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--- workshops:hpcprac3 [2017/07/05 09:26]
kevin created
+++ workshops:hpcprac3 [2021/12/09 16:42] (current)
@@ Line 1: / Line 1: @@
-=====MPI Practical Part I1=====
+=====Practical 3: MPI Part I=====
 ====Job Script====
@@ Line 9: / Line 9: @@
 **example.sh**:
-<code lang=bash>
+<code bash>
 #!/bin/bash
 #PBS -N example01
@@ Line 69: / Line 69: @@
 where //jobid// is replaced by the number of the job (looks like ''557809.sched01'').
+=====Task 1=====
+Create a sub-directory MPI in your Lustre directory:
+  cd ~/lustre
+  mkdir MPI
+  cd MPI
+  pwd
+The last command will display something like:
+  /home/student00/lustre/MPI
+Now use **nano** to create a file called hello_mpi.c
+<code C>
+/* C Example */
+#include <stdio.h>
+#include <mpi.h>
+int main (int argc, char *argv[])
+{
+  int rank, size;
+  MPI_Init (&argc, &argv);
+  MPI_Comm_rank (MPI_COMM_WORLD, &rank);
+  MPI_Comm_size (MPI_COMM_WORLD, &size);
+  printf( "Hello world from process %d of %d\n", rank, size );
+  MPI_Finalize();
+  return 0;
+}
+</code>
+Compile this with the **mpicc** MPI C compiler:
+  mpicc -o hello_mpi.x  mpi_hello.c
+> Those of you who prefer Fortran will need to compile your hello_mpi.f90 with the **mpif90** compiler instead.
+<code Fortran>
+!  Fortran example
+program hello
+include 'mpif.h'
+integer rank, size, ierror
+call MPI_INIT(ierror)
+call MPI_COMM_SIZE(MPI_COMM_WORLD, size, ierror)
+call MPI_COMM_RANK(MPI_COMM_WORLD, rank, ierror)
+print*, 'node', rank, ': Hello world'
+call MPI_FINALIZE(ierror)
+end
+</code>
+> Compile the Fortran example with:
+  mpif90 -o hello_mpi.x   mpi_hello.f90
+If you get an error message complaining that **mpicc** (or **mpif90**) is not found, then you forgot to load the necessary modules:
+<code bash>
+module unload gcc/6.1.0
+module load chpc/openmpi/2.0.2/gcc-5.1.0
+module list
+</code>
+The last command should display:
+<code>
+Currently Loaded Modulefiles:
+) gcc/5.1.0                      2) chpc/openmpi/2.0.2/gcc-5.1.0
+</code>
+Now create a job script file to run your first MPI program, and save it as //hello.pbs//:
+<code bash>
+#!/bin/bash
+#PBS -N Hello
+#PBS -l select=1:ncpus=24:mpiprocs=24
+#PBS -P Wchpc
+#PBS -q R522145
+#PBS -W group_list=training
+#PBS -l walltime=4:00:00
+module load chpc/openmpi/2.0.2/gcc-5.1.0
+cd /mnt/lustre/users/studentNN/MPI
+CWD=`pwd`
+echo "Working directory is $CWD"
+nproc=`cat $PBS_NODEFILE | wc -l`
+echo "nproc = $nproc"
+echo "Nodes used by this job:"
+cat $PBS_NODEFILE
+echo "Starting run..."
+echo "======="
+mpirun -n $nproc ./hello_mpi.x
+echo "======="
+echo "... done."
+</code>
+Launch the job script with **qsub**:
+  qsub hello.pbs
+Check its status with **qstat**:
+  qstat | grep student00
+> Replace the ''00'' above with your student account number!
+Once your job status has changed from ''R'' to ''F'' or ''E'' then look for the output:
+  ls
+The file you want to look at will be called something like //Hello.o99999// where the number at the end will be the job ID number:
+  cat Hello.o12345
+> Replace 12345 with the job number!
+=====Carry On=====
+Attempt the exercises in the {{:workshops:epcc-mpi-course-slides.pdf|slides}}.

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