P a g e 1. HPC Example for C with OpenMPI

Transcription

1 P a g e 1 HPC Example for C with OpenMPI

2 Revision History Version Date Prepared By Summary of Changes 1.0 Jul 3, 2017 Raymond Tsang Initial release 1.1 Jul 24, 2018 Ray Cheung Minor change HPC Example for C with OpenMPI P a g e 2

3 Table of Contents 1. Introduction Perform the test Job submission How to check the result Useful Reference... 9 P a g e 3

4 1. Introduction This document is shown a C example by using OpenMPI method running on the pilot HPC environment. For more information on Pilot HPC Platform, please refer this section "High Performance Computing Support Services" ( ) in the ITS website. For creating your Pilot HPC Platform account, please complete the online form ( ). P a g e 4

5 2. Perform the test 2.1 Create the testing directory $ mkdir -p $HOME/mpi_pi_c $ cd $HOME/mpi_pi_c 2.2 Prepare the C program (Filename: mpi_pi.c) #include "mpi.h" #include <stdio.h> #include <math.h> int main( int argc, char *argv[] ) { int n, myid, numprocs, i; double PI25DT = ; double mypi, pi, h, sum, x; MPI_Init(&argc,&argv); MPI_Comm_size(MPI_COMM_WORLD,&numprocs); MPI_Comm_rank(MPI_COMM_WORLD,&myid); while (1) { if (myid == 0) { printf("enter the number of intervals: (0 quits) "); scanf("%d",&n); MPI_Bcast(&n, 1, MPI_INT, 0, MPI_COMM_WORLD); if (n == 0) break; else { h = 1.0 / (double) n; sum = 0.0; for (i = myid + 1; i <= n; i += numprocs) { x = h * ((double)i - 0.5); sum += (4.0 / (1.0 + x*x)); mypi = h * sum; MPI_Reduce(&mypi, &pi, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD); if (myid == 0) printf("pi is approximately %.16f, Error is %.16f\n", pi, fabs(pi - PI25DT)); MPI_Finalize(); return 0; 2.3 Load the MPI user environment. You can select OpenMPI with gcc. For select OpenMPI, use the following $ module load openmpi gcc $ module list Currently Loaded Modulefiles: 1) openmpi gcc P a g e 5

6 $ which mpicc /hpcapps/openmpi gcc-5.3.0/bin/mpicc _ 2.4 Build the executable binary by using the selected MPI $ mpicc -o mpi_pi mpi_pi.c $ file mpi_pi mpi_pi: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux , not stripped 2.5 Prepare the input data file (Filename: input.dat) Prepare the job script file. _ For select OpenMPI, use the following (Filename: mpi_pi_c_openmpi.sbatch) #!/bin/bash -login #SBATCH --partition=h01gen #SBATCH --time=24:00:00 #SBATCH --ntasks=8 #SBATCH --mem-per-cpu=1024m #SBATCH --job-name="c Ex" module load openmpi gcc echo "Start time is `date` " mpirun mpi_pi < input.dat > result.out echo "End time is `date` " module unload openmpi gcc Example files can be found at: /hpcapps/examples/h01/c/ input.dat mpi_pi.c mpi_pi_c_openmpi.sbatch P a g e 6

7 3 Job submission 3.1 Submit the script (mpi_pi_c_openmpi.sbatch) to job queue. A job ID number will be returned. $ sbatch mpi_pi_c_openmpi.sbatch Submitted batch job Enquiry the submitted job status. $ squeue l Wed Mar 15 15:52: JOBID PARTITION NAME USER STATE TIME TIME_LIMI NODES NODELIST(REASON) 477 h01gen C Ex itsuser3 RUNNING 0: :00:00 2 its-h01-c[ ] Job status field name Explanation Example JOBID Unique Job id. 477 PARTITION Name of the job queue that the job has assigned. h01gen NAME Name for the job allocation C Ex USER Your NetID itsuser3 STATE Job current status. RUNNING PENDING = Job is pending for execution RUNNING = Job is executing SUSPENDED = Job has suspended CANCELLED = Job was cancelled COMPLETED = Job was completed TIME Time for the job executed 0:03 (3 seconds) TIME_LIMI The maximum execution time 7-00:00:00 (7 days) NODES Number of nodes assigned 2 NODELIST(REASON) Name of nodes has assigned its-h01-c[ ] P a g e 7

8 4 How to check the result 4.1 Check for any error messages for JobID $ more slurm-477.out Start time is Wed Mar 15 15:52:40 HKT 2017 End time is Wed Mar 15 15:53:42 HKT Check for result $ wc -l result.out 8 result.out $ cat result.out , Error is , Error is , Error is , Error is , Error is , Error is , Error is , Error is P a g e 8

9 5 Useful Reference Manpage for OpenMPI - mpicc URL: Manpage for OpenMPI - mpirun URL: Tutorials for SLURM sbatch URL: Tutorials for SLURM squeue URL: P a g e 9