James: Created page with "IMa2 is a serial program that is currently installed on ANDY at the CUNY HPC Center. It requires an input file and potentially several additional data files to run. Here we provide a script that will run the test input program supplied by the authors, 'ima2_testinput.u'. Completing this run may also require the prior file ('ima2_priorfile_4pops.txt') and the nested models file ('ima2_all_nested_models_2_pops.txt'). All these files can be copied out of the IMa2 installa..."

2022-10-20T20:07:42Z

Created page with "IMa2 is a serial program that is currently installed on ANDY at the CUNY HPC Center. It requires an input file and potentially several additional data files to run. Here we provide a script that will run the test input program supplied by the authors, 'ima2_testinput.u'. Completing this run may also require the prior file ('ima2_priorfile_4pops.txt') and the nested models file ('ima2_all_nested_models_2_pops.txt'). All these files can be copied out of the IMa2 installa..."

New page

IMa2 is a serial program that is currently installed on ANDY at the CUNY HPC Center. It requires an input file and potentially several additional data files to run. Here we provide a script
that will run the test input program supplied by the authors, 'ima2_testinput.u'. Completing this run may also require the prior file ('ima2_priorfile_4pops.txt') and the nested models file ('ima2_all_nested_models_2_pops.txt'). All these files can be copied out of the IMa2 installation examples directory, as follows:

<pre>
cp /share/apps/ima2/default/examples/ima2_testinput.u .
</pre>

A working SLURM batch script that will complete an IMa2 run is presented here:

<pre>
#!/bin/bash
#SBATCH --partition production
#SBATCH --job-name IMa2_serial
#SBATCH --nodes=1
#SBATCH --ntasks=1

# Find out name of master execution host (compute node)
echo -n ">>>> SLURM Master compute node is: "
hostname

# You must explicitly change to the working directory in SLURM
cd $SLURM_SUBMIT_DIR

# Point to the execution directory to run
echo ">>>> Begin IMa2 Serial Run ..."
echo ""
/share/apps/ima2/default/bin/IMa2 -i ima2_testinput.u -o ima2_testoutput.out -q2 -m1 -t3 -b10000 -l100
echo ""
echo ">>>> End IMa2 Serial Run ..."
</pre>

This script can be dropped into a file (say 'ima2_serial.job), and run with:

<pre>
qsub ima2_serial.job
</pre>

It should take less than a few minutes to run and will produce SLURM output and error files beginning
with the job name 'IMA2_serial'. It also produces IMa2's own output files. Details on the meaning
for the SLURM script are covered below in the SLURM section. The most important lines are the '#SBATCH --nodes=1 ntasks=1 mem=1920'. The first instructs SLURM to select 1 resource 'chunk' with 1
processor (core) and 1,920 MBs of memory in it for the job. The second instructs SLURM to place
this job wherever the least used resources are found (freely). The compute node that it finally
selects to run your job will be printed in the SLURM output file by the 'hostname' command.

Please take note of the IMa2 options used here. Details on each can be found in the IMa2 manual
referenced above.

IMA2 - Revision history