Testing and porting applications and workflows to CentOS 7 environment

These are basic instructions for using the Geyser and Caldera nodes that have been updated with CentOS and new software.

Interactive use

Add the flag -r cent74 to your invocation of any of the standard command scripts (execdav, execca, execgy, and execgpu).

Example:

execdav -r cent74

Batch jobs

Use the following sample job scripts as templates for batch submissions to the CentOS nodes. Once you are done writing your batch script, you can submit using sbatch as usual.

Earlier script examples included a source command for initializing the Slurm environment. That command is no longer needed and should be removed from scripts used in the CentOS 7 environment.

for tcsh users

#!/bin/tcsh
#SBATCH -J centos
#SBATCH -n 4
#SBATCH --ntasks-per-node=2
#SBATCH -t 05:00
#SBATCH -A project_code
#SBATCH -p dav
#SBATCH --reservation cent74
#SBATCH -o tcsh.log

### Set TMPDIR to avoid job failures
setenv TMPDIR /glade/scratch/$USER/temp
mkdir -p $TMPDIR

module load cdo/1.9.4

cdo -h

scontrol show job $SLURM_JOB_ID

For bash users

#!/bin/bash -l
#SBATCH -J centos
#SBATCH -n 4
#SBATCH --ntasks-per-node=2
#SBATCH -t 05:00
#SBATCH -A project_code
#SBATCH -p dav
#SBATCH --reservation cent74
#SBATCH -o bash.log

### Set TMPDIR to avoid job failures
export TMPDIR=/glade/scratch/$USER/temp
mkdir -p $TMPDIR

module load cdo/1.9.4

cdo -h

scontrol show job $SLURM_JOB_ID

Starting a VNC session

To start a VNC session on the CentOS 7 nodes from Cheyenne, Geyser, or Caldera, run the following (inserting your project code where indicated):

/glade/u/apps/dav/opt/usr/bin/vncserver_submit -a project_code

The default version of the vncserver_submit script will still put you on a Red Hat 6 node.

You will have access to a GNOME3 desktop. KDE also is available and can be activated by adding the option -d kde when calling the script.