1 / 7

SCI 1550 Revision

SCI 1550 Revision. 25/5 – 18/6/2004. 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. Software applications. Message Passing Interface MPICH 1.2.5 LAM 7.0.4

lei
Download Presentation

SCI 1550 Revision

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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.

More Related