Channnelflow 2.0 make fail

Installation
1

I am getting the following error while running “make -j” command, It seems that HDF5 library link error.
…
[ 41%] Linking CXX executable simulateflow
…/channelflow/libchflow.so: undefined reference to H5Gopen1' ../channelflow/libchflow.so: undefined reference toH5T_STD_U16LE_g’
…/channelflow/libchflow.so: undefined reference to curl_easy_perform' ../channelflow/libchflow.so: undefined reference toH5Dset_extent’
…/channelflow/libchflow.so: undefined reference to H5Pcreate' ../channelflow/libchflow.so: undefined reference toH5Tget_native_type’
…/channelflow/libchflow.so: undefined reference to curl_easy_getinfo' ../channelflow/libchflow.so: undefined reference toH5Aexists’
…/channelflow/libchflow.so: undefined reference to H5Pfill_value_defined' ../channelflow/libchflow.so: undefined reference toH5Pset_layout’
…/channelflow/libchflow.so: undefined reference to H5Tis_variable_str' ../channelflow/libchflow.so: undefined reference toH5Oopen’
…/channelflow/libchflow.so: undefined reference to H5Acreate1' ../channelflow/libchflow.so: undefined reference toH5Tget_size’
…/channelflow/libchflow.so: undefined reference to H5DSis_scale' ../channelflow/libchflow.so: undefined reference toH5Fflush’
…/channelflow/libchflow.so: undefined reference to H5Fopen' ../channelflow/libchflow.so: undefined reference toH5T_NATIVE_INT_g’
…/channelflow/libchflow.so: undefined reference to H5check_version' ../channelflow/libchflow.so: undefined reference toH5Pset_chunk_cache’
…/channelflow/libchflow.so: undefined reference to H5Pset_coll_metadata_write' ../channelflow/libchflow.so: undefined reference toH5DSdetach_scale’
…/channelflow/libchflow.so: undefined reference to H5Pget_layout' ../channelflow/libchflow.so: undefined reference toH5T_STD_U16BE_g’
…/channelflow/libchflow.so: undefined reference to curl_easy_init' ../channelflow/libchflow.so: undefined reference toH5T_STD_I8BE_g’
…/channelflow/libchflow.so: undefined reference to H5Pset_file_image_callbacks' ../channelflow/libchflow.so: undefined reference toH5Awrite’
…/channelflow/libchflow.so: undefined reference to H5Tget_member_type' ../channelflow/libchflow.so: undefined reference toH5Aclose’
…/channelflow/libchflow.so: undefined reference to H5Gunlink' ../channelflow/libchflow.so: undefined reference tocurl_easy_strerror’
…/channelflow/libchflow.so: undefined reference to H5Dget_create_plist' ../channelflow/libchflow.so: undefined reference toH5T_IEEE_F64LE_g’
…/channelflow/libchflow.so: undefined reference to H5Eauto_is_v2' ../channelflow/libchflow.so: undefined reference toH5Idec_ref’
…/channelflow/libchflow.so: undefined reference to H5Dget_space' ../channelflow/libchflow.so: undefined reference toH5DSget_scale_name’
…/channelflow/libchflow.so: undefined reference to H5Pset_all_coll_metadata_ops' ../channelflow/libchflow.so: undefined reference toH5Literate’
…/channelflow/libchflow.so: undefined reference to H5T_STD_I16LE_g' ../channelflow/libchflow.so: undefined reference toH5T_STD_U64BE_g’
…/channelflow/libchflow.so: undefined reference to H5Pget_chunk' ../channelflow/libchflow.so: undefined reference toH5Gcreate2’
…/channelflow/libchflow.so: undefined reference to H5Fget_create_plist' ../channelflow/libchflow.so: undefined reference toH5Aiterate2’
…/channelflow/libchflow.so: undefined reference to H5Iget_name' ../channelflow/libchflow.so: undefined reference toH5P_CLS_DATASET_ACCESS_ID_g’
…/channelflow/libchflow.so: undefined reference to H5Tget_member_name' ../channelflow/libchflow.so: undefined reference toH5Tget_member_value’
…/channelflow/libchflow.so: undefined reference to H5Sget_simple_extent_npoints' ../channelflow/libchflow.so: undefined reference toH5Eget_auto2’
…/channelflow/libchflow.so: undefined reference to H5Tset_cset' ../channelflow/libchflow.so: undefined reference toH5Aopen’
…/channelflow/libchflow.so: undefined reference to curl_version_info' ../channelflow/libchflow.so: undefined reference toH5Gget_objinfo’
…/channelflow/libchflow.so: undefined reference to H5Pset_link_creation_order' ../channelflow/libchflow.so: undefined reference toH5T_NATIVE_LLONG_g’
…/channelflow/libchflow.so: undefined reference to H5Tenum_insert' ../channelflow/libchflow.so: undefined reference toH5free_memory’
…/channelflow/libchflow.so: undefined reference to H5Tinsert' ../channelflow/libchflow.so: undefined reference toH5Tget_member_offset’
…/channelflow/libchflow.so: undefined reference to H5Pset_obj_track_times' ../channelflow/libchflow.so: undefined reference toH5T_NATIVE_SHORT_g’
…/channelflow/libchflow.so: undefined reference to H5Dread' ../channelflow/libchflow.so: undefined reference toH5Tset_strpad’
…/channelflow/libchflow.so: undefined reference to H5Fget_obj_ids' ../channelflow/libchflow.so: undefined reference toH5Pget_chunk_cache’
…/channelflow/libchflow.so: undefined reference to H5Gget_objname_by_idx' ../channelflow/libchflow.so: undefined reference toH5T_NATIVE_UCHAR_g’
…/channelflow/libchflow.so: undefined reference to H5Pset_fclose_degree' ../channelflow/libchflow.so: undefined reference toH5Tequal’
…/channelflow/libchflow.so: undefined reference to H5Pset_fletcher32' ../channelflow/libchflow.so: undefined reference toH5Pset_deflate’
…/channelflow/libchflow.so: undefined reference to H5Aopen_by_name' ../channelflow/libchflow.so: undefined reference toH5T_STD_I32BE_g’
…/channelflow/libchflow.so: undefined reference to H5Aget_space' ../channelflow/libchflow.so: undefined reference toH5Sget_simple_extent_ndims’
…/channelflow/libchflow.so: undefined reference to H5T_STD_U32BE_g' ../channelflow/libchflow.so: undefined reference toH5T_STD_U64LE_g’
…/channelflow/libchflow.so: undefined reference to curl_easy_cleanup' ../channelflow/libchflow.so: undefined reference toH5T_IEEE_F64BE_g’
…/channelflow/libchflow.so: undefined reference to H5Tset_size' ../channelflow/libchflow.so: undefined reference toH5P_CLS_GROUP_CREATE_ID_g’
…/channelflow/libchflow.so: undefined reference to H5DSget_num_scales' ../channelflow/libchflow.so: undefined reference toH5T_STD_I8LE_g’
…/channelflow/libchflow.so: undefined reference to H5Dopen1' ../channelflow/libchflow.so: undefined reference toH5Tarray_create1’
…/channelflow/libchflow.so: undefined reference to H5Fget_obj_count' ../channelflow/libchflow.so: undefined reference toH5Adelete’
…/channelflow/libchflow.so: undefined reference to H5Aget_type' ../channelflow/libchflow.so: undefined reference toH5Fcreate’
…/channelflow/libchflow.so: undefined reference to H5Pclose' ../channelflow/libchflow.so: undefined reference toH5T_STD_I32LE_g’
…/channelflow/libchflow.so: undefined reference to H5Screate_simple' ../channelflow/libchflow.so: undefined reference toH5Pset_fapl_core’
…/channelflow/libchflow.so: undefined reference to H5Tcommit1' ../channelflow/libchflow.so: undefined reference toH5Pget_nfilters’
…/channelflow/libchflow.so: undefined reference to H5Sselect_hyperslab' ../channelflow/libchflow.so: undefined reference toH5DSset_scale’
…/channelflow/libchflow.so: undefined reference to H5DSattach_scale' ../channelflow/libchflow.so: undefined reference toH5T_NATIVE_DOUBLE_g’
…/channelflow/libchflow.so: undefined reference to H5Pset_fill_time' ../channelflow/libchflow.so: undefined reference toH5Sget_simple_extent_dims’
…/channelflow/libchflow.so: undefined reference to H5Tget_array_dims1' ../channelflow/libchflow.so: undefined reference toH5P_CLS_DATASET_XFER_ID_g’
…/channelflow/libchflow.so: undefined reference to H5T_C_S1_g' ../channelflow/libchflow.so: undefined reference toH5T_STD_U8LE_g’
…/channelflow/libchflow.so: undefined reference to H5Lexists' ../channelflow/libchflow.so: undefined reference toH5Pget_version’
…/channelflow/libchflow.so: undefined reference to H5Tvlen_create' ../channelflow/libchflow.so: undefined reference toH5Dopen2’
…/channelflow/libchflow.so: undefined reference to H5Tcopy' ../channelflow/libchflow.so: undefined reference toH5Dget_type’
…/channelflow/libchflow.so: undefined reference to H5T_NATIVE_ULLONG_g' ../channelflow/libchflow.so: undefined reference toH5Pset_filter’
…/channelflow/libchflow.so: undefined reference to H5Screate' ../channelflow/libchflow.so: undefined reference toH5Gget_objtype_by_idx’
…/channelflow/libchflow.so: undefined reference to H5Pget_filter2' ../channelflow/libchflow.so: undefined reference toH5T_NATIVE_UINT_g’
…/channelflow/libchflow.so: undefined reference to H5T_IEEE_F32LE_g' ../channelflow/libchflow.so: undefined reference toH5T_STD_I16BE_g’
…/channelflow/libchflow.so: undefined reference to H5Pget_link_creation_order' ../channelflow/libchflow.so: undefined reference toH5Tget_super’
…/channelflow/libchflow.so: undefined reference to H5T_NATIVE_FLOAT_g' ../channelflow/libchflow.so: undefined reference toH5Pset_attr_creation_order’
…/channelflow/libchflow.so: undefined reference to H5Eset_auto2' ../channelflow/libchflow.so: undefined reference toH5Pset_libver_bounds’
…/channelflow/libchflow.so: undefined reference to H5Dget_access_plist' ../channelflow/libchflow.so: undefined reference toH5T_STD_U8BE_g’
…/channelflow/libchflow.so: undefined reference to H5Pset_shuffle' ../channelflow/libchflow.so: undefined reference toH5Aopen_name’
…/channelflow/libchflow.so: undefined reference to curl_easy_setopt' ../channelflow/libchflow.so: undefined reference toH5Aread’
…/channelflow/libchflow.so: undefined reference to H5Pset_file_image' ../channelflow/libchflow.so: undefined reference toH5Pset_dxpl_mpio’
…/channelflow/libchflow.so: undefined reference to H5Tget_order' ../channelflow/libchflow.so: undefined reference tocurl_global_init’
…/channelflow/libchflow.so: undefined reference to H5P_CLS_DATASET_CREATE_ID_g' ../channelflow/libchflow.so: undefined reference toH5Tget_nmembers’
…/channelflow/libchflow.so: undefined reference to H5T_STD_I64LE_g' ../channelflow/libchflow.so: undefined reference toH5Gget_create_plist’
…/channelflow/libchflow.so: undefined reference to H5Aget_num_attrs' ../channelflow/libchflow.so: undefined reference toH5Sclose’
…/channelflow/libchflow.so: undefined reference to H5Tget_array_ndims' ../channelflow/libchflow.so: undefined reference toH5Pset_fill_value’
…/channelflow/libchflow.so: undefined reference to H5T_STD_U32LE_g' ../channelflow/libchflow.so: undefined reference toH5Sget_simple_extent_type’
…/channelflow/libchflow.so: undefined reference to H5open' ../channelflow/libchflow.so: undefined reference toH5DSiterate_scales’
…/channelflow/libchflow.so: undefined reference to H5get_libversion' ../channelflow/libchflow.so: undefined reference toH5Eset_auto1’
…/channelflow/libchflow.so: undefined reference to H5Pset_chunk' ../channelflow/libchflow.so: undefined reference toH5Oclose’
…/channelflow/libchflow.so: undefined reference to H5P_CLS_FILE_CREATE_ID_g' ../channelflow/libchflow.so: undefined reference toH5Tclose’
…/channelflow/libchflow.so: undefined reference to H5Aopen_idx' ../channelflow/libchflow.so: undefined reference toH5Sselect_none’
…/channelflow/libchflow.so: undefined reference to H5T_NATIVE_SCHAR_g' ../channelflow/libchflow.so: undefined reference tocurl_global_cleanup’
…/channelflow/libchflow.so: undefined reference to H5Iinc_ref' ../channelflow/libchflow.so: undefined reference toH5Gopen2’
…/channelflow/libchflow.so: undefined reference to H5Pset_szip' ../channelflow/libchflow.so: undefined reference toH5Pget_fill_value’
…/channelflow/libchflow.so: undefined reference to H5Tenum_create' ../channelflow/libchflow.so: undefined reference toH5T_NATIVE_USHORT_g’
…/channelflow/libchflow.so: undefined reference to H5Eget_auto1' ../channelflow/libchflow.so: undefined reference toH5Dwrite’
…/channelflow/libchflow.so: undefined reference to H5Dclose' ../channelflow/libchflow.so: undefined reference toH5T_IEEE_F32BE_g’
…/channelflow/libchflow.so: undefined reference to H5Tget_class' ../channelflow/libchflow.so: undefined reference toH5Tcreate’
…/channelflow/libchflow.so: undefined reference to H5P_CLS_FILE_ACCESS_ID_g' ../channelflow/libchflow.so: undefined reference toH5Fclose’
…/channelflow/libchflow.so: undefined reference to H5Lmove' ../channelflow/libchflow.so: undefined reference toH5Gget_num_objs’
…/channelflow/libchflow.so: undefined reference to H5Gclose' ../channelflow/libchflow.so: undefined reference toH5Dcreate2’
…/channelflow/libchflow.so: undefined reference to H5T_STD_I64BE_g' ../channelflow/libchflow.so: undefined reference toH5Aget_name’
…/channelflow/libchflow.so: undefined reference to `H5Pset_fapl_mpio’
collect2: error: ld returned 1 exit status
make[2]: *** [programs/continuesoln] Error 1
make[1]: *** [programs/CMakeFiles/continuesoln_app.dir/all] Error 2

I am looking for suggestions.
Thank you.

2

Hi hemata,
Is CMake able to find the library at the correct location? Do you have any error/worning after running cmake command?
Could you check that variable HDF5_INCLUDE_DIR and HDF5_LIBRARY in the build directory, CMakeCache.txt, are pointing to the correct path?
Best,
Mirko

3

Hi Mirko,

I have tried running cmake but the configuration fails.Please find below my input and output:

INPUT:
cmake /home/arslan/channelflow -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/home/arslan -DFFTW_INCLUDE_DIR=/home/arslan/libs/fftw-3.3.8/include -DFFTW_LIBRARY=/home/arslan/libs/fftw-3.3.8/lib/libfftw3.a -DUSE_MPI=ON -DWITH_HDF5CXX=ON

OUTPUT:
CMake Error in /home/arslan/channelflow/build/CMakeFiles/CMakeTmp/CMakeLists.txt:
Imported target “MPI::MPI_C” includes non-existent path

"/opt/intel-2019/intelpython3/intel64/include"

in its INTERFACE_INCLUDE_DIRECTORIES. Possible reasons include:

  • The path was deleted, renamed, or moved to another location.

  • An install or uninstall procedure did not complete successfully.

  • The installation package was faulty and references files it does not
    provide.

CMake Error at /usr/local/share/cmake-3.12/Modules/FindMPI.cmake:1182 (try_compile):
Failed to generate test project build system.
Call Stack (most recent call first):
/usr/local/share/cmake-3.12/Modules/FindMPI.cmake:1223 (_MPI_try_staged_settings)
/usr/local/share/cmake-3.12/Modules/FindMPI.cmake:1483 (_MPI_check_lang_works)
CMakeLists.txt:109 (find_package)

– Configuring incomplete, errors occurred!