Had to upgrade cmake to 2.8.8 for another project (VisIT). Now the shared
configuration
cmake \
-DCMAKE_INSTALL_PREFIX:PATH=/scr_multipole/cary/contrib/hdf5-1.8.8-ser \
-DCMAKE_BUILD_TYPE:STRING=Release \
-DCMAKE_COLOR_MAKEFILE:BOOL=FALSE \
-DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \
-DCMAKE_C_COMPILER:FILEPATH='/usr/local/contrib/bin/gcc' \
-DCMAKE_CXX_COMPILER:FILEPATH='/usr/local/contrib/bin/g++' \
-DCMAKE_Fortran_COMPILER:FILEPATH='/usr/local/contrib/bin/gfortran' \
-DCMAKE_C_FLAGS:STRING='-pipe -fPIC' \
-DCMAKE_CXX_FLAGS:STRING='-pipe -fPIC' \
-DCMAKE_Fortran_FLAGS:STRING='-fPIC' \
-DBUILD_SHARED_LIBS:BOOL=ON \
-DCMAKE_SHARED_LINKER_FLAGS:STRING='-Wl,-rpath,$ORIGIN' \
-DCMAKE_SKIP_RPATH:BOOL=ON \
-DHDF5_BUILD_FORTRAN:BOOL=ON \
-DCMAKE_EXE_LINKER_FLAGS:STRING='-Wl,-rpath,/usr/local/contrib/gcc-4.6.3/lib64'
\
-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=TRUE \
-DHDF5_BUILD_HL_LIB:BOOL=ON \
/scr_multipole/cary/vorpalall/builds/hdf5-1.8.8
does not build on a Linux machine,
$ uname -a; gcc --version
Linux multipole.txcorp.com 2.6.32-220.17.1.el6.x86_64 #1 SMP Wed May 16
00:01:37 BST 2012 x86_64 x86_64 x86_64 GNU/Linux
gcc (GCC) 4.6.3
The failure is
Linking C shared library ../../bin/libhdf5_f90cstub.so
cd /scr_multipole/cary/vorpalall/builds/hdf5-1.8.8/sersh/fortran/src &&
/scr_multipole/cary/contrib/cmake-2.8.8-ser/bin/cmake -E cmake_link_script
CMakeFiles/hdf5_f90cstub.dir/link.txt --verbose=1
/usr/local/contrib/bin/gcc -fPIC -pipe -fPIC -std=c99 -fomit-frame-pointer
-finline-functions -fno-common -fmessage-length=0 -O3 -DNDEBUG
-Wl,-rpath,$ORIGIN -shared -Wl,-soname,libhdf5_f90cstub.so.7.2.0 -o
../../bin/libhdf5_f90cstub.so.1.8.8
CMakeFiles/hdf5_f90cstub.dir/__/H5f90i_gen.h.o
CMakeFiles/hdf5_f90cstub.dir/H5f90kit.c.o CMakeFiles/hdf5_f90cstub.dir/H5_f.c.o
CMakeFiles/hdf5_f90cstub.dir/H5Af.c.o CMakeFiles/hdf5_f90cstub.dir/H5Df.c.o
CMakeFiles/hdf5_f90cstub.dir/H5Ef.c.o CMakeFiles/hdf5_f90cstub.dir/H5Ff.c.o
CMakeFiles/hdf5_f90cstub.dir/H5Gf.c.o CMakeFiles/hdf5_f90cstub.dir/H5If.c.o
CMakeFiles/hdf5_f90cstub.dir/H5Lf.c.o CMakeFiles/hdf5_f90cstub.dir/H5Of.c.o
CMakeFiles/hdf5_f90cstub.dir/H5Pf.c.o CMakeFiles/hdf5_f90cstub.dir/H5Rf.c.o
CMakeFiles/hdf5_f90cstub.dir/H5Sf.c.o CMakeFiles/hdf5_f90cstub.dir/H5Tf.c.o
CMakeFiles/hdf5_f90cstub.dir/H5Zf.c.o ../../bin/libhdf5.so.1.8.8 -lm
CMakeFiles/hdf5_f90cstub.dir/__/H5f90i_gen.h.o: file not recognized: File
format not recognized
collect2: ld returned 1 exit status
make[2]: *** [bin/libhdf5_f90cstub.so.1.8.8] Error 1
Seems like the new cmake does not allow one to put header files in the library
source list.
Attached is the patch that allowed me to build hdf5-1.8.9 everywhere I need.
John Cary
diff -ruN hdf5-1.8.9/CMakeLists.txt hdf5-1.8.9-new/CMakeLists.txt
--- hdf5-1.8.9/CMakeLists.txt 2012-05-09 09:06:29.000000000 -0600
+++ hdf5-1.8.9-new/CMakeLists.txt 2012-07-01 08:38:25.000000000 -0600
@@ -478,7 +478,10 @@
IF (H5_HAVE_PARALLEL)
SET (LINK_LIBS ${LINK_LIBS} ${MPI_C_LIBRARIES})
IF (MPI_C_LINK_FLAGS)
- SET (CMAKE_EXE_LINKER_FLAGS ${MPI_C_LINK_FLAGS} ${CMAKE_EXE_LINKER_FLAGS})
+# JRC: only Windows does not use compiler wrapper
+ if (WIN32)
+ SET (CMAKE_EXE_LINKER_FLAGS "${MPI_LINK_FLAGS}
${CMAKE_EXE_LINKER_FLAGS}")
+ endif ()
ENDIF (MPI_C_LINK_FLAGS)
ENDIF (H5_HAVE_PARALLEL)
@@ -884,7 +887,7 @@
IF (EXISTS "${HDF5_SOURCE_DIR}/release_docs" AND IS_DIRECTORY
"${HDF5_SOURCE_DIR}/release_docs")
SET (release_files
${HDF5_SOURCE_DIR}/release_docs/CMake.txt
- ${HDF5_SOURCE_DIR}/release_docs/Using_CMake.txt
+ ${HDF5_SOURCE_DIR}/release_docs/USING_CMake.txt
${HDF5_SOURCE_DIR}/release_docs/COPYING
${HDF5_SOURCE_DIR}/release_docs/HISTORY-1_8.txt
${HDF5_SOURCE_DIR}/release_docs/INSTALL
diff -ruN hdf5-1.8.9/config/cmake/ConfigureChecks.cmake
hdf5-1.8.9-new/config/cmake/ConfigureChecks.cmake
--- hdf5-1.8.9/config/cmake/ConfigureChecks.cmake 2012-05-09
09:06:20.000000000 -0600
+++ hdf5-1.8.9-new/config/cmake/ConfigureChecks.cmake 2012-07-01
08:38:25.000000000 -0600
@@ -129,6 +129,7 @@
SET (WINDOWS)
IF (WIN32)
+ message(STATUS "CMAKE_CXX_COMPILER_ID = ${CMAKE_CXX_COMPILER_ID}.")
IF (MINGW)
SET (H5_HAVE_MINGW 1)
SET (WINDOWS 1) # MinGW tries to imitate Windows
@@ -136,9 +137,9 @@
SET (H5_HAVE_WIN32_API 1)
IF (NOT UNIX AND NOT CYGWIN AND NOT MINGW)
SET (WINDOWS 1)
- IF (MSVC)
+ IF (MSVC OR ${CMAKE_CXX_COMPILER_ID} STREQUAL "MSVC")
SET (H5_HAVE_VISUAL_STUDIO 1)
- ENDIF (MSVC)
+ ENDIF ()
ENDIF (NOT UNIX AND NOT CYGWIN AND NOT MINGW)
ENDIF (WIN32)
@@ -957,4 +958,4 @@
# problem converting from unsigned long long to long double */
IF (CYGWIN)
SET (H5_CYGWIN_ULLONG_TO_LDOUBLE_ROUND_PROBLEM 1)
-ENDIF (CYGWIN)
\ No newline at end of file
+ENDIF (CYGWIN)
diff -ruN hdf5-1.8.9/config/cmake/FindMPI.cmake
hdf5-1.8.9-new/config/cmake/FindMPI.cmake
--- hdf5-1.8.9/config/cmake/FindMPI.cmake 2012-05-09 09:06:20.000000000
-0600
+++ hdf5-1.8.9-new/config/cmake/FindMPI.cmake 1969-12-31 17:00:00.000000000
-0700
@@ -1,628 +0,0 @@
-# - Find a Message Passing Interface (MPI) implementation
-# The Message Passing Interface (MPI) is a library used to write
-# high-performance distributed-memory parallel applications, and
-# is typically deployed on a cluster. MPI is a standard interface
-# (defined by the MPI forum) for which many implementations are
-# available. All of them have somewhat different include paths,
-# libraries to link against, etc., and this module tries to smooth
-# out those differences.
-#
-# === Variables ===
-#
-# This module will set the following variables per language in your project,
-# where <lang> is one of C, CXX, or Fortran:
-# MPI_<lang>_FOUND TRUE if FindMPI found MPI flags for <lang>
-# MPI_<lang>_COMPILER MPI Compiler wrapper for <lang>
-# MPI_<lang>_COMPILE_FLAGS Compilation flags for MPI programs
-# MPI_<lang>_INCLUDE_PATH Include path(s) for MPI header
-# MPI_<lang>_LINK_FLAGS Linking flags for MPI programs
-# MPI_<lang>_LIBRARIES All libraries to link MPI programs against
-# Additionally, FindMPI sets the following variables for running MPI
-# programs from the command line:
-# MPIEXEC Executable for running MPI programs
-# MPIEXEC_NUMPROC_FLAG Flag to pass to MPIEXEC before giving
-# it the number of processors to run on
-# MPIEXEC_PREFLAGS Flags to pass to MPIEXEC directly
-# before the executable to run.
-# MPIEXEC_POSTFLAGS Flags to pass to MPIEXEC after other flags
-# === Usage ===
-#
-# To use this module, simply call FindMPI from a CMakeLists.txt file, or
-# run find_package(MPI), then run CMake. If you are happy with the auto-
-# detected configuration for your language, then you're done. If not, you
-# have two options:
-# 1. Set MPI_<lang>_COMPILER to the MPI wrapper (mpicc, etc.) of your
-# choice and reconfigure. FindMPI will attempt to determine all the
-# necessary variables using THAT compiler's compile and link flags.
-# 2. If this fails, or if your MPI implementation does not come with
-# a compiler wrapper, then set both MPI_<lang>_LIBRARIES and
-# MPI_<lang>_INCLUDE_PATH. You may also set any other variables
-# listed above, but these two are required. This will circumvent
-# autodetection entirely.
-# When configuration is successful, MPI_<lang>_COMPILER will be set to the
-# compiler wrapper for <lang>, if it was found. MPI_<lang>_FOUND and other
-# variables above will be set if any MPI implementation was found for <lang>,
-# regardless of whether a compiler was found.
-#
-# When using MPIEXEC to execute MPI applications, you should typically use
-# all of the MPIEXEC flags as follows:
-# ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} PROCS
-# ${MPIEXEC_PREFLAGS} EXECUTABLE ${MPIEXEC_POSTFLAGS} ARGS
-# where PROCS is the number of processors on which to execute the program,
-# EXECUTABLE is the MPI program, and ARGS are the arguments to pass to the
-# MPI program.
-#
-# === Backward Compatibility ===
-#
-# For backward compatibility with older versions of FindMPI, these
-# variables are set, but deprecated:
-# MPI_FOUND MPI_COMPILER MPI_LIBRARY
-# MPI_COMPILE_FLAGS MPI_INCLUDE_PATH MPI_EXTRA_LIBRARY
-# MPI_LINK_FLAGS MPI_LIBRARIES
-# In new projects, please use the MPI_<lang>_XXX equivalents.
-
-#=============================================================================
-# Copyright 2001-2011 Kitware, Inc.
-# Copyright 2010-2011 Todd Gamblin tgamb...@llnl.gov
-# Copyright 2001-2009 Dave Partyka
-#
-# Distributed under the OSI-approved BSD License (the "License");
-# see accompanying file Copyright.txt for details.
-#
-# This software is distributed WITHOUT ANY WARRANTY; without even the
-# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the License for more information.
-#=============================================================================
-# (To distribute this file outside of CMake, substitute the full
-# License text for the above reference.)
-
-# include this to handle the QUIETLY and REQUIRED arguments
-include(${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake)
-include(GetPrerequisites)
-
-#
-# This part detects MPI compilers, attempting to wade through the mess of
compiler names in
-# a sensible way.
-#
-# The compilers are detected in this order:
-#
-# 1. Try to find the most generic availble MPI compiler, as this is usually
set up by
-# cluster admins. e.g., if plain old mpicc is available, we'll use it and
assume it's
-# the right compiler.
-#
-# 2. If a generic mpicc is NOT found, then we attempt to find one that matches
-# CMAKE_<lang>_COMPILER_ID. e.g. if you are using XL compilers, we'll try
to find mpixlc
-# and company, but not mpiicc. This hopefully prevents toolchain
mismatches.
-#
-# If you want to force a particular MPI compiler other than what we autodetect
(e.g. if you
-# want to compile regular stuff with GNU and parallel stuff with Intel), you
can always set
-# your favorite MPI_<lang>_COMPILER explicitly and this stuff will be ignored.
-#
-
-# Start out with the generic MPI compiler names, as these are most commonly
used.
-set(_MPI_C_COMPILER_NAMES mpicc mpcc mpicc_r mpcc_r)
-set(_MPI_CXX_COMPILER_NAMES mpicxx mpiCC mpcxx mpCC
mpic++ mpc++
- mpicxx_r mpiCC_r mpcxx_r mpCC_r
mpic++_r mpc++_r)
-set(_MPI_Fortran_COMPILER_NAMES mpif95 mpif95_r mpf95 mpf95_r
- mpif90 mpif90_r mpf90 mpf90_r
- mpif77 mpif77_r mpf77 mpf77_r)
-
-# GNU compiler names
-set(_MPI_GNU_C_COMPILER_NAMES mpigcc mpgcc mpigcc_r mpgcc_r)
-set(_MPI_GNU_CXX_COMPILER_NAMES mpig++ mpg++ mpig++_r mpg++_r)
-set(_MPI_GNU_Fortran_COMPILER_NAMES mpigfortran mpgfortran
mpigfortran_r mpgfortran_r
- mpig77 mpig77_r mpg77 mpg77_r)
-
-# Intel MPI compiler names
-set(_MPI_Intel_C_COMPILER_NAMES mpiicc)
-set(_MPI_Intel_CXX_COMPILER_NAMES mpiicpc mpiicxx mpiic++ mpiiCC)
-set(_MPI_Intel_Fortran_COMPILER_NAMES mpiifort mpiif95 mpiif90 mpiif77)
-
-# PGI compiler names
-set(_MPI_PGI_C_COMPILER_NAMES mpipgcc mppgcc)
-set(_MPI_PGI_CXX_COMPILER_NAMES mpipgCC mppgCC)
-set(_MPI_PGI_Fortran_COMPILER_NAMES mpipgf95 mpipgf90 mppgf95 mppgf90
mpipgf77 mppgf77)
-
-# XLC MPI Compiler names
-set(_MPI_XL_C_COMPILER_NAMES mpxlc mpxlc_r mpixlc
mpixlc_r)
-set(_MPI_XL_CXX_COMPILER_NAMES mpixlcxx mpixlC mpixlc++
mpxlcxx mpxlc++ mpixlc++ mpxlCC
- mpixlcxx_r mpixlC_r mpixlc++_r
mpxlcxx_r mpxlc++_r mpixlc++_r mpxlCC_r)
-set(_MPI_XL_Fortran_COMPILER_NAMES mpixlf95 mpixlf95_r mpxlf95
mpxlf95_r
- mpixlf90 mpixlf90_r mpxlf90
mpxlf90_r
- mpixlf77 mpixlf77_r mpxlf77
mpxlf77_r
- mpixlf mpixlf_r mpxlf
mpxlf_r)
-
-# append vendor-specific compilers to the list if we either don't know the
compiler id,
-# or if we know it matches the regular compiler.
-foreach (lang C CXX Fortran)
- foreach (id GNU Intel PGI XL)
- if (NOT CMAKE_${lang}_COMPILER_ID OR "${CMAKE_${lang}_COMPILER_ID}"
STREQUAL "${id}")
- list(APPEND _MPI_${lang}_COMPILER_NAMES
${_MPI_${id}_${lang}_COMPILER_NAMES})
- endif()
- unset(_MPI_${id}_${lang}_COMPILER_NAMES) # clean up the namespace here
- endforeach()
-endforeach()
-
-
-# Names to try for MPI exec
-set(_MPI_EXEC_NAMES mpiexec mpirun lamexec srun)
-
-# Grab the path to MPI from the registry if we're on windows.
-set(_MPI_PREFIX_PATH)
-if(WIN32)
- list(APPEND _MPI_PREFIX_PATH
"[HKEY_LOCAL_MACHINE\\SOFTWARE\\MPICH\\SMPD;binary]/..")
- list(APPEND _MPI_PREFIX_PATH "[HKEY_LOCAL_MACHINE\\SOFTWARE\\MPICH2;Path]")
- list(APPEND _MPI_PREFIX_PATH "$ENV{ProgramW6432}/MPICH2/")
-endif()
-
-# Build a list of prefixes to search for MPI.
-foreach(SystemPrefixDir ${CMAKE_SYSTEM_PREFIX_PATH})
- foreach(MpiPackageDir ${_MPI_PREFIX_PATH})
- if(EXISTS ${SystemPrefixDir}/${MpiPackageDir})
- list(APPEND _MPI_PREFIX_PATH "${SystemPrefixDir}/${MpiPackageDir}")
- endif()
- endforeach()
-endforeach()
-
-
-#
-# interrogate_mpi_compiler(lang try_libs)
-#
-# Attempts to extract compiler and linker args from an MPI compiler. The
arguments set
-# by this function are:
-#
-# MPI_<lang>_INCLUDE_PATH MPI_<lang>_LINK_FLAGS MPI_<lang>_FOUND
-# MPI_<lang>_COMPILE_FLAGS MPI_<lang>_LIBRARIES
-#
-# MPI_<lang>_COMPILER must be set beforehand to the absolute path to an MPI
compiler for
-# <lang>. Additionally, MPI_<lang>_INCLUDE_PATH and MPI_<lang>_LIBRARIES may
be set
-# to skip autodetection.
-#
-# If try_libs is TRUE, this will also attempt to find plain MPI libraries in
the usual
-# way. In general, this is not as effective as interrogating the compilers,
as it
-# ignores language-specific flags and libraries. However, some MPI
implementations
-# (Windows implementations) do not have compiler wrappers, so this approach
must be used.
-#
-function (interrogate_mpi_compiler lang try_libs)
- # MPI_${lang}_NO_INTERROGATE will be set to a compiler name when the
*regular* compiler was
- # discovered to be the MPI compiler. This happens on machines like the Cray
XE6 that use
- # modules to set cc, CC, and ftn to the MPI compilers. If the user
force-sets another MPI
- # compiler, MPI_${lang}_COMPILER won't be equal to
MPI_${lang}_NO_INTERROGATE, and we'll
- # inspect that compiler anew. This allows users to set new compilers w/o
rm'ing cache.
- string(COMPARE NOTEQUAL "${MPI_${lang}_NO_INTERROGATE}"
"${MPI_${lang}_COMPILER}" interrogate)
-
- # If MPI is set already in the cache, don't bother with interrogating the
compiler.
- if (interrogate AND ((NOT MPI_${lang}_INCLUDE_PATH) OR (NOT
MPI_${lang}_LIBRARIES)))
- if (MPI_${lang}_COMPILER)
- # Check whether the -showme:compile option works. This indicates that we
have either OpenMPI
- # or a newer version of LAM-MPI, and implies that -showme:link will also
work.
- execute_process(
- COMMAND ${MPI_${lang}_COMPILER} -showme:compile
- OUTPUT_VARIABLE MPI_COMPILE_CMDLINE OUTPUT_STRIP_TRAILING_WHITESPACE
- ERROR_VARIABLE MPI_COMPILE_CMDLINE ERROR_STRIP_TRAILING_WHITESPACE
- RESULT_VARIABLE MPI_COMPILER_RETURN)
-
- if (MPI_COMPILER_RETURN EQUAL 0)
- # If we appear to have -showme:compile, then we should
- # also have -showme:link. Try it.
- execute_process(
- COMMAND ${MPI_${lang}_COMPILER} -showme:link
- OUTPUT_VARIABLE MPI_LINK_CMDLINE OUTPUT_STRIP_TRAILING_WHITESPACE
- ERROR_VARIABLE MPI_LINK_CMDLINE ERROR_STRIP_TRAILING_WHITESPACE
- RESULT_VARIABLE MPI_COMPILER_RETURN)
-
- if (MPI_COMPILER_RETURN EQUAL 0)
- # We probably have -showme:incdirs and -showme:libdirs as well,
- # so grab that while we're at it.
- execute_process(
- COMMAND ${MPI_${lang}_COMPILER} -showme:incdirs
- OUTPUT_VARIABLE MPI_INCDIRS OUTPUT_STRIP_TRAILING_WHITESPACE
- ERROR_VARIABLE MPI_INCDIRS ERROR_STRIP_TRAILING_WHITESPACE)
-
- execute_process(
- COMMAND ${MPI_${lang}_COMPILER} -showme:libdirs
- OUTPUT_VARIABLE MPI_LIBDIRS OUTPUT_STRIP_TRAILING_WHITESPACE
- ERROR_VARIABLE MPI_LIBDIRS ERROR_STRIP_TRAILING_WHITESPACE)
-
- else()
- # reset things here if something went wrong.
- set(MPI_COMPILE_CMDLINE)
- set(MPI_LINK_CMDLINE)
- endif()
- endif ()
-
- # Older versions of LAM-MPI have "-showme". Try to find that.
- if (NOT MPI_COMPILER_RETURN EQUAL 0)
- execute_process(
- COMMAND ${MPI_${lang}_COMPILER} -showme
- OUTPUT_VARIABLE MPI_COMPILE_CMDLINE OUTPUT_STRIP_TRAILING_WHITESPACE
- ERROR_VARIABLE MPI_COMPILE_CMDLINE ERROR_STRIP_TRAILING_WHITESPACE
- RESULT_VARIABLE MPI_COMPILER_RETURN)
- endif()
-
- # MVAPICH uses -compile-info and -link-info. Try them.
- if (NOT MPI_COMPILER_RETURN EQUAL 0)
- execute_process(
- COMMAND ${MPI_${lang}_COMPILER} -compile-info
- OUTPUT_VARIABLE MPI_COMPILE_CMDLINE OUTPUT_STRIP_TRAILING_WHITESPACE
- ERROR_VARIABLE MPI_COMPILE_CMDLINE ERROR_STRIP_TRAILING_WHITESPACE
- RESULT_VARIABLE MPI_COMPILER_RETURN)
-
- # If we have compile-info, also have link-info.
- if (MPI_COMPILER_RETURN EQUAL 0)
- execute_process(
- COMMAND ${MPI_${lang}_COMPILER} -link-info
- OUTPUT_VARIABLE MPI_LINK_CMDLINE OUTPUT_STRIP_TRAILING_WHITESPACE
- ERROR_VARIABLE MPI_LINK_CMDLINE ERROR_STRIP_TRAILING_WHITESPACE
- RESULT_VARIABLE MPI_COMPILER_RETURN)
- endif()
-
- # make sure we got compile and link. Reset vars if something's wrong.
- if (NOT MPI_COMPILER_RETURN EQUAL 0)
- set(MPI_COMPILE_CMDLINE)
- set(MPI_LINK_CMDLINE)
- endif()
- endif()
-
- # MPICH just uses "-show". Try it.
- if (NOT MPI_COMPILER_RETURN EQUAL 0)
- execute_process(
- COMMAND ${MPI_${lang}_COMPILER} -show
- OUTPUT_VARIABLE MPI_COMPILE_CMDLINE OUTPUT_STRIP_TRAILING_WHITESPACE
- ERROR_VARIABLE MPI_COMPILE_CMDLINE ERROR_STRIP_TRAILING_WHITESPACE
- RESULT_VARIABLE MPI_COMPILER_RETURN)
- endif()
-
- if (MPI_COMPILER_RETURN EQUAL 0)
- # We have our command lines, but we might need to copy
MPI_COMPILE_CMDLINE
- # into MPI_LINK_CMDLINE, if we didn't find the link line.
- if (NOT MPI_LINK_CMDLINE)
- set(MPI_LINK_CMDLINE ${MPI_COMPILE_CMDLINE})
- endif()
- else()
- message(STATUS "Unable to determine MPI from MPI driver
${MPI_${lang}_COMPILER}")
- set(MPI_COMPILE_CMDLINE)
- set(MPI_LINK_CMDLINE)
- endif()
-
- # Here, we're done with the interrogation part, and we'll try to extract
args we care
- # about from what we learned from the compiler wrapper scripts.
-
- # If interrogation came back with something, extract our variable from
the MPI command line
- if (MPI_COMPILE_CMDLINE OR MPI_LINK_CMDLINE)
- # Extract compile flags from the compile command line.
- string(REGEX MATCHALL "(^| )-[Df]([^\" ]+|\"[^\"]+\")"
MPI_ALL_COMPILE_FLAGS "${MPI_COMPILE_CMDLINE}")
- set(MPI_COMPILE_FLAGS_WORK)
-
- foreach(FLAG ${MPI_ALL_COMPILE_FLAGS})
- if (MPI_COMPILE_FLAGS_WORK)
- set(MPI_COMPILE_FLAGS_WORK "${MPI_COMPILE_FLAGS_WORK} ${FLAG}")
- else()
- set(MPI_COMPILE_FLAGS_WORK ${FLAG})
- endif()
- endforeach()
-
- # Extract include paths from compile command line
- string(REGEX MATCHALL "(^| )-I([^\" ]+|\"[^\"]+\")"
MPI_ALL_INCLUDE_PATHS "${MPI_COMPILE_CMDLINE}")
- foreach(IPATH ${MPI_ALL_INCLUDE_PATHS})
- string(REGEX REPLACE "^ ?-I" "" IPATH ${IPATH})
- string(REGEX REPLACE "//" "/" IPATH ${IPATH})
- list(APPEND MPI_INCLUDE_PATH_WORK ${IPATH})
- endforeach()
-
- # try using showme:incdirs if extracting didn't work.
- if (NOT MPI_INCLUDE_PATH_WORK)
- set(MPI_INCLUDE_PATH_WORK ${MPI_INCDIRS})
- separate_arguments(MPI_INCLUDE_PATH_WORK)
- endif()
-
- # If all else fails, just search for mpi.h in the normal include paths.
- if (NOT MPI_INCLUDE_PATH_WORK)
- set(MPI_HEADER_PATH "MPI_HEADER_PATH-NOTFOUND" CACHE FILEPATH
"Cleared" FORCE)
- find_path(MPI_HEADER_PATH mpi.h
- HINTS ${_MPI_BASE_DIR} ${_MPI_PREFIX_PATH}
- PATH_SUFFIXES include)
- set(MPI_INCLUDE_PATH_WORK ${MPI_HEADER_PATH})
- endif()
-
- # Extract linker paths from the link command line
- string(REGEX MATCHALL "(^| |-Wl,)-L([^\" ]+|\"[^\"]+\")"
MPI_ALL_LINK_PATHS "${MPI_LINK_CMDLINE}")
- set(MPI_LINK_PATH)
- foreach(LPATH ${MPI_ALL_LINK_PATHS})
- string(REGEX REPLACE "^(| |-Wl,)-L" "" LPATH ${LPATH})
- string(REGEX REPLACE "//" "/" LPATH ${LPATH})
- list(APPEND MPI_LINK_PATH ${LPATH})
- endforeach()
-
- # try using showme:libdirs if extracting didn't work.
- if (NOT MPI_LINK_PATH)
- set(MPI_LINK_PATH ${MPI_LIBDIRS})
- separate_arguments(MPI_LINK_PATH)
- endif()
-
- # Extract linker flags from the link command line
- string(REGEX MATCHALL "(^| )-Wl,([^\" ]+|\"[^\"]+\")"
MPI_ALL_LINK_FLAGS "${MPI_LINK_CMDLINE}")
- set(MPI_LINK_FLAGS_WORK)
- foreach(FLAG ${MPI_ALL_LINK_FLAGS})
- if (MPI_LINK_FLAGS_WORK)
- set(MPI_LINK_FLAGS_WORK "${MPI_LINK_FLAGS_WORK} ${FLAG}")
- else()
- set(MPI_LINK_FLAGS_WORK ${FLAG})
- endif()
- endforeach()
-
- # Extract the set of libraries to link against from the link command
- # line
- string(REGEX MATCHALL "(^| )-l([^\" ]+|\"[^\"]+\")" MPI_LIBNAMES
"${MPI_LINK_CMDLINE}")
-
- # Determine full path names for all of the libraries that one needs
- # to link against in an MPI program
- foreach(LIB ${MPI_LIBNAMES})
- string(REGEX REPLACE "^ ?-l" "" LIB ${LIB})
- # MPI_LIB is cached by find_library, but we don't want that. Clear
it first.
- set(MPI_LIB "MPI_LIB-NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
- find_library(MPI_LIB NAMES ${LIB} HINTS ${MPI_LINK_PATH})
-
- if (MPI_LIB)
- list(APPEND MPI_LIBRARIES_WORK ${MPI_LIB})
- elseif (NOT MPI_FIND_QUIETLY)
- message(WARNING "Unable to find MPI library ${LIB}")
- endif()
- endforeach()
-
- # Sanity check MPI_LIBRARIES to make sure there are enough libraries
- list(LENGTH MPI_LIBRARIES_WORK MPI_NUMLIBS)
- list(LENGTH MPI_LIBNAMES MPI_NUMLIBS_EXPECTED)
- if (NOT MPI_NUMLIBS EQUAL MPI_NUMLIBS_EXPECTED)
- set(MPI_LIBRARIES_WORK "MPI_${lang}_LIBRARIES-NOTFOUND")
- endif()
- endif()
-
- elseif(try_libs)
- # If we didn't have an MPI compiler script to interrogate, attempt to
find everything
- # with plain old find functions. This is nasty because MPI
implementations have LOTS of
- # different library names, so this section isn't going to be very
generic. We need to
- # make sure it works for MS MPI, though, since there are no compiler
wrappers for that.
- find_path(MPI_HEADER_PATH mpi.h
- HINTS ${_MPI_BASE_DIR} ${_MPI_PREFIX_PATH}
- PATH_SUFFIXES include Inc)
- set(MPI_INCLUDE_PATH_WORK ${MPI_HEADER_PATH})
-
- # Decide between 32-bit and 64-bit libraries for Microsoft's MPI
- if("${CMAKE_SIZEOF_VOID_P}" EQUAL 8)
- set(MS_MPI_ARCH_DIR amd64)
- else()
- set(MS_MPI_ARCH_DIR i386)
- endif()
-
- set(MPI_LIB "MPI_LIB-NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
- find_library(MPI_LIB
- NAMES mpi mpich mpich2 msmpi
- HINTS ${_MPI_BASE_DIR} ${_MPI_PREFIX_PATH}
- PATH_SUFFIXES lib lib/${MS_MPI_ARCH_DIR} Lib Lib/${MS_MPI_ARCH_DIR})
- set(MPI_LIBRARIES_WORK ${MPI_LIB})
-
- # Right now, we only know about the extra libs for C++.
- # We could add Fortran here (as there is usually libfmpich, etc.), but
- # this really only has to work with MS MPI on Windows.
- # Assume that other MPI's are covered by the compiler wrappers.
- if (${lang} STREQUAL CXX)
- set(MPI_LIB "MPI_LIB-NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
- find_library(MPI_LIB
- NAMES mpi++ mpicxx cxx mpi_cxx
- HINTS ${_MPI_BASE_DIR} ${_MPI_PREFIX_PATH}
- PATH_SUFFIXES lib)
- if (MPI_LIBRARIES_WORK AND MPI_LIB)
- set(MPI_LIBRARIES_WORK ${MPI_LIBRARIES_WORK} ${MPI_LIB})
- endif()
- endif()
-
- if (${lang} STREQUAL Fortran)
- set(MPI_LIB "MPI_LIB-NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
- find_library(MPI_LIB
- NAMES fmpi fmpich fmpich2 fmpich2g
- HINTS ${_MPI_BASE_DIR} ${_MPI_PREFIX_PATH}
- PATH_SUFFIXES lib)
- if (MPI_LIBRARIES_WORK AND MPI_LIB)
- set(MPI_LIBRARIES_WORK ${MPI_LIBRARIES_WORK} ${MPI_LIB})
- endif()
- endif()
-
- if (NOT MPI_LIBRARIES_WORK)
- set(MPI_LIBRARIES_WORK "MPI_${lang}_LIBRARIES-NOTFOUND")
- endif()
- endif()
-
- # If we found MPI, set up all of the appropriate cache entries
- set(MPI_${lang}_COMPILE_FLAGS ${MPI_COMPILE_FLAGS_WORK} CACHE STRING "MPI
${lang} compilation flags" FORCE)
- set(MPI_${lang}_INCLUDE_PATH ${MPI_INCLUDE_PATH_WORK} CACHE STRING "MPI
${lang} include path" FORCE)
- set(MPI_${lang}_LINK_FLAGS ${MPI_LINK_FLAGS_WORK} CACHE STRING "MPI
${lang} linking flags" FORCE)
- set(MPI_${lang}_LIBRARIES ${MPI_LIBRARIES_WORK} CACHE STRING "MPI
${lang} libraries to link against" FORCE)
- mark_as_advanced(MPI_${lang}_COMPILE_FLAGS MPI_${lang}_INCLUDE_PATH
MPI_${lang}_LINK_FLAGS MPI_${lang}_LIBRARIES)
-
- # clear out our temporary lib/header detectionv variable here.
- set(MPI_LIB "MPI_LIB-NOTFOUND" CACHE INTERNAL "Scratch
variable for MPI lib detection" FORCE)
- set(MPI_HEADER_PATH "MPI_HEADER_PATH-NOTFOUND" CACHE INTERNAL "Scratch
variable for MPI header detection" FORCE)
- endif()
-
- # finally set a found variable for each MPI language
- if (MPI_${lang}_INCLUDE_PATH AND MPI_${lang}_LIBRARIES)
- set(MPI_${lang}_FOUND TRUE PARENT_SCOPE)
- else()
- set(MPI_${lang}_FOUND FALSE PARENT_SCOPE)
- endif()
-endfunction()
-
-
-# This function attempts to compile with the regular compiler, to see if MPI
programs
-# work with it. This is a last ditch attempt after we've tried interrogating
mpicc and
-# friends, and after we've tried to find generic libraries. Works on machines
like
-# Cray XE6, where the modules environment changes what MPI version cc, CC, and
ftn use.
-function(try_regular_compiler lang success)
- set(scratch_directory ${CMAKE_CURRENT_BINARY_DIR}${CMAKE_FILES_DIRECTORY})
- if (${lang} STREQUAL Fortran)
- set(test_file ${scratch_directory}/cmake_mpi_test.f90)
- file(WRITE ${test_file}
- "program hello\n"
- "include 'mpif.h'\n"
- "integer ierror\n"
- "call MPI_INIT(ierror)\n"
- "call MPI_FINALIZE(ierror)\n"
- "end\n")
- else()
- if (${lang} STREQUAL CXX)
- set(test_file ${scratch_directory}/cmake_mpi_test.cpp)
- else()
- set(test_file ${scratch_directory}/cmake_mpi_test.c)
- endif()
- file(WRITE ${test_file}
- "#include <mpi.h>\n"
- "int main(int argc, char **argv) {\n"
- " MPI_Init(&argc, &argv);\n"
- " MPI_Finalize();\n"
- "}\n")
- endif()
- try_compile(compiler_has_mpi ${scratch_directory} ${test_file})
- if (compiler_has_mpi)
- set(MPI_${lang}_NO_INTERROGATE ${CMAKE_${lang}_COMPILER} CACHE STRING
"Whether to interrogate MPI ${lang} compiler" FORCE)
- set(MPI_${lang}_COMPILER ${CMAKE_${lang}_COMPILER} CACHE STRING "MPI
${lang} compiler" FORCE)
- set(MPI_${lang}_COMPILE_FLAGS "" CACHE STRING "MPI
${lang} compilation flags" FORCE)
- set(MPI_${lang}_INCLUDE_PATH "" CACHE STRING "MPI
${lang} include path" FORCE)
- set(MPI_${lang}_LINK_FLAGS "" CACHE STRING "MPI
${lang} linking flags" FORCE)
- set(MPI_${lang}_LIBRARIES "" CACHE STRING "MPI
${lang} libraries to link against" FORCE)
- endif()
- set(${success} ${compiler_has_mpi} PARENT_SCOPE)
- unset(compiler_has_mpi CACHE)
-endfunction()
-
-# End definitions, commence real work here.
-
-# Most mpi distros have some form of mpiexec which gives us something we can
reliably look for.
-find_program(MPIEXEC
- NAMES ${_MPI_EXEC_NAMES}
- PATHS ${_MPI_PREFIX_PATH}
- PATH_SUFFIXES bin
- DOC "Executable for running MPI programs.")
-
-# call get_filename_component twice to remove mpiexec and the directory it
exists in (typically bin).
-# This gives us a fairly reliable base directory to search for /bin /lib and
/include from.
-get_filename_component(_MPI_BASE_DIR "${MPIEXEC}" PATH)
-get_filename_component(_MPI_BASE_DIR "${_MPI_BASE_DIR}" PATH)
-
-set(MPIEXEC_NUMPROC_FLAG "-np" CACHE STRING "Flag used by MPI to specify the
number of processes for MPIEXEC; the next option will be the number of
processes.")
-set(MPIEXEC_PREFLAGS "" CACHE STRING "These flags will be directly
before the executable that is being run by MPIEXEC.")
-set(MPIEXEC_POSTFLAGS "" CACHE STRING "These flags will come after all
flags given to MPIEXEC.")
-set(MPIEXEC_MAX_NUMPROCS "2" CACHE STRING "Maximum number of processors
available to run MPI applications.")
-mark_as_advanced(MPIEXEC MPIEXEC_NUMPROC_FLAG MPIEXEC_PREFLAGS
MPIEXEC_POSTFLAGS MPIEXEC_MAX_NUMPROCS)
-
-
-#=============================================================================
-# Backward compatibility input hacks. Propagate the FindMPI hints to C and
-# CXX if the respective new versions are not defined. Translate the old
-# MPI_LIBRARY and MPI_EXTRA_LIBRARY to respective MPI_${lang}_LIBRARIES.
-#
-# Once we find the new variables, we translate them back into their old
-# equivalents below.
-foreach (lang C CXX)
- # Old input variables.
- set(_MPI_OLD_INPUT_VARS COMPILER COMPILE_FLAGS INCLUDE_PATH LINK_FLAGS)
-
- # Set new vars based on their old equivalents, if the new versions are not
already set.
- foreach (var ${_MPI_OLD_INPUT_VARS})
- if (NOT MPI_${lang}_${var} AND MPI_${var})
- set(MPI_${lang}_${var} "${MPI_${var}}")
- endif()
- endforeach()
-
- # Special handling for MPI_LIBRARY and MPI_EXTRA_LIBRARY, which we nixed in
the
- # new FindMPI. These need to be merged into MPI_<lang>_LIBRARIES
- if (NOT MPI_${lang}_LIBRARIES AND (MPI_LIBRARY OR MPI_EXTRA_LIBRARY))
- set(MPI_${lang}_LIBRARIES ${MPI_LIBRARY} ${MPI_EXTRA_LIBRARY})
- endif()
-endforeach()
-#=============================================================================
-
-
-# This loop finds the compilers and sends them off for interrogation.
-foreach (lang C CXX Fortran)
- if (CMAKE_${lang}_COMPILER_WORKS)
- # If the user supplies a compiler *name* instead of an absolute path,
assume that we need to find THAT compiler.
- if (MPI_${lang}_COMPILER)
- is_file_executable(MPI_${lang}_COMPILER MPI_COMPILER_IS_EXECUTABLE)
- if (NOT MPI_COMPILER_IS_EXECUTABLE)
- # Get rid of our default list of names and just search for the name
the user wants.
- set(_MPI_${lang}_COMPILER_NAMES ${MPI_${lang}_COMPILER})
- set(MPI_${lang}_COMPILER "MPI_${lang}_COMPILER-NOTFOUND" CACHE
FILEPATH "Cleared" FORCE)
- # If the user specifies a compiler, we don't want to try to search
libraries either.
- set(try_libs FALSE)
- endif()
- else()
- set(try_libs TRUE)
- endif()
-
- find_program(MPI_${lang}_COMPILER
- NAMES ${_MPI_${lang}_COMPILER_NAMES}
- PATHS "${MPI_HOME}/bin" "$ENV{MPI_HOME}/bin" ${_MPI_PREFIX_PATH})
- interrogate_mpi_compiler(${lang} ${try_libs})
- mark_as_advanced(MPI_${lang}_COMPILER)
-
- # last ditch try -- if nothing works so far, just try running the regular
compiler and
- # see if we can create an MPI executable.
- set(regular_compiler_worked 0)
- if (NOT MPI_${lang}_LIBRARIES OR NOT MPI_${lang}_INCLUDE_PATH)
- try_regular_compiler(${lang} regular_compiler_worked)
- endif()
-
- if (regular_compiler_worked)
- find_package_handle_standard_args(MPI_${lang} DEFAULT_MSG
MPI_${lang}_COMPILER)
- else()
- find_package_handle_standard_args(MPI_${lang} DEFAULT_MSG
MPI_${lang}_LIBRARIES MPI_${lang}_INCLUDE_PATH)
- endif()
- endif()
-endforeach()
-
-
-#=============================================================================
-# More backward compatibility stuff
-#
-# Bare MPI sans ${lang} vars are set to CXX then C, depending on what was
found.
-# This mimics the behavior of the old language-oblivious FindMPI.
-set(_MPI_OLD_VARS FOUND COMPILER INCLUDE_PATH COMPILE_FLAGS LINK_FLAGS
LIBRARIES)
-if (MPI_CXX_FOUND)
- foreach (var ${_MPI_OLD_VARS})
- set(MPI_${var} ${MPI_CXX_${var}})
- endforeach()
-elseif (MPI_C_FOUND)
- foreach (var ${_MPI_OLD_VARS})
- set(MPI_${var} ${MPI_C_${var}})
- endforeach()
-else()
- # Note that we might still have found Fortran, but you'll need to use
MPI_Fortran_FOUND
- set(MPI_FOUND FALSE)
-endif()
-
-# Chop MPI_LIBRARIES into the old-style MPI_LIBRARY and MPI_EXTRA_LIBRARY, and
set them in cache.
-if (MPI_LIBRARIES)
- list(GET MPI_LIBRARIES 0 MPI_LIBRARY_WORK)
- set(MPI_LIBRARY ${MPI_LIBRARY_WORK} CACHE FILEPATH "MPI library to link
against" FORCE)
-else()
- set(MPI_LIBRARY "MPI_LIBRARY-NOTFOUND" CACHE FILEPATH "MPI library to link
against" FORCE)
-endif()
-
-list(LENGTH MPI_LIBRARIES MPI_NUMLIBS)
-if (MPI_NUMLIBS GREATER 1)
- set(MPI_EXTRA_LIBRARY_WORK ${MPI_LIBRARIES})
- list(REMOVE_AT MPI_EXTRA_LIBRARY_WORK 0)
- set(MPI_EXTRA_LIBRARY ${MPI_EXTRA_LIBRARY_WORK} CACHE STRING "Extra MPI
libraries to link against" FORCE)
-else()
- set(MPI_EXTRA_LIBRARY "MPI_EXTRA_LIBRARY-NOTFOUND" CACHE STRING "Extra MPI
libraries to link against" FORCE)
-endif()
-#=============================================================================
-
-# unset these vars to cleanup namespace
-unset(_MPI_OLD_VARS)
-unset(_MPI_PREFIX_PATH)
-unset(_MPI_BASE_DIR)
-foreach (lang C CXX Fortran)
- unset(_MPI_${lang}_COMPILER_NAMES)
-endforeach()
diff -ruN hdf5-1.8.9/fortran/src/CMakeLists.txt
hdf5-1.8.9-new/fortran/src/CMakeLists.txt
--- hdf5-1.8.9/fortran/src/CMakeLists.txt 2012-05-09 09:06:28.000000000
-0600
+++ hdf5-1.8.9-new/fortran/src/CMakeLists.txt 2012-07-01 08:38:45.000000000
-0600
@@ -85,7 +85,7 @@
#-----------------------------------------------------------------------------
SET (f90CStub_C_SRCS
# generated files
- ${HDF5_F90_BINARY_DIR}/H5f90i_gen.h
+ # ${HDF5_F90_BINARY_DIR}/H5f90i_gen.h
# normal distribution
${HDF5_F90_SRC_SOURCE_DIR}/H5f90kit.c
@@ -104,6 +104,11 @@
${HDF5_F90_SRC_SOURCE_DIR}/H5Tf.c
${HDF5_F90_SRC_SOURCE_DIR}/H5Zf.c
)
+foreach (src ${f90CStub_C_SRCS})
+set_source_files_properties(${src}
+ PROPERTIES OBJECT_DEPENDS ${HDF5_F90_BINARY_DIR}/H5f90i_gen.h
+)
+endforeach ()
IF (H5_HAVE_PARALLEL)
SET (f90CStub_C_SRCS
diff -ruN hdf5-1.8.9/hl/fortran/src/CMakeLists.txt
hdf5-1.8.9-new/hl/fortran/src/CMakeLists.txt
--- hdf5-1.8.9/hl/fortran/src/CMakeLists.txt 2012-05-09 09:06:19.000000000
-0600
+++ hdf5-1.8.9-new/hl/fortran/src/CMakeLists.txt 2012-07-01
08:38:25.000000000 -0600
@@ -26,7 +26,8 @@
SET (HDF5_HL_F90_HEADERS ${HDF5_HL_F90_SRC_SOURCE_DIR}/H5LTf90proto.h)
SET_SOURCE_FILES_PROPERTIES (${HDF5_HL_F90_HEADERS} PROPERTIES LANGUAGE C)
-ADD_LIBRARY (${HDF5_HL_F90_C_LIB_TARGET} ${LIB_TYPE} ${HDF5_HL_F90_C_SRCS}
${HDF5_HL_F90_HEADERS})
+# ADD_LIBRARY (${HDF5_HL_F90_C_LIB_TARGET} ${LIB_TYPE} ${HDF5_HL_F90_C_SRCS}
${HDF5_HL_F90_HEADERS})
+ADD_LIBRARY (${HDF5_HL_F90_C_LIB_TARGET} ${LIB_TYPE} ${HDF5_HL_F90_C_SRCS})
TARGET_LINK_LIBRARIES (${HDF5_HL_F90_C_LIB_TARGET} ${HDF5_F90_C_LIB_TARGET}
${HDF5_HL_LIB_TARGET})
SET_GLOBAL_VARIABLE (HDF5_LIBRARIES_TO_EXPORT
"${HDF5_LIBRARIES_TO_EXPORT};${HDF5_HL_F90_C_LIB_TARGET}")
H5_SET_LIB_OPTIONS (${HDF5_HL_F90_C_LIB_TARGET} ${HDF5_HL_F90_C_LIB_NAME}
${LIB_TYPE})
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