PALMA-NG

Overview

palma3 is the login node to a newer part of the PALMA system. It has various queues/partitions for different purposes:

  • u0dawin: A queue for general purpose. It is usable for everyone, even without being a member of the groups that have submittet a proposal for PALMA. It replaces the old ZIVHPC cluster
  • k20gpu: Four nodes equipped with 3 K20 nVidia Tesla accelerators each
  • normal: 44 nodes with 32 Broadwell CPU cores each. (Not fully installed yet)
  • zivsmp: A SMP machine with 512 GB RAM. The old login node of ZIVHPC. (not available yet)
  • phi: 2 Nodes with 4 Intel Xeon Phi accelerators each. (not available yet).

The batch system

The batch system on PALMA3 is SLURM, but there is a wrapper for PBS installed, so most of your skripts should still be able to work. If you want to switch to SLURM, this document might help you: https://slurm.schedmd.com/rosetta.pdf

When using PBS skript, there are some differences to PALMA:

  • The first line of the submit script has to be #!/bin/bash
  • A queue is called partition in terms of SLURM. These terms will be used synonymous here.
  • The variable $PBS_O_WORKDIR will not be set. Instead you will start in the directory in which the script resides.
  • For using the "module add" command, you will have to source some scripts first: "source /etc/profile.d/modules.sh; source /etc/profile.d/modules_local.sh"

Submit a job

Create a file for example called submit.cmd

#!/bin/bash

# set the number of nodes
#SBATCH --nodes=1

# set the number of CPU cores per node
#SBATCH -n 8

# set a partition
#SBATCH -p u0dawin

# set max wallclock time
#SBATCH --time=24:00:00

# set name of job
#SBATCH --job-name=test123

# mail alert at start, end and abortion of execution
#SBATCH --mail-type=ALL

# set an output file
#SBATCH -o output.dat

# send mail to this address
#SBATCH --mail-user=your_account@uni-muenster.de

# In the u0dawin queue, you will need the following line
source /etc/profile.d/modules.sh; source /etc/profile.d/modules_local.sh

# run the application
./program

You can send your submission to the batch system with the command "sbatch submit.cmd"

A detailed description can be found here: http://slurm.schedmd.com/sbatch.html

Show running jobs

  • squeue
  • qstat
  • showq

Show information about the queues

scontrol show partition

Running interactive jobs with SLURM

Use for example the following command:

srun -p u0dawin -N 1 --ntasks-per-node=8 --pty bash

This starts a job in the u0dawin queue/partition on one node with eight cores.

-- Holger Angenent - 2016-08-22

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Topic revision: r7 - 2016-09-07 - HolgerAngenent
 
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