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doku:vsc5quickstart [2023/01/05 22:16] – [Submit a Job] goldenbergdoku:vsc5quickstart [2023/05/17 15:00] – msiegel
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 ====== Quick start guide for VSC-5 ====== ====== Quick start guide for VSC-5 ======
- 
-**Status: 2022/04** 
- 
-This page is under construction. 
  
 ===== Connecting ===== ===== Connecting =====
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-===== Loading Modules & Spack Environments =====+===== Software installations =====
  
-Different CPUs come with different compilers, so we use +==== New SPACK without environments ====
-the new spack feature ''environment'' to make sure to choose the right +
-package. +
  
-On login the default ''spack environment'' (zen3) is loaded +Having worked with spack environments for some time, we have encountered several severe issues which have convinced us that we need to find a more practical way of maintaining software packages at VSC.
-automatically, so only modules that run on AMD processors are visible +
-with ''spack find''.+
  
-On VSC5 no default modules are loaded. Please do that by yourself +There are now three separate spack installation trees corresponding to the CPU/GPU architectures on VSC:
-using ''spack load <module>'' or ''module load <module>''. +
  
-Find the official SPACK documentation at https://spack.readthedocs.io/+  * skylake - Intel CPUs; works on Intel Skylake and Cascadelake CPUs 
 +  * zen - AMD CPUs; works on Zen 2 and 3 CPUs 
 +  * cuda-zen - AMD CPUs + NVIDIA GPUs; works on all nodes equipped with graphics cards
  
- +By default the spack installation tree suitable for the current compute/login node is activated and will be indicated by a **prefix** on the command line, e.g.:
-==== List Spack Environments ==== +
- +
-Type ''spack env list'' to see which environments are available and +
-which one is active.+
  
 <code> <code>
-$ spack env list +zen [user@l51 ~]$
-==> 2 environments +
-    cascadelake  zen3+
 </code> </code>
  
-The current ''spack environment'' is also shown in your prompt:+Read more about SPACK at: 
 +  * [[doku:spack-transition | Transition to new SPACK without Environments]] 
 +  * [[doku:spack]] 
 +  * [[https://spack.readthedocs.io/en/latest/basic_usage.html|Official documentation of SPACK]]
  
-<code> 
-(zen3) [myname@l55 ~]# 
-</code> 
  
-Mind that if your prompt is changed later, like when loading a ''python +==== Load a module ====
-environment'' using ''conda'', the correct ''spack environment'' might +
-not be shown correctly in your prompt.+
  
-When a spack environment is activated, the command ''spack find -l'' lists those packages available for the active +Most software is installed via SPACK, so you can use spack commands like ''spack find -ld xyz'' to get details about the installation. All these installations also provide a module, find available modules with ''module avail xyz'', and load with ''module load xyz''. See [[doku:spack|SPACK - a package manager for HPC systems]] for more information.
-environment.+
  
-The command ''module avail'' will also show only those modules that are compatible with the active +Some software is still installed by hand, find available modules with ''module avail xyz'', and load with ''module load xyz''.
-spack environment.+
  
  
-==== Change Spack Environment ==== +===== Compile code =====
- +
-If you want to look for a certain package that belongs to another +
-architecture, first change the spack environment: +
- +
-<code> +
-$ spacktivate <myenv> +
-$ spacktivate cascadelake +
-</code> +
- +
-Only then ''spack find'' will show the modules for the active environment (e.g. ''cascadelake''). +
- +
- +
-==== Save Spack Environment ==== +
- +
-The following creates a load script for your current spack environment +
-with all loaded modules: +
- +
-<code> +
-$ spack env loads -r  +
-</code> +
- +
-This creates a file called ''loads'' in the environment +
-directory. Sourcing that file in bash will make the environment +
-available to the user. The ''source loads'' command can be included in +
-''.bashrc'' files. The loads file may also be copied out of the +
-environment, renamed, etc. +
- +
- +
-==== Load a Module ==== +
- +
-Please always use spack, see [[doku:spack|SPACK - a package manager for +
-HPC systems]]. +
- +
- +
-===== Compile Code =====+
  
 A program needs to be compiled on the hardware it will later run A program needs to be compiled on the hardware it will later run
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 128 physical cores (core-id 0-127) and 256 virtual cores available. 128 physical cores (core-id 0-127) and 256 virtual cores available.
  
-The A100 GPU nodes have 512GB RAM and the NVIDIA A100 cards have 40GB RAM each. +The A100 GPU nodes have 512GB RAM and the two NVIDIA A100 cards have 40GB RAM each. 
-At the moment 40 GPU nodes are installed.+60 A100 nodes are installed.
  
 +The A40 GPU nodes have 256GB RAM and the two NVIDIA A40 cards have 46GB each.
 +45 A40 nodes are installed.
 <code> <code>
 $ nvidia-smi $ nvidia-smi
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 ===== SLURM ===== ===== SLURM =====
-**For the exact partition/queue setup see [[doku:vsc5_queue|Queue | Partition setup on VSC-5]]** +For the partition/queue setup see [[doku:vsc5_queue|Queue | Partition setup on VSC-5]]. 
- +type ''sinfo -o %P'' to see the available partitions.
-The following partitions are currently available: +
-<code> +
-$ sinfo -o %P +
-PARTITION +
-zen2_0256_a40x2 -> AMD CPU nodes with 2x AMD Epyc (Milan) and 2x NIVIDA A40 and 256GB RAM +
-jupyter -> reserved for the jupyterhub +
-login5 -> login nodes, not an actual slurm partition +
-zen3_2048 -> AMD CPU nodes with 2x AMD Epyc (Milan) and 2TB RAM +
-zen3_1024 -> AMD CPU nodes with 2x AMD Epyc (Milan) and 1TB RAM +
-zen3_0512* -> The default partition. AMD CPU nodes with 2x AMD Epyc (Milan) and 512GB RAM +
-cascadelake_0384 -> Intel CPU nodes with 2x Intel Cascadelake and 384GB RAM +
-zen3_0512_a100x2 -> AMD CPU nodes with 2x AMD Epyc (Milan) and 2x NIVIDA A100 and 512GB RAM +
- +
-</code> +
- +
-==== QoS ==== +
- +
-The following QoS are available for normal (=non private) projects: +
- +
-^QOS name ^ gives access to partition ^description^ +
-| | |  +
-|zen3_0512 | zen3_0512 | default | +
-|zen3_1024 | zen3_1024 | +
-|zen3_2048 | zen3_2048 | +
-|cascadelake_0384 | cascadelake_0384 | +
-|zen2_0256_a40x2 | zen2_0256_a40x2 | +
-|zen3_0512_a100x2 | zen3_0512_a100x2 | +
-|zen3_0512_devel | 5 nodes on zen3_0512 | +
  
 ==== Submit a Job ==== ==== Submit a Job ====
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 #SBATCH -J <meaningful name for job> #SBATCH -J <meaningful name for job>
 #SBATCH -N 1 #SBATCH -N 1
-#SBATCH --gres=gpu:2 
 ./my_program ./my_program
 </file> </file>
  • doku/vsc5quickstart.txt
  • Last modified: 2023/05/17 15:28
  • by msiegel