The GFI computing system: Difference between revisions

Latest revision as of 09:57, 2 March 2020

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 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 UiB support * https://hjelp.uib.no in any case of problems or questions. You may give your support request some ref. to HPC or "Group of scientific computing"

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 (click 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, 36 cores, 72 threads, 2.3GHz, 25MB L3 cache

1.5 TB DDR4-2666 memory

2 NVIDIA Tesla GPU, 12 GB

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.

There is no queue system on the new cyclone.

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

Different software configurations can 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.

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

@@ Line 3: / Line 3: @@
 '''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.
+Please notify the UiB support [https://hjelp.uib.no * https://hjelp.uib.no] in any case of problems or questions. You may give your support request some ref. to HPC or "Group of scientific computing"
@@ Line 20: / Line 20: @@
 ==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.
+Users should be able to use the system in interactive use (click 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
@@ Line 40: / Line 40: @@
 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
+* Intel Xeon Gold 6140M, 36 cores, 72 threads, 2.3GHz, 25MB L3 cache
 * 1.5 TB DDR4-2666 memory
@@ Line 52: / Line 52: @@
 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.
+* For transition, you will need to recompile your code (if it is compiled code) for the operating system CentOS linux.
-* There is no queue system on the new cyclone. Users can submit to the hexagon queue from cyclone (acts as login node).
+* There is no queue system on the new cyclone.
-* There is a 30-50% resource limitation per user. This will keep individual users from accidentally brining down the system.
+* There is a 30-50% resource limitation per user. This will keep individual users from accidentally bringing down the system.
-* Different software configurations cand be activated using the command module
+* Different software configurations can be activated using the command module
 * Access to data storage will be maintained using existing paths, such as /Data/gfi.