Add HDF5options.cmake files for serial and parallel tests on HPC

machines (where tests are to be run as batch jobs.
Add README_HPC file with instructions for setting up configuration
to use batch scripts for running tests on HPC machines and some
pointers for cross compiling.

3 files changed, 313 insertions, 0 deletions

diff --git a/config/cmake/scripts/HPC/par-HDF5options.cmake b/config/cmake/scripts/HPC/par-HDF5options.cmake
new file mode 100644
index 0000000..0527995
--- /dev/null
+++ b/config/cmake/scripts/HPC/par-HDF5options.cmake
@@ -0,0 +1,117 @@
+#
+# 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 "${ADD_BUILD_OPTIONS} -DXXX:YY=ZZZZ")                 ###
+#############################################################################################
+
+### uncomment/comment and change the following lines for other configuration options
+
+#############################################################################################
+####      maximum parallel processor count for build and test       ####
+set (MAX_PROC_COUNT 8)
+
+#############################################################################################
+####      alternate toolsets       ####
+#set (CMAKE_GENERATOR_TOOLSET "Intel C++ Compiler 17.0")
+
+#############################################################################################
+####      Only build static libraries       ####
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_SHARED_LIBS:BOOL=OFF")
+####      Add PICC option on linux/mac       ####
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_ANSI_CFLAGS:STRING=-fPIC")
+
+#############################################################################################
+####      fortran enabled      ####
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=ON")
+    ### enable Fortran 2003 depends on HDF5_BUILD_FORTRAN
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_F2003:BOOL=ON")
+####      fortran disabled      ####
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=OFF")
+    ### enable Fortran 2003 depends on HDF5_BUILD_FORTRAN
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_F2003:BOOL=OFF")
+
+#############################################################################################
+####      java enabled      ####
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=ON")
+####      java disabled      ####
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=OFF")
+
+#############################################################################################
+### change install prefix (default use INSTALLDIR value)
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_INSTALL_PREFIX:PATH=${INSTALLDIR}")
+
+#############################################################################################
+####      ext libraries       ####
+
+### ext libs from tgz
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=TGZ -DTGZPATH:PATH=${CTEST_SCRIPT_DIRECTORY}")
+### ext libs from git
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=GIT")
+### ext libs on system
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=NO")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_LIBRARY:FILEPATH=some_location/lib/zlib.lib -DZLIB_INCLUDE_DIR:PATH=some_location/include")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DSZIP_LIBRARY:FILEPATH=some_location/lib/szlib.lib -DSZIP_INCLUDE_DIR:PATH=some_location/include")
+
+### disable using ext zlib
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF")
+### disable using ext szip
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_ENCODING:BOOL=OFF")
+
+####      package examples       ####
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACK_EXAMPLES:BOOL=ON -DHDF5_EXAMPLES_COMPRESSED:STRING=HDF5Examples-1.10.9-Source.tar.gz -DHDF5_EXAMPLES_COMPRESSED_DIR:PATH=${CTEST_SCRIPT_DIRECTORY}")
+
+#############################################################################################
+### enable parallel builds
+
+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")
+
+#############################################################################################
+### enable thread-safety builds
+
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_THREADSAFE:BOOL=ON")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PARALLEL:BOOL=OFF")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=OFF")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=OFF")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_HL_LIB:BOOL=OFF")
+
+#############################################################################################
+### disable test program builds
+
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_TESTING:BOOL=OFF")
+
+#############################################################################################
+### disable packaging
+
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_NO_PACKAGES:BOOL=ON")
+### Create install package with external libraries (szip, zlib)
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACKAGE_EXTLIBS:BOOL=ON")
+
+#############################################################################################
+### use a toolchain file
+
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/craype.cmake")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/intel.cmake")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/GCC.cmake")
+
+#options to run test scripts in batch commands
+set (LOCAL_BATCH_TEST ON)
+set (LOCAL_BATCH_SCRIPT_COMMAND "sbatch")
+set (LOCAL_BATCH_SCRIPT_NAME "knl_ctestS.sl")
+set (LOCAL_BATCH_SCRIPT_PARALLEL_NAME "knl_ctestP.sl")
+set(MPIEXEC_EXECUTABLE "srun")
+
+#############################################################################################
diff --git a/config/cmake/scripts/HPC/ser-HDF5options.cmake b/config/cmake/scripts/HPC/ser-HDF5options.cmake
new file mode 100644
index 0000000..71266ec
--- /dev/null
+++ b/config/cmake/scripts/HPC/ser-HDF5options.cmake
@@ -0,0 +1,117 @@
+#
+# Copyright by The HDF Group.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
+#
+#############################################################################################
+####  Change default configuration of options in config/cmake/cacheinit.cmake file        ###
+####  format: set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DXXX:YY=ZZZZ")                 ###
+#############################################################################################
+
+### uncomment/comment and change the following lines for other configuration options
+
+#############################################################################################
+####      maximum parallel processor count for build and test       ####
+#set (MAX_PROC_COUNT 8)
+
+#############################################################################################
+####      alternate toolsets       ####
+#set (CMAKE_GENERATOR_TOOLSET "Intel C++ Compiler 17.0")
+
+#############################################################################################
+####      Only build static libraries       ####
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_SHARED_LIBS:BOOL=OFF")
+####      Add PICC option on linux/mac       ####
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_ANSI_CFLAGS:STRING=-fPIC")
+
+#############################################################################################
+####      fortran enabled      ####
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=ON")
+    ### enable Fortran 2003 depends on HDF5_BUILD_FORTRAN
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_F2003:BOOL=ON")
+####      fortran disabled      ####
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=OFF")
+    ### enable Fortran 2003 depends on HDF5_BUILD_FORTRAN
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_F2003:BOOL=OFF")
+
+#############################################################################################
+####      java enabled      ####
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=ON")
+####      java disabled      ####
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=OFF")
+
+#############################################################################################
+### change install prefix (default use INSTALLDIR value)
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_INSTALL_PREFIX:PATH=${INSTALLDIR}")
+
+#############################################################################################
+####      ext libraries       ####
+
+### ext libs from tgz
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=TGZ -DTGZPATH:PATH=${CTEST_SCRIPT_DIRECTORY}")
+### ext libs from git
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=GIT")
+### ext libs on system
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=NO")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_LIBRARY:FILEPATH=some_location/lib/zlib.lib -DZLIB_INCLUDE_DIR:PATH=some_location/include")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DSZIP_LIBRARY:FILEPATH=some_location/lib/szlib.lib -DSZIP_INCLUDE_DIR:PATH=some_location/include")
+
+### disable using ext zlib
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF")
+### disable using ext szip
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_ENCODING:BOOL=OFF")
+
+####      package examples       ####
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACK_EXAMPLES:BOOL=ON -DHDF5_EXAMPLES_COMPRESSED:STRING=HDF5Examples-1.10.9-Source.tar.gz -DHDF5_EXAMPLES_COMPRESSED_DIR:PATH=${CTEST_SCRIPT_DIRECTORY}")
+
+#############################################################################################
+### enable parallel builds
+
+#set (ADD_BUILD_OPTIONS "${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 "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_THREADSAFE:BOOL=OFF")
+
+#############################################################################################
+### enable thread-safety builds
+
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_THREADSAFE:BOOL=ON")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PARALLEL:BOOL=OFF")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=OFF")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=OFF")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_HL_LIB:BOOL=OFF")
+
+#############################################################################################
+### disable test program builds
+
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_TESTING:BOOL=OFF")
+
+#############################################################################################
+### disable packaging
+
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_NO_PACKAGES:BOOL=ON")
+### Create install package with external libraries (szip, zlib)
+set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACKAGE_EXTLIBS:BOOL=ON")
+
+#############################################################################################
+### use a toolchain file
+
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/intel.cmake")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/crayle.cmake")
+#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/GCC.cmake")
+
+#options to run test scripts in batch commands
+set (LOCAL_BATCH_TEST ON)
+set (LOCAL_BATCH_SCRIPT_COMMAND "sbatch")
+set (LOCAL_BATCH_SCRIPT_NAME "knl_ctestS.sl")
+set (LOCAL_BATCH_SCRIPT_PARALLEL_NAME "knl_ctestP.sl")
+set(MPIEXEC_EXECUTABLE "srun")
+
+#############################################################################################
diff --git a/release_docs/README_HPC b/release_docs/README_HPC
new file mode 100644
index 0000000..bdeab67
--- /dev/null
+++ b/release_docs/README_HPC
@@ -0,0 +1,79 @@
+HDF5 version 1.11.4 currently under development
+
+HDF5 source tar files with the HPC prefix are intended for use on clusters where 
+configuration and build steps will be done on a login node and executable and
+lib files that are built will be run on compute nodes.  
+
+Note these differences from the regular CMake tar and zip files:
+  - Test programs produced by this tar file will be run using batch scripts. 
+  - Serial and parallel HDF5options.cmake files, using parallel options by default.
+
+Note also that options are now available in HDF5 source to facilitate use of 
+toolchain files for using cross compilers available on login nodes to compile
+HDF5 for compute nodes.
+
+Instructions to configure build and test HDF5 using CMake:
+
+1. The cmake version must be 3.10 or later (cmake --version).
+2. Load or switch modules and set CC, FC, CXX for compilers desired.
+3. run build-unix.sh to configure, build, test and package HDF5 with CMake.
+
+Contents:
+
+build-unix.sh           Simple script for running CMake to configure, build, 
+                        test, and package HDF5.
+CTestScript.cmake       CMake script to configure, build, test and package 
+                        HDF5.
+hdf5-<version>          HDF5 source for <version>.
+HDF5config.cmake        CMake script to configure, build, test and package
+                        HDF5. 
+HDF5Examples            Source for HDF5 Examples.
+HDF5options.cmake       symlink to parallel or serial HDF5options.cmake files.
+                        Default is parallel file, which builds and tests both
+                        serial and parallel C and Fortran wrappers.
+                        To build serial only, C Fortran and C++ wrappers, delete
+                        The HDF5options.cmake link and run 
+                        'ln -s ser-HDF5options.cmake HDF5options.cmake' to switch.  
+par-HDF5options.cmake   Options file for HDF5 serial and parallel build and test.
+ser-HDF5options.cmake   Options file for HDF5 serial only build and test.
+SZip.tar.gz             Source for building SZip.
+ZLib.tar.gz             Source for buildng Zlib.
+
+
+To cross compile with this HPC-CMake tar.gz HDF5 source file:
+On Cray XC40  haswell login node for knl compute nodes using CMake and Cray modules:
+        1.  Uncomment line in HDF5options.txt to use a toolchain file - line 106 for
+            config/toolchain/crayle.cmake.
+        2.  Uncomment lines 110, 111, and 115 - 122 of HDF5options.cmake.
+            Line 110 allows configuring to complete on the haswell node.
+            Line 111 switches the compiler to build files for knl nodes.
+            Lines 115 - 122 set up test files to use sbatch to run build tests
+            in batch jobs on a knl compute node with 6 processes.
+        3.  Compiler module may be the default PrgEnv-intel/6.0.4 to use 
+            intel/18.0.2 or other intel, PrgEnv-cray/6.0.4 to use cce/8.7.4,
+            or PrgEnv-gnu/6.0.4 for GCC compilers.  PrgEnv-pgi/6.0.4 is also 
+            available but has not been tested with this tar file.
+        4.  These CMake options are set in config/toolchain/crayle.cmake:
+                set(CMAKE_SYSTEM_NAME Linux)
+                set(CMAKE_COMPILER_VENDOR "CrayLinuxEnvironment")
+                set(CMAKE_C_COMPILER cc)
+                set(CMAKE_CXX_COMPILER c++)
+                set(CMAKE_Fortran_COMPILER ftn)
+                set(CMAKE_CROSSCOMPILING_EMULATOR "")
+
+        5.  Settings for two other cross-compiling options are also in the 
+            config/toolchain files which do not seem to be necessary with the 
+            Cray PrgEnv-* modules
+            a.  HDF5_USE_PREGEN.  This option, along with the HDF5_USE_PREGEN_DIR
+                CMake variable would allow the use of an appropriate H5Tinit.c 
+                file with type information generated on a compute node to be used
+                when cross compiling for those compute nodes.  The use of the 
+                variables in lines 110 and 111 of HDF5options.cmake file seem to
+                preclude needing this option with the available Cray modules and
+                CMake options.
+            b.  HDF5_BATCH_H5DETECT and associated CMake variables.  This option
+                when properly configured will run H5detect in a batch job on a
+                compute node at the beginning of the CMake build process.  It 
+                was also found to be unnecessary with the available Cray modules
+                and CMake options.
+-