Yanked all MPI-1 calls

Added batch scripts in bin/batch.

14 files changed, 207 insertions, 11 deletions

diff --git a/MANIFEST b/MANIFEST
index e37f8c9..cec5cf6 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -96,6 +96,17 @@
 ./bin/timekeeper                    _DO_NOT_DISTRIBUTE_
 ./bin/trace
 ./bin/yodconfigure
+./bin/batch/ctestP.lsf.in.cmake
+./bin/batch/ctestP.sl.in.cmake
+./bin/batch/ctestS.lsf.in.cmake
+./bin/batch/ctestS.sl.in.cmake
+./bin/batch/knl_ctestP.sl.in.cmake
+./bin/batch/knl_ctestS.sl.in.cmake
+./bin/batch/knl_H5detect.sl.in.cmake
+./bin/batch/ctest.qsub.in.cmake
+./bin/batch/ray_ctestP.lsf.in.cmake
+./bin/batch/ray_ctestS.lsf.in.cmake
+./bin/batch/raybsub
 
 ./config/COPYING
 ./config/BlankForm
diff --git a/bin/batch/ctest.qsub.in.cmake b/bin/batch/ctest.qsub.in.cmake
new file mode 100755
index 0000000..702fca7
--- /dev/null
+++ b/bin/batch/ctest.qsub.in.cmake
@@ -0,0 +1,21 @@
+#!/bin/bash -l
+if [ $# -gt 0 ]; then
+    SUMMARY_FILE=$1
+fi
+ACCOUNT_ID=@ACCOUNT_ID@
+
+echo "Run parallel test command. Test output will be in build/${SUMMARY_FILE}"
+CTEST_CMD=`which ctest`
+
+#SKIPTESTS <<KEYWORD:script inserts list of skips tests here -- don't remove>>
+
+cd @HDF5_BINARY_DIR@
+if [[ $SUMMARY_FILE == *"ctestS"* ]]; then
+  CMD="${CTEST_CMD} . -E MPI_TEST_ -C Release -j 32 -T test"
+else
+  CMD="${CTEST_CMD} . -R MPI_TEST_ ${SKIP_TESTS} -C Release -T test"
+fi
+
+qsub -t 60 -n 1 -q debug-flat-quad -A ${ACCOUNT_ID} ${CMD} >& ${SUMMARY_FILE}
+
+echo "Done running ctest parallel command."
diff --git a/bin/batch/ctestP.lsf.in.cmake b/bin/batch/ctestP.lsf.in.cmake
new file mode 100644
index 0000000..3fdd5ce
--- /dev/null
+++ b/bin/batch/ctestP.lsf.in.cmake
@@ -0,0 +1,19 @@
+#!/bin/tcsh
+### LSF syntax
+#BSUB -nnodes 1                  #number of nodes
+#BSUB -W 30                      #walltime in minutes
+#BSUB -G guests                  #account
+#BSUB -e ctestPerrors.txt        #stderr
+#BSUB -o ctestPoutput.txt        #stdout
+#BSUB -J hdf5_ctestP             #job
+##BSUB -q pbatch                 #queue to use
+#BSUB -q pdebug
+
+##date; hostname
+##echo -n 'JobID is '; echo $LSB_JOBID
+
+cd @HDF5_BINARY_DIR@
+echo "Run parallel test command. Test output will be in build/ctestP.out"
+ctest . -R MPI_TEST_ -C Release -T test >& ctestP.out
+
+echo "Done running ctest parallel command."
diff --git a/bin/batch/ctestP.sl.in.cmake b/bin/batch/ctestP.sl.in.cmake
new file mode 100644
index 0000000..1069fa9
--- /dev/null
+++ b/bin/batch/ctestP.sl.in.cmake
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+#SBATCH --nodes=1
+#SBATCH -t 00:30:00
+#SBATCH --mail-type=BEGIN,END,FAIL
+##SBATCH --mail-user=<username>@sandia.gov
+#SBATCH --export=ALL
+#SBATCH --job-name=h5_ctestP
+
+cd @HDF5_BINARY_DIR@
+ctest . -R MPI_TEST_ -C Release -T test >& ctestP.out
+
+echo "Done running ctestP.sl"
+
diff --git a/bin/batch/ctestS.lsf.in.cmake b/bin/batch/ctestS.lsf.in.cmake
new file mode 100644
index 0000000..a01d39b
--- /dev/null
+++ b/bin/batch/ctestS.lsf.in.cmake
@@ -0,0 +1,18 @@
+#!/bin/tcsh
+### LSF syntax
+#BSUB -nnodes 1                  #number of nodes
+#BSUB -W 29                      #walltime in minutes
+#BSUB -G guests                  #account
+#BSUB -e ctestSerrors.txt        #stderr
+#BSUB -o ctestSoutput.txt        #stdout
+#BSUB -J hdf5_ctestS             #job
+##BSUB -q pbatch                 #queue to use
+#BSUB -q pdebug
+
+cd @HDF5_BINARY_DIR@
+echo "Run command. Test output will be in build/ctestS.out"
+ctest . -E MPI_TEST_ -C Release -j 32 -T test >& ctestS.out
+
+##$CMD  >& ctestS.out
+echo "Done running command."
+
diff --git a/bin/batch/ctestS.sl.in.cmake b/bin/batch/ctestS.sl.in.cmake
new file mode 100644
index 0000000..4f96bb9
--- /dev/null
+++ b/bin/batch/ctestS.sl.in.cmake
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+#SBATCH --nodes=1
+#SBATCH -t 00:30:00
+#SBATCH --mail-type=BEGIN,END,FAIL
+##SBATCH --mail-user=<username>@sandia.gov
+#SBATCH --export=ALL
+#SBATCH --job-name=h5_ctestS
+
+cd @HDF5_BINARY_DIR@
+CMD="ctest . -E MPI_TEST_ -C Release -j 32 -T test"
+
+echo "Run $CMD. Test output will be in build/ctestS.out"
+$CMD  >& ctestS.out
+echo "Done running $CMD"
diff --git a/bin/batch/knl_H5detect.sl.in.cmake b/bin/batch/knl_H5detect.sl.in.cmake
new file mode 100644
index 0000000..39a3ef3
--- /dev/null
+++ b/bin/batch/knl_H5detect.sl.in.cmake
@@ -0,0 +1,20 @@
+#!/bin/bash
+
+#SBATCH -p knl -C quad
+#SBATCH --nodes=1
+#SBATCH -t 00:10:00
+#SBATCH --mail-type=BEGIN,END,FAIL
+#SBATCH --mail-user=<username>@sandia.gov
+#SBATCH --export=ALL
+#SBATCH --job-name=knl_h5detect
+
+
+# Inputs:  Build directory, output file name, executable file name (username/email if available).
+PROGNAME=H5detect
+OUTPUT=H5Tinit.c
+
+CMD="@HDF5_BINARY_DIR@/bin/${PROGNAME} @HDF5_GENERATED_SOURCE_DIR@/${OUTPUT}"
+echo "Run $CMD"
+srun -n 1 $CMD
+echo "Done running $CMD"
+
diff --git a/bin/batch/knl_ctestP.sl.in.cmake b/bin/batch/knl_ctestP.sl.in.cmake
new file mode 100644
index 0000000..f985fbb
--- /dev/null
+++ b/bin/batch/knl_ctestP.sl.in.cmake
@@ -0,0 +1,16 @@
+#!/bin/bash
+
+#SBATCH -p knl -C quad,cache
+#SBATCH --nodes=1
+#SBATCH -t 00:30:00
+#SBATCH --mail-type=BEGIN,END,FAIL
+##SBATCH --mail-user=<username>@sandia.gov
+#SBATCH --export=ALL
+#SBATCH --job-name=h5_ctestP
+
+cd @HDF5_BINARY_DIR@
+#run parallel tests except t_cache_image test
+ctest . -R MPI_TEST_ -C Release -T test >& ctestP.out
+
+echo "Done running $CMD"
+
diff --git a/bin/batch/knl_ctestS.sl.in.cmake b/bin/batch/knl_ctestS.sl.in.cmake
new file mode 100644
index 0000000..af6353b
--- /dev/null
+++ b/bin/batch/knl_ctestS.sl.in.cmake
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+#SBATCH -p knl -C quad,cache
+#SBATCH --nodes=1
+#SBATCH -t 00:30:00
+#SBATCH --mail-type=BEGIN,END,FAIL
+##SBATCH --mail-user=<username>@sandia.gov
+#SBATCH --export=ALL
+#SBATCH --job-name=h5_ctestS
+
+cd @HDF5_BINARY_DIR@
+CMD="ctest . -E MPI_TEST_ -C Release -j 32 -T test"
+
+echo "Run $CMD. Test output will be in build/ctestS.out"
+$CMD  >& ctestS.out
+echo "Done running $CMD"
+
diff --git a/bin/batch/ray_ctestP.lsf.in.cmake b/bin/batch/ray_ctestP.lsf.in.cmake
new file mode 100644
index 0000000..7067a65
--- /dev/null
+++ b/bin/batch/ray_ctestP.lsf.in.cmake
@@ -0,0 +1,20 @@
+#!/bin/tcsh
+### LSF syntax
+#BSUB -n 6                       #number of nodes
+#BSUB -R "span[ptile=6]"
+#BSUB -W 30                      #walltime in minutes
+#BSUB -G guests                  #account
+#BSUB -e ctestPerrors.txt        #stderr
+#BSUB -o ctestPoutput.txt        #stdout
+#BSUB -J hdf5_ctestP             #job
+##BSUB -q pbatch                 #queue to use
+#BSUB -q pdebug
+
+##date; hostname
+##echo -n 'JobID is '; echo $LSB_JOBID
+
+cd @HDF5_BINARY_DIR@
+echo "Run parallel test command. Test output will be in build/ctestP.out"
+ctest . -R 'MPI_TEST_' -C Release -T test >& ctestP.out
+
+echo "Done running ctest parallel command."
diff --git a/bin/batch/ray_ctestS.lsf.in.cmake b/bin/batch/ray_ctestS.lsf.in.cmake
new file mode 100644
index 0000000..da20438
--- /dev/null
+++ b/bin/batch/ray_ctestS.lsf.in.cmake
@@ -0,0 +1,18 @@
+#!/bin/tcsh
+### LSF syntax
+#BSUB -n 1                       #number of nodes
+#BSUB -W 29                      #walltime in minutes
+#BSUB -G guests                  #account
+#BSUB -e ctestSerrors.txt        #stderr
+#BSUB -o ctestSoutput.txt        #stdout
+#BSUB -J hdf5_ctestS             #job
+##BSUB -q pbatch                 #queue to use
+#BSUB -q pdebug
+
+cd @HDF5_BINARY_DIR@
+echo "Run command. Test output will be in build/ctestS.out"
+ctest . -E 'MPI_TEST_' -C Release -j 32 -T test >& ctestS.out
+
+##$CMD  >& ctestS.out
+echo "Done running command."
+
diff --git a/bin/batch/raybsub b/bin/batch/raybsub
new file mode 100755
index 0000000..19dceef
--- /dev/null
+++ b/bin/batch/raybsub
@@ -0,0 +1,7 @@
+#!/bin/tcsh
+
+# ray.llnl.gov requires a '<' with bsub for submitting .lsf batch jobs.
+# CMake is reluctant to pass the '<', so we put it in this script and use
+# the script to submit the bsub command on ray.
+
+bsub < $1
diff --git a/src/H5.c b/src/H5.c
index 9845945..ab7d45c 100644
--- a/src/H5.c
+++ b/src/H5.c
@@ -131,7 +131,7 @@ H5_init_library(void)
         if (mpi_initialized && !mpi_finalized) {
             int key_val;
 
-            if(MPI_SUCCESS != (mpi_code = MPI_Comm_create_keyval(MPI_NULL_COPY_FN, 
+            if(MPI_SUCCESS != (mpi_code = MPI_Comm_create_keyval(MPI_COMM_NULL_COPY_FN, 
                                                                  (MPI_Comm_delete_attr_function *)H5_mpi_delete_cb, 
                                                                  &key_val, NULL)))
                 HMPI_GOTO_ERROR(FAIL, "MPI_Comm_create_keyval failed", mpi_code)
diff --git a/testpar/t_cache.c b/testpar/t_cache.c
index 0493cb6..25ffbc8 100644
--- a/testpar/t_cache.c
+++ b/testpar/t_cache.c
@@ -1171,15 +1171,15 @@ setup_derived_types(void)
     struct mssg_t sample; /* used to compute displacements */
 
     /* setup the displacements array */
-    if ( ( MPI_SUCCESS != MPI_Address(&sample.req, &displs[0]) ) ||
-         ( MPI_SUCCESS != MPI_Address(&sample.src, &displs[1]) ) ||
-         ( MPI_SUCCESS != MPI_Address(&sample.dest, &displs[2]) ) ||
-         ( MPI_SUCCESS != MPI_Address(&sample.mssg_num, &displs[3]) ) ||
-         ( MPI_SUCCESS != MPI_Address(&sample.base_addr, &displs[4]) ) ||
-         ( MPI_SUCCESS != MPI_Address(&sample.len, &displs[5]) ) ||
-         ( MPI_SUCCESS != MPI_Address(&sample.ver, &displs[6]) ) ||
-         ( MPI_SUCCESS != MPI_Address(&sample.count, &displs[7]) ) ||
-         ( MPI_SUCCESS != MPI_Address(&sample.magic, &displs[8]) ) ) {
+    if ( ( MPI_SUCCESS != MPI_Get_address(&sample.req, &displs[0]) ) ||
+         ( MPI_SUCCESS != MPI_Get_address(&sample.src, &displs[1]) ) ||
+         ( MPI_SUCCESS != MPI_Get_address(&sample.dest, &displs[2]) ) ||
+         ( MPI_SUCCESS != MPI_Get_address(&sample.mssg_num, &displs[3]) ) ||
+         ( MPI_SUCCESS != MPI_Get_address(&sample.base_addr, &displs[4]) ) ||
+         ( MPI_SUCCESS != MPI_Get_address(&sample.len, &displs[5]) ) ||
+         ( MPI_SUCCESS != MPI_Get_address(&sample.ver, &displs[6]) ) ||
+         ( MPI_SUCCESS != MPI_Get_address(&sample.count, &displs[7]) ) ||
+         ( MPI_SUCCESS != MPI_Get_address(&sample.magic, &displs[8]) ) ) {
 
         nerrors++;
         success = FALSE;
@@ -1199,7 +1199,7 @@ setup_derived_types(void)
 
     if ( success ) {
 
-        result = MPI_Type_struct(9, block_len, displs, mpi_types, &mpi_mssg_t);
+        result = MPI_Type_create_struct(9, block_len, displs, mpi_types, &mpi_mssg_t);
 
         if ( result != MPI_SUCCESS ) {