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An error occurs when linking mkl pardiso using cmake in linux.

Donghee
Beginner
1,117 Views

I am trying to compile a program that uses both the blas function and the pardiso function.

However, it works fine on Windows, but a link error occurs on Linux.

And if comment out pardiso in the code below, the link works fine, but if  use pardiso, a link error occurs.

It seems to work well when using only blas, so when using pardiso, there seems to be additional work to be done, but I have no idea what it is.

 

I am linking the static version library of mkl, and I am using Parallel Studio 2019 Update5 Cluster Edition.

 

Below is my code.

==========================================================

#include <iostream>
#include "mkl.h"

using namespace std;

void gmatgvec_mkl(const double a[], const double b[], const int m, const int n, double c[])
{
const double alpha = 1.0;
const double beta = 0.0;

if (m == 0 || n == 0) return;

cblas_dgemv(CblasColMajor, CblasNoTrans,
m, n, alpha, &a[0], m, &b[0], 1, beta, &c[0], 1);
}

int main(int argc, char* argv[])
{
cout << "Hello CMake. - project 1" << endl;

double matA[2 * 2];
double vecB[2];
double vecC[2];

matA[0] = 1.0;
matA[1] = 2.0;
matA[2] = 3.0;
matA[3] = 4.0;

vecB[0] = 5.0;
vecB[1] = 6.0;

gmatgvec_mkl(matA, vecB, 2, 2, vecC);

cout << "vecC[0] = " << vecC[0] << endl;
cout << "vecC[1] = " << vecC[1] << endl;

if (argc > 10) {
PARDISO(NULL, NULL, NULL,
NULL, NULL, NULL, NULL,
NULL, NULL, NULL, NULL,
NULL, NULL, NULL, NULL,
NULL);
}

return 0;
}

==========================================================

 

Below is my cmake file.

==========================================================

CMAKE_MINIMUM_REQUIRED (VERSION 2.8.12)

IF(NOT WIN32)
SET(CMAKE_C_COMPILER "$ENV{HOME}/intel/bin/icc")
SET(CMAKE_CXX_COMPILER "$ENV{HOME}/intel/bin/icpc")

SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -v")
SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,--no-undefined")
ENDIF()

PROJECT ("CMakeMKL")

IF(WIN32)
SET(MKL_INCLUDE "C:\\Program Files (x86)\\IntelSWTools\\compilers_and_libraries_2019.5.281\\windows\\mkl\\include")
SET(MKL_LIBRARY "C:\\Program Files (x86)\\IntelSWTools\\compilers_and_libraries_2019.5.281\\windows\\mkl\\lib\\intel64")
SET(ICPC_LIBRARY "C:\\Program Files (x86)\\IntelSWTools\\compilers_and_libraries_2019.5.281\\windows\\compiler\\lib\\intel64")
ELSE()
SET(MKL_INCLUDE "$ENV{HOME}/intel/mkl/include")
SET(MKL_LIBRARY "$ENV{HOME}/intel/mkl/lib/intel64")
SET(ICPC_LIBRARY "$ENV{HOME}/intel/lib/intel64")
ENDIF()

ADD_EXECUTABLE (${PROJECT_NAME}
CMakeProject1.cpp
)

TARGET_INCLUDE_DIRECTORIES(${PROJECT_NAME} PUBLIC
${MKL_INCLUDE}
)

IF(WIN32)
TARGET_LINK_LIBRARIES(${PROJECT_NAME} ${MKL_LIBRARY}\\mkl_intel_lp64.lib)
TARGET_LINK_LIBRARIES(${PROJECT_NAME} ${MKL_LIBRARY}\\mkl_intel_thread.lib)
TARGET_LINK_LIBRARIES(${PROJECT_NAME} ${MKL_LIBRARY}\\mkl_core.lib)
TARGET_LINK_LIBRARIES(${PROJECT_NAME} ${ICPC_LIBRARY}\\libiomp5md.lib)
ELSE()
#SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,-rpath=${MKL_LIBRARY}")
#SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,-rpath=${ICPC_LIBRARY}")
#SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,-rpath-link=${MKL_LIBRARY}")
#SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,-rpath-link=${ICPC_LIBRARY}")
#SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,--start-group ${MKL_LIBRARY}/libmkl_intel_lp64.a ${MKL_LIBRARY}/libmkl_intel_thread.a ${MKL_LIBRARY}/libmkl_core.a -Wl,--end-group -liomp5 -lpthread -lm -ldl")

TARGET_LINK_LIBRARIES(${PROJECT_NAME} ${MKL_LIBRARY}/libmkl_intel_lp64.a)
TARGET_LINK_LIBRARIES(${PROJECT_NAME} ${MKL_LIBRARY}/libmkl_intel_thread.a)
TARGET_LINK_LIBRARIES(${PROJECT_NAME} ${MKL_LIBRARY}/libmkl_core.a)
TARGET_LINK_LIBRARIES(${PROJECT_NAME} ${ICPC_LIBRARY}/libiomp5.a)

TARGET_LINK_LIBRARIES(${PROJECT_NAME} pthread)
TARGET_LINK_LIBRARIES(${PROJECT_NAME} dl)
TARGET_LINK_LIBRARIES(${PROJECT_NAME} m)
ENDIF()

===================================================

 

 

Below is the linker error message.

==========================================================

[1/2] Building CXX object CMakeFiles/CMakeMKL.dir/CMakeProject1.cpp.o
[2/2] Linking CXX executable CMakeMKL
FAILED: CMakeMKL
: && /home/dbae/intel/bin/icpc -g -v -Wl,--no-undefined -rdynamic CMakeFiles/CMakeMKL.dir/CMakeProject1.cpp.o -o CMakeMKL /home/dbae/intel/mkl/lib/intel64/libmkl_intel_lp64.a /home/dbae/intel/mkl/lib/intel64/libmkl_intel_thread.a /home/dbae/intel/mkl/lib/intel64/libmkl_core.a /home/dbae/intel/lib/intel64/libiomp5.a -lpthread -ldl -lm && :
icpc version 19.0.5.281 (gcc version 4.8.5 compatibility)
/home/dbae/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom -mGLOB_em64t=TRUE -mP1OPT_version=19.0-intel64 -mGLOB_diag_file=CMakeFiles/CMakeMKL.dir/CMakeProject1.cpp.diag -mGLOB_long_size_64 -mGLOB_routine_pointer_size_64 -mP1OPT_print_version=FALSE -mCG_use_gas_got_workaround=F -mP2OPT_align_option_used=TRUE -mGLOB_gcc_version=485 "-mGLOB_options_string=-g -v -Wl,--no-undefined -rdynamic -o CMakeMKL -lpthread -ldl -lm" -mGLOB_cxx_limited_range=FALSE -mCG_extend_parms=FALSE -mGLOB_compiler_bin_directory=/home/dbae/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64 -mP3OPT_emit_line_numbers -mGLOB_debug_target=GLOB_DEBUG_TARGET_ALL -mDEBUG_info_level=2 -mDEBUG_use_indirect_strings=TRUE -mIPOPT_ninl_debug_info=TRUE -mDEBUG_emit_dwarf_inline_info=TRUE -mDEBUG_debug_ranges=TRUE -mGLOB_debug_format=GLOB_DEBUG_FORMAT_DWARF40 -mGLOB_as_output_backup_file_name=/tmp/icpcGA3opZas_.s -mGLOB_dashboard_use_source_name -mIPOPT_activate -mGLOB_product_id_code=0x22006d90 -mP3OPT_use_mspp_call_convention -mP2OPT_subs_out_of_bound=FALSE -mP2OPT_disam_type_based_disam=2 -mP2OPT_disam_assume_ansi_c -mP2OPT_checked_disam_ansi_alias=TRUE -mGLOB_ansi_alias -mPGOPTI_value_profile_use=T -mGLOB_opt_report_use_source_name -mP2OPT_il0_array_sections=TRUE -mGLOB_offload_mode=1 -mP2OPT_offload_unique_var_string=icpc0174938581JqCV9F -mP2OPT_hlo -mP2OPT_hpo_rtt_control=0 -mIPOPT_args_in_regs=0 -mP2OPT_disam_assume_nonstd_intent_in=FALSE -mGLOB_imf_mapping_library=/home/dbae/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/libiml_attr.so -mP2OPT_hlo_embed_loopinfo -mPGOPTI_gen_threadsafe_level=0 -mIPOPT_link -mIPOPT_ipo_activate -mIPOPT_mo_activate -mIPOPT_source_files_list=/tmp/icpcslisxQwR0s -mIPOPT_mo_global_data -mIPOPT_link_script_file=/tmp/icpcscriptuZD6ce "-mIPOPT_cmdline_link="/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crt1.o" "/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crti.o" "/usr/lib/gcc/x86_64-redhat-linux/4.8.5/crtbegin.o" "-export-dynamic" "--eh-frame-hdr" "--build-id" "-dynamic-linker" "/lib64/ld-linux-x86-64.so.2" "-m" "elf_x86_64" "-o" "CMakeMKL" "-L/home/dbae/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin" "-L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/" "-L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64" "-L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/" "-L/lib/../lib64" "-L/lib/../lib64/" "-L/usr/lib/../lib64" "-L/usr/lib/../lib64/" "-L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../" "-L/lib64" "-L/lib/" "-L/usr/lib64" "-L/usr/lib" "--no-undefined" "CMakeFiles/CMakeMKL.dir/CMakeProject1.cpp.o" "/home/dbae/intel/mkl/lib/intel64/libmkl_intel_lp64.a" "/home/dbae/intel/mkl/lib/intel64/libmkl_intel_thread.a" "/home/dbae/intel/mkl/lib/intel64/libmkl_core.a" "/home/dbae/intel/lib/intel64/libiomp5.a" "-lpthread" "-ldl" "-L/home/dbae/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin" "-Bstatic" "-limf" "-Bdynamic" "-lm" "-Bdynamic" "-Bstatic" "-limf" "-lsvml" "-lirng" "-Bdynamic" "-lstdc++" "-lm" "-Bstatic" "-lipgo" "-ldecimal" "--as-needed" "-Bdynamic" "-lcilkrts" "--no-as-needed" "-lstdc++" "-lgcc" "-lgcc_s" "-Bstatic" "-lirc" "-lsvml" "-Bdynamic" "-lc" "-lgcc" "-lgcc_s" "-Bstatic" "-lirc_s" "-Bdynamic" "-ldl" "-lc" "/usr/lib/gcc/x86_64-redhat-linux/4.8.5/crtend.o" "/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crtn.o"" -mIPOPT_il_in_obj -mIPOPT_ipo_activate_warn=FALSE -mIPOPT_obj_output_file_name=/tmp/ipo_icpcrAJlQT.o -mIPOPT_whole_archive_fixup_file_name=/tmp/icpcwarchn1fqPv -mGLOB_linker_version=2.27 -mGLOB_linker=ld -mGLOB_driver_tempfile_name=/tmp/icpctempfileuXX82g -mP3OPT_asm_target=P3OPT_ASM_TARGET_GAS -mGLOB_async_unwind_tables=TRUE -mGLOB_obj_output_file=/tmp/ipo_icpcrAJlQT.o -mGLOB_source_dialect=GLOB_SOURCE_DIALECT_NONE -mP1OPT_source_file_name=ipo_out.c CMakeFiles/CMakeMKL.dir/CMakeProject1.cpp.o -mIPOPT_object_files=T -mIPOPT_assembly_files=/tmp/icpcalisUlmkeq -mIPOPT_generated_tempfiles=/tmp/icpcelisNDkoqb -mIPOPT_embedded_object_base_name=/tmp/icpceobj8tcvCW -mIPOPT_cmdline_link_new_name=/tmp/icpcllispX7EOH
ld /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crt1.o /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.8.5/crtbegin.o -export-dynamic --eh-frame-hdr --build-id -dynamic-linker /lib64/ld-linux-x86-64.so.2 -m elf_x86_64 -o CMakeMKL -L/home/dbae/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/ -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/ -L/lib/../lib64 -L/lib/../lib64/ -L/usr/lib/../lib64 -L/usr/lib/../lib64/ -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../ -L/lib64 -L/lib/ -L/usr/lib64 -L/usr/lib --no-undefined CMakeFiles/CMakeMKL.dir/CMakeProject1.cpp.o /home/dbae/intel/mkl/lib/intel64/libmkl_intel_lp64.a /home/dbae/intel/mkl/lib/intel64/libmkl_intel_thread.a /home/dbae/intel/mkl/lib/intel64/libmkl_core.a /home/dbae/intel/lib/intel64/libiomp5.a -lpthread -ldl -L/home/dbae/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin -Bstatic -limf -Bdynamic -lm -Bdynamic -Bstatic -limf -lsvml -lirng -Bdynamic -lstdc++ -lm -Bstatic -lipgo -ldecimal --as-needed -Bdynamic -lcilkrts --no-as-needed -lstdc++ -lgcc -lgcc_s -Bstatic -lirc -lsvml -Bdynamic -lc -lgcc -lgcc_s -Bstatic -lirc_s -Bdynamic -ldl -lc /usr/lib/gcc/x86_64-redhat-linux/4.8.5/crtend.o /usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crtn.o
/home/dbae/intel/mkl/lib/intel64/libmkl_core.a(pardiso_lp64.o): In function `mkl_pds_lp64_pardiso':
pardiso_lp64_h.f:(.text+0x18a): undefined reference to `mkl_pds_lp64_pds_get_omp_num_threads'
pardiso_lp64_h.f:(.text+0x198): undefined reference to `mkl_pds_lp64_pds_get_num_threads'
pardiso_lp64_h.f:(.text+0x1a4): undefined reference to `mkl_pds_lp64_pds_get_omp_num_threads'
pardiso_lp64_h.f:(.text+0x1b0): undefined reference to `mkl_pds_lp64_pds_get_num_threads'
pardiso_lp64_h.f:(.text+0x31b): undefined reference to `mkl_pds_lp64_get_dynamic_pardiso'
pardiso_lp64_h.f:(.text+0x351): undefined reference to `mkl_pds_lp64_pardiso_max_threads'
/home/dbae/intel/mkl/lib/intel64/libmkl_core.a(pds_pardiso_lp64.o): In function `mkl_pds_lp64_dist_pardiso':
pds_pardiso.c:(.text+0x828): undefined reference to `mkl_pds_lp64_pds_refinement_real'
pds_pardiso.c:(.text+0x8ed): undefined reference to `mkl_pds_lp64_pds_refinement_cmplx'
/home/dbae/intel/mkl/lib/intel64/libmkl_core.a(pds_factorization_lp64.o): In function `mkl_pds_lp64_pds_factorization':
pds_factorization.c:(.text+0x25): undefined reference to `mkl_pds_lp64_pds_copy_a2l_value_omp_cmplx'
pds_factorization.c:(.text+0x2f): undefined reference to `mkl_pds_lp64_pds_copy_a2l_value_omp_real'
pds_factorization.c:(.text+0x86): undefined reference to `mkl_pds_lp64_pds_fct_omp_driver_cmplx'
pds_factorization.c:(.text+0x95): undefined reference to `mkl_pds_lp64_pds_fct_omp_driver_real'
/home/dbae/intel/mkl/lib/intel64/libmkl_core.a(pardiso_c_lp64.o): In function `mkl_pds_lp64_pardiso_c':
pardiso_c.c:(.text+0x8df9): undefined reference to `mkl_pds_lp64_convert_to_vbsr'
/home/dbae/intel/mkl/lib/intel64/libmkl_core.a(kernel_dispatch_lp64.o): In function `mkl_pds_lp64_kernel_dispatch':
kernel_dispatch.c:(.text+0x2ff): undefined reference to `mkl_pds_lp64_pds_slv_nrhs_seq_real'
kernel_dispatch.c:(.text+0x37f): undefined reference to `mkl_pds_lp64_pds_slv_nrhs_par_real'
kernel_dispatch.c:(.text+0x408): undefined reference to `mkl_pds_lp64_pds_slv_nrhs_seq_cmplx'
kernel_dispatch.c:(.text+0x485): undefined reference to `mkl_pds_lp64_pds_slv_nrhs_par_cmplx'
kernel_dispatch.c:(.text+0x57c): undefined reference to `mkl_pds_lp64_iter_ref_seq_nrhs_real'
kernel_dispatch.c:(.text+0x5fa): undefined reference to `mkl_pds_lp64_iter_ref_par_nrhs_real'
kernel_dispatch.c:(.text+0x692): undefined reference to `mkl_pds_lp64_iter_ref_seq_nrhs_cmplx'
kernel_dispatch.c:(.text+0x70d): undefined reference to `mkl_pds_lp64_iter_ref_par_nrhs_cmplx'
kernel_dispatch.c:(.text+0x80d): undefined reference to `mkl_pds_lp64_pds_sym_indef_diag_fct_slv_seq_cmplx'
kernel_dispatch.c:(.text+0x8ad): undefined reference to `mkl_pds_lp64_pds_sym_indef_bk_fct_slv_seq_cmplx'
kernel_dispatch.c:(.text+0x95b): undefined reference to `mkl_pds_lp64_pds_sym_indef_diag_fct_slv_cmplx'
kernel_dispatch.c:(.text+0x9fb): undefined reference to `mkl_pds_lp64_pds_sym_indef_bk_fct_slv_cmplx'
kernel_dispatch.c:(.text+0xaa8): undefined reference to `mkl_pds_lp64_pds_her_pos_fct_slv_seq_cmplx'
kernel_dispatch.c:(.text+0xb48): undefined reference to `mkl_pds_lp64_pds_her_pos_fct_slv_cmplx'
kernel_dispatch.c:(.text+0xc09): undefined reference to `mkl_pds_lp64_pds_unsym_fct_slv_seq_cmplx'
kernel_dispatch.c:(.text+0xcbd): undefined reference to `mkl_pds_lp64_pds_unsym_fct_slv_cmplx'
kernel_dispatch.c:(.text+0xd60): undefined reference to `mkl_pds_lp64_pds_sym_pos_fct_slv_seq_real'
kernel_dispatch.c:(.text+0xdf6): undefined reference to `mkl_pds_lp64_pds_sym_pos_fct_slv_real'
kernel_dispatch.c:(.text+0xea2): undefined reference to `mkl_pds_lp64_pds_unsym_fct_slv_seq_real'
kernel_dispatch.c:(.text+0xf38): undefined reference to `mkl_pds_lp64_pds_unsym_fct_slv_t_seq_real'
kernel_dispatch.c:(.text+0xfd7): undefined reference to `mkl_pds_lp64_pds_unsym_fct_slv_real'
kernel_dispatch.c:(.text+0x106d): undefined reference to `mkl_pds_lp64_pds_unsym_fct_slv_t_real'
kernel_dispatch.c:(.text+0x111e): undefined reference to `mkl_pds_lp64_pds_sym_indef_diag_fct_slv_seq_real'

.

.

.

.

 

==========================================================

 

 

No matter how much I google it, it doesn't fix it. please help me please!

0 Kudos
1 Solution
VidyalathaB_Intel
Moderator
1,102 Views

Hi,

 

Thanks for reaching out to us.

>>but a link error occurs on Linux.

I could reproduce the issue from my end with the provided CMake file.

Since the issue comes during the linking stage, I tried modifying your CMakeLists.txt at the target_link_libraries command as shown below (you can comment out the remaining target_link_libraries commands (for Linux) and just insert this single line.

 

TARGET_LINK_LIBRARIES(${PROJECT_NAME} "-Wl,--start-group" ${MKL_LIBRARY}/libmkl_intel_lp64.a ${MKL_LIBRARY}/libmkl_intel_thread.a ${MKL_LIBRARY}/libmkl_core.a "-Wl,--end-group -liomp5 -lpthread -lm -ldl")

 

After the above change, it works successfully. I don't see the linking errors which we saw before.

Here is the output :

VidyalathaB_Intel_0-1651738965910.png

 

Please try it and let me know if you still face any issues.

 

Regards,

Vidya.

 

View solution in original post

0 Kudos
3 Replies
VidyalathaB_Intel
Moderator
1,103 Views

Hi,

 

Thanks for reaching out to us.

>>but a link error occurs on Linux.

I could reproduce the issue from my end with the provided CMake file.

Since the issue comes during the linking stage, I tried modifying your CMakeLists.txt at the target_link_libraries command as shown below (you can comment out the remaining target_link_libraries commands (for Linux) and just insert this single line.

 

TARGET_LINK_LIBRARIES(${PROJECT_NAME} "-Wl,--start-group" ${MKL_LIBRARY}/libmkl_intel_lp64.a ${MKL_LIBRARY}/libmkl_intel_thread.a ${MKL_LIBRARY}/libmkl_core.a "-Wl,--end-group -liomp5 -lpthread -lm -ldl")

 

After the above change, it works successfully. I don't see the linking errors which we saw before.

Here is the output :

VidyalathaB_Intel_0-1651738965910.png

 

Please try it and let me know if you still face any issues.

 

Regards,

Vidya.

 

0 Kudos
Donghee
Beginner
1,064 Views

Thank you so much Vidya!

I'm very happy that the problem that has been going on for several weeks has been resolved!

0 Kudos
VidyalathaB_Intel
Moderator
1,060 Views

Hi,


Thanks for accepting our solution and glad to know that it worked.

As the issue is resolved we are closing this thread. Please post a new question if you need any additional assistance from Intel as this thread will no longer be monitored.


Have a Great Day!


Regards,

Vidya.


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Reply