feat: add/intel mpi example

example/hello-world-intel-mpi/README.md

@@ -0,0 +1,10 @@
+# Hello World Intel MPI
+
+This example shows requesting using the intel MPI snippet, which means adding a custom setup and run
+command to your code. An hpc-* flavored family is required (which is the default).
+
+```bash
+GOOGLE_PROJECT=myproject
+snakemake --jobs 1 --executor googlebatch --googlebatch-region us-central1 --googlebatch-project ${GOOGLE_PROJECT} --default-storage-provider s3 --default-storage-prefix s3://my-snakemake-testing --googlebatch-snippets intel-mpi
+```
+

example/hello-world-intel-mpi/Snakefile

@@ -0,0 +1,57 @@
+# https://github.com/snakemake/snakemake/blob/main/tests/test_slurm_mpi/Snakefile
+# Note that in reality, the mpi, account, and partition resources should be specified
+# via --default-resources, in order to keep such infrastructure specific details out of the
+# workflow definition.
+
+
+localrules:
+    all,
+    clean,
+    copy,
+
+rule all:
+    input:
+        "pi.calc",
+
+rule clean:
+    shell:
+        "rm -f pi.calc"
+
+rule copy:
+    input:
+        local("pi_MPI.c"),
+    output:
+        "pi_MPI.c",
+    log:
+        "logs/copy.log",
+    resources:
+        mem_mb=0,
+    shell:
+        "cp {input} {output} &> {log}"
+
+rule compile:
+    input:
+        "pi_MPI.c",
+    output:
+        "pi_MPI",
+    log:
+        "logs/compile.log",
+    resources:
+        mem_mb=0,
+    shell:
+        "mpicc -o {output} {input} &> {log}"
+
+rule calc_pi:
+    input:
+        "pi_MPI",
+    output:
+        "pi.calc",
+    log:
+        "logs/calc_pi.log",
+    resources:
+        mem_mb=0,
+        tasks=1,
+        mpi="mpiexec",
+    shell:
+        "chmod +x {input};"
+        "{resources.mpi} -hostfile $BATCH_HOSTS_FILE -n {resources.tasks} {input} 10 > {output};"

example/hello-world-intel-mpi/pi_MPI.c

@@ -0,0 +1,66 @@
+#include <stdio.h>
+#include <math.h>
+#include "stdlib.h"
+#include "mpi.h"
+
+
+double f(double x){
+  return ( 4.0/(1.0 + x*x) );
+}
+
+
+int main(int argc,char *argv[])
+{
+
+  int myrank, size;
+
+  MPI_Init(&argc, &argv);
+  MPI_Comm_size(MPI_COMM_WORLD, &size);
+  MPI_Comm_rank(MPI_COMM_WORLD, &myrank);
+
+  long long int i, n;
+  double PI25DT = 3.141592653589793238462643;
+  double mypi, pi, h, mysum, x;
+
+
+
+  /* Argument handling from command line */
+  if( 2 == argc ){
+    n = atoll(argv[1]);
+  }else{
+    if( 0 == myrank ){
+      n = 10000000;
+      printf("Too many or no argument given; using n = %d instead.\n", n);
+    }
+  }
+
+
+  MPI_Bcast(&n, 1, MPI_LONG_LONG_INT, 0, MPI_COMM_WORLD);
+
+  h = 1.0/( (double)n );
+  mysum = 0.0;
+
+  for(i = myrank+1 ; i <= n ; i += size){
+    x = h*((double)i - 0.5);
+    mysum = mysum + f(x);
+  }
+
+  mypi = h*mysum;
+
+  MPI_Reduce(&mypi, &pi, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD);
+
+  /* Output result if myrank==0 */
+  if( 0 == myrank ){
+    char* filename = argv[1];   
+    FILE *fp;
+    char buf[0x100];    
+    snprintf(buf, sizeof(buf), "%s", filename);
+    fp = fopen(buf, "w+");
+    fprintf(fp, "\nUsing %d processes and the value n = %d.\n",size,n);
+    fprintf(fp, "Calculated pi: %.16f, with error %.16f\n\n", pi, fabs(pi - PI25DT));
+    fclose(fp);    
+  }
+
+  MPI_Finalize();
+  return 0;
+}

snakemake_executor_plugin_googlebatch/snippets/intel-mpi/run.sh

@@ -8,6 +8,6 @@ source /opt/intel/mpi/latest/env/vars.sh
 if [ $BATCH_TASK_INDEX = 0 ]; then
   ls
   which mpirun
-  echo "{% if resources.mpi %}{{ resources.mpi }}{% else %}mpiexec{% endif %} -hostfile $BATCH_HOSTS_FILE -n {{ settings.tasks }} -ppn {{ settings.tasks_per_node }} {{ command }}"
-  {% if resources.mpi %}{{ resources.mpi }}{% else %}mpiexec{% endif %} -hostfile $BATCH_HOSTS_FILE -n {{ settings.tasks }} -ppn {{ settings.tasks_per_node }} {{ command }}
+  echo "{{ command }}"
+  {{ command }}
 fi