[petsc-users] Pestc-matlab issue
Yongxiang Lei
leiyongxiang1205 at gmail.com
Fri Jun 17 12:52:34 CDT 2022
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
/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
/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
/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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