List of installed softwares
GNU Compiler collection, gcc, gfortran etc.
Intel compilers, icc, ifort they can be accessed setting the environment variable using the command
source /opt/intel/composer_xe_2011_sp1.8.273/bin/compilervars_global.sh intel64
or you may add this line to the end of your ~/.bashrc file
There are 6 choices of mpi, please select appropriate environment.
NOTE: Most of the case the default choice (1) might work OK
The MPI environment can be changed using the command
mpi-selector-menu
- mpich2-intel
- openmpi-1.4-gcc-i386
- openmpi-1.4-gcc-x86_64
- rocks-openmpi-1.4.3
- sun-ct-8.2.1-i386
- sun-ct-8.2.1-x86_64
SAGE – compiled using Intel Compilers located at
/opt/sage-4.7.2-linux-64bit
Software for molecular modelling
NAMD
/opt/NAMD_CVS-2012-01-16_Linux-x86_64
GROMACS
/opt/bio/gromacs —-using gnu compiler
/opt/icr/gromacs-4.5.3 —–using intel compiler the queues that are available can be viewed using
qstat -q
the queues are listed in the increasing order of the CPUTIME and decreasing order of priority
There are 16 nodes in this cluster individual nodes can be
accessed by ssh using their name compute-0-0 to compute-0-15
Some useful openPBS commands to manage jobs
qstat -q <queuename> List jobs in a specific queue
qstat -u <username> List jobs for a particular user
qsub <script> Submit a job to the default queue (submit)
qsub -q <queue> <script> Submit a job to a particular queue.
qsub -I <script> Submit a job for an interactive run (will return a prompt when job is run)
qsub -h <script> Submit a job and put a hold on it
(useful for starting jobs with dependencies)
qrls <jobid> release a hold on a job
qdel <jobid> stop and remove a job from pbs
Model script to submit parallel job –
save the lines between begin and end in file for e.g. sub.sh
and make necessary changes.
submit the job in a queue using
qsub sub.sh
————-parallel–openMP——————begin
1 #!/bin/bash
2 #PBS -j oe
3 #specify queue name
4 #PBS -q short1
5 #specify job name
6 #PBS -N jobname
7 #specify number of cpus to be assigned
8 #PBS -l ncpus=8
9 #PBS -V
10 #Set the number of OpenMP threads
11 #if you are using open MP
12 export OMP_NUM_THREADS=8
13 #to locate here it is running
14 echo “Running on: “
15 cat ${PBS_NODEFILE}
16 echo
17 echo “Program Output begins: “
18 cd ${PBS_O_WORKDIR}
19 ./<your_parallel_executable_name>
—————parallel————————end
Script for serial job
————serial——————–begin
1 #!/bin/bash
2 #PBS -j oe
3 #specify queue name
4 #PBS -q short1
5 #specify job name
6 #PBS -N jobname
7 #specify time required for job completion
8 #PBS -l walltime=10:00:00
9 #to locate where it is running
10 echo “Running on: “
11 cat ${PBS_NODEFILE}
12 echo
13 echo “Program Output begins: “
14 cd ${PBS_O_WORKDIR}
15 ./<your_serial_sexecutable_name>
————–serial———————–end
- These are minimal scripts only, you may improve by using online reference material on openPBS and torque
- JOBS SUBMISSION IN THIS CLUSTER STRICTLY BY OpenPBS QUEUING SYSTEM – See the quick start reference above
- List of queues
test 00:30:00 — 20
short1 02:00:00 — 20
short2 08:00:00 — 15
day 24:00:00 — 15
threeday 72:00:00 — 15
week 168:00:0 — 15
verylong 480:00:0 — 15
serial 720:00:0 — 60
infinite 1440:00: — 10
Mail your suggestion/comments to hpc@iitmandi.ac.in