[petsc-users] Pestc-matlab issue

Fri Jun 17 13:07:19 CDT 2022

  Please send configure.log and make.log to petsc-maint at mcs.anl.gov <mailto:petsc-maint at mcs.anl.gov> 


> On Jun 17, 2022, at 1:52 PM, Yongxiang Lei <leiyongxiang1205 at gmail.com> wrote:
> 
> Dear concerns,
> 
> I met such issues when I  confirm that my Matlab installation is finished. I am also sure that the g++ version is given. Could you please check this problem for me?  The related information is given as follows. 
> 
> Looking forward to hearing from you
> Best regards
> Xiang
> 
> >> mex -setup cpp
> MEX configured to use 'g++' for C++ language compilation.
> .........................................................................................................
> [ADS+u2192020 at cos8-25136ecf ~]$ g++ --version
> g++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-13)
> Copyright (C) 2018 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions.  There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
> .............................................................................................................
> export PETSC_DIR=$PWD
> export PETSC_ARCH=linux-debug
> ./configure \
>   --CC=$HOME/sfw/linux/openmpi-4.0.2/bin/mpicc \
>   --CXX=$HOME/sfw/linux/openmpi-4.0.2/bin/mpicxx \
>   --FC=$HOME/sfw/linux/openmpi-4.0.2/bin/mpif90 \
>   --with-debugging=1 \
>   --download-hypre=1 \
>   --download-fblaslapack=1 \
>   --with-x=0\
>   --with-matlab-dir=/home/ADS/u2192020/Matlab2022/ \
>   --with-matlab-engine=1 \
>   --with-matlab-engine-dir=/home/ADS/u2192020/Matlab2022/extern/engines/
> =========================================
> =========================================
> Now to check if the libraries are working do:
> make PETSC_DIR=/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB PETSC_ARCH=linux-debug check
> =========================================
> [ADS+u2192020 at cos8-25136ecf PETSc-MATLAB]$ make -j4 check
> Running check examples to verify correct installation
> Using PETSC_DIR=/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB and PETSC_ARCH=linux-debug
> gmake[3]: [/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/lib/petsc/conf/rules:320: ex19.PETSc] Error 2 (ignored)
> *******************Error detected during compile or link!*******************
> See http://www.mcs.anl.gov/petsc/documentation/faq.html <http://www.mcs.anl.gov/petsc/documentation/faq.html>
> /home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/src/snes/tutorials ex19
> *********************************************************************************
> /home/ADS/u2192020/sfw/linux/openmpi-4.0.2/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -g3 -O0  -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -g3 -O0    -I/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/include -I/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/linux-debug/include -I/home/ADS/u2192020/Matlab2022/extern/include     ex19.c  -Wl,-rpath,/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/linux-debug/lib -L/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/linux-debug/lib -Wl,-rpath,/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/linux-debug/lib -L/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/linux-debug/lib -Wl,-rpath,/home/ADS/u2192020/Matlab2022/bin/glnxa64 -L/home/ADS/u2192020/Matlab2022/bin/glnxa64 -Wl,-rpath,/home/ADS/u2192020/Matlab2022/extern/lib/glnxa64 -L/home/ADS/u2192020/Matlab2022/extern/lib/glnxa64 -Wl,-rpath,/home/ADS/u2192020/sfw/linux/openmpi-4.0.2/lib -L/home/ADS/u2192020/sfw/linux/openmpi-4.0.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/8 -L/usr/lib/gcc/x86_64-redhat-linux/8 -lpetsc -lHYPRE -lflapack -lfblas -lm -leng -lmex -lmx -lmat -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl -o ex19
> //home/ADS/u2192020/Matlab2022/bin/glnxa64/libmwopccore.so: undefined reference to `std::__cxx11::basic_ostringstream<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::basic_ostringstream()@GLIBCXX_3.4.26'
> //home/ADS/u2192020/Matlab2022/bin/glnxa64/libmwfoundation_matlabdata_matlab.so: undefined reference to `std::logic_error::logic_error(std::logic_error&&)@GLIBCXX_3.4.26'
> /home/ADS/u2192020/Matlab2022/bin/glnxa64/libmex.so: undefined reference to `std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::basic_ostringstream()@GLIBCXX_3.4.26'
> /home/ADS/u2192020/Matlab2022/bin/glnxa64/libmx.so: undefined reference to `std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::basic_stringstream()@GLIBCXX_3.4.26'
> collect2: error: ld returned 1 exit status
> gmake[4]: *** [<builtin>: ex19] Error 1
> 1,5c1,10
> < lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
> <   0 SNES Function norm 0.0406612 
> <   1 SNES Function norm 4.12227e-06 
> <   2 SNES Function norm 6.098e-11 
> < Number of SNES iterations = 2
> ---
> > --------------------------------------------------------------------------
> > mpiexec was unable to launch the specified application as it could not access
> > or execute an executable:
> > 
> > Executable: ./ex19
> > Node: cos8-25136ecf
> > 
> > while attempting to start process rank 0.
> > --------------------------------------------------------------------------
> > 2 total processes failed to start
> /home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/src/snes/tutorials
> Possible problem with ex19 running with hypre, diffs above
> =========================================
> gmake[3]: [/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/lib/petsc/conf/rules:374: ex5f.PETSc] Error 2 (ignored)
> *******************Error detected during compile or link!*******************
> See http://www.mcs.anl.gov/petsc/documentation/faq.html <http://www.mcs.anl.gov/petsc/documentation/faq.html>
> /home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/src/snes/tutorials ex5f
> *********************************************************
> /home/ADS/u2192020/sfw/linux/openmpi-4.0.2/bin/mpif90 -fPIC -Wall -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -g -O0   -fPIC -Wall -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -g -O0    -I/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/include -I/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/linux-debug/include -I/home/ADS/u2192020/Matlab2022/extern/include     ex5f.F90  -Wl,-rpath,/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/linux-debug/lib -L/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/linux-debug/lib -Wl,-rpath,/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/linux-debug/lib -L/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/linux-debug/lib -Wl,-rpath,/home/ADS/u2192020/Matlab2022/bin/glnxa64 -L/home/ADS/u2192020/Matlab2022/bin/glnxa64 -Wl,-rpath,/home/ADS/u2192020/Matlab2022/extern/lib/glnxa64 -L/home/ADS/u2192020/Matlab2022/extern/lib/glnxa64 -Wl,-rpath,/home/ADS/u2192020/sfw/linux/openmpi-4.0.2/lib -L/home/ADS/u2192020/sfw/linux/openmpi-4.0.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/8 -L/usr/lib/gcc/x86_64-redhat-linux/8 -lpetsc -lHYPRE -lflapack -lfblas -lm -leng -lmex -lmx -lmat -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl -o ex5f
> //home/ADS/u2192020/Matlab2022/bin/glnxa64/libmwopccore.so: undefined reference to `std::__cxx11::basic_ostringstream<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::basic_ostringstream()@GLIBCXX_3.4.26'
> //home/ADS/u2192020/Matlab2022/bin/glnxa64/libmwfoundation_matlabdata_matlab.so: undefined reference to `std::logic_error::logic_error(std::logic_error&&)@GLIBCXX_3.4.26'
> /home/ADS/u2192020/Matlab2022/bin/glnxa64/libmex.so: undefined reference to `std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::basic_ostringstream()@GLIBCXX_3.4.26'
> /home/ADS/u2192020/Matlab2022/bin/glnxa64/libmx.so: undefined reference to `std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::basic_stringstream()@GLIBCXX_3.4.26'
> collect2: error: ld returned 1 exit status
> gmake[4]: *** [/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/lib/petsc/conf/test:43: ex5f] Error 1
> gmake[3]: [/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/lib/petsc/conf/rules:320: ex31.PETSc] Error 2 (ignored)
> *******************Error detected during compile or link!*******************
> See http://www.mcs.anl.gov/petsc/documentation/faq.html <http://www.mcs.anl.gov/petsc/documentation/faq.html>
> /home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/src/vec/vec/tutorials ex31
> *********************************************************************************
> /home/ADS/u2192020/sfw/linux/openmpi-4.0.2/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -g3 -O0  -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -g3 -O0    -I/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/include -I/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/linux-debug/include -I/home/ADS/u2192020/Matlab2022/extern/include     ex31.c  -Wl,-rpath,/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/linux-debug/lib -L/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/linux-debug/lib -Wl,-rpath,/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/linux-debug/lib -L/home/ADS/u2192020/sfw/petsc/PETSc-MATLAB/linux-debug/lib -Wl,-rpath,/home/ADS/u2192020/Matlab2022/bin/glnxa64 -L/home/ADS/u2192020/Matlab2022/bin/glnxa64 -Wl,-rpath,/home/ADS/u2192020/Matlab2022/extern/lib/glnxa64 -L/home/ADS/u2192020/Matlab2022/extern/lib/glnxa64 -Wl,-rpath,/home/ADS/u2192020/sfw/linux/openmpi-4.0.2/lib -L/home/ADS/u2192020/sfw/linux/openmpi-4.0.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/8 -L/usr/lib/gcc/x86_64-redhat-linux/8 -lpetsc -lHYPRE -lflapack -lfblas -lm -leng -lmex -lmx -lmat -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl -o ex31
> //home/ADS/u2192020/Matlab2022/bin/glnxa64/libmwopccore.so: undefined reference to `std::__cxx11::basic_ostringstream<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::basic_ostringstream()@GLIBCXX_3.4.26'
> //home/ADS/u2192020/Matlab2022/bin/glnxa64/libmwfoundation_matlabdata_matlab.so: undefined reference to `std::logic_error::logic_error(std::logic_error&&)@GLIBCXX_3.4.26'
> /home/ADS/u2192020/Matlab2022/bin/glnxa64/libmex.so: undefined reference to `std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::basic_ostringstream()@GLIBCXX_3.4.26'
> /home/ADS/u2192020/Matlab2022/bin/glnxa64/libmx.so: undefined reference to `std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::basic_stringstream()@GLIBCXX_3.4.26'
> collect2: error: ld returned 1 exit status
> gmake[4]: *** [<builtin>: ex31] Error 1
> Completed test examples
> [ADS+u2192020 at cos8-25136ecf PETSc-MATLAB]$ 

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