Difference: PALMA3 (19 vs. 20)

Revision 202017-03-02 - HolgerAngenent

Line: 1 to 1
 
META TOPICPARENT name="HPC"

PALMA-NG

Line: 21 to 21
 
  • p0kapp: 1 nodes for exclusive usage
  • hims: 4 nodes for exclusive usage
Added:
>
>
 

Software/The module concept

The software on palma-ng can be accessed via modules. These are small script that set environment variables (like PATH and LD_LIBRARY_PATH) pointing to the locations where the software is installed (this is mostly on network drives so that the software is available on every node in the cluster). The module system we use here is LMOD (1). In contrast to the older environment modules we used on PALMA I and NWZPHI, there is the new command "module spider". Please find more information on this below.

Line: 48 to 48
 
  • goolfc/2016.10 Only on the k20gpu nodes for CUDA

If you want to use the Intel compiler, you can type for example the following:

Deleted:
<
<
 
module add intel/2016b
Changed:
<
<
module av
>
>
module av
  and you will see the software that has been compiled with this version. Alternatively you can use the "module spider" command.
Line: 126 to 124
 

Starting jobs with MPI-parallel codes

mpirun will get all necessary information from SLURM, if submitted appropriately. If you for example want to start 128 MPI ranks distributed to four nodes, you could do this the following way:

Deleted:
<
<
 
srun -p normal --nodes=2 --ntasks=128 --ntasks-per-node=64 --pty bash
Changed:
<
<
mpirun ./program
>
>
mpirun ./program
  or for an non-interactive run or put those parameters in the batch script.
Line: 135 to 131
 or for an non-interactive run or put those parameters in the batch script.

For starting hybrid jobs (meaning that they are using MPI and OpenMP parallelization at the same time), you can use the --cpus-per-task switch.

Deleted:
<
<
 
srun -p normal --nodes=2 --ntasks=64 --ntasks-per-node=32 --cpus-per-task=2 --pty bash
Changed:
<
<
OMP_NUM_THREADS=2 mpirun ./program
>
>
OMP_NUM_THREADS=2 mpirun ./program
 

Show information about the queues

scontrol show partition
Line: 205 to 215
 
scontrol requeue <jobid>

-- Holger Angenent - 2016-08-22

Added:
>
>
 
META FILEATTACHMENT attachment="llview.png" attr="" comment="" date="1481027490" name="llview.png" path="llview.png" size="50475" user="h_5fzimm01" version="2"
Added:
>
>
META FILEATTACHMENT attachment="palma-ng_batchsystem.png" attr="" comment="" date="1488459211" name="palma-ng_batchsystem.png" path="palma-ng_batchsystem.png" size="24143" user="h_5fzimm01" version="2"
 
This site is powered by the TWiki collaboration platform Powered by PerlCopyright © 2008-2022 by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding ZIVwiki? Send feedback
Datenschutzerklärung Impressum