Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)

* commit '6eaef5ebd61b8019f66f51d3fe74ec3c1b1d4f0f':
  Reorder lines in HDF5config.cmake so that additions to end of $HPC-HDF5options scripts will take precedence.
  updated -E option
  remove -M option
  added -M HPC to ctest command
  fixed missing paralle test
  Adding cross-compilation for theta (ANL) and qsub (COBALT) batch controls.

14 files changed, 93 insertions, 79 deletions

diff --git a/MANIFEST b/MANIFEST
index 41edffb..c3dc0e9 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -92,10 +92,6 @@
 ./bin/timekeeper      _DO_NOT_DISTRIBUTE_
 ./bin/trace
 ./bin/yodconfigure
-./bin/batch/cori_ctestP.sl.in.cmake
-./bin/batch/cori_ctestS.sl.in.cmake
-./bin/batch/cori_knl_ctestP.sl.in.cmake
-./bin/batch/cori_knl_ctestS.sl.in.cmake
 ./bin/batch/ctestP.lsf.in.cmake
 ./bin/batch/ctestP.sl.in.cmake
 ./bin/batch/ctestS.lsf.in.cmake
@@ -103,6 +99,7 @@
 ./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
@@ -3407,6 +3404,7 @@
 # CMake-specific HPC Scripts
 ./config/cmake/scripts/HPC/sbatch-HDF5options.cmake
 ./config/cmake/scripts/HPC/bsub-HDF5options.cmake
+./config/cmake/scripts/HPC/qsub-HDF5options.cmake
 ./config/cmake/scripts/HPC/raybsub-HDF5options.cmake
 
 # Files generated by autogen
diff --git a/bin/batch/cori_ctestP.sl.in.cmake b/bin/batch/cori_ctestP.sl.in.cmake
deleted file mode 100644
index 287fe3c..0000000
--- a/bin/batch/cori_ctestP.sl.in.cmake
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/bin/bash
-
-#SBATCH -C haswell
-#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@
-CMD="ctest . -R MPI_TEST_ -E t_cache_image -C Release -T test"
-
-echo "Run $CMD. Test output will be in build/ctestP.out"
-$CMD >& ctestP.out
-echo "Done running $CMD"
-
diff --git a/bin/batch/cori_ctestS.sl.in.cmake b/bin/batch/cori_ctestS.sl.in.cmake
deleted file mode 100644
index 50bef6b..0000000
--- a/bin/batch/cori_ctestS.sl.in.cmake
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/bin/bash
-
-#SBATCH -C haswell
-#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/cori_knl_ctestP.sl.in.cmake b/bin/batch/cori_knl_ctestP.sl.in.cmake
deleted file mode 100644
index 82378ec..0000000
--- a/bin/batch/cori_knl_ctestP.sl.in.cmake
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/bin/bash
-
-#SBATCH -C knl,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@
-CMD="ctest . -R MPI_TEST_ -E t_cache_image -C Release -T test"
-
-echo "Run $CMD. Test output will be in build/ctestP.out"
-$CMD >& ctestP.out
-echo "Done running $CMD"
-
diff --git a/bin/batch/cori_knl_ctestS.sl.in.cmake b/bin/batch/cori_knl_ctestS.sl.in.cmake
deleted file mode 100644
index c6d9e83..0000000
--- a/bin/batch/cori_knl_ctestS.sl.in.cmake
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/bin/bash
-
-#SBATCH -C knl,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/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
index 2777f39..3fdd5ce 100644
--- a/bin/batch/ctestP.lsf.in.cmake
+++ b/bin/batch/ctestP.lsf.in.cmake
@@ -14,6 +14,6 @@
 
 cd @HDF5_BINARY_DIR@
 echo "Run parallel test command. Test output will be in build/ctestP.out"
-ctest . -R 'TEST_PAR|PH5DIFF|PERFORM' -E t_cache_image -C Release -T test >& 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
index 592d37d..6399de7 100644
--- a/bin/batch/ctestP.sl.in.cmake
+++ b/bin/batch/ctestP.sl.in.cmake
@@ -8,7 +8,7 @@
 #SBATCH --job-name=h5_ctestP
 
 cd @HDF5_BINARY_DIR@
-ctest . -R MPI_TEST_ -E t_cache_image -C Release -T test >& ctestP.out
+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
index 7ef5af5..a01d39b 100644
--- a/bin/batch/ctestS.lsf.in.cmake
+++ b/bin/batch/ctestS.lsf.in.cmake
@@ -11,7 +11,7 @@
 
 cd @HDF5_BINARY_DIR@
 echo "Run command. Test output will be in build/ctestS.out"
-ctest . -E 'TEST_PAR|PH5DIFF|PERFORM' -C Release -j 32 -T test >& 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/knl_ctestP.sl.in.cmake b/bin/batch/knl_ctestP.sl.in.cmake
index 73c5ac5..f985fbb 100644
--- a/bin/batch/knl_ctestP.sl.in.cmake
+++ b/bin/batch/knl_ctestP.sl.in.cmake
@@ -10,7 +10,7 @@
 
 cd @HDF5_BINARY_DIR@
 #run parallel tests except t_cache_image test
-ctest . -R MPI_TEST_ -E t_cache_image -C Release -T test >& ctestP.out
+ctest . -R MPI_TEST_ -C Release -T test >& ctestP.out
 
 echo "Done running $CMD"
 
diff --git a/bin/batch/ray_ctestP.lsf.in.cmake b/bin/batch/ray_ctestP.lsf.in.cmake
index 082276a..7067a65 100644
--- a/bin/batch/ray_ctestP.lsf.in.cmake
+++ b/bin/batch/ray_ctestP.lsf.in.cmake
@@ -15,6 +15,6 @@
 
 cd @HDF5_BINARY_DIR@
 echo "Run parallel test command. Test output will be in build/ctestP.out"
-ctest . -R 'MPI_TEST_' -E t_cache_image -C Release -T test >& ctestP.out
+ctest . -R 'MPI_TEST_' -C Release -T test >& ctestP.out
 
 echo "Done running ctest parallel command."
diff --git a/config/cmake/scripts/CTestScript.cmake b/config/cmake/scripts/CTestScript.cmake
index e234057..e1fe85a 100644
--- a/config/cmake/scripts/CTestScript.cmake
+++ b/config/cmake/scripts/CTestScript.cmake
@@ -280,7 +280,11 @@ message (STATUS "Dashboard script configuration:\n${vars}\n")
         if (LOCAL_BATCH_SCRIPT_COMMAND STREQUAL "raybsub")
           execute_process (COMMAND ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_COMMAND} ${LOCAL_BATCH_SCRIPT_ARGS} ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_NAME})
         else ()
-          execute_process (COMMAND ${LOCAL_BATCH_SCRIPT_COMMAND} ${LOCAL_BATCH_SCRIPT_ARGS} ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_NAME})
+          if (LOCAL_BATCH_SCRIPT_COMMAND STREQUAL "qsub")
+            execute_process (COMMAND ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_NAME} ctestS.out)
+          else ()
+            execute_process (COMMAND ${LOCAL_BATCH_SCRIPT_COMMAND} ${LOCAL_BATCH_SCRIPT_ARGS} ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_NAME})
+          endif()
         endif ()
         message(STATUS "Check for existence of ${CTEST_BINARY_DIRECTORY}/Testing/${TAG_CONTENTS}/Test.xml")
         execute_process(COMMAND ls ${CTEST_BINARY_DIRECTORY}/Testing/${TAG_CONTENTS}/Test.xml RESULT_VARIABLE result OUTPUT_QUIET ERROR_QUIET)
@@ -299,7 +303,11 @@ message (STATUS "Dashboard script configuration:\n${vars}\n")
           if (LOCAL_BATCH_SCRIPT_COMMAND STREQUAL "raybsub")
             execute_process (COMMAND ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_COMMAND} ${LOCAL_BATCH_SCRIPT_ARGS} ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_PARALLEL_NAME})
           else ()
-            execute_process (COMMAND ${LOCAL_BATCH_SCRIPT_COMMAND} ${LOCAL_BATCH_SCRIPT_ARGS} ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_PARALLEL_NAME})
+            if (LOCAL_BATCH_SCRIPT_COMMAND STREQUAL "qsub")
+              execute_process (COMMAND ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_NAME} ctestP.out)
+            else ()
+              execute_process (COMMAND ${LOCAL_BATCH_SCRIPT_COMMAND} ${LOCAL_BATCH_SCRIPT_ARGS} ${CTEST_BINARY_DIRECTORY}/${LOCAL_BATCH_SCRIPT_PARALLEL_NAME})
+            endif ()
           endif ()
           message(STATUS "Check for existence of ${CTEST_BINARY_DIRECTORY}/Testing/${TAG_CONTENTS}/Test.xml")
           execute_process(COMMAND ls ${CTEST_BINARY_DIRECTORY}/Testing/${TAG_CONTENTS}/Test.xml RESULT_VARIABLE result OUTPUT_QUIET ERROR_QUIET)
diff --git a/config/cmake/scripts/HDF5config.cmake b/config/cmake/scripts/HDF5config.cmake
index 0d85b42..44ed531 100644
--- a/config/cmake/scripts/HDF5config.cmake
+++ b/config/cmake/scripts/HDF5config.cmake
@@ -44,7 +44,7 @@ set (CTEST_SOURCE_VERSEXT "")
 #CTEST_CONFIGURATION_TYPE - Release, Debug, RelWithDebInfo
 #CTEST_SOURCE_NAME - name of source folder; HDF5-1.10.0
 #MODEL - CDash group name
-#HPC - run alternate configurations for HPC machines; sbatch, bsub, raybsub
+#HPC - run alternate configurations for HPC machines; sbatch, bsub, raybsub, qsub
 #MPI - enable MPI;
 if (DEFINED CTEST_SCRIPT_ARG)
     # transform ctest script arguments of the form
@@ -179,7 +179,6 @@ if (NOT DEFINED HPC)
 else ()
   set (CTEST_SITE "${SITE_OS_NAME}")
   set (CTEST_CMAKE_GENERATOR "Unix Makefiles")
-  include (${CTEST_SOURCE_DIRECTORY}/config/cmake/scripts/HPC/${HPC}-HDF5options.cmake)
 endif ()
 ###################################################################
 
@@ -229,6 +228,9 @@ if (WIN32)
 else ()
   set (BINFILEBASE "HDF5-${CTEST_SOURCE_VERSION}${CTEST_SOURCE_VERSEXT}")
   include (${CTEST_SCRIPT_DIRECTORY}/HDF5options.cmake)
+  if (DEFINED HPC)
+    include (${CTEST_SOURCE_DIRECTORY}/config/cmake/scripts/HPC/${HPC}-HDF5options.cmake)
+  endif ()
   include (${CTEST_SCRIPT_DIRECTORY}/CTestScript.cmake)
   if (APPLE)
     if (EXISTS "${CTEST_BINARY_DIRECTORY}/${BINFILEBASE}-Darwin.dmg")
diff --git a/config/cmake/scripts/HPC/qsub-HDF5options.cmake b/config/cmake/scripts/HPC/qsub-HDF5options.cmake
new file mode 100644
index 0000000..51c3891
--- /dev/null
+++ b/config/cmake/scripts/HPC/qsub-HDF5options.cmake
@@ -0,0 +1,51 @@
+#
+# Copyright by The HDF Group.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
+#
+#############################################################################################
+####  Change default configuration of options in config/cmake/cacheinit.cmake file        ###
+####  format: set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DXXX:YY=ZZZZ")                 ###
+#############################################################################################
+
+### uncomment/comment and change the following lines for other configuration options
+
+#############################################################################################
+### enable parallel builds
+if (DEFINED MPI)
+  # maximum parallel processor count for build and test       ####
+  set (MAX_PROC_COUNT 8)
+  set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PARALLEL:BOOL=ON")
+  set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=OFF")
+  set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=OFF")
+  set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_THREADSAFE:BOOL=OFF")
+endif ()
+#############################################################################################
+### options to run test scripts in batch commands
+set (LOCAL_BATCH_SCRIPT_NAME "ctest.qsub")
+set (LOCAL_BATCH_SCRIPT_PARALLEL_NAME "ctest.qsub")
+if (DEFINED KNL)
+  ### some additions and alternatives to cross compile on haswell for knl
+  set (COMPUTENODE_HWCOMPILE_MODULE "craype-mic-knl")
+  set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/crayle.cmake")
+endif ()
+set (LOCAL_BATCH_SCRIPT_COMMAND "qsub")
+set (LOCAL_BATCH_TEST "TRUE")
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_TEST:BOOL=ON")
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_SCRIPT_NAME:STRING=${LOCAL_BATCH_SCRIPT_NAME}")
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DLOCAL_BATCH_SCRIPT_PARALLEL_NAME:STRING=${LOCAL_BATCH_SCRIPT_PARALLEL_NAME}")
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_EXECUTABLE:STRING=aprun")
+# Option to suppress writing job statistics; to avoid issues with h5diff comparisons.
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_PREFLAGS:STRING=-q")
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_NUMPROC_FLAG:STRING=-n")
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DMPIEXEC_MAX_NUMPROCS:STRING=6")
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DACCOUNT_ID:STRING=${LOCAL_BATCH_SCRIPT_ARGS}")
+
+#############################################################################################
+#############################################################################################