gfi - User contributions [en]

Meteorology Calendar Autumn 2024

2024-11-12T08:07:50Z

Csp001: Updated topic of my talk.

The Meteorology Group Lunch Meeting takes place on Thursday at 12:05 in U105 in the GFI cantina, where you can also join online in Zoom.

At the start of each meeting, we will have an information exchange of 5-10 minutes to have updates on subjects such as recent and upcoming conferences or past weather events.

For the Autumn semester 2024 [mailto:stephan.kral@uib.no Stephan Kral] and [mailto:qidi.yu@uib.no Qidi Yu] are in charge of organizing the seminar speakers. So please send them an email if you would like to present something.

For presentations please keep contributions between '''15''' and max. '''25''' minutes to leave enough time to discuss the material. We will have maximum one long presentation per meeting and can accommodate an additional couple of shorter ones, which can be project presentations or other group-related issues.

It is also possible to join on Zoom via https://uib.zoom.us/j/68473038190?pwd=T3JzY0Z5UXQ4ZUdmcE56c0VrcFhhQT09

Back to [[Meteorology_Calendar|main Calendar]]
{| class="wikitable" border="1"
|+Itinerary:
|-
! width="100" |Date
! width="180" |Who
! width="120" |Length
! width="600" |Title
! width="300" |Room
|-
|22-08-24|| Fernando Sanches Lopes||25 min|| Modelling lifetime and damage evolution of LEP coating configurations subject to rain erosion based on climatology of hydrometeor size distributions
+ Semester Kick-Off
|U105
|-
|29-08-24|| Mauro Ghirardelli||45 min || PhD trial lecture||U105
|-
|05-09-24|| Eigo Tochimoto||25 min|| A composite study of extratropical cyclones accompanied by split fronts in the Northwestern Pacific||U105
|-
|12-09-24|| <s>Sanaz Zarif</s>||<s>25 min</s>|| <s>PhD project description</s>||<s>U105</s>
|-
|19-09-24|| Cos Zwart||25 min|| Introduction ||U105
|-
|26-09-24|| Mari Steinslid ||25 min|| Advancing the Understanding of the Atmospheric Water Cycle in Numerical Weather Prediction Models by Model-data Comparisons at Native Time-step Resolution ||U105
|-
|03-10-24|| Fumiaki Ogawa||30 min|| Moist dynamics in mid-latitude storm tracks near ocean fronts: recent results and future research||U105
|-
|10-10-24|| || || Autumn Vacation||
|-
|17-10-24|| Andrea Marcheggiani||25 min|| Effects of cold-air outbreaks on near-surface baroclinicity||U105
|-
|24-10-24|| Ida Haven||25 min|| Observations of latent heat fluxes over the Greenland ice sheat||U105
|-
|31-10-24|| Sanaz Zarif||25 min|| Molecular diffusivity of stable water isotopes||U105
|-
|07-11-24|| <s>Josh Dorrington<s>||<s>25 min<s>|| <s>Forecasts and projections of extreme rainfall using dynamical precursors<s>||U105
|-
|14-11-24|| Josh Dorrington||25 min|| Forecasts and projections of extreme rainfall using dynamical precursors ||U105
|-
|21-11-24|| ||...|| ||U105
|-
|28-11-24|| Clemens Spensberger||25 min|| Attributing momentum fluxes to weather||U105
|-
|05-12-24|| ||...|| ||U105
|-
|12-12-24|| ||...|| ||U105
|-
|19-12-24|| ||...|| ||U105
|-
|}

Meteorology Calendar Autumn 2024

2024-10-25T09:28:13Z

Csp001: Add myself to the speaker list

The Meteorology Group Lunch Meeting takes place on Thursday at 12:05 in U105 in the GFI cantina, where you can also join online in Zoom.

At the start of each meeting, we will have an information exchange of 5-10 minutes to have updates on subjects such as recent and upcoming conferences or past weather events.

For the Autumn semester 2024 [mailto:stephan.kral@uib.no Stephan Kral] and [mailto:qidi.yu@uib.no Qidi Yu] are in charge of organizing the seminar speakers. So please send them an email if you would like to present something.

For presentations please keep contributions between '''15''' and max. '''25''' minutes to leave enough time to discuss the material. We will have maximum one long presentation per meeting and can accommodate an additional couple of shorter ones, which can be project presentations or other group-related issues.

It is also possible to join on Zoom via https://uib.zoom.us/j/68473038190?pwd=T3JzY0Z5UXQ4ZUdmcE56c0VrcFhhQT09

Back to [[Meteorology_Calendar|main Calendar]]
{| class="wikitable" border="1"
|+Itinerary:
|-
! width="100" |Date
! width="180" |Who
! width="120" |Length
! width="600" |Title
! width="300" |Room
|-
|22-08-24|| Fernando Sanches Lopes||25 min|| Modelling lifetime and damage evolution of LEP coating configurations subject to rain erosion based on climatology of hydrometeor size distributions
+ Semester Kick-Off
|U105
|-
|29-08-24|| Mauro Ghirardelli||45 min || PhD trial lecture||U105
|-
|05-09-24|| Eigo Tochimoto||25 min|| A composite study of extratropical cyclones accompanied by split fronts in the Northwestern Pacific||U105
|-
|12-09-24|| <s>Sanaz Zarif</s>||<s>25 min</s>|| <s>PhD project description</s>||<s>U105</s>
|-
|19-09-24|| Cos Zwart||25 min|| Introduction ||U105
|-
|26-09-24|| Mari Steinslid ||25 min|| Advancing the Understanding of the Atmospheric Water Cycle in Numerical Weather Prediction Models by Model-data Comparisons at Native Time-step Resolution ||U105
|-
|03-10-24|| Fumiaki Ogawa||30 min|| Moist dynamics in mid-latitude storm tracks near ocean fronts: recent results and future research||U105
|-
|10-10-24|| || || Autumn Vacation||
|-
|17-10-24|| Andrea Marcheggiani||25 min|| Effects of cold-air outbreaks on near-surface baroclinicity||U105
|-
|24-10-24|| Ida Haven||25 min|| Observations of latent heat fluxes over the Greenland ice sheat||U105
|-
|31-10-24|| ||...|| ||U105
|-
|07-11-24|| Josh Dorrington||25 min|| Forecasts and projections of extreme rainfall using dynamical precursors||U105
|-
|14-11-24|| ||...|| ||U105
|-
|21-11-24|| ||...|| ||U105
|-
|28-11-24|| Clemens Spensberger||25 min|| Jet life cycles||U105
|-
|05-12-24|| ||...|| ||U105
|-
|12-12-24|| ||...|| ||U105
|-
|19-12-24|| ||...|| ||U105
|-
|}

ERA5 reanalysis data

2023-09-22T10:46:35Z

Csp001: Adding detected_features folder and a little clean-up.

GFI is building up an archive of ERA5 reanalysis data on the local linux system cyclone.hpc.uib.no. ERA5 supersedes the ERA-Interim reanalysis data, which ended in August 2019. More information about the ERA5 reanalysis data set is available [https://www.ecmwf.int/en/forecasts/datasets/reanalysis-datasets/era5 at ECMWF's ERA5 websites].

The ERA5 data files are available in two different CF-compatible netCDF formats (ETH Zurich format and Bergen format) at

/Data/gfi/share/era5

== Data in ETH Zurich format ==

Data in the ETH Zurich format is collected in one subfolder:

ml/ 3-hourly data on a regular 0.5 deg lat-lon grid, with model-level and pressure level files (see below)

Data in the '''ml'''-folder are contained in subdirectories for each year and month:

ml/yyyy/mm/[B|H|P|Z]yyyymmdd_hh

where yyyy is the year, mm the two-digit month, dd the two-digit day, and hh the two-digit hours, and Bxxx, Hxxx, Pxxx, Zxxx are different file types, as described in the table below. This format is the same used at the [https://iac.ethz.ch/group/atmospheric-dynamics.html Atmospheric Dynamics group at IAC, ETH Zürich, Switzerland]; the [https://www.imk-tro.kit.edu/7425.php LSDP group at Karlsruhe Institute of Technology, Germany]; and the [https://www.weizmann.ac.il/EPS/raveh-rubin/ Dynamical Meteorology Group, Weizmann Institute of Science, Rehovot, Israel].

Until now, the years 1999-2018 have been retrieved. The period will successively be extended back to 1979, and forward in time.

The data files contain the following variables:

{| class="wikitable"
|+ '''ERA5 data files in ETH Zurich format format'''
|-
|File name
|colspan="2"|Pyyyymmdd_hh
|colspan="1"|Zyyyymmdd_hh
|colspan="1"|Hyyyymmdd_hh
|colspan="1"|Byyyymmdd_hh
|-
|Leveltype
|Model level
|Surface
|Pressure
|Pressure
|Surface
|-
|Variables
|T, Q, U, V, OMEGA, LWC, IWC, RWC, SWC
|LSP, CP, SF, SSHF, SLHF, BLH, TCC, U10M, V10M, MSL, PS, SSTK
|Z, T, Q, U, V
|Z
|PS, MSL, TCC, U10M, V10M, SSTK, CI, D2M, T2M, TCW, TCWV, VIWVD, E, MN2T, MX2T, SI, TTR, TTRC, WG10, LSP, CP, SF, SSHF, SLHF, BLH
|-
|Levels
|40-137
| -
|900, 850, 800, 700, 600, 500, 400, 300, 250, 200, 100 hPa
|1000, 975, 950, 925, 900, 875, 850, 825, 800, 775, 750, 700, 650, 600, 550, 500, 450, 400, 350, 300, 250, 225, 200, 175, 150, 125, 100, 70, 50, 30, 20, 10, 70, 5, 3, 2, 1 hPa
| -
|-
|Times available
|colspan="5"|00, 03, 06, 09, 12, 15, 18, 21 UTC
|}

Note that the variables LSP, CP, SF, SSHF, SLHF, and BLH are derived as prognostic variables from the short-range forecast. Data valid at 00, 03, 06, 09 UTC are 06, 09, 12, 15 h forecast of the 18 UTC forecast of the previous day. Accordingly, data valid at 12, 15, 18, 21 UTC are 06, 09, 12, 15 h forecast of the 06 UTC forecast. The prognostic variables are accumulated over the previous 1 h.

Please see [https://confluence.ecmwf.int/display/CKB/ERA5%3A+data+documentation ECMWF ERA5 data documentation] for parameter abbreviations.

'''Conditions of use:''' When using the ERA5 data from this archive please make sure to reference "[https://cds.climate.copernicus.eu/cdsapp#!/home Copernicus Climate Change Service (C3S) (2017): ERA5: Fifth generation of ECMWF atmospheric reanalyses of the global climate. Copernicus Climate Change Service Climate Data Store (CDS)], date of citation" and acknowledge "ECMWF for providing ERA-5 data“. Also, please acknowledge "Michael Sprenger (ETH Zurich)“ for the support in providing the data.

== Data in Bergen format ==

Data in the Bergen format is in the following subfolders:

pl/ Pressure level data.
pl_tendencies/ Diabatic temperature tendencies on pressure levels.
pv2/ Data on the PV2-surface.
sfc/ Single-level data.
detected_features/ Weather events identified by various detection algorithms.
slope/ Isentropic slope data and its tendencies.

Data in these folders is organised in one file per month, variable and level, for example:

pl/ea.[ans|for].yyyymm.plev.var

This data is completely available for 1979-2022. Specifically, we have the following data available

{| class="wikitable"
|+ '''ERA5 data files in Bergen format'''
|-
!colspan="1"|Folder
!colspan="1"|Data available (see [https://confluence.ecmwf.int/display/CKB/ERA5%3A+data+documentation] for parameter abbreviations)
!colspan="1"|Details
|-
| rowspan=2 | '''sfc/'''
|blh, msl, siconc, sp, sst, t2m, tcwv, u10, v10, viewvf, vinwf
|Instantaneous (ans)
|-
|cp, lsp, slhf, sshf, ssrd, ssr, strd, str, tsr, ttr
|Accumulated over previous 3 hours (for)
|-
|'''pl/'''
|t, q, z, u, v, w
|Instantaneous (ans)
|-
|'''pl_tendencies/'''
|mttlwrcs, mttlwr, mttpm, mttswrcs, mttswr
|Accumulated over previous 3 hours (for)
|-
|'''pv2/'''
|u, v, pt, pres
|Instantaneous (ans)
|}

The folder '''detected_features/''' contains detected cyclones, anticyclones, fronts, jet axes, moisture transport axes, cold-air outbreaks, frontal volumes, Rossby wave breaking, and blocking events. For details on the different weather features refer to the '''README''' in the folder.

The folder '''slope/''' contains data deriving from the isentropic slope framework (see [https://doi.org/10.1002/qj.2605 Papritz and Spengler, 2015], for more details):

{| class="wikitable"
!colspan="1"|Variable name
!colspan="1"|Description
!colspan="1"|Equation
!colspan="1"|Units
!colspan="1"|Notes
|-
|slope
|Slope of isentropic surface
| S = abs(gradθz)
|m m-1
|Instantaneous
|-
|tilt
|Tendency in slope due to tilting
| gradθz /S · gradθ wid
|m m-1 s-1
|Instantaneous
|-
|diab
|Tendency in slope due to diabatic heating
| -dz/dθ gradθz /S · gradθ (dθ/dt)
|m m-1 s-1
|Accumulated over 6-hour period centred on instantaneous time step (stored as instantaneous, ans)
|-
|iadv
|Tendency in slope due to isentropic advection
| '''u''' · gradθS
|m m-1 s-1
|Instantaneous
|-
|w_ci
|Cross isentropic vertical velocity
| w - wiu
|m s-1
|Instantaneous
|-
|mask_slope
|Combination of masks from slope, diab and tilt
| -
|0-1
|Instantaneous
|}

ERA5 reanalysis data

2023-09-14T10:56:48Z

Csp001: Separating more cleanly which folders contain which format.

GFI is building up an archive of ERA5 reanalysis data on the local linux system cyclone.hpc.uib.no. ERA5 supersedes the ERA-Interim reanalysis data, which ended in August 2019. More information about the ERA5 reanalysis data set is available [https://www.ecmwf.int/en/forecasts/datasets/reanalysis-datasets/era5 at ECMWF's ERA5 websites].

The ERA5 data files are available in two different CF-compatible netCDF formats at

/Data/gfi/share/era5

== Data in ETH Zurich format ==

Data in the ETH Zurich format is collected in one subfolder:

ml/ 3-hourly data on a regular 0.5 deg lat-lon grid, with model-level and pressure level files (see below)

Data in the '''ml'''-folder are contained in subdirectories for each year and month:

ml/yyyy/mm/[B|H|P|Z]yyyymmdd_hh

where yyyy is the year, mm the two-digit month, dd the two-digit day, and hh the two-digit hours, and Bxxx, Hxxx, Pxxx, Zxxx are different file types, as described in the table below. This format is the same used at the [https://iac.ethz.ch/group/atmospheric-dynamics.html Atmospheric Dynamics group at IAC, ETH Zürich, Switzerland]; the [https://www.imk-tro.kit.edu/7425.php LSDP group at Karlsruhe Institute of Technology, Germany]; and the [https://www.weizmann.ac.il/EPS/raveh-rubin/ Dynamical Meteorology Group, Weizmann Institute of Science, Rehovot, Israel].

Until now, the years 1999-2018 have been retrieved. The period will successively be extended back to 1979, and forward in time.

The data files contain the following variables:

{| class="wikitable"
|+ '''ERA5 data files in ETH Zurich format format'''
|-
|File name
|colspan="2"|Pyyyymmdd_hh
|colspan="1"|Zyyyymmdd_hh
|colspan="1"|Hyyyymmdd_hh
|colspan="1"|Byyyymmdd_hh
|-
|Leveltype
|Model level
|Surface
|Pressure
|Pressure
|Surface
|-
|Variables
|T, Q, U, V, OMEGA, LWC, IWC, RWC, SWC
|LSP, CP, SF, SSHF, SLHF, BLH, TCC, U10M, V10M, MSL, PS, SSTK
|Z, T, Q, U, V
|Z
|PS, MSL, TCC, U10M, V10M, SSTK, CI, D2M, T2M, TCW, TCWV, VIWVD, E, MN2T, MX2T, SI, TTR, TTRC, WG10, LSP, CP, SF, SSHF, SLHF, BLH
|-
|Levels
|40-137
| -
|900, 850, 800, 700, 600, 500, 400, 300, 250, 200, 100 hPa
|1000, 975, 950, 925, 900, 875, 850, 825, 800, 775, 750, 700, 650, 600, 550, 500, 450, 400, 350, 300, 250, 225, 200, 175, 150, 125, 100, 70, 50, 30, 20, 10, 70, 5, 3, 2, 1 hPa
| -
|-
|Times available
|colspan="5"|00, 03, 06, 09, 12, 15, 18, 21 UTC
|}

Note that the variables LSP, CP, SF, SSHF, SLHF, and BLH are derived as prognostic variables from the short-range forecast. Data valid at 00, 03, 06, 09 UTC are 06, 09, 12, 15 h forecast of the 18 UTC forecast of the previous day. Accordingly, data valid at 12, 15, 18, 21 UTC are 06, 09, 12, 15 h forecast of the 06 UTC forecast. The prognostic variables are accumulated over the previous 1 h.

Please see [https://confluence.ecmwf.int/display/CKB/ERA5%3A+data+documentation ECMWF ERA5 data documentation] for parameter abbreviations.

'''Conditions of use:''' When using the ERA5 data from this archive please make sure to reference "[https://cds.climate.copernicus.eu/cdsapp#!/home Copernicus Climate Change Service (C3S) (2017): ERA5: Fifth generation of ECMWF atmospheric reanalyses of the global climate. Copernicus Climate Change Service Climate Data Store (CDS)], date of citation" and acknowledge "ECMWF for providing ERA-5 data“. Also, please acknowledge "Michael Sprenger (ETH Zurich)“ for the support in providing the data.

== Data in Bergen format ==

Data in the Bergen format is in the following subfolders:

pl/ pressure level data following the format of ERA-interim.
pl_tendencies/ diabatic temperature tendencies on pressure levels, following the format of ERA-interim.
pv2/ Data on the PV2-surface following the format of ERA-interim.
sfc/ Single-level data following the format of ERA-interim.
slope/ Isentropic slope data and its tendencies following the format of ERA-interim

Data in these folders is organised in one file per month, variable and level, for example:

pl/ea.[ans|for].yyyymm.plev.var

This data is completely available for 1979-2022. Specifically, we have the following data available

{| class="wikitable"
|+ '''ERA5 data files in Bergen format'''
|-
!colspan="1"|Folder
!colspan="1"|Data available (see [https://confluence.ecmwf.int/display/CKB/ERA5%3A+data+documentation] for parameter abbreviations)
!colspan="1"|Details
|-
| rowspan=2 | '''sfc/'''
|blh, msl, siconc, sp, sst, t2m, tcwv, u10, v10, viewvf, vinwf
|Instantaneous (ans)
|-
|cp, lsp, slhf, sshf, ssrd, ssr, strd, str, tsr, ttr
|Accumulated over previous 3 hours (for)
|-
|'''pl/'''
|t, q, z, u, v, w
|Instantaneous (ans)
|-
|'''pl_tendencies/'''
|mttlwrcs, mttlwr, mttpm, mttswrcs, mttswr
|Accumulated over previous 3 hours (for)
|-
|'''pv2/'''
|u, v, pt, pres
|Instantaneous (ans)
|}

The folder '''slope/''' contains data deriving from the isentropic slope framework (see [https://doi.org/10.1002/qj.2605 Papritz and Spengler, 2015], for more details):

{| class="wikitable"
!colspan="1"|Variable name
!colspan="1"|Description
!colspan="1"|Equation
!colspan="1"|Units
!colspan="1"|Notes
|-
|slope
|Slope of isentropic surface
| S = abs(gradθz)
|m m-1
|Instantaneous
|-
|tilt
|Tendency in slope due to tilting
| gradθz /S · gradθ wid
|m m-1 s-1
|Instantaneous
|-
|diab
|Tendency in slope due to diabatic heating
| -dz/dθ gradθz /S · gradθ (dθ/dt)
|m m-1 s-1
|Accumulated over 6-hour period centred on instantaneous time step (stored as instantaneous, ans)
|-
|iadv
|Tendency in slope due to isentropic advection
| '''u''' · gradθS
|m m-1 s-1
|Instantaneous
|-
|w_ci
|Cross isentropic vertical velocity
| w - wiu
|m s-1
|Instantaneous
|-
|mask_slope
|Combination of masks from slope, diab and tilt
| -
|0-1
|Instantaneous
|}

ERA5 reanalysis data

2023-03-20T13:31:10Z

Csp001: Adding file name pattern for pl, sfc, and pv2-data.

Documentation of the ERA5 archive at GFI

GFI is building up an archive of ERA5 reanalysis data on the local linux system cyclone.hpc.uib.no. ERA5 supersedes the ERA-Interim reanalysis data, which ended in August 2019. More information about the ERA5 reanalysis data set is available [https://www.ecmwf.int/en/forecasts/datasets/reanalysis-datasets/era5 at ECMWF's ERA5 websites].

The ERA5 data files are available in a CF-compatible netCDF format on cyclone.hpc.uib.no and other computers that mount the UiB linux system at

/Data/gfi/share/era5

At GFI, we share the data format with the [https://iac.ethz.ch/group/atmospheric-dynamics.html Atmospheric Dynamics group at IAC, ETH Zürich, Switzerland]; the [https://www.imk-tro.kit.edu/7425.php LSDP group at Karlsruhe Institute of Technology, Germany]; and the [https://www.weizmann.ac.il/EPS/raveh-rubin/ Dynamical Meteorology Group, Weizmann Institute of Science, Rehovot, Israel]. The data are organised as follows

ml/ 3-hourly data on a regular 0.5 deg lat-lon grid, with model-level and pressure level files (see below)
pl/ pressure level data following the format of ERA-interim.
pl_tendencies/ diabatic temperature tendencies on pressure levels, following the format of ERA-interim.
pv2/ Data on the PV2-surface following the format of ERA-interim.
sfc/ Single-level data following the format of ERA-interim.

Data in the '''ml'''-folder are contained in subdirectories for each year and month:

ml/yyyy/mm/[B|H|P|Z]yyyymmdd_hh

where yyyy is the year, mm the two-digit month, dd the two-digit day, and hh the two-digit hours, and Bxxx, Hxxx, Pxxx, Zxxx are different file types, as described in the table below.

Until now, the years 1999-2018 have been retrieved, the period will successively be extended back to 1979, and forward in time.

Data in the '''pl_*''', '''sfc''' and '''pv2'''-folders is organised in one file per month, variable and level, for example:

pl/ea.[ans|for].YYYYMM.PLEV.VAR

This data is completely available for 1979-2020.

The data files contain the following variables:

{| class="wikitable"
!colspan="6"|ERA5 data files
|-
|File name
|colspan="2"|Pyyyymmdd_hh
|colspan="1"|Zyyyymmdd_hh
|colspan="1"|Hyyyymmdd_hh
|colspan="1"|Byyyymmdd_hh
|-
|Leveltype
|Model level
|Surface
|Pressure
|Pressure
|Surface
|-
|Variables
|T, Q, U, V, OMEGA, LWC, IWC, RWC, SWC
|LSP, CP, SF, SSHF, SLHF, BLH, TCC, U10M, V10M, MSL, PS, SSTK
|Z, T, Q, U, V
|Z
|PS, MSL, TCC, U10M, V10M, SSTK, CI, D2M, T2M, TCW, TCWV, VIWVD, E, MN2T, MX2T, SI, TTR, TTRC, WG10, LSP, CP, SF, SSHF, SLHF, BLH
|-
|Levels
|40-137
| -
|900, 850, 800, 700, 600, 500, 400, 300, 250, 200, 100 hPa
|1000, 975, 950, 925, 900, 875, 850, 825, 800, 775, 750, 700, 650, 600, 550, 500, 450, 400, 350, 300, 250, 225, 200, 175, 150, 125, 100, 70, 50, 30, 20, 10, 70, 5, 3, 2, 1 hPa
| -
|-
|Times available
|colspan="5"|00, 03, 06, 09, 12, 15, 18, 21 UTC
|}

Note that the variables LSP, CP, SF, SSHF, SLHF, and BLH are derived as prognostic variables from the short-range forecast. Data valid at 00, 03, 06, 09 UTC are 06, 09, 12, 15 h forecast of the 18 UTC forecast of the previous day. Accordingly, data valid at 12, 15, 18, 21 UTC are 06, 09, 12, 15 h forecast of the 06 UTC forecast. The prognostic variables are accumulated over the previous 1 h.

Please see [https://confluence.ecmwf.int//display/CKB/ERA5+data+documentation#ERA5datadocumentation-Parameterlistings ECMWF ERA5 data documentation] for parameter abbreviations.

'''Conditions of use:''' When using the ERA5 data from this archive please make sure to reference "[https://cds.climate.copernicus.eu/cdsapp#!/home Copernicus Climate Change Service (C3S) (2017): ERA5: Fifth generation of ECMWF atmospheric reanalyses of the global climate. Copernicus Climate Change Service Climate Data Store (CDS)], date of citation" and acknowledge "ECMWF for providing ERA-5 data“. Also, please acknowledge "Michael Sprenger (ETH Zurich)“ for the support in providing the data.

ERA5 reanalysis data

2023-03-20T13:25:01Z

Csp001: Updating info on the pl and pl_tendency data.

Documentation of the ERA5 archive at GFI

GFI is building up an archive of ERA5 reanalysis data on the local linux system cyclone.hpc.uib.no. ERA5 supersedes the ERA-Interim reanalysis data, which ended in August 2019. More information about the ERA5 reanalysis data set is available [https://www.ecmwf.int/en/forecasts/datasets/reanalysis-datasets/era5 at ECMWF's ERA5 websites].

The ERA5 data files are available in a CF-compatible netCDF format on cyclone.hpc.uib.no and other computers that mount the UiB linux system at

/Data/gfi/share/era5

At GFI, we share the data format with the [https://iac.ethz.ch/group/atmospheric-dynamics.html Atmospheric Dynamics group at IAC, ETH Zürich, Switzerland]; the [https://www.imk-tro.kit.edu/7425.php LSDP group at Karlsruhe Institute of Technology, Germany]; and the [https://www.weizmann.ac.il/EPS/raveh-rubin/ Dynamical Meteorology Group, Weizmann Institute of Science, Rehovot, Israel]. The data are organised as follows

ml/ 3-hourly data on a regular 0.5 deg lat-lon grid, with model-level and pressure level files (see below)
pl/ pressure level data following the format of ERA-interim.
pl_tendencies/ diabatic temperature tendencies on pressure levels, following the format of ERA-interim.

Data files are contained in subdirectories for each year and month:

ml/yyyy/mm/[B|H|P|Z]yyyymmdd_hh

where yyyy is the year, mm the two-digit month, dd the two-digit day, and hh the two-digit hours, and Bxxx, Hxxx, Pxxx, Zxxx are different file types, as described in the table below.

Until now, the years 1999-2018 have been retrieved, the period will successively be extended back to 1979, and forward in time.

The data files contain the following variables:

{| class="wikitable"
!colspan="6"|ERA5 data files
|-
|File name
|colspan="2"|Pyyyymmdd_hh
|colspan="1"|Zyyyymmdd_hh
|colspan="1"|Hyyyymmdd_hh
|colspan="1"|Byyyymmdd_hh
|-
|Leveltype
|Model level
|Surface
|Pressure
|Pressure
|Surface
|-
|Variables
|T, Q, U, V, OMEGA, LWC, IWC, RWC, SWC
|LSP, CP, SF, SSHF, SLHF, BLH, TCC, U10M, V10M, MSL, PS, SSTK
|Z, T, Q, U, V
|Z
|PS, MSL, TCC, U10M, V10M, SSTK, CI, D2M, T2M, TCW, TCWV, VIWVD, E, MN2T, MX2T, SI, TTR, TTRC, WG10, LSP, CP, SF, SSHF, SLHF, BLH
|-
|Levels
|40-137
| -
|900, 850, 800, 700, 600, 500, 400, 300, 250, 200, 100 hPa
|1000, 975, 950, 925, 900, 875, 850, 825, 800, 775, 750, 700, 650, 600, 550, 500, 450, 400, 350, 300, 250, 225, 200, 175, 150, 125, 100, 70, 50, 30, 20, 10, 70, 5, 3, 2, 1 hPa
| -
|-
|Times available
|colspan="5"|00, 03, 06, 09, 12, 15, 18, 21 UTC
|}

Note that the variables LSP, CP, SF, SSHF, SLHF, and BLH are derived as prognostic variables from the short-range forecast. Data valid at 00, 03, 06, 09 UTC are 06, 09, 12, 15 h forecast of the 18 UTC forecast of the previous day. Accordingly, data valid at 12, 15, 18, 21 UTC are 06, 09, 12, 15 h forecast of the 06 UTC forecast. The prognostic variables are accumulated over the previous 1 h.

Please see [https://confluence.ecmwf.int//display/CKB/ERA5+data+documentation#ERA5datadocumentation-Parameterlistings ECMWF ERA5 data documentation] for parameter abbreviations.

'''Conditions of use:''' When using the ERA5 data from this archive please make sure to reference "[https://cds.climate.copernicus.eu/cdsapp#!/home Copernicus Climate Change Service (C3S) (2017): ERA5: Fifth generation of ECMWF atmospheric reanalyses of the global climate. Copernicus Climate Change Service Climate Data Store (CDS)], date of citation" and acknowledge "ECMWF for providing ERA-5 data“. Also, please acknowledge "Michael Sprenger (ETH Zurich)“ for the support in providing the data.

File:Get started cyclone.pdf

2022-12-05T14:05:48Z

Csp001: Csp001 uploaded a new version of File:Get started cyclone.pdf

Step by step guide for Jupyter on cyclone.

Using cyclone

2022-09-21T09:53:11Z

Csp001: /* Accessing the data from your own machines */

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>CDO</code>, <code>CDO/1.9.5-foss-2018b</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* ghostview
*: ''<no module required>''
* grads
*: ''<no module required>''
* Matlab
*: <code>Matlab</code>, <code>Matlab/2018a</code>, <code>Matlab/2012a</code>
* ncdump and other netCDF utilities
*: <code>netCDF</code>, <code>netCDF/4.6.1-foss-2018b</code>
* NCL
*: <code>NCL</code>, <code>NCL/6.5.0</code>
* nco
*: <code>NCO</code>, <code>NCO/4.7.4-foss-2018b</code>
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: ''First'' choose and load the python module for the python version that you want to use, either <code>Python/2.7.15-foss-2018b</code> for python 2.7.15, or <code>Python/3.7.0-foss-2018b</code> for python 3.7.0.
*: ''Then'', as a temporary solution, many scientific python packages are installed in the following virtual environments:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.15.
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3-2021a/bin/activate</code> for python 3.7.0.
*: For the pygrib module, <code>ecCodes/2.7.3-foss-2018b</code> is required in addition.
* R
*: ''<no module required>''

=== Text editors ===

* emacs
*: Is installed globally, but requires <code>util-linux/2.32-GCCcore-7.3.0</code> to work.
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>. '''Note''': The library is called <code>libopenblas</code>, so you'll need to compile with <code>-lopenblas</code>.
* eccodes (replacement for grib_api)
*: <code>ecCodes/2.7.3-foss-2018b</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>. '''Note''': The library is called <code>libscalapack</code>, so you'll need to compile with <code>-lscalapack</code>.
* MPI
*: <code>OpenMPI/3.1.1-GCC-7.3.0-2.30</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>
* proj
*: <code>PROJ/5.0.0-foss-2018b</code>

=== Jupyter & Jupyterhub ===

Here is a step by step guide to setup and use Jupyter based on the <code>dynpie3</code> environment.

[[File:Get started cyclone.pdf|thumb|Step by step guide for Jupyter on cyclone]]

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://uib.no;<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://uib.no;<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.
Alternatively you can mount the network drive with sshfs to a dedicated directory using <code>sshfs</code> (install with <code>sudo apt install sshfs</code>):
<pre>mkdir ~/cyclone_gfi
From UiB network: sshfs -o follow_symlinks <user name>@cyclone.hpc.uib.no:/gfi/ ~/cyclone_gfi/
From ext. networks: sshfs -o follow_symlinks <user name>@sync.uib.no:/gfi/ ~/cyclone_gfi/
Unmount with: fusermount -u ~/cyclone_gfi</pre>
On Windows you can mount by navigating to <code>File Explorer > Map network drive</code> and enter <code>\\leo.hpc.uib.no\gfi</code>. Make sure to enable <code>Connect using different credentials</code> and fill in <code><user name>@uib.no</code> and your PW.

== Displaying GUIs on your screen ==

The ssh-login command at the top of this wiki enables trusted X11 forwarding (the <code>-Y</code> option), which allows you to display Graphical User Interfaces (GUIs) on your screen. This way you may be able to run software on a high performance system in a more userfriendly way than by just operating via the terminal. To make this work properly you may have to edit the ssh configuration file (<code>/etc/ssh/ssh_config</code> on linux systems) by adding or uncommenting the following two lines:

<pre>X11Forwarding yes
ForwardX11Trusted yes</pre>

Editing this file requires superuser priviliges so you may have to ask the IT department for support. For Mac the solution should be pretty similar, windows requires additional software like PuTTY (for establishing an ssh-connection) and an XServer (e.g. VcXsrv).

Using cyclone

2022-02-07T12:46:47Z

Csp001: Add instructions for jupyter

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>CDO</code>, <code>CDO/1.9.5-foss-2018b</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* ghostview
*: ''<no module required>''
* grads
*: ''<no module required>''
* Matlab
*: <code>Matlab</code>, <code>Matlab/2018a</code>, <code>Matlab/2012a</code>
* ncdump and other netCDF utilities
*: <code>netCDF</code>, <code>netCDF/4.6.1-foss-2018b</code>
* NCL
*: <code>NCL</code>, <code>NCL/6.5.0</code>
* nco
*: <code>NCO</code>, <code>NCO/4.7.4-foss-2018b</code>
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: ''First'' choose and load the python module for the python version that you want to use, either <code>Python/2.7.15-foss-2018b</code> for python 2.7.15, or <code>Python/3.7.0-foss-2018b</code> for python 3.7.0.
*: ''Then'', as a temporary solution, many scientific python packages are installed in the following virtual environments:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.15.
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3-2021a/bin/activate</code> for python 3.7.0.
*: For the pygrib module, <code>ecCodes/2.7.3-foss-2018b</code> is required in addition.
* R
*: ''<no module required>''

=== Text editors ===

* emacs
*: Is installed globally, but requires <code>util-linux/2.32-GCCcore-7.3.0</code> to work.
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>. '''Note''': The library is called <code>libopenblas</code>, so you'll need to compile with <code>-lopenblas</code>.
* eccodes (replacement for grib_api)
*: <code>ecCodes/2.7.3-foss-2018b</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>. '''Note''': The library is called <code>libscalapack</code>, so you'll need to compile with <code>-lscalapack</code>.
* MPI
*: <code>OpenMPI/3.1.1-GCC-7.3.0-2.30</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>
* proj
*: <code>PROJ/5.0.0-foss-2018b</code>

=== Jupyter & Jupyterhub ===

Here is a step by step guide to setup and use Jupyter based on the <code>dynpie3</code> environment.

[[File:Get started cyclone.pdf|thumb|Step by step guide for Jupyter on cyclone]]

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.
Alternatively you can mount the network drive with sshfs to a dedicated directory using <code>sshfs</code> (install with <code>sudo apt install sshfs</code>):
<pre>mkdir ~/cyclone_gfi
From UiB network: sshfs -o follow_symlinks <user name>@cyclone.hpc.uib.no:/gfi/ ~/cyclone_gfi/
From ext. networks: sshfs -o follow_symlinks <user name>@sync.uib.no:/gfi/ ~/cyclone_gfi/
Unmount with: fusermount -u ~/cyclone_gfi</pre>
On Windows you can mount by navigating to <code>File Explorer > Map network drive</code> and enter <code>\\leo.hpc.uib.no\gfi</code>. Make sure to enable <code>Connect using different credentials</code> and fill in <code><user name>@uib.no</code> and your PW.

== Displaying GUIs on your screen ==

The ssh-login command at the top of this wiki enables trusted X11 forwarding (the <code>-Y</code> option), which allows you to display Graphical User Interfaces (GUIs) on your screen. This way you may be able to run software on a high performance system in a more userfriendly way than by just operating via the terminal. To make this work properly you may have to edit the ssh configuration file (<code>/etc/ssh/ssh_config</code> on linux systems) by adding or uncommenting the following two lines:

<pre>X11Forwarding yes
ForwardX11Trusted yes</pre>

Editing this file requires superuser priviliges so you may have to ask the IT department for support. For Mac the solution should be pretty similar, windows requires additional software like PuTTY (for establishing an ssh-connection) and an XServer (e.g. VcXsrv).

File:Get started cyclone.pdf

2022-02-07T12:44:17Z

Csp001:

Step by step guide for Jupyter on cyclone.

Using cyclone

2021-01-07T09:56:23Z

Csp001: New virtualenv.

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>CDO</code>, <code>CDO/1.9.5-foss-2018b</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* ghostview
*: ''<no module required>''
* grads
*: ''<no module required>''
* Matlab
*: <code>Matlab</code>, <code>Matlab/2018a</code>, <code>Matlab/2012a</code>
* ncdump and other netCDF utilities
*: <code>netCDF</code>, <code>netCDF/4.6.1-foss-2018b</code>
* NCL
*: <code>NCL</code>, <code>NCL/6.5.0</code>
* nco
*: <code>NCO</code>, <code>NCO/4.7.4-foss-2018b</code>
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: ''First'' choose and load the python module for the python version that you want to use, either <code>Python/2.7.15-foss-2018b</code> for python 2.7.15, or <code>Python/3.7.0-foss-2018b</code> for python 3.7.0.
*: ''Then'', as a temporary solution, many scientific python packages are installed in the following virtual environments:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.15.
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3-2021a/bin/activate</code> for python 3.7.0.
*: For the pygrib module, <code>ecCodes/2.7.3-foss-2018b</code> is required in addition.
* R
*: ''<no module required>''

=== Text editors ===

* emacs
*: Is installed globally, but requires <code>util-linux/2.32-GCCcore-7.3.0</code> to work.
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>. '''Note''': The library is called <code>libopenblas</code>, so you'll need to compile with <code>-lopenblas</code>.
* eccodes (replacement for grib_api)
*: <code>ecCodes/2.7.3-foss-2018b</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>. '''Note''': The library is called <code>libscalapack</code>, so you'll need to compile with <code>-lscalapack</code>.
* MPI
*: <code>OpenMPI/3.1.1-GCC-7.3.0-2.30</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>
* proj
*: <code>PROJ/5.0.0-foss-2018b</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2020-11-16T10:00:36Z

Csp001: Update virtualenv for python3

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>CDO</code>, <code>CDO/1.9.5-foss-2018b</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* ghostview
*: ''<no module required>''
* grads
*: ''<no module required>''
* Matlab
*: <code>Matlab</code>, <code>Matlab/2018a</code>, <code>Matlab/2012a</code>
* ncdump and other netCDF utilities
*: <code>netCDF</code>, <code>netCDF/4.6.1-foss-2018b</code>
* NCL
*: <code>NCL</code>, <code>NCL/6.5.0</code>
* nco
*: <code>NCO</code>, <code>NCO/4.7.4-foss-2018b</code>
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: ''First'' choose and load the python module for the python version that you want to use, either <code>Python/2.7.15-foss-2018b</code> for python 2.7.15, or <code>Python/3.7.0-foss-2018b</code> for python 3.7.0.
*: ''Then'', as a temporary solution, many scientific python packages are installed in the following virtual environments:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.15.
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3-2020a/bin/activate</code> for python 3.7.0.
*: For the pygrib module, <code>ecCodes/2.7.3-foss-2018b</code> is required in addition.
* R
*: ''<no module required>''

=== Text editors ===

* emacs
*: Is installed globally, but requires <code>util-linux/2.32-GCCcore-7.3.0</code> to work.
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>. '''Note''': The library is called <code>libopenblas</code>, so you'll need to compile with <code>-lopenblas</code>.
* eccodes (replacement for grib_api)
*: <code>ecCodes/2.7.3-foss-2018b</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>. '''Note''': The library is called <code>libscalapack</code>, so you'll need to compile with <code>-lscalapack</code>.
* MPI
*: <code>OpenMPI/3.1.1-GCC-7.3.0-2.30</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>
* proj
*: <code>PROJ/5.0.0-foss-2018b</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2019-04-10T09:57:18Z

Csp001: /* Data analysis and plotting */ Clarify that python need to be loaded before being able to use the virtualenvs.

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>CDO</code>, <code>CDO/1.9.5-foss-2018b</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* ghostview
*: ''<no module required>''
* grads
*: ''<no module required>''
* Matlab
*: <code>Matlab</code>, <code>Matlab/2018a</code>, <code>Matlab/2012a</code>
* ncdump and other netCDF utilities
*: <code>netCDF</code>, <code>netCDF/4.6.1-foss-2018b</code>
* NCL
*: <code>NCL</code>, <code>NCL/6.5.0</code>
* nco
*: <code>NCO</code>, <code>NCO/4.7.4-foss-2018b</code>
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: ''First'' choose and load the python module for the python version that you want to use, either <code>Python/2.7.15-foss-2018b</code> for python 2.7.15, or <code>Python/3.7.0-foss-2018b</code> for python 3.7.0.
*: ''Then'', as a temporary solution, many scientific python packages are installed in the following virtual environments:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.15.
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3/bin/activate</code> for python 3.7.0.
*: For the pygrib module, <code>ecCodes/2.7.3-foss-2018b</code> is required in addition.
* R
*: ''<no module required>''

=== Text editors ===

* emacs
*: Is installed globally, but requires <code>util-linux/2.32-GCCcore-7.3.0</code> to work.
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>. '''Note''': The library is called <code>libopenblas</code>, so you'll need to compile with <code>-lopenblas</code>.
* eccodes (replacement for grib_api)
*: <code>ecCodes/2.7.3-foss-2018b</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>. '''Note''': The library is called <code>libscalapack</code>, so you'll need to compile with <code>-lscalapack</code>.
* MPI
*: <code>OpenMPI/3.1.1-GCC-7.3.0-2.30</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>
* proj
*: <code>PROJ/5.0.0-foss-2018b</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2018-11-26T13:34:06Z

Csp001: /* Compilers and libraries */

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>CDO</code>, <code>CDO/1.9.5-foss-2018b</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* ghostview
*: ''<no module required>''
* grads
*: ''<no module required>''
* Matlab
*: <code>Matlab</code>, <code>Matlab/2018a</code>, <code>Matlab/2012a</code>
* ncdump and other netCDF utilities
*: <code>netCDF</code>, <code>netCDF/4.6.1-foss-2018b</code>
* NCL
*: <code>NCL</code>, <code>NCL/6.5.0</code>
* nco
*: <code>NCO</code>, <code>NCO/4.7.4-foss-2018b</code>
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: Temporary solution, use one of the two below commands to enable the virtual environment:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.15, based on <code>Python/2.7.15-foss-2018b</code>
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3/bin/activate</code> for python 3.7.0, based on <code>Python/3.7.0-foss-2018b</code>.
*: For the pygrib module, <code>ecCodes/2.7.3-foss-2018b</code> is required in addition.
* R
*: ''<no module required>''

=== Text editors ===

* emacs
*: Is installed globally, but requires <code>util-linux/2.32-GCCcore-7.3.0</code> to work.
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>. '''Note''': The library is called <code>libopenblas</code>, so you'll need to compile with <code>-lopenblas</code>.
* eccodes (replacement for grib_api)
*: <code>ecCodes/2.7.3-foss-2018b</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>. '''Note''': The library is called <code>libscalapack</code>, so you'll need to compile with <code>-lscalapack</code>.
* MPI
*: <code>OpenMPI/3.1.1-GCC-7.3.0-2.30</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>
* proj
*: <code>PROJ/5.0.0-foss-2018b</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2018-11-26T10:03:57Z

Csp001: /* Text editors */

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>CDO</code>, <code>CDO/1.9.5-foss-2018b</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* ghostview
*: ''<no module required>''
* grads
*: ''<no module required>''
* Matlab
*: <code>Matlab</code>, <code>Matlab/2018a</code>, <code>Matlab/2012a</code>
* ncdump and other netCDF utilities
*: <code>netCDF</code>, <code>netCDF/4.6.1-foss-2018b</code>
* NCL
*: <code>NCL</code>, <code>NCL/6.5.0</code>
* nco
*: <code>NCO</code>, <code>NCO/4.7.4-foss-2018b</code>
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: Temporary solution, use one of the two below commands to enable the virtual environment:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.15, based on <code>Python/2.7.15-foss-2018b</code>
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3/bin/activate</code> for python 3.7.0, based on <code>Python/3.7.0-foss-2018b</code>.
*: For the pygrib module, <code>ecCodes/2.7.3-foss-2018b</code> is required in addition.
* R
*: ''<no module required>''

=== Text editors ===

* emacs
*: Is installed globally, but requires <code>util-linux/2.32-GCCcore-7.3.0</code> to work.
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>
* eccodes (replacement for grib_api)
*: <code>ecCodes/2.7.3-foss-2018b</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>
* MPI
*: <code>OpenMPI/3.1.1-GCC-7.3.0-2.30</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>
* proj
*: <code>PROJ/5.0.0-foss-2018b</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2018-11-26T10:03:30Z

Csp001: /* Available software */

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>CDO</code>, <code>CDO/1.9.5-foss-2018b</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* ghostview
*: ''<no module required>''
* grads
*: ''<no module required>''
* Matlab
*: <code>Matlab</code>, <code>Matlab/2018a</code>, <code>Matlab/2012a</code>
* ncdump and other netCDF utilities
*: <code>netCDF</code>, <code>netCDF/4.6.1-foss-2018b</code>
* NCL
*: <code>NCL</code>, <code>NCL/6.5.0</code>
* nco
*: <code>NCO</code>, <code>NCO/4.7.4-foss-2018b</code>
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: Temporary solution, use one of the two below commands to enable the virtual environment:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.15, based on <code>Python/2.7.15-foss-2018b</code>
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3/bin/activate</code> for python 3.7.0, based on <code>Python/3.7.0-foss-2018b</code>.
*: For the pygrib module, <code>ecCodes/2.7.3-foss-2018b</code> is required in addition.
* R
*: ''<no module required>''

=== Text editors ===

* emacs
*: <code>util-linux/2.32-GCCcore-7.3.0</code>
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>
* eccodes (replacement for grib_api)
*: <code>ecCodes/2.7.3-foss-2018b</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>
* MPI
*: <code>OpenMPI/3.1.1-GCC-7.3.0-2.30</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>
* proj
*: <code>PROJ/5.0.0-foss-2018b</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2018-11-05T14:09:18Z

Csp001: /* Data analysis and plotting */

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>CDO</code>, <code>CDO/1.9.5-foss-2018b</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* ghostview
*: ''<no module required>''
* grads
*: ''<no module required>''
* Matlab
*: <code>Matlab</code>, <code>Matlab/2018a</code>, <code>Matlab/2012a</code>
* ncdump and other netCDF utilities
*: <code>netCDF</code>, <code>netCDF/4.6.1-foss-2018b</code>
* NCL
*: <code>NCL</code>, <code>NCL/6.5.0</code>
* nco
*: <code>NCO</code>, <code>NCO/4.7.4-foss-2018b</code>
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: Temporary solution, use one of the two below commands to enable the virtual environment:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.15, based on <code>Python/2.7.15-foss-2018b</code>
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3/bin/activate</code> for python 3.7.0, based on <code>Python/3.7.0-foss-2018b</code>.
*: For the pygrib module, <code>ecCodes/2.7.3-foss-2018b</code> is required in addition.
* R
*: ''<no module required>''

=== Text editors ===

* emacs
*: ''<no module required>''
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>
* eccodes (replacement for grib_api)
*: <code>ecCodes/2.7.3-foss-2018b</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>
* MPI
*: <code>OpenMPI/3.1.1-GCC-7.3.0-2.30</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>
* proj
*: <code>PROJ/5.0.0-foss-2018b</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2018-10-10T14:25:51Z

Csp001: /* Data analysis and plotting */

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>CDO</code>, <code>CDO/1.9.5-foss-2018b</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* ghostview
*: ''<no module required>''
* grads
*: ''<no module required>''
* Matlab
*: <code>Matlab</code>, <code>Matlab/2018a</code>, <code>Matlab/2012a</code>
* NCL
*: <code>NCL</code>, <code>NCL/6.5.0</code>
* nco
*: ''<no module required>''
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: Temporary solution, use one of the two below commands to enable the virtual environment:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.15, based on <code>Python/2.7.15-foss-2018b</code>
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3/bin/activate</code> for python 3.7.0, based on <code>Python/3.7.0-foss-2018b</code>.
*: For the pygrib module, <code>ecCodes/2.7.3-foss-2018b</code> is required in addition.
* R
*: ''<no module required>''

=== Text editors ===

* emacs
*: ''<no module required>''
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>
* eccodes (replacement for grib_api)
*: <code>ecCodes/2.7.3-foss-2018b</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>
* MPI
*: <code>OpenMPI/3.1.1-GCC-7.3.0-2.30</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>
* proj
*: <code>PROJ/5.0.0-foss-2018b</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2018-10-10T14:07:46Z

Csp001: /* Data analysis and plotting */

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>CDO</code>, <code>CDO/1.9.5-foss-2018b</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* ghostview
*: ''<no module required>''
* grads
*: ''<no module required>''
* Matlab
*: <code>Matlab</code>, <code>Matlab/2018a</code>, <code>Matlab/2012a</code>
* NCL
*: <code>NCL</code>, <code>NCL/6.5.0</code>
* nco
*: ''<no module required>''
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: Temporary solution, use one of the two below commands to enable the virtual environment:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.15, based on <code>Python/2.7.15-foss-2018b</code>
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3/bin/activate</code> for python 3.7.0, based on <code>Python/3.7.0-foss-2018b</code>.
*: For the pygrib module, <code>grib_api/1.24.0-foss-2018b</code> is required in addition.
* R
*: ''<no module required>''

=== Text editors ===

* emacs
*: ''<no module required>''
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>
* eccodes (replacement for grib_api)
*: <code>ecCodes/2.7.3-foss-2018b</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>
* MPI
*: <code>OpenMPI/3.1.1-GCC-7.3.0-2.30</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>
* proj
*: <code>PROJ/5.0.0-foss-2018b</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2018-10-08T11:23:27Z

Csp001: /* Compilers and libraries */

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>CDO</code>, <code>CDO/1.9.5-foss-2018b</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* ghostview
*: ''<no module required>''
* grads
*: ''<no module required>''
* Matlab
*: <code>Matlab</code>, <code>Matlab/2018a</code>, <code>Matlab/2012a</code>
* NCL
*: <code>NCL</code>, <code>NCL/6.5.0</code>
* nco
*: ''<no module required>''
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: Temporary solution, use one of the two below commands to enable the virtual environment:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.5.
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3/bin/activate</code> for python 3.4.9.
*: For the pygrib module, <code>grib_api/1.24.0-foss-2018b</code> is required in addition. '''Note''': These virtual environments will at some point be replaced by ones based on the new python versions 2.7.15 and 3.7.0 that are now available on cyclone. This change will be announced on dynlib-users@gfi.uib.no, please contact Clemens Spensberger if you are not on this list and like to be informed.
* R
*: ''<no module required>''

=== Text editors ===

* emacs
*: ''<no module required>''
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>
* eccodes (replacement for grib_api)
*: <code>ecCodes/2.7.3-foss-2018b</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>
* MPI
*: <code>OpenMPI/3.1.1-GCC-7.3.0-2.30</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>
* proj
*: <code>PROJ/5.0.0-foss-2018b</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2018-10-08T09:44:18Z

Csp001: /* Data analysis and plotting */

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>CDO</code>, <code>CDO/1.9.5-foss-2018b</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* ghostview
*: ''<no module required>''
* grads
*: ''<no module required>''
* Matlab
*: <code>Matlab</code>, <code>Matlab/2018a</code>, <code>Matlab/2012a</code>
* NCL
*: <code>NCL</code>, <code>NCL/6.5.0</code>
* nco
*: ''<no module required>''
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: Temporary solution, use one of the two below commands to enable the virtual environment:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.5.
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3/bin/activate</code> for python 3.4.9.
*: For the pygrib module, <code>grib_api/1.24.0-foss-2018b</code> is required in addition. '''Note''': These virtual environments will at some point be replaced by ones based on the new python versions 2.7.15 and 3.7.0 that are now available on cyclone. This change will be announced on dynlib-users@gfi.uib.no, please contact Clemens Spensberger if you are not on this list and like to be informed.
* R
*: ''<no module required>''

=== Text editors ===

* emacs
*: ''<no module required>''
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>
* MPI
*: <code>OpenMPI/3.1.1-GCC-7.3.0-2.30</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>
* proj
*: <code>PROJ/5.0.0-foss-2018b</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2018-10-06T09:48:18Z

Csp001: /* Compilers and libraries */

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>CDO</code>, <code>CDO/1.9.5-foss-2018b</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* ghostview
*: ''<no module required>''
* grads
*: ''<no module required>''
* Matlab
*: <code>Matlab</code>, <code>Matlab/2018a</code>, <code>Matlab/2012a</code>
* NCL
*: ''Currently unavailable''
* nco
*: ''<no module required>''
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: Temporary solution, use one of the two below commands to enable the virtual environment:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.5.
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3/bin/activate</code> for python 3.4.9.
*: For the pygrib module, <code>grib_api/1.24.0-foss-2018b</code> is required in addition. '''Note''': These virtual environments will at some point be replaced by ones based on the new python versions 2.7.15 and 3.7.0 that are now available on cyclone. This change will be announced on dynlib-users@gfi.uib.no, please contact Clemens Spensberger if you are not on this list and like to be informed.
* R
*: ''<no module required>''

=== Text editors ===

* emacs
*: ''<no module required>''
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>
* MPI
*: <code>OpenMPI/3.1.1-GCC-7.3.0-2.30</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>
* proj
*: <code>PROJ/5.0.0-foss-2018b</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2018-10-06T09:43:31Z

Csp001: /* Available software */

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>CDO</code>, <code>CDO/1.9.5-foss-2018b</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* ghostview
*: ''<no module required>''
* grads
*: ''<no module required>''
* Matlab
*: <code>Matlab</code>, <code>Matlab/2018a</code>, <code>Matlab/2012a</code>
* NCL
*: ''Currently unavailable''
* nco
*: ''<no module required>''
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: Temporary solution, use one of the two below commands to enable the virtual environment:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.5.
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3/bin/activate</code> for python 3.4.9.
*: For the pygrib module, <code>grib_api/1.24.0-foss-2018b</code> is required in addition. '''Note''': These virtual environments will at some point be replaced by ones based on the new python versions 2.7.15 and 3.7.0 that are now available on cyclone. This change will be announced on dynlib-users@gfi.uib.no, please contact Clemens Spensberger if you are not on this list and like to be informed.
* R
*: ''<no module required>''

=== Text editors ===

* emacs
*: ''<no module required>''
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2018-10-05T13:36:01Z

Csp001: /* Data analysis and plotting */

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>CDO</code>, <code>CDO/1.9.5-foss-2018b</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* Matlab
*: <code>Matlab</code>, <code>Matlab/2018a</code>
* NCL
*: ''Currently unavailable''
* nco
*: ''Currently unavailable''
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: Temporary solution, use one of the two below commands to enable the virtual environment:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.5.
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3/bin/activate</code> for python 3.4.9.
*: For the pygrib module, <code>grib_api/1.24.0-foss-2018b</code> is required in addition. '''Note''': These virtual environments will at some point be replaced by ones based on the new python versions 2.7.15 and 3.7.0 that are now available on cyclone. This change will be announced on dynlib-users@gfi.uib.no, please contact Clemens Spensberger if you are not on this list and like to be informed.
* R
*: ''Currently unavailable''

=== Text editors ===

* emacs
*: ''<no module required>''
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2018-10-05T11:43:35Z

Csp001: /* Data analysis and plotting */

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>CDO</code>, <code>CDO/1.9.5-foss-2018b</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* Matlab
*: ''Currently unavailable''
* NCL
*: ''Currently unavailable''
* nco
*: ''Currently unavailable''
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: Temporary solution, use one of the two below commands to enable the virtual environment:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.5.
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3/bin/activate</code> for python 3.4.9.
*: For the pygrib module, <code>grib_api/1.24.0-foss-2018b</code> is required in addition. '''Note''': These virtual environments will at some point be replaced by ones based on the new python versions 2.7.15 and 3.7.0 that are now available on cyclone. This change will be announced on dynlib-users@gfi.uib.no, please contact Clemens Spensberger if you are not on this list and like to be informed.
* R
*: ''Currently unavailable''

=== Text editors ===

* emacs
*: ''<no module required>''
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2018-10-05T11:40:08Z

Csp001: /* Compilers and libraries */

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Hexagon-specific modules are now no longer listed and available on cyclone. All packages listed with this command should work, so please report to <code>support@hpc.uib.no</code> if they do not.

=== Data analysis and plotting ===

* CDO
*: <code>cdo</code>, <code>cdo/1.6.2</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* Matlab
*: ''Currently unavailable''
* NCL
*: ''Currently unavailable''
* nco
*: ''Currently unavailable''
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: Temporary solution, use one of the two below commands to enable the virtual environment:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.5.
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3/bin/activate</code> for python 3.4.9.
*: For the pygrib module, <code>grib_api/1.24.0-foss-2018b</code> is required in addition. '''Note''': These virtual environments will at some point be replaced by ones based on the new python versions 2.7.15 and 3.7.0 that are now available on cyclone. This change will be announced on dynlib-users@gfi.uib.no, please contact Clemens Spensberger if you are not on this list and like to be informed.
* R
*: ''Currently unavailable''

=== Text editors ===

* emacs
*: ''<no module required>''
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* HDF5 libraries
*: <code>HDF5/1.10.2-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>
* netcdf
*: For C-libaries: <code>netCDF/4.6.1-foss-2018b</code>,
*: For Fortran-libraries <code>netCDF-Fortran/4.4.4-foss-2018b</code>, compile with option <code>-I/shared/apps/netCDF-Fortran/4.4.4-foss-2018b/include</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2018-10-05T09:36:13Z

Csp001: /* Available software */

Using cyclone

2018-10-05T09:33:59Z

Csp001: /* Compilers and libraries */

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Please be aware that some of these modules will be specific to hexagon and it's cray architecture. Hence module names containing "cray" might not work on cyclone, although some exceptions are known to exist, see <code>netcdf</code> and <code>ncview</code>. Vice-versa, if the module name contains "foss", the module will be specific to cyclone and might not work on hexagon.

=== Data analysis and plotting ===

* CDO
*: <code>cdo</code>, <code>cdo/1.6.2</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* Matlab
*: ''Currently unavailable''
* NCL
*: ''Currently unavailable''
* nco
*: ''Currently unavailable''
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: Temporary solution, use one of the two below commands to enable the virtual environment:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.5.
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3/bin/activate</code> for python 3.4.9.
*: For the pygrib module, <code>grib_api/1.24.0-foss-2018b</code> is required in addition. '''Note''': These virtual environments will at some point be replaced by ones based on the new python versions 2.7.15 and 3.7.0 that are now available on cyclone. This change will be announced on dynlib-users@gfi.uib.no, please contact Clemens Spensberger if you are not on this list and like to be informed.
* R
*: ''Currently unavailable''

=== Text editors ===

* emacs
*: ''<no module required>''
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>
* netcdf
*: <code>netCDF/4.6.1-foss-2018b</code>, <code>netCDF-Fortran/4.4.4-foss-2018b</code>
* HDF5 libraries
*: <code>module load HDF5/1.10.2-foss-2018b</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2018-10-05T09:31:57Z

Csp001:

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Please be aware that some of these modules will be specific to hexagon and it's cray architecture. Hence module names containing "cray" might not work on cyclone, although some exceptions are known to exist, see <code>netcdf</code> and <code>ncview</code>. Vice-versa, if the module name contains "foss", the module will be specific to cyclone and might not work on hexagon.

=== Data analysis and plotting ===

* CDO
*: <code>cdo</code>, <code>cdo/1.6.2</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* Matlab
*: ''Currently unavailable''
* NCL
*: ''Currently unavailable''
* nco
*: ''Currently unavailable''
* ncview
*: <code>ncview</code>, <code>ncview/2.1.7-foss-2018b</code>. Load only when needed! The package is currently known to break some GUI programs like gedit and gvim.
* python, plus selection of scientific packages
*: Temporary solution, use one of the two below commands to enable the virtual environment:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.5.
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3/bin/activate</code> for python 3.4.9.
*: For the pygrib module, <code>grib_api/1.24.0-foss-2018b</code> is required in addition. '''Note''': These virtual environments will at some point be replaced by ones based on the new python versions 2.7.15 and 3.7.0 that are now available on cyclone. This change will be announced on dynlib-users@gfi.uib.no, please contact Clemens Spensberger if you are not on this list and like to be informed.
* R
*: ''Currently unavailable''

=== Text editors ===

* emacs
*: ''<no module required>''
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>. '''Note the upper-case''' module name, there is also a small-case <code>gcc</code>.
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>
* netcdf
*: <code>netCDF/4.6.1-foss-2018b</code>, <code>netCDF-Fortran/4.4.4-foss-2018b</code>
* HDF5 libraries
*: <code>module load HDF5/1.10.2-foss-2018b</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2018-10-05T09:21:03Z

Csp001:

Using cyclone

2018-10-05T08:11:38Z

Csp001: /* Text editors */

Using cyclone

2018-10-05T08:11:11Z

Csp001:

Using cyclone

2018-10-05T08:10:23Z

Csp001:

Using cyclone

2018-10-04T13:31:22Z

Csp001:

== Connection and first steps ==

Use ssh to connect
<pre>ssh -Y <username>@cyclone.hpc.uib.no</pre>
or just simply:
<pre>ssh -Y cyclone.hpc.uib.no</pre>
if you're connecting from a computer where you are logged in under the same name. When you are connecting for the first time, you will be asked to verify a signature. Reply "yes" to this question.

=== Home directories ===

<code>cyclone.hpc.uib.no</code> shares home directories with the new hexagon cluster. These home directories are separate from your standard UiB home directory. The contents of your home directories will not be synced, so you will manually need to transfer your scripts to the new system.

=== How to access software ===

In contrast to the old skd-cyclone, most scientific software is only available through software modules. Modules need to be loaded manually before the respective software can be used. We use software modules, because they provide are a clean and handy way to offer conflicting software or software versions: Instead of updating software and potentially breaking user scripts and programs new software is then made available in parallel to those that require it.

=== Start-up scripts ===

It might be handy to automatically load modules for software that you use frequently every time you login to cyclone. To accomplish that for bash, there are two relevant files, <code>$HOME/.bashrc</code> and <code>$HOME/.bash_profile</code> . <code>.bash_profile</code> should contain things that need to be defined at login time only, like <code>PATH</code> and other environment variables, startup programs, etc. You just need things once, not in every shell you open. In most cases, you also need the things from <code>.bashrc</code> in your login shell. That's why <code>.bash_profile</code> sources <code>.bashrc</code> as well, but .bashrc doesn't usually source <code>.bash_profile</code>. In contrast, <code>.bashrc</code> should typically contain things you want to set in every shell you open, like aliases, functions, etc. These are per shell session items that are not inherited from environment ([https://unix.stackexchange.com/questions/346336/why-have-both-bash-profile-and-bashrc source and detailed explanation]).

==== An example <code>.bash_profile</code> for inspiration ====

<pre>module load cdo/1.6.9
module load ncarg/6.3.0-login

alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi</pre>

==== An example <code>.bash_profile</code> for inspiration ====

<pre>alias rm="rm -i"
alias cp="cp -i"
alias erai="cd /Data/skd/share/Reanalysis/ERA_INTERIM/6HOURLY/"</pre>

== Available software ==

Below is a list of frequently used software and which module to load on the new cyclone. Relevant module names are printed like for <code>matlab/2015b</code>. Modules can be loaded by <code>module load <module name></code>, and unloaded <code>module unload <module name></code>. [[Using modules on cyclone|More details on the module system]].

To list all available modules, use the command
<pre>module avail</pre>

Please be aware that some of these modules will be specific to hexagon and it's cray architecture. Hence module names containing "cray" might not work on cyclone, although some exceptions are known to exist, see <code>netcdf</code> and <code>ncview</code>. Vice-versa, if the module name contains "foss", the module will be specific to cyclone and might not work on hexagon.

=== Data analysis and plotting ===

* CDO
*: <code>cdo</code>, <code>cdo/1.6.2</code>
* Dynlib
*: See temporary solution for python. Requires in addition <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code> and <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>.
* Matlab
*: <code>matlab</code>, <code>matlab/2015b</code>
* NCL
*: <code>ncarg</code>, <code>ncarg/6.0.0-login</code>
* nco
*: <code>nco</code>
* ncview
*: <code>ncview</code>, based on the <code>cray-netcdf</code> package.
* python, plus selection of scientific packages
*: Temporary solution, use one of the two below commands to enable the virtual environment:
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie2/bin/activate</code> for python 2.7.
*: <code>source /Data/gfi/users/local/share/virtualenv/dynpie3/bin/activate</code> for python 3.4.
*: For the pygrib module, <code>grib_api/1.24.0-foss-2018b</code> is required in addition.
* R
*: <code>R</code>, <code>R/3.2.5</code>

=== Text editors ===

* emacs
*: <code>emacs</code>
* gedit
*: ''<no module required>''
* gvim
*: ''<no module required>''
* vi(m)
*: ''<no module required>''

=== Compilers and libraries ===

* blas
*: <code>OpenBLAS/0.3.1-GCC-7.3.0-2.30</code>
* gcc, gfortran
*: <code>GCC</code>, <code>GCC/7.3.0-2.30</code>. '''Note the upper-case''' module name, there is also a small-case <code>gcc</code>.
* grib_api
*: <code>grib_api/1.24.0-foss-2018b</code>
* lapack
*: <code>ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1</code>
* netcdf
*: netCDF libraries installed in the folder <code>/opt/cray/netcdf/4.4.1.1/GNU/5.1</code>. You'll hence need to include <code>-I/opt/cray/netcdf/4.4.1.1/GNU/5.1/include -L/opt/cray/netcdf/4.4.1.1/GNU/5.1/lib</code> in your compile command.
* HDF5 libraries
*: <code>module load HDF5/1.10.2-foss-2018b</code>

== Accessing the data from your own machines ==

Note: From your personal machines you will need to be connected to the UiB VPN to be able to mount the following network drives.

On MacOS you can mount folders through <code>Finder > Go > Connect to Server ...</code>. In the dialogue window that pops up, enter
<pre>smb://<user name>@leo.hpc.uib.no/gfi</pre>
as the '''Server Address'''. You might want to replace <code>gfi</code> by <code>skd</code> to access the skd disks if that is your primary affiliation.
On Ubuntu this is very similar: <code>Files > Go > Enter Location ...</code>. Enter the address: <pre>smb://<user name>@leo.hpc.uib.no/gfi</pre> and enter your password in the next pop-up window, while keeping "UiB" in the "Domain" field.

Using cyclone

2018-10-02T13:57:05Z

Csp001: /* Available software */

Using cyclone

2018-10-02T13:55:52Z

Csp001: /* Available software */

The GFI computing system

2018-09-29T13:52:56Z

Csp001:

The Geophysical Institute has acquired a new computing system named '''cyclone.hpc.uib.no''' which replaces the system '''skd-cyclone.klientdrift.uib.no''' from Summer 2018.

'''A detailed overview over the system [[:File:GFI_cyclone_overview.pdf|can be downloaded here as PDF presentation]].''' The following page contains the system specifications, users might instead want to learn [[Using cyclone]] or [[Using modules on cyclone]].

Please notify the HPC support [mailto:support@hpc.uib.no support@hpc.uib.no] in any case of problems or questions.

==Users==

The intended users for this system are:

* BSc students (coursework)

* MSc students (coursework, thesis)

* PhD students

* researchers

==Requirements==

Users should be able to use the system in interactive use (klick and point, typing) and in batch use (using shell scripts). Typical tasks are data analysis, plotting. GFI will also run routine data processing of observations and forecasts on this system.

Therefore, we required the system to be or have

* low threshold access (easy to use)

* interactive use

* safe usage (against unintentional overuse)

* optimized for serial I/O (as is typical for post-processing tasks)

* single-node parallelisation jobs

* lifetime of 5-7 years

==Computing performance==

The computing performance has been enhanced substantially: The new system is a Dell PowerEdge R740 Server configuration with the following characteristics:

* Intel Xeon Gold 6140M, 18 cores, 72 threads, 2.3GHz, 25MB L3 cache

* 1.5 TB DDR4-2666 memory

* 2 NVIDIA Tesla GPU, 12 GB

[[File:dell.jpg|400px]]

==System characteristics==

Here are the key facts about using the new system

* For transition, you will need to recompile your code (if it is compiled code) for the operating system CentOS linux. This is the same operating system as on the UiB high-performace compute system Hexagon.

* There is no queue system on the new cyclone. Users can submit to the hexagon queue from cyclone (acts as login node).

* There is a 30-50% resource limitation per user. This will keep individual users from accidentally brining down the system.

* Different software configurations cand be activated using the command module

* Access to data storage will be maintained using existing paths, such as /Data/gfi.

* The same and additional software packages are available (your suggestions?)

* The system is maintained by the experts from UiB's HPC group. This should be an advantage for GFI.

==GPU acceleration==

The new cyclone is equipped with very advanced computing power. There are two Tesla P100 Graphics Processing Units (GPUs) build into the server. This will boost parallel computation power for software that can make use of this feature. Native programming languages, standard libraries, as well as Matlab and python can make use of GPU acceleration for compute operations. GFI is planning on offering courses to introduce to GPU programming.

[[File:NVIDIA_GPU.jpg|400px]]

Here are the facts about the GPU accelerators:

* each Tesla P100 has 3584 cores

* memory of 12 GB per GPU

* both GPUs can also be used in combination

* programming using CUDA, DirectCompute, OpenCL, OpenACC

* some libraries are already optimized for GPU usage

* first optimisation step are OpenACC compiler statements

* bottleneck in GPU programming is to get data on/off the GPU

Using modules on cyclone

2018-09-29T13:50:45Z

Csp001:

== Using modules on cyclone==

This page documents how to use Modulefiles on the Abel (HPC for UiO) and Colossus (HPC for TSD) clusters. Same procedure applies on cyclone. For some specific documentation on available modules refer to [[Using cyclone]].

To simplify setting up environments for compilers, MPI-versions and some installed applications, the clusters have the [http://modules.sourceforge.net Environment Modules package] installed. This provides means for dynamic modification of a user's environment via modulefiles.

Each modulefile contains the information needed to configure the shell for an environment. Typically, a modulefile modifies environment variables like PATH, MANPATH, LD_LIBRARY_PATH, CPATH and PKG_CONFIG_PATH to give access to an application or library.

Modulefiles can be used from most shells, as well as Perl and Python. Modulefiles can be loaded/unloaded on the command line or within your scripts by typing:

<code>
module load modulefile

module unload modulefile
</code>

(On Colossus, the module commands can only be used in job scripts.) You can also ask for a specific version of a modulefile:

<code>
module load modulefile/version
</code>

For the purpose of reproducability, we encourage users to load specific versions of modulefiles. Also, we recommend using

<code>
module purge
</code>

prior to any module load commands in job scripts, to prevent inheriting environment variables set by module commands in the shell used when submitting the job.

The available modulefiles can be listed by module avail. Example output:

<nowiki>
$ module avail
------------------------ /usr/share/Modules/modulefiles -------------------------
dot module-cvs module-info modules null use.own

--------------------------- /cluster/etc/modulefiles ----------------------------
454apps/2.8(default) mcmcphase/2.0(default)
R/2.15.1(default) microbiomeutil/20110519(default)
R/2.15.1.shlib migrate/3.3.2(default)
abyss/1.3.4(default) mothur/1.26.0(default)
adf/2010.02b(default) mrbayes/3.2.1(default)
adf/2012.01b muscle/3.8.31(default)
ampliconnoise/1.25(default) ncl/2.1.18(default)
beagle/1.0(default) newbler/2.8(default)
[...]
</nowiki>

You can also specify a name:

<nowiki>
$ module avail blast
--------------------------- /cluster/etc/modulefiles ----------------------------
blast/2.2.26(default) blast+/2.2.26(default)
</nowiki>

You will get a list of current loaded modulefiles by

<nowiki>
$ module list
Currently Loaded Modulefiles:
1) intel/2011.10 2) R/2.15.1
</nowiki>

A help text exists for most of the modulefiles; to view it, type

<code>
module help modulefile
</code>

To view exactly what a modulefile is doing to your environment, type

<code>
module show modulefile
</code>

For further documentation, please refer to the [http://modules.sourceforge.net Environment Modules homepage]

'''Personalize default modulefiles'''

You may add loading of modulefiles to your .bash_profile file to make sure your favorite modulefile is always loaded when logging in. For instance, to always have the intel modulefile load on login, add:

<code>
module load intel
</code>

to the .bash_profile file.

Using cyclone

2018-09-29T13:48:40Z

Csp001: /* Accessing the data from your own machines */

Using cyclone

2018-09-29T13:41:45Z

Csp001: /* Available software */

Using cyclone

2018-09-29T13:12:23Z

Csp001:

Using cyclone

2018-09-29T13:09:49Z

Csp001: Created page with "== Connection and first steps == Use ssh to connect <pre>ssh -Y <username>@cyclone.hpc.uib.no</pre> or just simply: <pre>ssh -Y cyclone.hpc.uib.no</pre> if you're connecting..."

Main Page

2018-09-29T12:45:05Z

Csp001: /* IT */

== Geophysical Institute ==

[[File:GFI.jpg]]

==Research and PhD/Postdoc Groups==
===[[Meteorology]]===
===[[ResClim Bergen subgroup]]===

==IT==
===[[The GFI computing system]]===
===[[Using cyclone]]===
===[[Using modules on cyclone]]===
===[[Bedymo]]===
===[[Dynlib]]===
===[[Forecast plotting]]===
===[[Git]]===
===[[NCL]]===
===[[Python]]===
===[[WRF]]===
===[[WaterSip]]===
===[[Using the queue system on skd-cyclone]]===

==Social Activities and Groups==
===[[Football]]===
===[[Gale Brewing Club]]===
===[[Geosupen]]===
===[[GFI-social]]===
===[[Kakeklubben]]===
===[[Music]]===
===[[PhD Forum]]===
===[[Schafkopf]]===
===[[Volleyball]]===

[[Category:IT]]

Dynlib utils functions

2017-09-18T14:14:46Z

Csp001: Outdated and obsolete, to be deleted.

Dynlib diag functions

2017-09-18T14:14:08Z

Csp001: Outdated and obsolete, to be deleted.

Dynlib derivatives functions

2017-09-18T14:13:22Z

Csp001: Outdated and obsolete, to be deleted.

Git

2017-09-18T14:09:45Z

Csp001: Updated paths

The development of [[Bedymo]] and [[Dynlib]] is coordinated with the version control system [http://git-scm.com git]. git is a ''distributed'' version control system in that there is no central repository required, as would be for older systems like [http://subversion.apache.org/ svn (subversion)] or [http://cvs.nongnu.org/ cvs]. Any central repository is only central by ''convention''.

== Background ==

=== Common ideas behind all version control systems ===

All version control systems store the history of a set of files and directories in a '''repository''', and are able to restore the file as it used to be in a previous version. In addition to the actual changes in the file(s) all systems also keep meta-information like the editing user, the date and time of the changes as well as a small description of the changes. The development of the project is tracked through '''commits''', which creates and stores a new '''version''' or '''revision''' of all changed files.

=== Distributed version control ===

In a distributed version control system like git, there is no central repository. Every copy of the repository is technically equal, and is equally able to crate new '''versions'''. In a non-distributed version control system, only the central repository residing on a (publicly available) server is able to create new versions. Hence, you need connection to that server to be able to commit changes.

=== Advantages of distributed version control ===

Apart from the ability to track changes and view the entire history of the project also when offline (on a cruise, plane, conference or summer school with limited connectivity) the main advantage of distributed version control systems lies in the flexibility of the work flow, which can be easily setup to match the work groups inner workings: Often several people work on the same tool or model, but develop in different directions. Using the setup suggested below those people can still share bug fixes easily and merge there developments in the end.

=== Disadvantages of distributed version control ===

The added flexibility of a distributed system comes at the cost of loosing an intuitive way to address the different revisions. Using a central repository, one simply increases an internal revision counter, such that revision 765 supersedes revision 764. Without a central repository there is noone that could assign those kind of numbers. git uses the SHA1-hash of the commited files as an identifier for the revision, e.g. something like <code>bbe0e301cb39b597a49b3819ccf8b0d08d817d2e</code>. One need however only type the first couple of symbols until the identifier becomes unique. In this example taken from dynlib, <code>bbe0</code> is enough to uniquely identify the revision. In addition one can always manually assign human-friendlier names such as <code>gamma-0.4.2</code> for the above revision.

== Usage for [[Bedymo]] and [[Dynlib]] ==

All instructions are shown here for dynlib. The setup for bedymo is indentical, so that you need only replace dynlib by bedymo to obtain the corresponding command for bedymo.

=== Obtaining dynlib ===

# The official source code repository resides a shared user directory. The <code>clone</code> command copies the entire repository into a dynlib folder in your current working directory.
#:<code>git clone /Data/gfi/users/local/src/dynlib.git</code>
# Change into the dynlib folder.
#:<code>cd dynlib</code>
# Compile the library.
#:<code>./compile</code>

=== Updating dynlib ===

# The repository you cloned from is saved in the git configuration as <code>origin</code> designating your ''source repository''. That's where the following command fetches updates from.
#:<code>git pull</code>
# Re-Compile the library.
#:<code>./compile</code>

=== Fetching updates by some other user ===

Let's assume the user <code>tsp065</code> has coded some very interesting routines that have however not yet found thier way in the official respository.
#Then, if <code>tsp065</code> followed the instructions in the [[#Developing dynlib]] section, you can add Thomas' repository as one of your ''remote repositories'' by
#:<code>git remote add thomas /Data/gfi/users/local/src/dynlib_tsp065.git</code>
#:The name <code>thomas</code> is an aribtrary name for the remote repository.
# Then you can fetch updates from Thomas' respository just like from the official one.
#:<code>git pull thomas</code>
# Re-Compile the library.
#:<code>./compile</code>

== Developing Bedymo and Dynlib ==

=== Locally saving your changes ===

Suppose you have edited some of the Fortran95 source code files, and want to save and share them.
# Then first you have to commit the new version into your local development repository.
#:<code>git commit -a</code>
#:Give a sensible and brief description of your changes in the editor that is opened (automatically)

=== Setup of your personal publicly shared repository ===

# Creating a ''bare'' repository for sharing.
#:<code>git clone --bare . /Data/gfi/users/local/src/dynlib_<your-ID>.git</code>
# It is convenient to again setup a named ''remote repository''.
#:<code>git remote add own /Data/gfi/users/local/src/dynlib_<your-ID>.git</code>

=== Sharing your changes ===

# Then you have to ''push'' your new version to a repository that other people can read.
#:<code>git push own</code>

== More information ==

# [http://git-scm.com/book The git book]

Dynlib

2017-09-18T14:04:59Z

Csp001: /* Obtaining dynlib */

== [http://folk.uib.no/csp001/dynlib_doc/ Documentation] ==

The steps necessary to obtain dynlib are described below. A more thorough documentation is compiled in [http://folk.uib.no/csp001/dynlib_doc/ the main documentation website].

== Use the centrally installed dynlib ==

Dynlib is installed centrally for python 2.7 and python 3.4 in the python environments at <code>/Data/gfi/users/local/share/virtualenv/dynpie2</code> and <code>/Data/gfi/users/local/share/virtualenv/dynpie3</code>. You'll only have to activate one of these python enviroments to start using dynlib:
<pre>source /Data/gfi/users/local/share/virtualenv/dynpieX/bin/activate</pre>
In this command <code>X=2</code> for python 2.7 and <code>X=3</code> for python 3.4. For convenience add this command to your <code>~/.bash_profile</code> to activate the respective python environment automatically at each login.

'''Note''': For some types of login <code>.bash_profile</code> is not taken into account. In case you'll experience problems create a symbolic link <code>~/.bashrc</code> to point to the <code>~/.bash_profile</code> and re-login.

== Quick start to developing with dynlib ==

The following procedure is only necessary if you want to start developing dynlib further, for example if you want to add your own functions to dynlib. If you only want to use dynlib, the procedure in the above section is all you need.

=== Obtaining dynlib ===

# Copying the source code repository
#:<code>$ git clone /Data/gfi/users/local/src/dynlib.git</code>
#:To clone the repository to your laptop or any machine outside the UiB network, use
#:<code>$ git clone <username>@login.uib.no:/Data/gfi/users/local/src/dynlib.git</code>
# Change into the dynlib folder
#:<code>$ cd dynlib</code>
# Compile the library
#:<code>$ ./compile</code>
# (known broken right now) Make sure everything works as expected
#:<code>$ ./test</code>
# To use your personal development version of dynlib instead of the centrally installed one, create a symlink in your scripts folder that points to the development version
#:<code><in script folder>$ ln -s <path-to-dynlib>/lib dynlib</code>
Happy developing!

=== Editing the Fortran code ===

The fortran code lives in <code>lib/fortran</code> directory. At the moment there are 16 source code files 
<nowiki>$ ls *.f90
config.f90 detect_lines.f90 ellipse.f90 stat.f90
const.f90 detect_rwb_contour.f90 interpol.f90 tend.f90
derivatives.f90 diag.f90 kind.f90 thermodyn.f90
detect.f90 diag_tend.f90 sphere.f90 utils.f90</nowiki>
The most important are <code>diag.f90</code> which contains subroutines that calculate various diagnostics, and <code>detect.f90</code> which contains feature detection algorithms. Changed Fortran sources need to be recompiled, again using
:<code>$ ./compile</code>

=== [[git|Version control]] ===

The changes you made to the source code files can be listed by
:<code>$ git status</code>
or viewed in detailed diff-comparisons by
:<code>$ git diff</code>
or for one file only
:<code>$ git diff <filename></code>

In case you want to undo your changes, you can revert any file to the last committed version by
:<code>git checkout <filename></code>

Commit your changes from time to time and give a sensible and brief description of your changes in the editor that is opened (automatically)
:<code>$ git commit -a</code>
The commit is then stored in your copy of the source code repository, but not yet available for others, which allows you to also commit work-in-progress.

A more thorough introduction to the version control system is given [[git|here]] or on the [http://git-scm.com/book official documentation].

=== Using the Fortran functions ===

An example python script which calculates deformation using the Fortran function is provided in the [http://folk.uib.no/csp001/dynlib_doc/examples.html documentation].

== Dynlib functions ==

The functions are classified into different categories. All functions and categories listed in the [http://folk.uib.no/csp001/dynlib_doc/apidoc.html API documentation].

[[Category:Dynlib]]
[[Category:Libraries]]

Dynlib

2017-09-18T14:04:15Z

Csp001: /* Obtaining dynlib */

== [http://folk.uib.no/csp001/dynlib_doc/ Documentation] ==

The steps necessary to obtain dynlib are described below. A more thorough documentation is compiled in [http://folk.uib.no/csp001/dynlib_doc/ the main documentation website].

== Use the centrally installed dynlib ==

Dynlib is installed centrally for python 2.7 and python 3.4 in the python environments at <code>/Data/gfi/users/local/share/virtualenv/dynpie2</code> and <code>/Data/gfi/users/local/share/virtualenv/dynpie3</code>. You'll only have to activate one of these python enviroments to start using dynlib:
<pre>source /Data/gfi/users/local/share/virtualenv/dynpieX/bin/activate</pre>
In this command <code>X=2</code> for python 2.7 and <code>X=3</code> for python 3.4. For convenience add this command to your <code>~/.bash_profile</code> to activate the respective python environment automatically at each login.

'''Note''': For some types of login <code>.bash_profile</code> is not taken into account. In case you'll experience problems create a symbolic link <code>~/.bashrc</code> to point to the <code>~/.bash_profile</code> and re-login.

== Quick start to developing with dynlib ==

The following procedure is only necessary if you want to start developing dynlib further, for example if you want to add your own functions to dynlib. If you only want to use dynlib, the procedure in the above section is all you need.

=== Obtaining dynlib ===

# Copying the source code repository
#:<code>$ git clone /Data/gfi/users/local/src/dynlib.git</code>
#:To clone the repository to your laptop or any machine outside the UiB network, use
#:<code>$ git clone <username>@login.uib.no:/Data/gfi/users/local/src/dynlib.git</code>
# Change into the dynlib folder
#:<code>$ cd dynlib</code>
# Compile the library
#:<code>$ ./compile</code>
# (known broken right now) Make sure everything works as expected
#:<code>$ ./test</code>
# To use your personal development version of dynlib instead of the centrally installed one, create a symlink in your scripts folder that points to the development version
#:<code><in script folder>$ ln -s <path-to-dynlib>/lib dynlib
Happy developing!

=== Editing the Fortran code ===

The fortran code lives in <code>lib/fortran</code> directory. At the moment there are 16 source code files 
<nowiki>$ ls *.f90
config.f90 detect_lines.f90 ellipse.f90 stat.f90
const.f90 detect_rwb_contour.f90 interpol.f90 tend.f90
derivatives.f90 diag.f90 kind.f90 thermodyn.f90
detect.f90 diag_tend.f90 sphere.f90 utils.f90</nowiki>
The most important are <code>diag.f90</code> which contains subroutines that calculate various diagnostics, and <code>detect.f90</code> which contains feature detection algorithms. Changed Fortran sources need to be recompiled, again using
:<code>$ ./compile</code>

=== [[git|Version control]] ===

The changes you made to the source code files can be listed by
:<code>$ git status</code>
or viewed in detailed diff-comparisons by
:<code>$ git diff</code>
or for one file only
:<code>$ git diff <filename></code>

In case you want to undo your changes, you can revert any file to the last committed version by
:<code>git checkout <filename></code>

Commit your changes from time to time and give a sensible and brief description of your changes in the editor that is opened (automatically)
:<code>$ git commit -a</code>
The commit is then stored in your copy of the source code repository, but not yet available for others, which allows you to also commit work-in-progress.

A more thorough introduction to the version control system is given [[git|here]] or on the [http://git-scm.com/book official documentation].

=== Using the Fortran functions ===

An example python script which calculates deformation using the Fortran function is provided in the [http://folk.uib.no/csp001/dynlib_doc/examples.html documentation].

== Dynlib functions ==

The functions are classified into different categories. All functions and categories listed in the [http://folk.uib.no/csp001/dynlib_doc/apidoc.html API documentation].

[[Category:Dynlib]]
[[Category:Libraries]]

Dynlib

2017-09-18T14:00:38Z

Csp001: /* Using the Fortran functions */

== [http://folk.uib.no/csp001/dynlib_doc/ Documentation] ==

The steps necessary to obtain dynlib are described below. A more thorough documentation is compiled in [http://folk.uib.no/csp001/dynlib_doc/ the main documentation website].

== Use the centrally installed dynlib ==

Dynlib is installed centrally for python 2.7 and python 3.4 in the python environments at <code>/Data/gfi/users/local/share/virtualenv/dynpie2</code> and <code>/Data/gfi/users/local/share/virtualenv/dynpie3</code>. You'll only have to activate one of these python enviroments to start using dynlib:
<pre>source /Data/gfi/users/local/share/virtualenv/dynpieX/bin/activate</pre>
In this command <code>X=2</code> for python 2.7 and <code>X=3</code> for python 3.4. For convenience add this command to your <code>~/.bash_profile</code> to activate the respective python environment automatically at each login.

'''Note''': For some types of login <code>.bash_profile</code> is not taken into account. In case you'll experience problems create a symbolic link <code>~/.bashrc</code> to point to the <code>~/.bash_profile</code> and re-login.

== Quick start to developing with dynlib ==

The following procedure is only necessary if you want to start developing dynlib further, for example if you want to add your own functions to dynlib. If you only want to use dynlib, the procedure in the above section is all you need.

=== Obtaining dynlib ===

# Create a new folder for the project that'll use dynlib, and go into that directory.
#:<code>$ mkdir <project-name></code>
#:<code>$ cd <project-name></code>
# Copying the source code repository
#:<code>$ git clone /Data/gfi/users/local/src/dynlib.git</code>
#:To clone the repository to your laptop or any machine outside the UiB network, use
#:<code>$ git clone <username>@login.uib.no:/Data/gfi/users/local/src/dynlib.git</code>
# Change into the dynlib folder
#:<code>$ cd dynlib</code>
# Compile the library
#:<code>$ ./compile</code>
# (known broken right now) Make sure everything works as expected
#:<code>$ ./test</code>
Happy developing!

=== Editing the Fortran code ===

The fortran code lives in <code>lib/fortran</code> directory. At the moment there are 16 source code files 
<nowiki>$ ls *.f90
config.f90 detect_lines.f90 ellipse.f90 stat.f90
const.f90 detect_rwb_contour.f90 interpol.f90 tend.f90
derivatives.f90 diag.f90 kind.f90 thermodyn.f90
detect.f90 diag_tend.f90 sphere.f90 utils.f90</nowiki>
The most important are <code>diag.f90</code> which contains subroutines that calculate various diagnostics, and <code>detect.f90</code> which contains feature detection algorithms. Changed Fortran sources need to be recompiled, again using
:<code>$ ./compile</code>

=== [[git|Version control]] ===

The changes you made to the source code files can be listed by
:<code>$ git status</code>
or viewed in detailed diff-comparisons by
:<code>$ git diff</code>
or for one file only
:<code>$ git diff <filename></code>

In case you want to undo your changes, you can revert any file to the last committed version by
:<code>git checkout <filename></code>

Commit your changes from time to time and give a sensible and brief description of your changes in the editor that is opened (automatically)
:<code>$ git commit -a</code>
The commit is then stored in your copy of the source code repository, but not yet available for others, which allows you to also commit work-in-progress.

A more thorough introduction to the version control system is given [[git|here]] or on the [http://git-scm.com/book official documentation].

=== Using the Fortran functions ===

An example python script which calculates deformation using the Fortran function is provided in the [http://folk.uib.no/csp001/dynlib_doc/examples.html documentation].

== Dynlib functions ==

The functions are classified into different categories. All functions and categories listed in the [http://folk.uib.no/csp001/dynlib_doc/apidoc.html API documentation].

[[Category:Dynlib]]
[[Category:Libraries]]