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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

make

command I get the following

[ 15%] Built target integral_util_obj
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2

and 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.o

I 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: 445

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: 445

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: 445

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?

Offline

#8 2018-07-31 10:34:26

Ignacio
Administrator
From: Uppsala
Registered: 2015-11-03
Posts: 445

Re: Installation problem with HDF5

I can only suggest to try gcc compilers instead of intel

Offline

#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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