List of installed softwares (HPC)

............................................

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

1. mpich2-intel

2. openmpi-1.4-gcc-i386

3. openmpi-1.4-gcc-x86_64

4. rocks-openmpi-1.4.3

5. sun-ct-8.2.1-i386

6. 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 List jobs in a specific queue

qstat -u List jobs for a particular user

qsub Submit a job to the default queue (submit)

qsub -q Submit a job to a particular queue.

qsub -I Submit a job for an interactive run



(will return a prompt when job is run)

qsub -h Submit a job and put a hold on it

(useful for starting jobs with dependencies)

qrls release a hold on a job

qdel 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 ./



---------------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 ./

--------------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 it_helpdesk@iitmandi.ac.in