Brief Introduction to HPC Computing

A brief introduction to the usage of the HPC facilities, targeted at new and unexperienced HPC users is given below. The introduction is based on various minimal examples that illustrate how to compile serial and parallel programs as well as how to submit and monitor actual jobs using SGE.

Misc

how to use local storage for I/O intense serial jobs (or parallel jobs that run on a single host)

Consider the examplary C program myExample_tempdir.c

 
#include <stdio.h>

int main(int argc, char *argv[]) {
  FILE *myFile;

  myFile=fopen("my_data/myData.out","w");
  fprintf(myFile,"Test output to local scratch directory\n");

  fclose(myFile);
}
  

which assumes that there is a directory my_data in the current working directory to which the file myData.out with a certain content (here the sequence of characters Test output to local scratch directory) will be written.

In oder to compile the program via the current gcc compiler, you could first set the stage by loading the proper modules, e.g.

 module clear
 module load sge
 module load gcc/4.7.1

and then compiling via

  gcc myExample_tempdir.c -o myExample_tempdir

to yield the binary myExample_tempdir.

At this point bear in mind that we do not want to execute the binary right away! Instead, we would like to leave it to SGE to determine a proper queue instance (guided by the resources we subsequently will specify for the job) on a host with at least one free slot, where the job will be executed. A proper job submission script, here called myProg_tempdir.sge, that takes care of creating the folder my_data needed by the program myExample_tempdir in order to store its output in a temporal directory on the executing host reads

 
#!/bin/bash

####### which shell to use
#$ -S /bin/bash

####### change to directory where job was submitted from
#$ -cwd

####### maximum walltime of the job (hh:mm:ss)
#$ -l h_rt=0:10:0

####### memory per job slot
#$ -l h_vmem=100M

####### since working with local storage, no need to request disk space

####### name of the job
#$ -N tmpdir_test

####### change current working directory to the local /scratch/<jobId>.<x>.<qInst>
####### directory, available as TMPDIR on the executing host with HOSTNAME
cd $TMPDIR

####### write details to <jobName>.o<jobId> output file
echo "HOSTNAME = " $HOSTNAME
echo "TMPDIR   = " $TMPDIR

####### create output directory on executing host (parent folder is TMPDIR)
mkdir my_data

####### run program
$HOME/wmwr/my_examples/tempdir_example/myExample_tempdir

####### copy the output to the directory the job was submitted from
cp -a ./my_data $HOME/wmwr/my_examples/tempdir/
  

Submitting the script via

 qsub myProg_tempdir.sge

enqueues the respective job, here having jobId 703914. After successful termination of the job, the folder my_data appears in the working directory from which the job was originally submitted from. Also, the two job status files tmpdir_test.e703914 and tmpdir_test.o703914 where created that might contain further details associated with the job. The latter file should contain the name of the host on which the job actually ran and the name of the temporal directory. And indeed, cat tmpdir_test.o703914 reveals the file content

 HOSTNAME =  mpcs001
 TMPDIR   =  /scratch/703914.1.mpc_std_shrt.q

Further, the file my_data/myData.out contains the line

 Test output to local scratch directory

as expected.