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#1 2018-07-26 14:47:09
- Cayo
- Member
- Registered: 2018-07-26
- Posts: 5
Installation problem with HDF5
Hello,
I am new to MOLCAS and I am having problems with the installation.
I am trying to install the parallel version, using Intel compilers and libraries and while running the
makecommand I get the following
[ 15%] Built target integral_util_obj
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2and more above in the output,
[ 8%] Building C object CMakeFiles/hdf5_util_obj.dir/src/hdf5_util/mh5_capi.c.o
/home/cayo/OpenMolcas/src/hdf5_util/mh5_capi.c(18): catastrophic error: cannot open source file "hdf5.h"
#include "hdf5.h"
^
compilation aborted for /home/cayo/OpenMolcas/src/hdf5_util/mh5_capi.c (code 4)
CMakeFiles/hdf5_util_obj.dir/build.make:86: recipe for target 'CMakeFiles/hdf5_util_obj.dir/src/hdf5_util/mh5_capi.c.o' failed
make[2]: *** [CMakeFiles/hdf5_util_obj.dir/src/hdf5_util/mh5_capi.c.o] Error 4
CMakeFiles/Makefile2:2069: recipe for target 'CMakeFiles/hdf5_util_obj.dir/all' failed
make[1]: *** [CMakeFiles/hdf5_util_obj.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 8%] Building Fortran object CMakeFiles/integral_util_obj.dir/src/integral_util/closep.f.oI have no idea how to solve this problem... Any help will be appreciated.
Thanks in advance,
Cayo Gonçalves
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#2 2018-07-26 20:54:32
- Ignacio
- Administrator
- From: Uppsala
- Registered: 2015-11-03
- Posts: 1,012
Re: Installation problem with HDF5
It seems your HDF5 installation is broken or at least not correctly detected by CMake. You could try disabling it by adding -D HDF5=OFF to the cmake options.
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#3 2018-07-26 21:47:55
- Cayo
- Member
- Registered: 2018-07-26
- Posts: 5
Re: Installation problem with HDF5
Hello Ignacio,
Thank you very much for your reply.
Yes, but Hdf5 would be especially important to my work and I would like to keep it on. It is a fresh Ubuntu installation, and I installed it just with
sudo apt-get install hdf5-tools hdfview Offline
#4 2018-07-27 14:37:37
- Ignacio
- Administrator
- From: Uppsala
- Registered: 2015-11-03
- Posts: 1,012
Re: Installation problem with HDF5
Maybe you need a development package like libhdf5-dev.
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#5 2018-07-27 14:50:51
- Cayo
- Member
- Registered: 2018-07-26
- Posts: 5
Re: Installation problem with HDF5
Hello, Ignacio.
Thank you again. You are correct. I installed the development package and it worked for HDF5, but now I am getting a different error:
In file included from /home/cayo/OpenMolcas/src/misc_util/ceil.c(11):
/opt/intel/compilers_and_libraries_2017.7.259/linux/compiler/include/math.h(1300): error: identifier "_LIB_VERSION_TYPE" is undefined
_LIBIMF_EXT _LIB_VERSIONIMF_TYPE _LIBIMF_PUBVAR _LIB_VERSIONIMF;
^
compilation aborted for /home/cayo/OpenMolcas/src/misc_util/ceil.c (code 2)
CMakeFiles/misc_util_obj.dir/build.make:3686: recipe for target 'CMakeFiles/misc_util_obj.dir/src/misc_util/ceil.c.o' failed
make[2]: *** [CMakeFiles/misc_util_obj.dir/src/misc_util/ceil.c.o] Error 2
CMakeFiles/Makefile2:3505: recipe for target 'CMakeFiles/misc_util_obj.dir/all' failed
make[1]: *** [CMakeFiles/misc_util_obj.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....The ccmake gives me:
ACMLROOT
BIBER_COMPILER /usr/bin/biber
BIBTEX_COMPILER /usr/bin/bibtex
BIGOT OFF
BLOCK OFF
BOUNDS OFF
BUILD_SHARED_LIBS OFF
BUILD_STATIC_LIB OFF
CHEMPS2 OFF
CMAKE_AR /usr/bin/ar
CMAKE_BUILD_TYPE Release
CMAKE_COLOR_MAKEFILE ON
CMAKE_CXX_FLAGS_DEBUG
CMAKE_CXX_FLAGS_DEFAULT
CMAKE_CXX_FLAGS_FAST
CMAKE_CXX_FLAGS_GARBLE
CMAKE_CXX_FLAGS_RELEASE
CMAKE_CXX_FLAGS_RELWITHDEBINFO
CMAKE_C_COMPILER /opt/intel/bin/icc
CMAKE_C_FLAGS
CMAKE_C_FLAGS_DEBUG -debug -Wall
CMAKE_C_FLAGS_DEFAULT -std=gnu99
CMAKE_C_FLAGS_FAST -O2
CMAKE_C_FLAGS_GARBLE -O2 -debug -Wall
CMAKE_C_FLAGS_MINSIZEREL -Os -DNDEBUG
CMAKE_C_FLAGS_RELEASE -O2
CMAKE_C_FLAGS_RELWITHDEBINFO -O2 -debug -Wall
CMAKE_EXE_LINKER_FLAGS
CMAKE_EXE_LINKER_FLAGS_DEBUG
CMAKE_EXE_LINKER_FLAGS_MINSIZE
CMAKE_EXE_LINKER_FLAGS_RELEASE
CMAKE_EXE_LINKER_FLAGS_RELWITH
CMAKE_EXPORT_COMPILE_COMMANDS OFF
CMAKE_Fortran_COMPILER /opt/intel/bin/ifort
CMAKE_Fortran_FLAGS
CMAKE_Fortran_FLAGS_DEBUG -debug -traceback -warn all,nointerfaces,nodeclarations
CMAKE_Fortran_FLAGS_DEFAULT -fpp
CMAKE_Fortran_FLAGS_FAST -fast
CMAKE_Fortran_FLAGS_GARBLE -O2 -debug -traceback -warn all,nointerfaces,nodeclarations
CMAKE_Fortran_FLAGS_MINSIZEREL -Os
CMAKE_Fortran_FLAGS_RELEASE -O2 -traceback
CMAKE_Fortran_FLAGS_RELWITHDEB -O2 -debug -traceback -warn all,nointerfaces,nodeclarations
CMAKE_INSTALL_PREFIX /opt/molcas
CMAKE_LINKER /usr/bin/ld
CMAKE_MAKE_PROGRAM /usr/bin/make
CMAKE_MODULE_LINKER_FLAGS
CMAKE_MODULE_LINKER_FLAGS_DEBU
CMAKE_MODULE_LINKER_FLAGS_MINS
CMAKE_MODULE_LINKER_FLAGS_RELE
CMAKE_MODULE_LINKER_FLAGS_RELW
CMAKE_NM /usr/bin/nm
CMAKE_OBJCOPY /usr/bin/objcopy
CMAKE_OBJDUMP /usr/bin/objdump
CMAKE_RANLIB /usr/bin/ranlib
CMAKE_SHARED_LINKER_FLAGS
CMAKE_SHARED_LINKER_FLAGS_DEBU
CMAKE_SHARED_LINKER_FLAGS_MINS
CMAKE_SHARED_LINKER_FLAGS_RELE
CMAKE_SHARED_LINKER_FLAGS_RELW
CMAKE_SKIP_INSTALL_RPATH OFF
CMAKE_SKIP_RPATH OFF
CMAKE_STATIC_LINKER_FLAGS
CMAKE_STATIC_LINKER_FLAGS_DEBU
CMAKE_STATIC_LINKER_FLAGS_MINS
CMAKE_STATIC_LINKER_FLAGS_RELE
CMAKE_STATIC_LINKER_FLAGS_RELW
CMAKE_STRIP /usr/bin/strip
CMAKE_VERBOSE_MAKEFILE OFF
CTEST OFF
CUBLAS OFF
CUDAROOT
DEBUGPRINT OFF
DEBUGTRACE OFF
DEBUG_DEFS
DEFMOLCASDISK 20000
DEFMOLCASMEM 2048
DMRG OFF
DMRG_DEBUG OFF
DVIPDF_CONVERTER /usr/bin/dvipdfm
DVIPS_CONVERTER /usr/bin/dvips
EFPLIB OFF
EXPERT OFF
EXTRA
FDE OFF
GA ON
GA_INCLUDE_PATH /usr/local/include
GCOV OFF
GEN1INT OFF
GIT /usr/bin/git
GPERFTOOLS OFF
GRID_IT OFF
GROMACS OFF
GROMACS_DIR
HDF5 ON
HDF5_C_COMPILER_EXECUTABLE /usr/bin/h5cc
HDF5_C_LIBRARY_dl /usr/lib/x86_64-linux-gnu/libdl.so
HDF5_C_LIBRARY_hdf5 /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so
HDF5_C_LIBRARY_m /usr/lib/x86_64-linux-gnu/libm.so
HDF5_C_LIBRARY_pthread /usr/lib/x86_64-linux-gnu/libpthread.so
HDF5_C_LIBRARY_sz /usr/lib/x86_64-linux-gnu/libsz.so
HDF5_C_LIBRARY_z /usr/lib/x86_64-linux-gnu/libz.so
HDF5_DIFF_EXECUTABLE /usr/bin/h5diff
HDF5_DIR HDF5_DIR-NOTFOUND
HTLATEX_COMPILER /usr/bin/htlatex
LATEX2HTML_CONVERTER LATEX2HTML_CONVERTER-NOTFOUND
LATEXMK /usr/bin/latexmk
LATEX_COMPILER /usr/bin/latex
LIBARMCI /usr/local/lib/libarmci.a
LIBGA /usr/local/lib/libga.a
LIBMKL_BLACS /opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_ilp64.so
LIBMKL_CORE /opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/intel64/libmkl_core.so
LIBMKL_INTERFACE /opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/intel64/libmkl_intel_ilp64.so
LIBMKL_SCALAPACK /opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/intel64/libmkl_scalapack_ilp64.so
LIBMKL_SEQUENTIAL /opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/intel64/libmkl_sequential.so
LIBMKL_THREADING /opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/intel64/libmkl_intel_thread.so
LINALG MKL
LUALATEX_COMPILER /usr/bin/lualatex
MAKEINDEX_COMPILER /usr/bin/makeindex
MKLROOT /opt/intel/compilers_and_libraries_2017.7.259/linux/mkl
MKL_INCLUDE_PATH /opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/include
MKL_LIBRARY_PATH /opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/intel64
MPI ON
MPIEXEC_EXECUTABLE /opt/intel/compilers_and_libraries_2017.7.259/linux/mpi/intel64/bin/mpiexec
MPIEXEC_MAX_NUMPROCS 6
MPIEXEC_NUMPROC_FLAG -n
MPIEXEC_POSTFLAGS
MPIEXEC_PREFLAGS
MPI_C_ADDITIONAL_INCLUDE_DIRS
MPI_C_COMPILER /opt/intel/compilers_and_libraries_2017.7.259/linux/mpi/intel64/bin/mpiicc
MPI_C_COMPILE_DEFINITIONS
MPI_C_COMPILE_OPTIONS
MPI_C_HEADER_DIR /opt/intel/compilers_and_libraries_2017.7.259/linux/mpi/intel64/include
MPI_C_LIB_NAMES mpifort;mpi;mpigi;dl;rt;pthread
MPI_C_LINK_FLAGS -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /opt/intel/compilers_and_libraries_2017.7.259/l
MPI_Fortran_ADDITIONAL_INCLUDE
MPI_Fortran_COMPILER /opt/intel/compilers_and_libraries_2017.7.259/linux/mpi/intel64/bin/mpiifort
MPI_Fortran_COMPILE_DEFINITION
MPI_Fortran_COMPILE_OPTIONS
MPI_Fortran_F77_HEADER_DIR /opt/intel/compilers_and_libraries_2017.7.259/linux/mpi/intel64/include
MPI_Fortran_LIB_NAMES mpifort;mpi;mpigi;dl;rt;pthread
MPI_Fortran_LINK_FLAGS -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /opt/intel/compilers_and_libraries_2017.7.259/l
MPI_Fortran_MODULE_DIR /opt/intel/compilers_and_libraries_2017.7.259/linux/mpi/intel64/include
MPI_LAUNCHER /opt/intel/compilers_and_libraries_2017.7.259/linux/mpi/intel64/bin/mpiexec -n $MOLCAS_NPROCS
MPI_dl_LIBRARY /usr/lib/x86_64-linux-gnu/libdl.so
MPI_mpi_LIBRARY /opt/intel/compilers_and_libraries_2017.7.259/linux/mpi/intel64/lib/release_mt/libmpi.so
MPI_mpifort_LIBRARY /opt/intel/compilers_and_libraries_2017.7.259/linux/mpi/intel64/lib/libmpifort.so
MPI_mpigi_LIBRARY /opt/intel/compilers_and_libraries_2017.7.259/linux/mpi/intel64/lib/libmpigi.a
MPI_pthread_LIBRARY /usr/lib/x86_64-linux-gnu/libpthread.so
MPI_rt_LIBRARY /usr/lib/x86_64-linux-gnu/librt.so
MSYM OFF
NECI OFF
NEVPT2 OFF
NVBLAS OFF
OPENBLASROOT
OPENMP OFF
PDFLATEX_COMPILER /usr/bin/pdflatex
PDFTOPS_CONVERTER /usr/bin/pdftops
PERL /usr/bin/perl
PS2PDF_CONVERTER /usr/bin/ps2pdf14
PYTHON_EXECUTABLE /usr/bin/python3
RUNSCRIPT $program $input
SER_LAUNCHER
TOOLS OFF
WFA OFF
XELATEX_COMPILER /usr/bin/xelatex
XIAR /opt/intel/bin/xiar
XINDY_COMPILER XINDY_COMPILER-NOTFOUND Any idea how to solve this new problem?
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#6 2018-07-28 18:22:27
- Ignacio
- Administrator
- From: Uppsala
- Registered: 2015-11-03
- Posts: 1,012
Re: Installation problem with HDF5
I have never seen that, but it seems to be discussed in https://software.intel.com/en-us/forums … pic/760979
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#7 2018-07-30 20:24:50
- Cayo
- Member
- Registered: 2018-07-26
- Posts: 5
Re: Installation problem with HDF5
Hello Ignacio,
Thanks again. I did saw this post previously but when you sent it there was an option that I tried and worked. Someone suggested to comment the _LIB_VERSION_TYPE in math.h (it seems to me like a conflict with another file with same name at /usr/include/math.h). So, I did comment this in the /opt/intel/compilers_and_libraries_2017.7.259/linux/compiler/include/math.h file like following:
//_LIBIMF_EXTERN_C _LIB_VERSIONIMF_TYPE _LIBIMF_PUBVAR _LIB_VERSIONIMF;
_LIBIMF_EXTERN_C _LIBIMF_PUBVAR _LIB_VERSIONIMF;Then I almost finished, but there is a new error now:
[ 87%] Building Fortran object CMakeFiles/caspt2.dir/src/caspt2/offdns.f.o
ld: bin/guessorb.exe: hidden symbol `__intel_cpu_features_init_x' in /opt/intel/compilers_and_libraries_2017.7.259/linux/compiler/lib/intel64_lin/libirc.a(cpu_feature_disp.o) is referenced by DSO
ld: final link failed: Bad value
CMakeFiles/guessorb.exe.dir/build.make:104: recipe for target 'bin/guessorb.exe' failed
make[2]: *** [bin/guessorb.exe] Error 1
CMakeFiles/Makefile2:953: recipe for target 'CMakeFiles/guessorb.exe.dir/all' failed
make[1]: *** [CMakeFiles/guessorb.exe.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....Can you help me with this one?
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#8 2018-07-31 10:34:26
- Ignacio
- Administrator
- From: Uppsala
- Registered: 2015-11-03
- Posts: 1,012
Re: Installation problem with HDF5
I can only suggest to try gcc compilers instead of intel
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#9 2018-07-31 14:45:38
- Cayo
- Member
- Registered: 2018-07-26
- Posts: 5
Re: Installation problem with HDF5
Hello Ignacio,
Well, my goal was to use MOLCAS with intel compilers. It compiles with gcc and MKL, but I can't use intel mpi, otherwise I get new problems.
So, in the end I will stay with the serial compilation, using gcc and gfortran.
Thanks for all the help.
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