Update cmake macros and java arg format

4 files changed, 86 insertions, 10 deletions

diff --git a/config/cmake/jrunTest.cmake b/config/cmake/jrunTest.cmake
index 95c7583..fc49275 100644
--- a/config/cmake/jrunTest.cmake
+++ b/config/cmake/jrunTest.cmake
@@ -51,6 +51,8 @@ message (STATUS "COMMAND: ${TEST_TESTER} -Xmx1024M -Dorg.slf4j.simpleLogger.defa
 
 if (WIN32 AND NOT MINGW)
   set (ENV{PATH} "$ENV{PATH}\\;${TEST_LIBRARY_DIRECTORY}")
+else ()
+  set (ENV{LD_LIBRARY_PATH} "$ENV{LD_LIBRARY_PATH}:${TEST_LIBRARY_DIRECTORY}")
 endif ()
 
 # run the test program, capture the stdout/stderr and the result var
@@ -64,6 +66,7 @@ execute_process (
     RESULT_VARIABLE TEST_RESULT
     OUTPUT_FILE ${TEST_OUTPUT}
     ERROR_FILE ${TEST_OUTPUT}.err
+    OUTPUT_VARIABLE TEST_OUT
     ERROR_VARIABLE TEST_ERROR
 )
 
@@ -126,11 +129,22 @@ if (NOT TEST_SKIP_COMPARE)
       file (WRITE ${TEST_FOLDER}/${TEST_REFERENCE} "${TEST_STREAM}")
     endif ()
 
-    # now compare the output with the reference
-    execute_process (
-        COMMAND ${CMAKE_COMMAND} -E compare_files ${TEST_FOLDER}/${TEST_OUTPUT} ${TEST_FOLDER}/${TEST_REFERENCE}
-        RESULT_VARIABLE TEST_RESULT
-    )
+    if (NOT TEST_SORT_COMPARE)
+      # now compare the output with the reference
+      execute_process (
+          COMMAND ${CMAKE_COMMAND} -E compare_files ${TEST_FOLDER}/${TEST_OUTPUT} ${TEST_FOLDER}/${TEST_REFERENCE}
+          RESULT_VARIABLE TEST_RESULT
+      )
+    else ()
+      file (STRINGS ${TEST_FOLDER}/${TEST_OUTPUT} v1)
+      file (STRINGS ${TEST_FOLDER}/${TEST_REFERENCE} v2)
+      list (SORT v1)
+      list (SORT v2)
+      if (NOT v1 STREQUAL v2)
+        set(TEST_RESULT 1)
+      endif ()
+    endif ()
+
     if (TEST_RESULT)
       set (TEST_RESULT 0)
       file (STRINGS ${TEST_FOLDER}/${TEST_OUTPUT} test_act)
diff --git a/config/cmake/scripts/CTestScript.cmake b/config/cmake/scripts/CTestScript.cmake
index e234057..e1fe85a 100755
--- 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 8f0c9fa..2a80277 100755
--- a/config/cmake/scripts/HDF5config.cmake
+++ b/config/cmake/scripts/HDF5config.cmake
@@ -44,7 +44,7 @@ set (CTEST_SOURCE_VERSEXT "-snap1")
 #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
@@ -177,8 +177,8 @@ if (NOT DEFINED HPC)
     endif ()
   endif ()
 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 ()
 ###################################################################
 
@@ -203,7 +203,7 @@ endif ()
 #####       Following controls source update                  #####
 #set (LOCAL_UPDATE "TRUE")
 set (REPOSITORY_URL "https://git@bitbucket.hdfgroup.org/scm/hdffv/hdf5.git")
-set (REPOSITORY_BRANCH "hdf5_1_10_5")
+set (REPOSITORY_BRANCH "hdf5_1_10_6")
 
 #uncomment to use a compressed source file: *.tar on linux or mac *.zip on windows
 #set(CTEST_USE_TAR_SOURCE "${CTEST_SOURCE_VERSION}")
@@ -228,6 +228,9 @@ if (WIN32)
 else ()
   set (BINFILEBASE "HDF5-${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}")
+
+#############################################################################################
+#############################################################################################