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SeismicData / asdf-library

Adaptable Seismic Data Format
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cmake issue with HDF5 lib #17

Closed chukren closed 8 years ago

chukren commented 8 years ago

line19 in CMakeLists.txt find_package(HDF5 1.8.0 REQUIRED) will find the HDF5_LIBRARIES by itself and will not be successful at least on Titan, therefor cause issues like "Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS) (Required ..." This can be resolved by safely comment out line 19 and indicating library manually (already done in instruction). Suggested by Matthieu.

ghost commented 8 years ago

Hi, I can build the library without specifying hdf5 library manually. Can you try this?

export PATH=$PATH:/opt/cray/hdf5-parllel/1.8.12/gnu/48 module load cray-hdf5-parallel/1.8.12

Then cmake .. (without any hdf5 library manual location)

and it should build the makefile. I verified this works oh Titan a few minutes ago. You will need to specify the boost library manually (a bit of a pain but it's on the documentation on the main page).

chukren commented 8 years ago

I mean the problem is the "find_package(HDF5 1.8.0 REQUIRED)" may fail and the find_package() needs some help to find the lib for you in some case. Indicating the lib manually will be more flexible.

ghost commented 8 years ago

OK, well I will comment it out by default and close the issue, with instructions for user to specify the hdf5 library manually. I think the point of cmake is to not have to do this sort of thing, but it does seem safer to expect users to locate hdf5 manually.

chukren commented 8 years ago

Also, there is one more thing you might want to clean up.

In Titan configuration: -DBoost_NO_SYSTEM_PATHS=TRUE but -DBOOST_INCLUDE_DIRS is missing (will cause boost compiling issue)

but in CMakeLists.txt set(Boost_NO_SYSTEM_PATHS FALSE) if (Boost_NO_SYSTEM_PATHS) set(BOOST_ROOT /tigress/jas11/packages/boost) set(BOOST_INCLUDE_DIRS "${BOOST_ROOT}/include") set(BOOST_LIBRARY_DIRS "${BOOST_ROOT}/lib") endif (Boost_NO_SYSTEM_PATHS)

Might need to remind user to check CMakeLists.txt carefully.

QuLogic commented 8 years ago

To provide the hint to CMake, you can define the environment variable HDF5_ROOT. I don't think commenting out a check for a required dependency is the correct course of action.

chukren commented 8 years ago

Or use find_package() if the lib is not explicitly indicated in the command line.

QuLogic commented 8 years ago

Please post the CMake log from the unchanged files?

ghost commented 8 years ago 
The system is: Linux - 3.0.101-0.46-default - x86_64
Compiling the C compiler identification source file "CMakeCCompilerId.c" succeeded.
Compiler: /opt/cray/craype/2.4.2/bin/cc 
Build flags: 
Id flags: 

The output was:
0

Compilation of the C compiler identification source "CMakeCCompilerId.c" produced "a.out"

The C compiler identification is GNU, found in "/lustre/atlas/proj-shared/geo111/test_asdf/asdf-library/build/CMakeFiles/2.8.10.2/CompilerIdC/a.out"

Compiling the CXX compiler identification source file "CMakeCXXCompilerId.cpp" succeeded.
Compiler: /opt/cray/craype/2.4.2/bin/CC 
Build flags: 
Id flags: 

The output was:
0

Compilation of the CXX compiler identification source "CMakeCXXCompilerId.cpp" produced "a.out"

The CXX compiler identification is GNU, found in "/lustre/atlas/proj-shared/geo111/test_asdf/asdf-library/build/CMakeFiles/2.8.10.2/CompilerIdCXX/a.out"

Determining if the C compiler works passed with the following output:
Change Dir: /lustre/atlas/proj-shared/geo111/test_asdf/asdf-library/build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/gmake "cmTryCompileExec1361376955/fast"
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gmake[1]: Entering directory `/lustre/atlas1/geo111/proj-shared/test_asdf/asdf-library/build/CMakeFiles/CMakeTmp'
/autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/bin/cmake -E cmake_progress_report /lustre/atlas/proj-shared/geo111/test_asdf/asdf-library/build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec1361376955.dir/testCCompiler.c.o
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Linking C executable cmTryCompileExec1361376955
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Change Dir: /lustre/atlas/proj-shared/geo111/test_asdf/asdf-library/build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/gmake "cmTryCompileExec2798752675/fast"
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    arg [-L/opt/nvidia/cudatoolkit7.0/7.0.28-1.0502.10280.4.1/nvvm/lib64] ==> dir [/opt/nvidia/cudatoolkit7.0/7.0.28-1.0502.10280.4.1/nvvm/lib64]
    arg [-L/opt/cray/nvidia/default/lib64] ==> dir [/opt/cray/nvidia/default/lib64]
    arg [-L/opt/cray/rca/1.0.0-2.0502.60530.1.63.gem/lib64] ==> dir [/opt/cray/rca/1.0.0-2.0502.60530.1.63.gem/lib64]
    arg [-L/opt/cray/atp/1.8.3/libApp] ==> dir [/opt/cray/atp/1.8.3/libApp]
    arg [-L/opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2] ==> dir [/opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2]
    arg [-L/opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2/../../../../lib64] ==> dir [/opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2/../../../../lib64]
    arg [-L/lib/../lib64] ==> dir [/lib/../lib64]
    arg [-L/usr/lib/../lib64] ==> dir [/usr/lib/../lib64]
    arg [-L/opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2/../../..] ==> dir [/opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2/../../..]
    arg [CMakeFiles/cmTryCompileExec2798752675.dir/CMakeCCompilerABI.c.o] ==> ignore
    arg [-rpath=/opt/cray/gcc-libs] ==> ignore
    arg [-Bdynamic] ==> ignore
    arg [--as-needed] ==> ignore
    arg [-lcupti] ==> lib [cupti]
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    arg [-lcuda] ==> lib [cuda]
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    arg [-lAtpSigHandler] ==> lib [AtpSigHandler]
    arg [-lAtpSigHCommData] ==> lib [AtpSigHCommData]
    arg [--undefined=_ATP_Data_Globals] ==> ignore
    arg [--undefined=__atpHandlerInstall] ==> ignore
    arg [-lrca] ==> lib [rca]
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    arg [-lsci_gnu_48_mpi] ==> lib [sci_gnu_48_mpi]
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    arg [--as-needed] ==> ignore
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    arg [--as-needed] ==> ignore
    arg [-lmpich_gnu_48] ==> lib [mpich_gnu_48]
    arg [--no-as-needed] ==> ignore
    arg [--as-needed] ==> ignore
    arg [-lgfortran] ==> lib [gfortran]
    arg [-lquadmath] ==> lib [quadmath]
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    arg [--as-needed] ==> ignore
    arg [-lm] ==> lib [m]
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    arg [-lpthread] ==> lib [pthread]
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    arg [-lgcc] ==> lib [gcc]
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    arg [-lgcc_s] ==> lib [gcc_s]
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    arg [-lc] ==> lib [c]
    arg [-lgcc] ==> lib [gcc]
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    arg [-lgcc_s] ==> lib [gcc_s]
    arg [--no-as-needed] ==> ignore
    arg [/opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2/crtend.o] ==> ignore
    arg [/usr/lib/../lib64/crtn.o] ==> ignore
  remove lib [gcc]
  remove lib [gcc_s]
  remove lib [gcc]
  remove lib [gcc_s]
  collapse dir [/opt/cray/libsci/13.1.0/GNU/4.8/x86_64/lib] ==> [/opt/cray/libsci/13.1.0/GNU/4.8/x86_64/lib]
  collapse dir [/opt/cray/dmapp/default/lib64] ==> [/opt/cray/dmapp/default/lib64]
  collapse dir [/opt/cray/mpt/7.2.4/gni/mpich2-gnu/4.8/lib] ==> [/opt/cray/mpt/7.2.4/gni/mpich2-gnu/4.8/lib]
  collapse dir [/opt/nvidia/cudatoolkit7.0/7.0.28-1.0502.10280.4.1/lib64] ==> [/opt/nvidia/cudatoolkit7.0/7.0.28-1.0502.10280.4.1/lib64]
  collapse dir [/opt/nvidia/cudatoolkit7.0/7.0.28-1.0502.10280.4.1/extras/CUPTI/lib64] ==> [/opt/nvidia/cudatoolkit7.0/7.0.28-1.0502.10280.4.1/extras/CUPTI/lib64]
  collapse dir [/opt/nvidia/cudatoolkit7.0/7.0.28-1.0502.10280.4.1/nvvm/lib64] ==> [/opt/nvidia/cudatoolkit7.0/7.0.28-1.0502.10280.4.1/nvvm/lib64]
  collapse dir [/opt/cray/nvidia/default/lib64] ==> [/opt/cray/nvidia/default/lib64]
  collapse dir [/opt/cray/rca/1.0.0-2.0502.60530.1.63.gem/lib64] ==> [/opt/cray/rca/1.0.0-2.0502.60530.1.63.gem/lib64]
  collapse dir [/opt/cray/atp/1.8.3/libApp] ==> [/opt/cray/atp/1.8.3/libApp]
  collapse dir [/opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2] ==> [/opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2]
  collapse dir [/opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2/../../../../lib64] ==> [/opt/gcc/4.8.2/snos/lib64]
  collapse dir [/lib/../lib64] ==> [/lib64]
  collapse dir [/usr/lib/../lib64] ==> [/usr/lib64]
  collapse dir [/opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2/../../..] ==> [/opt/gcc/4.8.2/snos/lib]
  implicit libs: [cupti;cudart;cuda;AtpSigHandler;AtpSigHCommData;rca;sci_gnu_48_mpi;sci_gnu_48;mpich_gnu_48;gfortran;quadmath;m;pthread;c]
  implicit dirs: [/opt/cray/libsci/13.1.0/GNU/4.8/x86_64/lib;/opt/cray/dmapp/default/lib64;/opt/cray/mpt/7.2.4/gni/mpich2-gnu/4.8/lib;/opt/nvidia/cudatoolkit7.0/7.0.28-1.0502.10280.4.1/lib64;/opt/nvidia/cudatoolkit7.0/7.0.28-1.0502.10280.4.1/extras/CUPTI/lib64;/opt/nvidia/cudatoolkit7.0/7.0.28-1.0502.10280.4.1/nvvm/lib64;/opt/cray/nvidia/default/lib64;/opt/cray/rca/1.0.0-2.0502.60530.1.63.gem/lib64;/opt/cray/atp/1.8.3/libApp;/opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2;/opt/gcc/4.8.2/snos/lib64;/lib64;/usr/lib64;/opt/gcc/4.8.2/snos/lib]

Determining if the CXX compiler works passed with the following output:
Change Dir: /lustre/atlas/proj-shared/geo111/test_asdf/asdf-library/build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/gmake "cmTryCompileExec2418356033/fast"
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec2418356033.dir/build.make CMakeFiles/cmTryCompileExec2418356033.dir/build
gmake[1]: Entering directory `/lustre/atlas1/geo111/proj-shared/test_asdf/asdf-library/build/CMakeFiles/CMakeTmp'
/autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/bin/cmake -E cmake_progress_report /lustre/atlas/proj-shared/geo111/test_asdf/asdf-library/build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building CXX object CMakeFiles/cmTryCompileExec2418356033.dir/testCXXCompiler.cxx.o
/opt/cray/craype/2.4.2/bin/CC     -o CMakeFiles/cmTryCompileExec2418356033.dir/testCXXCompiler.cxx.o -c /lustre/atlas/proj-shared/geo111/test_asdf/asdf-library/build/CMakeFiles/CMakeTmp/testCXXCompiler.cxx
Linking CXX executable cmTryCompileExec2418356033
/autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec2418356033.dir/link.txt --verbose=1
/opt/cray/craype/2.4.2/bin/CC          CMakeFiles/cmTryCompileExec2418356033.dir/testCXXCompiler.cxx.o  -o cmTryCompileExec2418356033 -rdynamic 
gmake[1]: Leaving directory `/lustre/atlas1/geo111/proj-shared/test_asdf/asdf-library/build/CMakeFiles/CMakeTmp'

Detecting CXX compiler ABI info compiled with the following output:
Change Dir: /lustre/atlas/proj-shared/geo111/test_asdf/asdf-library/build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/gmake "cmTryCompileExec1105775271/fast"
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec1105775271.dir/build.make CMakeFiles/cmTryCompileExec1105775271.dir/build
gmake[1]: Entering directory `/lustre/atlas1/geo111/proj-shared/test_asdf/asdf-library/build/CMakeFiles/CMakeTmp'
/autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/bin/cmake -E cmake_progress_report /lustre/atlas/proj-shared/geo111/test_asdf/asdf-library/build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building CXX object CMakeFiles/cmTryCompileExec1105775271.dir/CMakeCXXCompilerABI.cpp.o
/opt/cray/craype/2.4.2/bin/CC     -o CMakeFiles/cmTryCompileExec1105775271.dir/CMakeCXXCompilerABI.cpp.o -c /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/CMakeCXXCompilerABI.cpp
Linking CXX executable cmTryCompileExec1105775271
/autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec1105775271.dir/link.txt --verbose=1
/opt/cray/craype/2.4.2/bin/CC        -v CMakeFiles/cmTryCompileExec1105775271.dir/CMakeCXXCompilerABI.cpp.o  -o cmTryCompileExec1105775271 -rdynamic  
Using built-in specs.
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COLLECT_LTO_WRAPPER=/opt/gcc/4.8.2/snos/libexec/gcc/x86_64-suse-linux/4.8.2/lto-wrapper
Target: x86_64-suse-linux
Configured with: ../cray-gcc-4.8.2/configure --prefix=/opt/gcc/4.8.2/snos --disable-nls --libdir=/opt/gcc/4.8.2/snos/lib --enable-languages=c,c++,fortran --with-gxx-include-dir=/opt/gcc/4.8.2/snos/include/g++ --with-slibdir=/opt/gcc/4.8.2/snos/lib --with-system-zlib --enable-shared --enable-__cxa_atexit --build=x86_64-suse-linux --with-mpc=/opt/gcc/mpc/0.8.1 --with-mpfr=/opt/gcc/mpfr/2.4.2 --with-gmp=/opt/gcc/gmp/4.3.2
Thread model: posix
gcc version 4.8.2 20131016 (Cray Inc.) (GCC) 
COMPILER_PATH=/opt/gcc/4.8.2/snos/libexec/gcc/x86_64-suse-linux/4.8.2/:/opt/gcc/4.8.2/snos/libexec/gcc/x86_64-suse-linux/4.8.2/:/opt/gcc/4.8.2/snos/libexec/gcc/x86_64-suse-linux/:/opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2/:/opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/
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 /opt/gcc/4.8.2/snos/libexec/gcc/x86_64-suse-linux/4.8.2/collect2 --eh-frame-hdr -m elf_x86_64 -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -o cmTryCompileExec1105775271 /usr/lib/../lib64/crt1.o /usr/lib/../lib64/crti.o /opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2/crtbegin.o -L/opt/cray/libsci/13.1.0/GNU/4.8/x86_64/lib -L/opt/cray/dmapp/default/lib64 -L/opt/cray/mpt/7.2.4/gni/mpich2-gnu/4.8/lib -L/opt/cray/dmapp/default/lib64 -L/opt/cray/mpt/7.2.4/gni/mpich2-gnu/4.8/lib -L/opt/nvidia/cudatoolkit7.0/7.0.28-1.0502.10280.4.1/lib64 -L/opt/nvidia/cudatoolkit7.0/7.0.28-1.0502.10280.4.1/extras/CUPTI/lib64 -L/opt/nvidia/cudatoolkit7.0/7.0.28-1.0502.10280.4.1/nvvm/lib64 -L/opt/cray/nvidia/default/lib64 -L/opt/cray/rca/1.0.0-2.0502.60530.1.63.gem/lib64 -L/opt/cray/atp/1.8.3/libApp -L/opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2 -L/opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2/../../.. CMakeFiles/cmTryCompileExec1105775271.dir/CMakeCXXCompilerABI.cpp.o -rpath=/opt/cray/gcc-libs -Bdynamic --as-needed -lcupti -lcudart --no-as-needed -lcuda --no-as-needed -lAtpSigHandler -lAtpSigHCommData --undefined=_ATP_Data_Globals --undefined=__atpHandlerInstall -lrca --as-needed -lsci_gnu_48_mpi --no-as-needed --as-needed -lsci_gnu_48 --no-as-needed --as-needed -lmpich_gnu_48 --no-as-needed --as-needed -lmpichcxx_gnu_48 --no-as-needed --as-needed -lgfortran -lquadmath --no-as-needed --as-needed -lm --no-as-needed --as-needed -lpthread --no-as-needed -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /opt/gcc/4.8.2/snos/lib/gcc/x86_64-suse-linux/4.8.2/crtend.o /usr/lib/../lib64/crtn.o
gmake[1]: Leaving directory `/lustre/atlas1/geo111/proj-shared/test_asdf/asdf-library/build/CMakeFiles/CMakeTmp'

Parsed CXX implicit link information from above output:
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Determining if the Fortran compiler works passed with the following output:
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gmake[1]: Entering directory `/lustre/atlas1/geo111/proj-shared/test_asdf/asdf-library/build/CMakeFiles/CMakeTmp'
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gmake[1]: Leaving directory `/lustre/atlas1/geo111/proj-shared/test_asdf/asdf-library/build/CMakeFiles/CMakeTmp'

Detecting Fortran compiler ABI info compiled with the following output:
Change Dir: /lustre/atlas/proj-shared/geo111/test_asdf/asdf-library/build/CMakeFiles/CMakeTmp

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QuLogic commented 8 years ago

Do you not use the HDF5 compiler wrappers?

Unfortunately, that doesn't actually show the HDF5 tests; I think maybe cmake --trace .. might?

ghost commented 8 years ago

Here is the output from cmake --trace ..

It is finding my local install of phdf5 on titan if I don't specify the location manually.

Running with trace output on.
-- The C compiler identification is GNU 4.8.2
-- The CXX compiler identification is GNU 4.8.2
-- Check for working C compiler: /opt/cray/craype/2.4.2/bin/cc
-- Check for working C compiler: /opt/cray/craype/2.4.2/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /opt/cray/craype/2.4.2/bin/CC
-- Check for working CXX compiler: /opt/cray/craype/2.4.2/bin/CC -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found HDF5: /ccs/home/jas11/lib/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (Required is at least version "1.8.0") 
-- Found MPI_C: /opt/cray/craype/2.4.2/bin/cc  
-- Found MPI_CXX: /opt/cray/craype/2.4.2/bin/CC  
-- Boost version: 1.57.0
-- Found the following Boost libraries:
--   system
-- Performing Test COMPILER_SUPPORTS_CXX11
-- Performing Test COMPILER_SUPPORTS_CXX11 - Success
-- Performing Test COMPILER_SUPPORTS_CXX0X
-- Performing Test COMPILER_SUPPORTS_CXX0X - Success
-- Found Doxygen: /usr/bin/doxygen (found version "1.5.6") 
-- The Fortran compiler identification is GNU
-- Check for working Fortran compiler: /opt/gcc/4.8.2/bin/gfortran
-- Check for working Fortran compiler: /opt/gcc/4.8.2/bin/gfortran  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /opt/gcc/4.8.2/bin/gfortran supports Fortran 90
-- Checking whether /opt/gcc/4.8.2/bin/gfortran supports Fortran 90 -- yes
-- Configuring done
-- Generating done
-- Build files have been written to: /lustre/atlas/proj-shared/geo111/test_asdf/asdf-library/build

I use the HDF5 compiler wrappers only if needed, not by default.

QuLogic commented 8 years ago

That doesn't appear to be the output of cmake --trace; it is extremely verbose. I don't understand though, why do you have a local install of HDF5 in your path if you don't want anything to use it?

ghost commented 8 years ago

I installed it on titan myself a while ago to test ASDF because I couldn't get the installed hdf5 to work properly. It seems to find it even if I manually specify the hdf5 location to cmake. I'll try using cmake --trace and get the full output.

ghost commented 8 years ago

Here is the cmake --trace output for the hdf5 relevant stuff:

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findlibrary(HDF5${LIB}_LIBRARY_DEBUG NAMES ${THIS_LIBRARY_SEARCHDEBUG} HINTS ${HDF5${LANGUAGE}_LIBRARY_DIRS} ENV HDF5_ROOT PATH_SUFFIXES lib Lib ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(286): findlibrary(HDF5${LIB}_LIBRARY_RELEASE NAMES ${THIS_LIBRARY_SEARCHRELEASE} HINTS ${HDF5${LANGUAGE}_LIBRARY_DIRS} ENV HDF5_ROOT PATH_SUFFIXES lib Lib ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(291): select_libraryconfigurations(HDF5${LIB} ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/SelectLibraryConfigurations.cmake(47): _set_library_name(HDF5_m RELEASE DEBUG ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/SelectLibraryConfigurations.cmake(37): if(HDF5_m_LIBRARY_RELEASE AND NOT HDF5_m_LIBRARY_DEBUG ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/SelectLibraryConfigurations.cmake(38): set(HDF5_m_LIBRARY_DEBUG ${HDF5_m_LIBRARY_RELEASE} ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/SelectLibraryConfigurations.cmake(39): set(HDF5_m_LIBRARY ${HDF5_m_LIBRARY_RELEASE} ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/SelectLibraryConfigurations.cmake(40): set(HDF5_m_LIBRARIES ${HDF5_m_LIBRARY_RELEASE} ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/SelectLibraryConfigurations.cmake(50): _set_library_name(HDF5_m DEBUG RELEASE ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/SelectLibraryConfigurations.cmake(37): if(HDF5_m_LIBRARY_DEBUG AND NOT HDF5_m_LIBRARY_RELEASE ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/SelectLibraryConfigurations.cmake(57): set(HDF5_m_LIBRARY ${HDF5_m_LIBRARY_RELEASE} ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/SelectLibraryConfigurations.cmake(58): set(HDF5_m_LIBRARIES ${HDF5_m_LIBRARY_RELEASE} ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/SelectLibraryConfigurations.cmake(60): if(HDF5_m_LIBRARY_DEBUG AND HDF5_m_LIBRARY_RELEASE AND NOT HDF5_m_LIBRARY_DEBUG STREQUAL HDF5_m_LIBRARY_RELEASE ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/SelectLibraryConfigurations.cmake(76): set(HDF5_m_LIBRARY ${HDF5_m_LIBRARY} CACHE FILEPATH The HDF5_m library ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/SelectLibraryConfigurations.cmake(79): if(HDF5_m_LIBRARY ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/SelectLibraryConfigurations.cmake(80): set(HDF5_m_FOUND TRUE ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/SelectLibraryConfigurations.cmake(83): mark_as_advanced(HDF5_m_LIBRARY HDF5_m_LIBRARY_RELEASE HDF5_m_LIBRARY_DEBUG ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(300): list(APPEND HDF5${LANGUAGE}_LIBRARIESDEBUG ${HDF5${LIB}_LIBRARY_DEBUG} ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(302): list(APPEND HDF5${LANGUAGE}_LIBRARIESRELEASE ${HDF5${LIB}_LIBRARY_RELEASE} ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(305): list(APPEND HDF5_LIBRARYDIRS ${HDF5${LANGUAGE}_LIBRARY_DIRS} ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(309): list(APPEND HDF5_LIBRARIESDEBUG ${HDF5${LANGUAGE}_LIBRARIES_DEBUG} ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(311): list(APPEND HDF5_LIBRARIESRELEASE ${HDF5${LANGUAGE}_LIBRARIES_RELEASE} ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(323): macro(_remove_duplicates_from_beginning _list_name ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(329): if(HDF5_INCLUDE_DIRS ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(330): _remove_duplicates_from_beginning(HDF5_INCLUDE_DIRS ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(324): list(REVERSE HDF5_INCLUDE_DIRS ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(325): list(REMOVE_DUPLICATES HDF5_INCLUDE_DIRS ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(326): list(REVERSE HDF5_INCLUDE_DIRS ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(332): if(HDF5_LIBRARIES_DEBUG ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(333): _remove_duplicates_from_beginning(HDF5_LIBRARIES_DEBUG ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(324): list(REVERSE HDF5_LIBRARIES_DEBUG ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(325): list(REMOVE_DUPLICATES HDF5_LIBRARIES_DEBUG ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(326): list(REVERSE HDF5_LIBRARIES_DEBUG ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(335): if(HDF5_LIBRARIES_RELEASE ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(336): _remove_duplicates_from_beginning(HDF5_LIBRARIES_RELEASE ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(324): list(REVERSE HDF5_LIBRARIES_RELEASE ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(325): list(REMOVE_DUPLICATES HDF5_LIBRARIES_RELEASE ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(326): list(REVERSE HDF5_LIBRARIES_RELEASE ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(338): if(HDF5_LIBRARY_DIRS ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(339): _remove_duplicates_from_beginning(HDF5_LIBRARY_DIRS ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(324): list(REVERSE HDF5_LIBRARY_DIRS ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(325): list(REMOVE_DUPLICATES HDF5_LIBRARY_DIRS ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(326): list(REVERSE HDF5_LIBRARY_DIRS ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(344): if(CMAKE_CONFIGURATION_TYPES OR CMAKE_BUILD_TYPE ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(352): else() /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(353): set(HDF5_LIBRARIES ${HDF5_LIBRARIES_RELEASE} ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(358): set(HDF5_IS_PARALLEL FALSE ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(359): foreach(_dir IN LISTS HDF5_INCLUDE_DIRS ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(360): if(EXISTS ${_dir}/H5pubconf.h ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(361): file(STRINGS ${_dir}/H5pubconf.h HDF5_HAVE_PARALLEL_DEFINE REGEX HAVE_PARALLEL 1 ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(364): if(HDF5_HAVE_PARALLEL_DEFINE ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(365): set(HDF5_IS_PARALLEL TRUE ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(360): if(EXISTS ${_dir}/H5pubconf.h ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(361): file(STRINGS ${_dir}/H5pubconf.h HDF5_HAVE_PARALLEL_DEFINE REGEX HAVE_PARALLEL 1 ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(364): if(HDF5_HAVE_PARALLEL_DEFINE ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(365): set(HDF5_IS_PARALLEL TRUE ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(369): set(HDF5_IS_PARALLEL ${HDF5_IS_PARALLEL} CACHE BOOL HDF5 library compiled with parallel IO support ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(371): mark_as_advanced(HDF5_IS_PARALLEL ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(375): if(HDF5_INCLUDE_DIRS ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(376): set(HDF5_INCLUDE_DIR ${HDF5_INCLUDE_DIRS} ) /autofs/nccs-svm1_sw/xk6/cmake/2.8.10.2/cle4.0_gnu4.7.2/share/cmake-2.8/Modules/FindHDF5.cmake(381): find_package_handle_standard_args(HDF5 DEFAULT_MSG HDF5_LIBRARIES HDF5_INCLUDE_DIRS )

QuLogic commented 8 years ago

Unfortunately, it's a bit difficult to say directly what's wrong from that log, too. Maybe we can go over this at the workshop next week.

QuLogic commented 8 years ago

Is it working now? We didn't change anything...

ghost commented 8 years ago

Yeah, it required exporting the hdf5 library variable. I updated the readme a little while back.

From: Elliott Sales de Andrade [notifications@github.com] Sent: Thursday, March 24, 2016 2:29 PM To: SeismicData/asdf-library Cc: James A. Smith Subject: Re: [asdf-library] cmake issue with HDF5 lib (#17)

Is it working now? We didn't change anything...

— You are receiving this because you modified the open/close state. Reply to this email directly or view it on GitHubhttps://github.com/SeismicData/asdf-library/issues/17#issuecomment-200983855