1. SCI 1550 Revision 25/5 – 18/6/2004

2. Summary • Hardware and Software of the PC cluster • Compiling and running of serial and parallel programs in C and Fortran • Submission of batch jobs into PBS • Monitoring the PBS job

3. Software applications • Message Passing Interface • MPICH 1.2.5 • LAM 7.0.4 • Mathematical related • SPRNG • ATLAS, SCALAPACK • MPITB for MATLAB • Computational Chemistry related • Gaussian, Q-CHEM • NAMD/VMD, Gamess, Gromacs, Amber

4. Compiling and running parallel programs in C • Using Makefile to compile • type make whenever you find Makefile • Run parallel programs using mpirun mpirun –np 4 –machinefile machines a.out -np : no of processes -machinefile : host file to run a.out : parallel executable file

5. Job submission using PBS • Prepare a job script #!/bin/bash #PBS –N jobname #PBS –l nodes=4 #PBS –l walltime=00:05:00 cd $PBS_O_WORKDIR NPROC=`wc –l < $PBS_NODEFILE` /u1/local/mpich-1.2.5/bin/mpirun –np $NPROC –machinefile $PBS_NODEFILE a.out • Submit job byqsub job.pbs

6. Managing running job in PBS • qstat is used to monitor the running job • qstat for querying job • qstat -B for querying server • qstat -Q for querying queue • qstat -f for full display • qdel delete a job in the PBS queue • qdel jobID

7. Exercise • Copy and untar the file rev.tar.gz from the directory /u1/local/share/sci1550/ • Compile and run the program withmpirun • Submit the job using cpir.pbs with nodes=2,4,6,8,10 and note the wall clock time.