Palmetto Cluster and deal.II

This guide is provided by Timo Heister.

Access palmetto

Log into login node (replace USERNAME with your clemson id):

ssh USERNAME@user.palmetto.clemson.edu

More info at http://citi.clemson.edu/palmetto/pages/userguide.html

Set up your account for using deal.II

Add the following lines to your .bash_profile (at the bottom):

export PATH=/home/heister/bin/cmake-$PATH

Interactive running

For compiling and running interactively, you NEED to be on one of the compute nodes:

qsub -I -l select=1:ncpus=16:mem=60gb:interconnect=fdr,walltime=1:00:00

See the user guide for more options (for example chip_type).

Every time you log into an interactive node, you need to load the modules I prepared before you can compile or run:

source /home/heister/shared-dealii/modules_8.4.1

Older versions are installed as /modules_8.3.0 and /modules (version 8.2.1).

Job submission

Example job file run.pbs needs to be copied into the directory where you want to run. You probably only need to edit:

  1. The number of nodes to run on ("select=X" in line 2)
  2. The total walltime if you need to run longer jobs
  3. The name of the program to run and optionally parameters (the "cmd=…" line)

Commands for job submission:

  1. submit a job (needs to be done from the login node and not a compute node!):
qsub run.pbs
  1. list jobs (running and queued) belonging to USERNAME:
qstat -u USERNAME
  1. cancel job (jobid is the first column in qstat):
qdel JOBID

Date: 2016-04-29T13:02+0100

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