support OpenMPI used to build mpi4py and PnetCDF

Author: wkliao

README.md

@@ -40,8 +40,16 @@ scalable I/O performance.
   export PNETCDF_DIR=/path/to/pnetcdf/dir
   pip install --no-build-isolation -e .
   ```
-* Testing -- Command `"make check"` tests all the programs available in folders
-  ["test/"](./test) and ["examples/"](./examples).
+* Testing
+  + Command `"make check"` tests all the programs available in folders
+  ["test/"](./test) and ["examples/"](./examples) by running one MPI process.
+  + Command `"make ptests"` tests all the programs by running more than one MPI
+    process.
+  + Note when using OpenMPI, use command below.
+    ```
+    make check  TESTMPIRUN="/path/to/OpenMPI/bin/mpirun --oversubscribe"
+    make ptests TESTMPIRUN="/path/to/OpenMPI/bin/mpirun --oversubscribe"
+    ```
 
 ### Additional Resources
 * [Example python programs](./examples#pnetcdf-python-examples) available in

examples/MNIST/Makefile

@@ -7,6 +7,8 @@ check_PROGRAMS = mnist_main.py
 
 MNIST_URL = https://raw.githubusercontent.com/pytorch/examples/main/mnist/main.py
 
+TESTMPIRUN = $(shell dirname ${CC})/mpirun
+
 all:
 
 mnist_main.py:
@@ -45,7 +47,7 @@ ptests check: mnist_main.py
 	@echo "======================================================================"
 	@echo "    examples/MNIST: Parallel testing on 4 MPI processes"
 	@echo "======================================================================"
-	@mpiexec -n 4 python mnist_main.py --batch-size 4 --test-batch-size 2 --epochs 3 --input-file mnist_images.nc
+	@${TESTMPIRUN} -n 4 python mnist_main.py --batch-size 4 --test-batch-size 2 --epochs 3 --input-file mnist_images.nc
 	@echo ""
 
 clean:

examples/Makefile

@@ -17,9 +17,10 @@ check_PROGRAMS = collective_write.py \
                  put_var.py \
                  get_var.py
 
-
+TESTMPIRUN = $(shell dirname ${CC})/mpirun
 TESTS_ENVIRONMENT  = export check_PROGRAMS="${check_PROGRAMS}";
 TESTS_ENVIRONMENT += export PNETCDF_DIR="${PNETCDF_DIR}";
+TESTS_ENVIRONMENT += export TESTMPIRUN="$(TESTMPIRUN)";
 
 OUTPUT_DIR = _tmp_output
 

examples/Pytorch_DDP/Makefile

@@ -6,8 +6,10 @@
 check_PROGRAMS = torch_ddp_skeleton.py
 
 
+TESTMPIRUN = $(shell dirname ${CC})/mpirun
 TESTS_ENVIRONMENT  = export check_PROGRAMS="${check_PROGRAMS}";
 TESTS_ENVIRONMENT += export PNETCDF_DIR="${PNETCDF_DIR}";
+TESTS_ENVIRONMENT += export TESTMPIRUN="$(TESTMPIRUN)";
 
 OUTPUT_DIR = _tmp_output
 

examples/Pytorch_DDP/parallel_run.sh

@@ -31,7 +31,7 @@ for prog in $check_PROGRAMS; do
    printf '%-60s' "Testing $prog"
 
    if test $prog = "torch_ddp_skeleton.py" ; then
-      CMD="mpiexec -n $NPROC python $prog -q"
+      CMD="${TESTMPIRUN} -n $NPROC python $prog -q"
    fi
    $CMD
    status=$?

examples/nonblocking/Makefile

@@ -7,9 +7,10 @@ check_PROGRAMS = nonblocking_write_def.py \
                  nonblocking_write.py \
                  nonblocking_read.py
 
-
+TESTMPIRUN = $(shell dirname ${CC})/mpirun
 TESTS_ENVIRONMENT  = export check_PROGRAMS="${check_PROGRAMS}";
 TESTS_ENVIRONMENT += export PNETCDF_DIR="${PNETCDF_DIR}";
+TESTS_ENVIRONMENT += export TESTMPIRUN="$(TESTMPIRUN)";
 
 OUTPUT_DIR = _tmp_output
 

examples/nonblocking/parallel_run.sh

@@ -61,9 +61,9 @@ for prog in $check_PROGRAMS; do
    printf '%-60s' "Testing $prog"
 
    if test "x$prog" = "xnonblocking_read.py" ; then
-      CMD="mpiexec -n $NPROC python $prog -q $OUT_DIR/nonblocking_write.nc"
+      CMD="${TESTMPIRUN} -n $NPROC python $prog -q $OUT_DIR/nonblocking_write.nc"
    else
-      CMD="mpiexec -n $NPROC python $prog -q $OUT_DIR/${prog%.*}.nc"
+      CMD="${TESTMPIRUN} -n $NPROC python $prog -q $OUT_DIR/${prog%.*}.nc"
    fi
    # echo "$CMD"
 

examples/parallel_run.sh

@@ -61,9 +61,9 @@ for prog in $check_PROGRAMS; do
    printf '%-60s' "Testing $prog"
 
    if test $prog = "get_var.py" ; then
-      CMD="mpiexec -n $NPROC python $prog -q $OUT_DIR/put_var.nc"
+      CMD="${TESTMPIRUN} -n $NPROC python $prog -q $OUT_DIR/put_var.nc"
    else
-      CMD="mpiexec -n $NPROC python $prog -q $OUT_DIR/${prog%.*}.nc"
+      CMD="${TESTMPIRUN} -n $NPROC python $prog -q $OUT_DIR/${prog%.*}.nc"
    fi
    $CMD
    status=$?

test/Makefile

@@ -50,7 +50,9 @@ check_PROGRAMS = tst_atts.py \
                  tst_wait.py \
                  tst_libver.py
 
+TESTMPIRUN = $(shell dirname ${CC})/mpirun
 TESTS_ENVIRONMENT = export check_PROGRAMS="${check_PROGRAMS}";
+TESTS_ENVIRONMENT += export TESTMPIRUN="$(TESTMPIRUN)";
 OUTPUT_DIR = _tmp_output
 
 all:

test/parallel_run.sh

@@ -31,9 +31,9 @@ for prog in ${check_PROGRAMS} ; do
    printf '%-60s' "Testing $prog "
 
    if test $prog = "tst_libver.py" ; then
-      CMD="mpiexec -n $NPROC python $prog -q"
+      CMD="${TESTMPIRUN} -n $NPROC python $prog -q"
    else
-      CMD="mpiexec -n $NPROC python $prog $OUT_DIR"
+      CMD="${TESTMPIRUN} -n $NPROC python $prog $OUT_DIR"
    fi
    $CMD
    status=$?