MATLAB and MKL FFTW wrapper

dr_sillekens — Wed, 24 Feb 2021 14:36:44 GMT

I am trying to use the MKL FFTW wrapper, however, I am stuck at something that doesn't provide google info.

It is compiling a matlab function from c. The c code expects FFTW.

Linux xxxxx 3.10.0-1160.11.1.el7.x86_64 #1 SMP Fri Dec 18 16:34:56 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

MATLAB R2020a

oneAPI MKL 2021

>> mex sspropc.c -v -I${MKLROOT}/include/fftw -L${MKLROOT}/lib/intel64 -L${MKLROOT}/interfaces/fftw3 ${MKLROOT}/lib/intel64/libmkl_intel_ilp64.a ${MKLROOT}/lib/intel64/libmkl_gnu_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_cdft_core.a LDFLAGS="$LDFLAGS -lgomp -lpthread -lm -ldl" CFLAGS="$CFLAGS -DMKL_ILP64 -m64 " Verbose mode is on. ... Looking for compiler 'gcc' ... ... Executing command 'which gcc' ...Yes ('/usr/bin/gcc'). ... Executing command 'gcc -dumpversion' ...Yes ('4.8.5'). ... Executing command 'gcc -print-file-name=libstdc++.so' ...Yes ('/usr/lib/gcc/x86_64-redhat-linux/4.8.5/libstdc++.so'). Found installed compiler 'gcc'. Options file details ------------------------------------------------------------------- Compiler location: /usr/bin/gcc Options file: /apps/matlab-r2020a/bin/glnxa64/mexopts/gcc_glnxa64.xml CMDLINE2 : /usr/bin/gcc -pthread -Wl,--no-undefined -Wl,-rpath-link,/apps/matlab-r2020a/bin/glnxa64 -lgomp -lpthread -lm -ldl -shared -O -Wl,--version-script,"/apps/matlab-r2020a/extern/lib/glnxa64/c_exportsmexfileversion.map" /tmp/mex_9932417573564106_21669/sspropc.o /tmp/mex_9932417573564106_21669/c_mexapi_version.o ${MKLROOT}/lib/intel64/libmkl_intel_ilp64.a ${MKLROOT}/lib/intel64/libmkl_gnu_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_cdft_core.a -L${MKLROOT}/lib/intel64 -L${MKLROOT}/interfaces/fftw3 -L"/apps/matlab-r2020a/bin/glnxa64" -lmx -lmex -lmat -lm -lstdc++ -o sspropc.mexa64 CC : /usr/bin/gcc DEFINES : -DMATLAB_DEFAULT_RELEASE=R2017b -DUSE_MEX_CMD -D_GNU_SOURCE -DMATLAB_MEX_FILE MATLABMEX : -DMATLAB_MEX_FILE CFLAGS : -fexceptions -fPIC -fno-omit-frame-pointer -pthread -DMKL_ILP64 -m64 INCLUDE : -I"${MKLROOT}/include/fftw" -I"/apps/matlab-r2020a/extern/include" -I"/apps/matlab-r2020a/simulink/include" COPTIMFLAGS : -O2 -fwrapv -DNDEBUG CDEBUGFLAGS : -g LD : /usr/bin/gcc LDFLAGS : -pthread -Wl,--no-undefined -Wl,-rpath-link,/apps/matlab-r2020a/bin/glnxa64 -lgomp -lpthread -lm -ldl LDTYPE : -shared FUNCTIONMAP : "/apps/matlab-r2020a/extern/lib/glnxa64/mexFunction.map" VERSIONMAP : "/apps/matlab-r2020a/extern/lib/glnxa64/c_exportsmexfileversion.map" LINKEXPORT : -Wl,--version-script,"/apps/matlab-r2020a/extern/lib/glnxa64/mexFunction.map" LINKEXPORTVER : -Wl,--version-script,"/apps/matlab-r2020a/extern/lib/glnxa64/c_exportsmexfileversion.map" LINKLIBS : ${MKLROOT}/lib/intel64/libmkl_intel_ilp64.a ${MKLROOT}/lib/intel64/libmkl_gnu_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_cdft_core.a -L${MKLROOT}/lib/intel64 -L${MKLROOT}/interfaces/fftw3 -L"/apps/matlab-r2020a/bin/glnxa64" -lmx -lmex -lmat -lm -lstdc++ LDOPTIMFLAGS : -O LDDEBUGFLAGS : -g MWCPPLIB : "/apps/matlab-r2020a/sys/os/glnxa64/libstdc++.so.6" OBJEXT : .o LDEXT : .mexa64 SETENV : CC="/usr/bin/gcc" CXX="g++" CFLAGS="-fexceptions -fPIC -fno-omit-frame-pointer -pthread -DMKL_ILP64 -m64 -DMATLAB_DEFAULT_RELEASE=R2017b -DUSE_MEX_CMD -D_GNU_SOURCE -DMATLAB_MEX_FILE " CXXFLAGS="-fexceptions -fPIC -fno-omit-frame-pointer -pthread -DMKL_ILP64 -m64 -std=c++11 -DMATLAB_DEFAULT_RELEASE=R2017b -DUSE_MEX_CMD -D_GNU_SOURCE -DMATLAB_MEX_FILE " COPTIMFLAGS="-O2 -fwrapv -DNDEBUG" CXXOPTIMFLAGS="-O2 -fwrapv -DNDEBUG" CDEBUGFLAGS="-g" CXXDEBUGFLAGS="-g" LD="/usr/bin/gcc" LDXX="g++" LDFLAGS="-pthread -Wl,--no-undefined -Wl,-rpath-link,/apps/matlab-r2020a/bin/glnxa64 -lgomp -lpthread -lm -ldl -shared ${MKLROOT}/lib/intel64/libmkl_intel_ilp64.a ${MKLROOT}/lib/intel64/libmkl_gnu_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_cdft_core.a -L${MKLROOT}/lib/intel64 -L${MKLROOT}/interfaces/fftw3 -L"/apps/matlab-r2020a/bin/glnxa64" -lmx -lmex -lmat -lm -lstdc++ -Wl,--version-script,"/apps/matlab-r2020a/extern/lib/glnxa64/mexFunction.map"" LDDEBUGFLAGS="-g" GCC : /usr/bin/gcc VER : 4.8.5 CPPLIBS : /usr/lib/gcc/x86_64-redhat-linux/4.8.5/libstdc++.so MATLABROOT : /apps/matlab-r2020a ARCH : glnxa64 SRC : "/home/uceeesi/code/ssprop-3.0.1/sspropc.c";"/apps/matlab-r2020a/extern/version/c_mexapi_version.c" OBJ : /tmp/mex_9932417573564106_21669/sspropc.o;/tmp/mex_9932417573564106_21669/c_mexapi_version.o OBJS : /tmp/mex_9932417573564106_21669/sspropc.o /tmp/mex_9932417573564106_21669/c_mexapi_version.o SRCROOT : /home/uceeesi/code/ssprop-3.0.1/sspropc DEF : /tmp/mex_9932417573564106_21669/sspropc.def EXP : "sspropc.exp" LIB : "sspropc.lib" EXE : sspropc.mexa64 ILK : "sspropc.ilk" MANIFEST : "sspropc.mexa64.manifest" TEMPNAME : sspropc EXEDIR : EXENAME : sspropc OPTIM : -O2 -fwrapv -DNDEBUG LINKOPTIM : -O CMDLINE1_0 : /usr/bin/gcc -c -DMATLAB_DEFAULT_RELEASE=R2017b -DUSE_MEX_CMD -D_GNU_SOURCE -DMATLAB_MEX_FILE -I"${MKLROOT}/include/fftw" -I"/apps/matlab-r2020a/extern/include" -I"/apps/matlab-r2020a/simulink/include" -fexceptions -fPIC -fno-omit-frame-pointer -pthread -DMKL_ILP64 -m64 -O2 -fwrapv -DNDEBUG "/home/uceeesi/code/ssprop-3.0.1/sspropc.c" -o /tmp/mex_9932417573564106_21669/sspropc.o CMDLINE1_1 : /usr/bin/gcc -c -DMATLAB_DEFAULT_RELEASE=R2017b -DUSE_MEX_CMD -D_GNU_SOURCE -DMATLAB_MEX_FILE -I"${MKLROOT}/include/fftw" -I"/apps/matlab-r2020a/extern/include" -I"/apps/matlab-r2020a/simulink/include" -fexceptions -fPIC -fno-omit-frame-pointer -pthread -DMKL_ILP64 -m64 -O2 -fwrapv -DNDEBUG "/apps/matlab-r2020a/extern/version/c_mexapi_version.c" -o /tmp/mex_9932417573564106_21669/c_mexapi_version.o ------------------------------------------------------------------- Building with 'gcc'. Warning: You are using gcc version '4.8.5-44)'. The version of gcc is not supported. The version currently supported with MEX is '6.3.x'. For a list of currently supported compilers see: https://www.mathworks.com/support/compilers/current_release. /usr/bin/gcc -c -DMATLAB_DEFAULT_RELEASE=R2017b -DUSE_MEX_CMD -D_GNU_SOURCE -DMATLAB_MEX_FILE -I"${MKLROOT}/include/fftw" -I"/apps/matlab-r2020a/extern/include" -I"/apps/matlab-r2020a/simulink/include" -fexceptions -fPIC -fno-omit-frame-pointer -pthread -DMKL_ILP64 -m64 -O2 -fwrapv -DNDEBUG "/home/uceeesi/code/ssprop-3.0.1/sspropc.c" -o /tmp/mex_9932417573564106_21669/sspropc.o /usr/bin/gcc -c -DMATLAB_DEFAULT_RELEASE=R2017b -DUSE_MEX_CMD -D_GNU_SOURCE -DMATLAB_MEX_FILE -I"${MKLROOT}/include/fftw" -I"/apps/matlab-r2020a/extern/include" -I"/apps/matlab-r2020a/simulink/include" -fexceptions -fPIC -fno-omit-frame-pointer -pthread -DMKL_ILP64 -m64 -O2 -fwrapv -DNDEBUG "/apps/matlab-r2020a/extern/version/c_mexapi_version.c" -o /tmp/mex_9932417573564106_21669/c_mexapi_version.o /usr/bin/gcc -pthread -Wl,--no-undefined -Wl,-rpath-link,/apps/matlab-r2020a/bin/glnxa64 -lgomp -lpthread -lm -ldl -shared -O -Wl,--version-script,"/apps/matlab-r2020a/extern/lib/glnxa64/c_exportsmexfileversion.map" /tmp/mex_9932417573564106_21669/sspropc.o /tmp/mex_9932417573564106_21669/c_mexapi_version.o ${MKLROOT}/lib/intel64/libmkl_intel_ilp64.a ${MKLROOT}/lib/intel64/libmkl_gnu_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_cdft_core.a -L${MKLROOT}/lib/intel64 -L${MKLROOT}/interfaces/fftw3 -L"/apps/matlab-r2020a/bin/glnxa64" -lmx -lmex -lmat -lm -lstdc++ -o sspropc.mexa64 Error using mex /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_avx512_mic_dfti_create_drmd.o): In function `commit': dfti_create_drmd.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_r2c_md_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_avx512_mic_dfti_create_dr1d.o): In function `commit': dfti_create_dr1d.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_r2c_1d_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_avx512_mic_dfti_create_dcmd.o): In function `commit': dfti_create_dcmd.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_c2c_md_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_avx512_mic_dfti_create_dc1d.o): In function `commit': dfti_create_dc1d.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_c2c_1d_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_avx512_dfti_create_drmd.o): In function `commit': dfti_create_drmd.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_r2c_md_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_avx512_dfti_create_dr1d.o): In function `commit': dfti_create_dr1d.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_r2c_1d_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_avx512_dfti_create_dcmd.o): In function `commit': dfti_create_dcmd.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_c2c_md_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_avx512_dfti_create_dc1d.o): In function `commit': dfti_create_dc1d.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_c2c_1d_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_avx2_dfti_create_drmd.o): In function `commit': dfti_create_drmd.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_r2c_md_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_avx2_dfti_create_dr1d.o): In function `commit': dfti_create_dr1d.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_r2c_1d_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_avx2_dfti_create_dcmd.o): In function `commit': dfti_create_dcmd.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_c2c_md_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_avx2_dfti_create_dc1d.o): In function `commit': dfti_create_dc1d.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_c2c_1d_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_avx_dfti_create_drmd.o): In function `commit': dfti_create_drmd.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_r2c_md_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_avx_dfti_create_dr1d.o): In function `commit': dfti_create_dr1d.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_r2c_1d_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_avx_dfti_create_dcmd.o): In function `commit': dfti_create_dcmd.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_c2c_md_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_avx_dfti_create_dc1d.o): In function `commit': dfti_create_dc1d.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_c2c_1d_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_mc3_dfti_create_drmd.o): In function `commit': dfti_create_drmd.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_r2c_md_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_mc3_dfti_create_dr1d.o): In function `commit': dfti_create_dr1d.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_r2c_1d_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_mc3_dfti_create_dcmd.o): In function `commit': dfti_create_dcmd.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_c2c_md_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_mc3_dfti_create_dc1d.o): In function `commit': dfti_create_dc1d.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_c2c_1d_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_mc_dfti_create_drmd.o): In function `commit': dfti_create_drmd.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_r2c_md_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_mc_dfti_create_dr1d.o): In function `commit': dfti_create_dr1d.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_r2c_1d_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_mc_dfti_create_dcmd.o): In function `commit': dfti_create_dcmd.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_c2c_md_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_mc_dfti_create_dc1d.o): In function `commit': dfti_create_dc1d.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_c2c_1d_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_def_dfti_create_drmd.o): In function `commit': dfti_create_drmd.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_r2c_md_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_def_dfti_create_dr1d.o): In function `commit': dfti_create_dr1d.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_r2c_1d_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_def_dfti_create_dcmd.o): In function `commit': dfti_create_dcmd.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_c2c_md_omp' /home/uceeesi/intel/oneapi/mkl/latest/lib/intel64/libmkl_core.a(_def_dfti_create_dc1d.o): In function `commit': dfti_create_dc1d.c:(.text+0x4): undefined reference to `mkl_dft_commit_node_d_c2c_1d_omp' collect2: error: ld returned 1 exit status

Re:MATLAB and MKL FFTW wrapper

RahulV_intel — Fri, 19 Mar 2021 06:31:17 GMT

Hi,

Could you please provide a small reproducer code and the build steps?

Also, specify your OS name and version.

Thanks,

Rahul

Re:MATLAB and MKL FFTW wrapper

Gennady_F_Intel — Fri, 19 Mar 2021 10:55:08 GMT

Is that FFTW3 wrappers for C?

Did you try to build this C code without mex file but using only icc/gcc compilers and the same linking mkl's line?

topic Re:MATLAB and MKL FFTW wrapper in Intel® oneAPI Math Kernel Library

MATLAB and MKL FFTW wrapper

Re:MATLAB and MKL FFTW wrapper

Re:MATLAB and MKL FFTW wrapper