Molcas Forum

lise

Member

From: Orsay

Registered: 2019-02-14

Posts: 11

Website

[SOLVED] problems in openmolcas generation with WFA and HDF5

hello,
I encountered problems during link phase of OpenMolcas18.09-360-g32519a5. That concerns link phasis of bin/caspt2.exe with -l lib/libmolcas.a, mh5_capi.c.o and the hdf5 functions.
System: CentOS Linux release 7.0.1406 (Core)
compiler: intel/14.0.5  (module load intel/14.0.5)

HDF5 version: 1.8.20 (notice that i don't use cmake so i don't have any cmake file directory to give to openmolcas -> HDF5_DIR)
Command Line:

# module load intel/14.0.5
# FC=ifort ./configure --prefix=/home/programmes/hdf5/1.8.20 --enable-cxx --enable-fortran --with-zlib
# make
# make install

HDF5 Installation successful

then OpenMolcas generation:

# module load intel/14.0.5
# cd build18.09_serial
# HDF5_ROOT=/home/programmes/hdf5/1.8.20 FC=ifort  cmake -D CMAKE_INSTALL_PREFIX=/home/programmes/OpenMolcas/v18.09/serial_WFA -D LINALG=MKL -D HDF5=ON -D WFA=ON -D ARMADILLO_INC=/usr/include/armadillo ../OpenMolcas18.09-360-g32519a5
# make >make_molcas.log 2>&1

I got this errors on lib/libmolcas.a:

Linking Fortran executable bin/caspt2.exe
/usr/bin/cmake -E cmake_link_script CMakeFiles/caspt2.exe.dir/link.txt --verbose=1
/home/programmes/intel/composer_xe_2013_sp1.5.212/composer_xe_2013_sp1.5.212/bin/intel64/ifort     -fpp -i8 -r8 -heap-arrays -O2 -traceback CMakeFiles/caspt2.exe.dir/src/caspt2/main.f.o CMakeFiles/caspt2.dir/src/caspt2/prinp_caspt2.f.o CMakeFiles/caspt2.dir/src/caspt2/getsgm2.f.o CMakeFiles/caspt2.dir/src/caspt2/hcoup.f.o CMakeFiles/caspt2.dir/src/caspt2/mkmaw_cp2.f.o CMakeFiles/caspt2.dir/src/caspt2/superindex.f.o CMakeFiles/caspt2.dir/src/caspt2/eqctl2.f.o CMakeFiles/caspt2.dir/src/caspt2/mltsca.f.o CMakeFiles/caspt2.dir/src/caspt2/caspt2.f.o CMakeFiles/caspt2.dir/src/caspt2/drt_rpt2.f.o CMakeFiles/caspt2.dir/src/caspt2/trachosz.f.o CMakeFiles/caspt2.dir/src/caspt2/traci_rpt2.f.o CMakeFiles/caspt2.dir/src/caspt2/rhsod_nosym.f.o CMakeFiles/caspt2.dir/src/caspt2/trimul.f.o CMakeFiles/caspt2.dir/src/caspt2/diadns.f.o CMakeFiles/caspt2.dir/src/caspt2/triang.f.o CMakeFiles/caspt2.dir/src/caspt2/grpini.f.o CMakeFiles/caspt2.dir/src/caspt2/mksmat.f.o CMakeFiles/caspt2.dir/src/caspt2/special.f.o CMakeFiles/caspt2.dir/src/caspt2/spec1c.f.o CMakeFiles/caspt2.dir/src/caspt2/mltctl.f.o CMakeFiles/caspt2.dir/src/caspt2/gdmat.f.o CMakeFiles/caspt2.dir/src/caspt2/pt2_get.f.o CMakeFiles/caspt2.dir/src/caspt2/halftrnsf.f.o CMakeFiles/caspt2.dir/src/caspt2/customh0.f.o CMakeFiles/caspt2.dir/src/caspt2/newfock.f.o CMakeFiles/caspt2.dir/src/caspt2/clsfls.f.o CMakeFiles/caspt2.dir/src/caspt2/mltdxp.f.o CMakeFiles/caspt2.dir/src/caspt2/ginit_cp2.f.o CMakeFiles/caspt2.dir/src/caspt2/nadiag.f.o CMakeFiles/caspt2.dir/src/caspt2/fock_rpt2.f.o CMakeFiles/caspt2.dir/src/caspt2/mkseg_cp2.f.o CMakeFiles/caspt2.dir/src/caspt2/fno_caspt2.f.o CMakeFiles/caspt2.dir/src/caspt2/trdns2d.f.o CMakeFiles/caspt2.dir/src/caspt2/exc1_cp2.f.o CMakeFiles/caspt2.dir/src/caspt2/sgmdia.f.o CMakeFiles/caspt2.dir/src/caspt2/drt0_cp2.f.o CMakeFiles/caspt2.dir/src/caspt2/print_ci_mix.f.o CMakeFiles/caspt2.dir/src/caspt2/fblock.f.o CMakeFiles/caspt2.dir/src/caspt2/dens2_rpt2.f.o CMakeFiles/caspt2.dir/src/caspt2/pt2wfn.f.o CMakeFiles/caspt2.dir/src/caspt2/intctl1.f.o CMakeFiles/caspt2.dir/src/caspt2/poly2.f.o CMakeFiles/caspt2.dir/src/caspt2/ham3.f.o CMakeFiles/caspt2.dir/src/caspt2/full2red.f.o CMakeFiles/caspt2.dir/src/caspt2/setup_cho.f.o CMakeFiles/caspt2.dir/src/caspt2/sizes.f.o CMakeFiles/caspt2.dir/src/caspt2/asind.f.o CMakeFiles/caspt2.dir/src/caspt2/fmat.f.o CMakeFiles/caspt2.dir/src/caspt2/cho_x_loc.f.o CMakeFiles/caspt2.dir/src/caspt2/rhsod.f.o CMakeFiles/caspt2.dir/src/caspt2/mklist.f.o CMakeFiles/caspt2.dir/src/caspt2/resdia.f.o CMakeFiles/caspt2.dir/src/caspt2/mkfg3.f.o CMakeFiles/caspt2.dir/src/caspt2/diafck.f.o CMakeFiles/caspt2.dir/src/caspt2/hefval.f.o CMakeFiles/caspt2.dir/src/caspt2/modop.f.o CMakeFiles/caspt2.dir/src/caspt2/chovec_io.f.o CMakeFiles/caspt2.dir/src/caspt2/poly3.f.o CMakeFiles/caspt2.dir/src/caspt2/done_caspt2.f.o CMakeFiles/caspt2.dir/src/caspt2/dex1_cp2.f.o CMakeFiles/caspt2.dir/src/caspt2/mkbmat.f.o CMakeFiles/caspt2.dir/src/caspt2/w1tw2.f.o CMakeFiles/caspt2.dir/src/caspt2/mkwwop.f.o CMakeFiles/caspt2.dir/src/caspt2/transfock.f.o CMakeFiles/caspt2.dir/src/caspt2/restr_rpt2.f.o CMakeFiles/caspt2.dir/src/caspt2/mkrhs.f.o CMakeFiles/caspt2.dir/src/caspt2/prwf1_cp2.f.o CMakeFiles/caspt2.dir/src/caspt2/eqctl1.f.o CMakeFiles/caspt2.dir/src/caspt2/trdtmp.f.o CMakeFiles/caspt2.dir/src/caspt2/h0spct.f.o CMakeFiles/caspt2.dir/src/caspt2/prwf_cp2.f.o CMakeFiles/caspt2.dir/src/caspt2/mkeps.f.o CMakeFiles/caspt2.dir/src/caspt2/wfnsizes.f.o CMakeFiles/caspt2.dir/src/caspt2/opnfls_caspt2.f.o CMakeFiles/caspt2.dir/src/caspt2/addrhs.f.o CMakeFiles/caspt2.dir/src/caspt2/pcg.f.o CMakeFiles/caspt2.dir/src/caspt2/compute_tr_dab.f.o CMakeFiles/caspt2.dir/src/caspt2/sgm.f.o CMakeFiles/caspt2.dir/src/caspt2/mltr1.f.o CMakeFiles/caspt2.dir/src/caspt2/trdact.f.o CMakeFiles/caspt2.dir/src/caspt2/modrhs.f.o CMakeFiles/caspt2.dir/src/caspt2/mkfg3dm.f.o CMakeFiles/caspt2.dir/src/caspt2/rhsall2.f.o CMakeFiles/caspt2.dir/src/caspt2/ga_striped.f.o CMakeFiles/caspt2.dir/src/caspt2/import_cho.f.o CMakeFiles/caspt2.dir/src/caspt2/poly0.f.o CMakeFiles/caspt2.dir/src/caspt2/orbctl.f.o CMakeFiles/caspt2.dir/src/caspt2/mkfop.f.o CMakeFiles/caspt2.dir/src/caspt2/sigma.f.o CMakeFiles/caspt2.dir/src/caspt2/readin_caspt2.f.o CMakeFiles/caspt2.dir/src/caspt2/creiph.f.o CMakeFiles/caspt2.dir/src/caspt2/par_sbmat.f.o CMakeFiles/caspt2.dir/src/caspt2/commWEW.f.o CMakeFiles/caspt2.dir/src/caspt2/trdns2a.f.o CMakeFiles/caspt2.dir/src/caspt2/exc2_cp2.f.o CMakeFiles/caspt2.dir/src/caspt2/pt2ini.f.o CMakeFiles/caspt2.dir/src/caspt2/ref_nato.f.o CMakeFiles/caspt2.dir/src/caspt2/diafop.f.o CMakeFiles/caspt2.dir/src/caspt2/dex2_cp2.f.o CMakeFiles/caspt2.dir/src/caspt2/transdref.f.o CMakeFiles/caspt2.dir/src/caspt2/dielmv.f.o CMakeFiles/caspt2.dir/src/caspt2/spec1a.f.o CMakeFiles/caspt2.dir/src/caspt2/add1ham.f.o CMakeFiles/caspt2.dir/src/caspt2/mltunf.f.o CMakeFiles/caspt2.dir/src/caspt2/allgather.f.o CMakeFiles/caspt2.dir/src/caspt2/tracho3.f.o CMakeFiles/caspt2.dir/src/caspt2/mcctl.f.o CMakeFiles/caspt2.dir/src/caspt2/sigma1_cp2.f.o CMakeFiles/caspt2.dir/src/caspt2/refwfn.f.o CMakeFiles/caspt2.dir/src/caspt2/mkdaw_cp2.f.o CMakeFiles/caspt2.dir/src/caspt2/mltmv.f.o CMakeFiles/caspt2.dir/src/caspt2/intctl2.f.o CMakeFiles/caspt2.dir/src/caspt2/procinp_caspt2.f.o CMakeFiles/caspt2.dir/src/caspt2/mktg3.f.o CMakeFiles/caspt2.dir/src/caspt2/mkrptorb.f.o CMakeFiles/caspt2.dir/src/caspt2/stini.f.o CMakeFiles/caspt2.dir/src/caspt2/excind.f.o CMakeFiles/caspt2.dir/src/caspt2/mkdref_rpt2.f.o CMakeFiles/caspt2.dir/src/caspt2/par_rhs.f.o CMakeFiles/caspt2.dir/src/caspt2/set_print_level.f.o CMakeFiles/caspt2.dir/src/caspt2/getdpref.f.o CMakeFiles/caspt2.dir/src/caspt2/pt2_put.f.o CMakeFiles/caspt2.dir/src/caspt2/grdctl.f.o CMakeFiles/caspt2.dir/src/caspt2/mkcoup_cp2.f.o CMakeFiles/caspt2.dir/src/caspt2/h0diag.f.o CMakeFiles/caspt2.dir/src/caspt2/mkfg3chemps2.f.o CMakeFiles/caspt2.dir/src/caspt2/nsind.f.o CMakeFiles/caspt2.dir/src/caspt2/pclose.f.o CMakeFiles/caspt2.dir/src/caspt2/offdns.f.o CMakeFiles/caspt2.dir/src/caspt2/fmat_cho.f.o CMakeFiles/caspt2.dir/src/caspt2/trdns1.f.o CMakeFiles/caspt2.dir/src/caspt2/synrhs.f.o CMakeFiles/caspt2.dir/src/caspt2/spec1d.f.o CMakeFiles/caspt2.dir/src/caspt2/afreez.f.o CMakeFiles/caspt2.dir/src/caspt2/traone.f.o CMakeFiles/caspt2.dir/src/caspt2/correl_orb.f.o CMakeFiles/caspt2.dir/src/caspt2/tracho2.f.o CMakeFiles/caspt2.dir/src/caspt2/lov_caspt2.f.o CMakeFiles/caspt2.dir/src/caspt2/mkpref_rpt2.f.o CMakeFiles/caspt2.dir/src/caspt2/natorb_caspt2.f.o CMakeFiles/caspt2.dir/src/caspt2/vcutil.f.o CMakeFiles/caspt2.dir/src/caspt2/fulltrnsf.f.o CMakeFiles/caspt2.dir/src/caspt2/cho_caspt2_rdinp.f.o CMakeFiles/caspt2.dir/src/caspt2/sbdiag.f.o CMakeFiles/caspt2.dir/src/caspt2/trdns2o.f.o CMakeFiles/caspt2.dir/src/caspt2/prpctl.f.o CMakeFiles/caspt2.dir/src/caspt2/nrcoup_cp2.f.o CMakeFiles/caspt2.dir/src/caspt2/dens.f.o CMakeFiles/caspt2.dir/src/caspt2/mkfg3cu4.f.o  -o bin/caspt2.exe -i_dynamic lib/libmolcas.a -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lirng -ldecimal -lcilkrts -lstdc++ -lirc -Wl,-rpath,::::::::::::::::::::::::::::::::::::::::::::::::: 
lib/libmolcas.a(mh5_capi.c.o): In function `mh5c_create_file':
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x49c): undefined reference to `H5open'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x4a2): undefined reference to `H5P_CLS_FILE_ACCESS_ID_g'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x4a7): undefined reference to `H5Pcreate'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x4b7): undefined reference to `H5Pset_fclose_degree'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x4cb): undefined reference to `H5check_version'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x4dd): undefined reference to `H5Fcreate'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x4e5): undefined reference to `H5open'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x4eb): undefined reference to `H5T_C_S1_g'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x4f0): undefined reference to `H5Tcopy'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x4fe): undefined reference to `H5Tset_size'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x50a): undefined reference to `H5Tset_strpad'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x511): undefined reference to `H5Screate'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x52f): undefined reference to `H5Acreate2'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x53a): undefined reference to `H5Sclose'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x541): undefined reference to `H5Tclose'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x549): undefined reference to `H5Aget_type'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x55a): undefined reference to `H5Awrite'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x564): undefined reference to `H5Fflush'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x56b): undefined reference to `H5Tclose'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x573): undefined reference to `H5Aclose'
lib/libmolcas.a(mh5_capi.c.o): In function `mh5c_open_file_rw':
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x5bc): undefined reference to `H5open'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x5c2): undefined reference to `H5P_CLS_FILE_ACCESS_ID_g'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x5c7): undefined reference to `H5Pcreate'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x5d7): undefined reference to `H5Pset_fclose_degree'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x5eb): undefined reference to `H5check_version'
.and so on.directly followed by
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x4715): undefined reference to `H5Sclose'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x471e): undefined reference to `H5Fflush'
/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c:(.text+0x474f): undefined reference to `H5Dread'
make[2]: *** [bin/caspt2.exe] Error 1
make[2]: Leaving directory `/beegfs/home/lise_didillon/build18.09_serial'
make[1]: *** [CMakeFiles/caspt2.exe.dir/all] Error 2
make[1]: Leaving directory `/beegfs/home/lise_didillon/build18.09_serial'
make: *** [all] Error 2

mh5_capi.c compile is OK:

[ 32%] Building C object CMakeFiles/hdf5_util_obj.dir/src/hdf5_util/mh5_capi.c.o
/home/programmes/intel/composer_xe_2013_sp1.5.212/composer_xe_2013_sp1.5.212/bin/intel64/icc  -D_I8_ -D_LINUX_ -D_MKL_ -D_MOLCAS_ -std=gnu99 -O2 -I/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/Include -I/home/lise_didillon/build18.09_serial/include -I/home/lise_didillon/build18.09_serial/mod -I/home/programmes/intel/composer_xe_2013_sp1.5.212/composer_xe_2013_sp1.5.212/mkl/include -I/home/programmes/hdf5/1.8.20/include -I/home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util -I/home/lise_didillon/build18.09_serial/mod/hdf5_util    -o CMakeFiles/hdf5_util_obj.dir/src/hdf5_util/mh5_capi.c.o   -c /home/lise_didillon/OpenMolcas18.09-360-g32519a5/src/hdf5_util/mh5_capi.c
make[2]: Leaving directory `/beegfs/home/lise_didillon/build18.09_serial'

I-ve tried also with:
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/programmes/hdf5/1.8.20/lib; export LD_LIBRARY_PATH
and with the static hdf5 libraries by adding to the line command:
-D UNIX=1 -D HDF5_USE_STATIC_LIBRARIES=1

But I've got the same errors...

2 things that can can have an effect:
- No HDF5_DIR to give as parameter in the cmake command line for OpenMolcas because I use configure and make: Do i have to use cmake v3
- /usr/include/armadillo is a file not a directory which only include all  the  armadillo include. The armadillo include files stay in /usr/include/armadillo_bits directory: Do I have to specify
-D ARMADILLO_INC=/usr/include/armadillo_bits instead of -D ARMADILLO_INC=/usr/include/armadillo

Thank you very much for any help
I will give you the CMakeCache.txt in a further message

Lise

lise

Member

From: Orsay

Registered: 2019-02-14

Posts: 11

Website

Re: [SOLVED] problems in openmolcas generation with WFA and HDF5

You will find here the CMakeCache.txt
If I use "-D UNIX=1 -D HDF5_USE_STATIC_LIBRARIES=1" instead of ".so" you find ".a" for all the hdf5 libraries

# cat CMakeCache.txt     
# This is the CMakeCache file.
# For build in directory: /home/lise_didillon/build18.09_serial
# It was generated by CMake: /usr/bin/cmake
# You can edit this file to change values found and used by cmake.
# If you do not want to change any of the values, simply exit the editor.
# If you do want to change a value, simply edit, save, and exit the editor.
# The syntax for the file is as follows:
# KEY:TYPE=VALUE
# KEY is the name of a variable in the cache.
# TYPE is a hint to GUI's for the type of VALUE, DO NOT EDIT TYPE!.
# VALUE is the current value for the KEY.

########################
# EXTERNAL cache entries
########################

//ACML path.
ACMLROOT:PATH=

//No help, variable specified on the command line.
ARMADILLO_INC:UNINITIALIZED=/usr/include/armadillo

//Do not allow any compiler warning (treat them as errors).
BIGOT:BOOL=OFF

//Activate BLOCK-DMRG support.
BLOCK:BOOL=OFF

//Enable bounds checking (only gfortran >= 4.8).
BOUNDS:BOOL=OFF

//Build dynamically-linked molcas library.
BUILD_SHARED_LIBS:BOOL=OFF

//Build statically-linked molcas library too.
BUILD_STATIC_LIB:BOOL=OFF

//Activate CheMPS2-DMRG support.
CHEMPS2:BOOL=OFF

//Path to a program.
CMAKE_AR:FILEPATH=/bin/ar

//Type of build, options are: None (CFLAGS/FFLAGS can be used),
// Debug, Garble, RelWithDebInfo, Release, Fast.
CMAKE_BUILD_TYPE:STRING=Release

//Enable/Disable color output during build.
CMAKE_COLOR_MAKEFILE:BOOL=ON

//CXX compiler.
CMAKE_CXX_COMPILER:FILEPATH=/home/programmes/intel/composer_xe_2013_sp1.5.212/composer_xe_2013_sp1.5.212/bin/intel64/icpc

//Flags used by the compiler during all build types.
CMAKE_CXX_FLAGS:STRING=

//C++ compiler flags used for debug builds.
CMAKE_CXX_FLAGS_DEBUG:STRING=-debug -Wall

//C++ compiler flags.
CMAKE_CXX_FLAGS_DEFAULT:STRING=' '

//C++ compiler flags used for fast release builds.
CMAKE_CXX_FLAGS_FAST:STRING=-O2

//C++ compiler flags used for garble builds.
CMAKE_CXX_FLAGS_GARBLE:STRING=-O2 -debug -Wall

//Flags used by the compiler during release minsize builds.
CMAKE_CXX_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG

//C++ compiler flags used for release builds.
CMAKE_CXX_FLAGS_RELEASE:STRING=-O2

//C++ compiler flags used for release builds with debug info.
CMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=-O2 -debug -Wall

//C compiler.
CMAKE_C_COMPILER:FILEPATH=/home/programmes/intel/composer_xe_2013_sp1.5.212/composer_xe_2013_sp1.5.212/bin/intel64/icc

//Flags used by the compiler during all build types.
CMAKE_C_FLAGS:STRING=

//C compiler flags used for debug builds.
CMAKE_C_FLAGS_DEBUG:STRING=-debug -Wall

//C compiler flags.
CMAKE_C_FLAGS_DEFAULT:STRING= -std=gnu99

//C compiler flags used for fast release builds.
CMAKE_C_FLAGS_FAST:STRING=-O2

//C compiler flags used for garble builds.
CMAKE_C_FLAGS_GARBLE:STRING=-O2 -debug -Wall

//Flags used by the compiler during release minsize builds.
CMAKE_C_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG

//C compiler flags used for release builds.
CMAKE_C_FLAGS_RELEASE:STRING=-O2

//C compiler flags used for release builds with debug info.
CMAKE_C_FLAGS_RELWITHDEBINFO:STRING=-O2 -debug -Wall

//Flags used by the linker.
CMAKE_EXE_LINKER_FLAGS:STRING=' '

//Flags used by the linker during debug builds.
CMAKE_EXE_LINKER_FLAGS_DEBUG:STRING=

//Flags used by the linker during release minsize builds.
CMAKE_EXE_LINKER_FLAGS_MINSIZEREL:STRING=

//Flags used by the linker during release builds.
CMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=

//Flags used by the linker during Release with Debug Info builds.
CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO:STRING=

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HDF5_m_LIBRARY_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: HDF5_m_LIBRARY_RELEASE
HDF5_m_LIBRARY_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: HDF5_z_LIBRARY
HDF5_z_LIBRARY-ADVANCED:INTERNAL=1
//ADVANCED property for variable: HDF5_z_LIBRARY_DEBUG
HDF5_z_LIBRARY_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: HDF5_z_LIBRARY_RELEASE
HDF5_z_LIBRARY_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: LATEXMK
LATEXMK-ADVANCED:INTERNAL=1
//STRINGS property for variable: LINALG
LINALG-STRINGS:INTERNAL=Internal;Runtime;MKL;ACML;OpenBLAS;Accelerate
//ADVANCED property for variable: MKLROOT
MKLROOT-ADVANCED:INTERNAL=0
//last value.
MKLROOT_LAST:INTERNAL=/home/programmes/intel/composer_xe_2013_sp1.5.212/composer_xe_2013_sp1.5.212/mkl
//ADVANCED property for variable: OPENBLASROOT
OPENBLASROOT-ADVANCED:INTERNAL=1
//ADVANCED property for variable: PERL
PERL-ADVANCED:INTERNAL=1
//ADVANCED property for variable: PYTHON_EXECUTABLE
PYTHON_EXECUTABLE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: SPHINX_EXECUTABLE
SPHINX_EXECUTABLE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: XIAR
XIAR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: XMLLINT
XMLLINT-ADVANCED:INTERNAL=1

Thank you for help

lise

Member

From: Orsay

Registered: 2019-02-14

Posts: 11

Website

Re: [SOLVED] problems in openmolcas generation with WFA and HDF5

I use cmake 2.8.11

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,012

Re: [SOLVED] problems in openmolcas generation with WFA and HDF5

When you run cmake, what does the output say about HDF5? For me it is:

Configuring HDF5 support:
-- HDF5_INCLUDE_PATH: /usr/include
-- HDF5_C_LIBRARIES: /usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- HDF5_CXX_LIBRARIES: /usr/lib/x86_64-linux-gnu/libhdf5_cpp.so;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so

If some of these are empty, you could try to manually define them (but note the first one is actually HDF5_INCLUDE_DIRS).

lise

Member

From: Orsay

Registered: 2019-02-14

Posts: 11

Website

Re: [SOLVED] problems in openmolcas generation with WFA and HDF5

Thank you!!

My command line:

# HDF5_ROOT=/home/programmes/hdf5/1.8.20 FC=ifort  cmake -D CMAKE_INSTALL_PREFIX=/home/programmes/OpenMolcas/v18.09/serial_WFA -D LINALG=MKL -D HDF5=ON -D WFA=ON -D ARMADILLO_INC=/usr/include/armadillo ../OpenMolcas18.09-360-g32519a5

The output:

Configuring HDF5 support:
-- Found HDF5: debug;/home/programmes/hdf5/1.8.20/lib/libhdf5_cpp.so;debug;/home/programmes/hdf5/1.8.20/lib/libhdf5.so;debug;/usr/lib64/libz.so;debug;/usr/lib64/libdl.so;debug;/usr/lib64/libm.so;optimized;/home/programmes/hdf5/1.8.20/lib/libhdf5_cpp.so;optimized;/home/programmes/hdf5/1.8.20/lib/libhdf5.so;optimized;/usr/lib64/libz.so;optimized;/usr/lib64/libdl.so;optimized;/usr/lib64/libm.so  
-- HDF5_INCLUDE_PATH: /home/programmes/hdf5/1.8.20/include
-- HDF5_C_LIBRARIES: 

HDF5_C_LIBRARIES is empty. is that OK?  does this variable contains a path or a libraries list?

lise

Member

From: Orsay

Registered: 2019-02-14

Posts: 11

Website

Re: [SOLVED] problems in openmolcas generation with WFA and HDF5

oh excuse me!  I see in your cmake output that HDF5_C_LIBRARY is a list of Librarie.
I will try to manually set it

lise

Member

From: Orsay

Registered: 2019-02-14

Posts: 11

Website

Re: [SOLVED] problems in openmolcas generation with WFA and HDF5

I never find how to manually set HDF5_C_LIBRARIES and HDF5_CXX_LIBRARIES. I have tried this (but it doesn't work)

# FC=ifort HDF5_ROOT=/home/programmes/hdf5/1.8.20 \
HDF5_C_LIBRARIES="/home/programmes/hdf5/1.8.20/lib/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so" \
HDF5_CXX_LIBRARIES="/home/programmes/hdf5/1.8.20/lib/libhdf5_cpp.so;/home/programmes/hdf5/1.8.20/lib/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so" \
cmake -D CMAKE_INSTALL_PREFIX=/home/programmes/OpenMolcas/v18.09/serial_WFA -D LINALG=MKL -D HDF5=ON -D WFA=ON -D ARMADILLO_INC=/usr/include/armadillo ../OpenMolcas18.09-360-g32519a5

I have tried also to set LD_LIBRARY_PATH as follow:

# LD_LIBRARY_PATH=/home/programmes/hdf5/1.8.20/lib:$LD_LIBRARY_PATH FC=ifort HDF5_ROOT=/home/programmes/hdf5/1.8.20 \
cmake -D CMAKE_INSTALL_PREFIX=/home/programmes/OpenMolcas/v18.09/serial_WFA -D LINALG=MKL -D HDF5=ON -D WFA=ON -D ARMADILLO_INC=/usr/include/armadillo ../OpenMolcas18.09-360-g32519a5

after that I run ldconfig

# ldconfig -n /home/programmes/hdf5/1.8.20/lib

it doesn't work

after that I directly modify at the end of CMakeFiles/caspt2.exe.dir/link.txt to add the libhdf5.a and run make:

-o bin/caspt2.exe -i_dynamic /home/programmes/hdf5/1.8.20/lib/libhdf5.a lib/libmolcas.a -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential lib/libwfa_molcas.a -lirng -ldecimal -lcilkrts -lstdc++ -lirc -lirng -ldecimal -lcilkrts -lstdc++ -lirc -Wl,-rpath,:::::::::::::::::::::::::::::::::::::::::::::::::

I have tried also in this part of line to replace the parameter i_dynamic by i-dynamic because i_dynamic don't exist (man ifort: -i-dynamic
              Links Intel-provided libraries dynamically. It is the  opposite
              of -i-static.)

at this point the last ideas are: use cmake3 instead of cmake 2.8.11; generate the rpm package with my hdf5 version and install it on my system
I don't know what to do.
could you help me?

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,012

Re: [SOLVED] problems in openmolcas generation with WFA and HDF5

If the problem is your definition is not picked up, it might be easier to modify the CMakeLists.txt file and insert your definition:

                if (HDF5_FOUND)
                        set(HDF5_C_LIBRARIES "insert your value here")
                        message ("-- HDF5_INCLUDE_DIRS: ${HDF5_INCLUDE_DIRS}")
                        message ("-- HDF5_C_LIBRARIES: ${HDF5_C_LIBRARIES}") 

Note also that, at least in my case, this is not just libhdf5.so, but also libpthread.so, libz.so, libdl.so and libm.so

About the -i_dynamic, that's cmake's own doing, updating cmake might help, but I believe it's harmless.

lise

Member

From: Orsay

Registered: 2019-02-14

Posts: 11

Website

Re: [SOLVED] problems in openmolcas generation with WFA and HDF5

It works!
So I add as you show me:

if (HDF5_FOUND) 
  set(HDF5_C_LIBRARIES "/home/programmes/hdf5/1.8.20/lib/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so")
  set(HDF5_CXX_LIBRARIES "/home/programmes/hdf5/1.8.20/lib/libhdf5_cpp.so;/home/programmes/hdf5/1.8.20/lib/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so")

I don't add libpthread, I don't now exactly  why but I refer to the previous output of cmake at the line mentioning the founded libraries: libhdf5, libz, etc.  libpthread was not mentioned so I conclude this library is not necessary.

Thank you very much
Best regards,
Lise