#1 2020-11-02 22:50:01

chenghui62000

Banned

From: Norway

Registered: 2018-06-19

Posts: 111

something wrong with superlu

Hi,

I tried to compile a parallel version of version 14.6, but for some reasons, it fails in the last step.
I follow the links of[https://code-aster.it/2019/01/12/code_aster-14-2-in-parallelo-su-ubuntu-bionic/] to do the compile.

The configure finished successfully as follows:

INCLUDES="${ASTER_PUBLIC}/hdf5-${HDF5_VER}/include ${ASTER_PUBLIC}/med-${MED_VER}/include ${ASTER_PUBLIC}/metis-${METIS_VER}/include ${ASTER_PUBLIC}/parmetis-${PARMETIS_VER}/include ${ASTER_PUBLIC}/ptscotch-${SCOTCH_VER}/include ${ASTER_PUBLIC}/mumps-${MUMPS_VER}_mpi/include ${ASTER_PUBLIC}/petsc-${PETSC_VER}/include ${ASTER_PUBLIC}/tfel-${MFRONT_VER}/include" LIBPATH="${ASTER_PUBLIC}/hdf5-${HDF5_VER}/lib ${ASTER_PUBLIC}/med-${MED_VER}/lib ${ASTER_PUBLIC}/metis-${METIS_VER}/lib ${ASTER_PUBLIC}/parmetis-${PARMETIS_VER}/lib ${ASTER_PUBLIC}/ptscotch-${SCOTCH_VER}/lib ${ASTER_PUBLIC}/scalapack-${SCALAPACK_VER}/lib ${ASTER_PUBLIC}/mumps-${MUMPS_VER}_mpi/lib ${ASTER_PUBLIC}/petsc-${PETSC_VER}/lib ${ASTER_PUBLIC}/tfel-${MFRONT_VER}/lib" ./waf configure --use-config=Ubuntu_mpi --prefix=${ASTER_ROOT}/${ASTER_VER}_mpi --install-tests --enable-mpi
checking environment... no found
executing: ./waf.engine configure --use-config=Ubuntu_mpi --prefix=/home/hui/p_aster//aster/14.6_mpi --install-tests --enable-mpi --out=build/std --jobs=4
Setting top to                           : /home/hui/dev/aster 
Setting out to                           : /home/hui/dev/aster/build/std 
Setting prefix to                        : /home/hui/p_aster/aster/14.6_mpi 
Searching configuration 'Ubuntu_mpi'... 
Checking for configuration               : Ubuntu_mpi 
Checking for 'gcc' (C compiler)          : mpicc 
Checking for 'g++' (C++ compiler)        : mpicxx 
Checking for 'gfortran' (Fortran compiler) : mpif90 
Checking for ''                          : yes 
Checking for ''                          : yes 
Checking for header mpi.h                : yes 
Checking for C compiler version          : gcc 7.5.0 
Checking for Fortran compiler version    : gfortran 7.5.0 
fortran link verbose flag                : -v 
Checking for OpenMP flag -fopenmp        : yes 
Getting fortran runtime link flags       : ok (-L/home/hui/p_aster//aster/public/hdf5-1.10.3/lib -L/home/hui/p_aster//aster/public/med-4.0.0/lib -L/home/hui/p_aster//aster/public/metis-5.1.0/lib -L/home/hui/p_aster//aster/public/parmetis-4.0.3/lib -L/home/hui/p_aster//aster/public/ptscotch-6.0.4/lib -L/home/hui/p_aster//aster/public/scalapack-2.0.2/lib -L/home/hui/p_aster//aster/public/mumps-5.1.2_mpi/lib -L/home/hui/p_aster//aster/public/petsc-3.14.0/lib -L/home/hui/p_aster//aster/public/tfel-3.1.1/lib -L/usr//lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -L/home/hui/p_aster//aster/public/hdf5-1.10.3/lib -L/home/hui/p_aster//aster/public/med-4.0.0/lib -L/home/hui/p_aster//aster/public/metis-5.1.0/lib -L/home/hui/p_aster//aster/public/parmetis-4.0.3/lib -L/home/hui/p_aster//aster/public/ptscotch-6.0.4/lib -L/home/hui/p_aster//aster/public/scalapack-2.0.2/lib -L/home/hui/p_aster//aster/public/mumps-5.1.2_mpi/lib -L/home/hui/p_aster//aster/public/petsc-3.14.0/lib -L/home/hui/p_aster//aster/public/tfel-3.1.1/lib -L/usr//lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Lnow -Lrelro -L/home/hui/p_aster//aster/public/hdf5-1.10.3/lib -L/home/hui/p_aster//aster/public/med-4.0.0/lib -L/home/hui/p_aster//aster/public/metis-5.1.0/lib -L/home/hui/p_aster//aster/public/parmetis-4.0.3/lib -L/home/hui/p_aster//aster/public/ptscotch-6.0.4/lib -L/home/hui/p_aster//aster/public/scalapack-2.0.2/lib -L/home/hui/p_aster//aster/public/mumps-5.1.2_mpi/lib -L/home/hui/p_aster//aster/public/petsc-3.14.0/lib -L/home/hui/p_aster//aster/public/tfel-3.1.1/lib -L/usr//lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/7/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/7/../../.. -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lquadmath -lm -lpthread -L/home/hui/p_aster//aster/public/hdf5-1.10.3/lib -L/home/hui/p_aster//aster/public/med-4.0.0/lib -L/home/hui/p_aster//aster/public/metis-5.1.0/lib -L/home/hui/p_aster//aster/public/parmetis-4.0.3/lib -L/home/hui/p_aster//aster/public/ptscotch-6.0.4/lib -L/home/hui/p_aster//aster/public/scalapack-2.0.2/lib -L/home/hui/p_aster//aster/public/mumps-5.1.2_mpi/lib -L/home/hui/p_aster//aster/public/petsc-3.14.0/lib -L/home/hui/p_aster//aster/public/tfel-3.1.1/lib -L/usr//lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib) 
Checking measure of VmSize during MPI_Init : ok (293324 kB) 
Checking for library pthread             : yes 
Checking for library dl                  : yes 
Checking for library util                : yes 
Checking for program 'python'            : /usr/bin/python3 
Checking for python version >= 3.5.0     : 3.6.9 
python-config                            : /usr/bin/python3-config 
Asking python-config for pyembed '--cflags --libs --ldflags --embed' flags : not found 
Asking python-config for pyembed '--cflags --libs --ldflags' flags : yes 
Testing pyembed configuration            : yes 
Asking python-config for pyext '--cflags --libs --ldflags' flags : yes 
Testing pyext configuration              : yes 
Checking for numpy                       : /usr/lib/python3/dist-packages/numpy/__init__.py 
Checking for numpy version               : 1.13.3 
Checking for numpy include               : ['/usr/lib/python3/dist-packages/numpy/core/include'] 
Checking for asrun                       : //home/hui/p_aster/aster/lib/python3.6/site-packages/asrun/__init__.py 
Getting platform                         : LINUX64 
Checking for library pthread             : yes 
Checking for library m                   : yes 
Checking for number of cores             : 4 
Checking for program 'python'            : /usr/bin/python3 
Checking for python module 'numpy'       : 1.13.3 
Checking for program 'ldd'               : /usr/bin/ldd 
Checking library blas                    : yes (blas) 
Checking library lapack                  : yes (lapack) 
Checking library blacs                   : yes (['blacsCinit-openmpi', 'blacsF77init-openmpi', 'blacs-openmpi']) 
Checking library scalapack               : yes (scalapack) 
Checking library optional                : yes (cblas) 
Checking for a program using blas/lapack : yes 
Checking for a program using blacs       : yes 
Checking for a program using omp thread  : yes (on 4 threads) 
Detected math libraries                  : ['pthread', 'm', 'blas', 'lapack', 'blacsCinit-openmpi', 'blacsF77init-openmpi', 'blacs-openmpi', 'scalapack', 'cblas'] 
Setting libm after files                 : yes ("-lm" removed from LINKFLAGS_CLIB) 
Checking for a program using blas/lapack : yes 
Checking for a program using blacs       : yes 
Checking for a program using omp thread  : yes (on 4 threads) 
Checking for library hdf5                : yes 
Checking for header hdf5.h               : yes 
Checking hdf5 version                    : 1.10.3 
Checking for API hdf5 v18                : default v18 
Checking size of hid_t integers          : 8 
Checking for library med                 : yes 
Checking for header med.h                : yes 
Checking size of med_int integers        : 4 
Checking size of med_idt integers        : 8 
Checking med version                     : 4.0.0 
Checking for library metis               : yes 
Checking for header metis.h              : yes 
Checking metis version                   : 5.1.0 
Checking for smumps_struc.h              : yes 
Checking for dmumps_struc.h              : yes 
Checking for cmumps_struc.h              : yes 
Checking for zmumps_struc.h              : yes 
Checking for mpif.h                      : yes 
Checking mumps version                   : 5.1.2 
Checking for library dmumps              : yes 
Checking for library zmumps              : yes 
Checking for library smumps              : yes 
Checking for library cmumps              : yes 
Checking for library mumps_common        : yes 
Checking for library pord                : yes 
Setting size of Mumps integers           : 4 
Checking for header scotch.h             : yes 
Checking scotch version                  : 6.0.4 
Checking for library esmumps             : yes 
Checking for library scotch              : yes 
Checking for library scotcherr           : yes 
Checking for library petsc               : yes 
Checking for library ml                  : yes 
Checking for library HYPRE               : yes 
Checking for library superlu             : yes 
Checking for library stdc++              : yes 
Checking for header petsc.h              : yes 
Checking petsc version                   : 3.8.2p0 
Reading build preferences from ~/.hgrc   : not found 
Compiling a simple fortran app           : yes 
Detecting whether we need a dummy main   : yes main 
Checking for fortran option              : yes (-fdefault-double-8 -fdefault-integer-8 -fdefault-real-8) 
Checking for fortran option              : yes (-Wimplicit-interface) 
Checking for fortran option              : yes (-Wintrinsic-shadow) 
Checking for fortran option              : yes (-fno-aggressive-loop-optimizations) 
Checking for fortran option              : yes (-ffree-line-length-none) 
Setting fortran compiler flags           : ['-fPIC', '-fdefault-double-8', '-fdefault-integer-8', '-fdefault-real-8', '-Wimplicit-interface', '-Wintrinsic-shadow', '-fno-aggressive-loop-optimizations', '-ffree-line-length-none'] 
Getting fortran mangling scheme          : ok ('_', '', 'lower-case') 
Checking size of integer4                : 4 
Checking the matching C type             : int 
Checking size of default integer         : 8 
Checking the matching C type             : long 
Checking size of logical                 : 1 
Checking size of simple precision real   : 4 
Checking the matching C type             : float 
Checking size of double precision real   : 8 
Checking the matching C type             : double 
Checking size of double complex          : 16 
Setting type for fortran string length   : unsigned int 
Setting size of blas/lapack integers     : 4 
Checking size of MPI_Fint integers       : 4 
Checking fpp stringify using #           : no 
Checking fpp stringify using ""          : yes 
Checking compilation with long lines     : yes 
Check for backtrace feature              : yes 
Check for tracebackqq feature            : no 
Checking for 'g++' (C++ compiler)        : mpicxx 
Checking for compiler flags -std=c++11   : yes 
Checking for library stdc++              : yes 
Checking for 'gcc' (C compiler)          : mpicc 
Getting C compiler flags                 : ['-fPIC'] 
Checking for library dl                  : yes 
Getting code_aster version               : [(14, 6, 0), 'b3490fa3b76c', 'v14', '11/06/2020', 'v14', 0] 
Checking for TFELHOME variable           : ['/home/hui/p_aster//aster/public/tfel-3.1.1'] 
Checking for program 'mfront'            : not found 
Check for msgfmt programs                : ['/usr/bin/msgfmt'] 
Check for xgettext programs              : ['/usr/bin/xgettext'] 
Check for msgmerge programs              : ['/usr/bin/msgmerge'] 
Check for lrelease programs              : not found 
Store execution environment              : yes 
Build list of testcases                  : yes 
Set tmp directory for `salome test`      : $ENV{ASTER_TMPDIR} 
Checking for program 'gmsh'              : not found 
Checking for program 'gmsh'              : not found 
Checking for program 'salome'            : not found 
Checking for program 'salome'            : not found 
Checking for program 'run_miss3d'        : not found 
Checking for program 'run_miss3d'        : not found 
Checking for program 'homard'            : /home/hui/p_aster//aster/public/homard-11.12/ASTER_HOMARD/homard 
Checking for program 'ecrevisse'         : not found 
Checking for program 'ecrevisse'         : not found 
Checking for program 'mfront'            : not found 
Checking for program 'mfront'            : not found 
Checking for program 'xmgrace'           : /usr/bin/xmgrace 
Checking for program 'gracebat'          : /usr/bin/gracebat 
Checking for 'data' repository           : /home/hui/dev/data not found 
Checking for 'validation' repository     : /home/hui/dev/validation not found 
Setting C debug flags                    : ['-g', '-O0'] 
Setting C optimization flags             : ['-O2'] 
Setting C++ debug flags                  : ['-g', '-O0'] 
Setting C++ optimization flags           : ['-O2'] 
Setting fortran debug flags              : ['-g', '-O0'] 
Getting fortran optimization flags       : ['-O2'] (VOLATILE is required) 
Write config file                        : debug/asterf_config.h 
Write config file                        : debug/asterc_config.h 
Write config file                        : release/asterf_config.h 
Write config file                        : release/asterc_config.h 
'configure' finished successfully (11.013s)

Then I compile with the command

  ./waf build -v

. and it gives me this error message:

hui@vmMint:~/dev/aster$ ./waf build -v
checking environment... no found
executing: ./waf.engine build -v --out=build/std --jobs=4
Waf: Entering directory `/home/hui/dev/aster/build/std/release'
[7331/8115] Compiling bibc/utilitai/superlu_wrapper.c
22:48:57 runner ['mpicc', '-fPIC', '-O2', '-g', '-fdebug-prefix-map=/build/python3.6-e9shER/python3.6-3.6.9=.', '-fstack-protector', '-g', '-fwrapv', '-O3', '-pthread', '-pthread', '-g', '-fdebug-prefix-map=/build/python3.6-e9shER/python3.6-3.6.9=.', '-fstack-protector', '-g', '-fwrapv', '-O3', '-I../../../../../p_aster/aster/public/hdf5-1.10.3/include', '-I../../../../../p_aster/aster/public/med-4.0.0/include', '-I../../../../../p_aster/aster/public/metis-5.1.0/include', '-I../../../../../p_aster/aster/public/parmetis-4.0.3/include', '-I../../../../../p_aster/aster/public/ptscotch-6.0.4/include', '-I../../../../../p_aster/aster/public/mumps-5.1.2_mpi/include', '-I../../../../../p_aster/aster/public/petsc-3.14.0/include', '-I../../../../../p_aster/aster/public/tfel-3.1.1/include', '-I../../../bibc/include', '-I../../../bibcxx/include', '-I../../../bibfor/include', '-I.', '-I/usr/include/python3.6m', '-I/usr/lib/python3/dist-packages/numpy/core/include', '-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi', '-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent', '-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include', '-I/usr/lib/x86_64-linux-gnu/openmpi/include', '-I/usr/lib/x86_64-linux-gnu/openmpi/lib', '-D_MAIN_=main', '-DNDEBUG', '-DNPY_NO_PREFIX', '-DNDEBUG', '../../../bibc/utilitai/superlu_wrapper.c', '-c', '-o/home/hui/dev/aster/build/std/release/bibc/utilitai/superlu_wrapper.c.1.o']
../../../bibc/utilitai/superlu_wrapper.c:39:10: fatal error: slu_ddefs.h: No such file or directory
 #include "slu_ddefs.h"
          ^~~~~~~~~~~~~
compilation terminated.

Waf: Leaving directory `/home/hui/dev/aster/build/std/release'
Build failed
 -> task in 'asterexec' failed with exit status 1: 
        {task 139930783187240: c superlu_wrapper.c -> superlu_wrapper.c.1.o}
['mpicc', '-fPIC', '-O2', '-g', '-fdebug-prefix-map=/build/python3.6-e9shER/python3.6-3.6.9=.', '-fstack-protector', '-g', '-fwrapv', '-O3', '-pthread', '-pthread', '-g', '-fdebug-prefix-map=/build/python3.6-e9shER/python3.6-3.6.9=.', '-fstack-protector', '-g', '-fwrapv', '-O3', '-I../../../../../p_aster/aster/public/hdf5-1.10.3/include', '-I../../../../../p_aster/aster/public/med-4.0.0/include', '-I../../../../../p_aster/aster/public/metis-5.1.0/include', '-I../../../../../p_aster/aster/public/parmetis-4.0.3/include', '-I../../../../../p_aster/aster/public/ptscotch-6.0.4/include', '-I../../../../../p_aster/aster/public/mumps-5.1.2_mpi/include', '-I../../../../../p_aster/aster/public/petsc-3.14.0/include', '-I../../../../../p_aster/aster/public/tfel-3.1.1/include', '-I../../../bibc/include', '-I../../../bibcxx/include', '-I../../../bibfor/include', '-I.', '-I/usr/include/python3.6m', '-I/usr/lib/python3/dist-packages/numpy/core/include', '-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi', '-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent', '-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include', '-I/usr/lib/x86_64-linux-gnu/openmpi/include', '-I/usr/lib/x86_64-linux-gnu/openmpi/lib', '-D_MAIN_=main', '-DNDEBUG', '-DNPY_NO_PREFIX', '-DNDEBUG', '../../../bibc/utilitai/superlu_wrapper.c', '-c', '-o/home/hui/dev/aster/build/std/release/bibc/utilitai/superlu_wrapper.c.1.o']

AlexKaz

Member

Registered: 2016-06-18

Posts: 7

Re: something wrong with superlu

Hi, I also try to compile CA with MPI.

There is an error with compilation

[7331/7331][100%][\][=============================================================================>][9m29.586s]
Waf: Leaving directory `/tmp/aster/aster-full-src-14.6.0/SRC/aster-14.6.0/build/std/release'
Build failed
-> task in 'asterexec' failed with exit status 1:
    {task 139981426616136: c superlu_wrapper.c -> superlu_wrapper.c.1.o}
['mpicc', '-fPIC', '-O2', '-g', '-fstack-protector-strong', '-g', '-fwrapv', '-O3', '-pthread', '-pthread', '-g', '-fstack-protector-strong', '-g', '-fwrapv', '-O3', '-I/opt/petsc-3.9.4/linux-metis-mumps/include', '-I/opt/petsc-3.9.4/include', '-I/usr/include/superlu', '-I/opt/parmetis-4.0.3/include', '-I/opt/mumps-5.1.2/include', '-I/opt/aster146p/public/hdf5-1.10.3/include', '-I/opt/aster146p/public/med-4.0.0/include', '-I/opt/aster146p/public/metis-5.1.0/include', '-I/opt/scotch-6.0.4/include', '-I/opt/OpenBLAS/include', '-I/opt/scalapack/include', '-I../../../bibc/include', '-I../../../bibcxx/include', '-I../../../bibfor/include', '-I.', '-I/usr/include/python3.5m', '-I/usr/lib/python3/dist-packages/numpy/core/include', '-I/usr/local/include', '-I/usr/local/lib', '-D_MAIN_=main', '-DNDEBUG', '-DNPY_NO_PREFIX', '-DNDEBUG', '../../../bibc/utilitai/superlu_wrapper.c', '-c', '-o/tmp/aster/aster-full-src-14.6.0/SRC/aster-14.6.0/build/std/release/bibc/utilitai/superlu_wrapper.c.1.o']

Problem maybe is in different version of superlu.

mpicc -fPIC -O2 -g -fstack-protector-strong -g -fwrapv -O3 -pthread -pthread -g -fstack-protector-strong -g -fwrapv -O3 -I/opt/petsc-3.9.4/linux-metis-mumps/include -I/opt/petsc-3.9.4/include -I/usr/include/superlu -I/opt/parmetis-4.0.3/include -I/opt/mumps-5.1.2/include -I/opt/aster146p/public/hdf5-1.10.3/include -I/opt/aster146p/public/med-4.0.0/include -I/opt/aster146p/public/metis-5.1.0/include -I/opt/scotch-6.0.4/include -I/opt/OpenBLAS/include -I/opt/scalapack/include -I../../../bibc/include -I../../../bibcxx/include -I../../../bibfor/include -I. -I/usr/include/python3.5m -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/local/include -I/usr/local/lib -D_MAIN_=main -DNDEBUG -DNPY_NO_PREFIX -DNDEBUG ../../../bibc/utilitai/superlu_wrapper.c -c -o/tmp/aster/aster-full-src-14.6.0/SRC/aster-14.6.0/build/std/release/bibc/utilitai/superlu_wrapper.c.1.o
...
extern void    dgstrf (superlu_options_t*, SuperMatrix*,
                ^
../../../bibc/utilitai/superlu_wrapper.c:114:5: error: too many arguments to function ‘dgstrf’
     dgstrf(&options, &AC, relax, panel_size, etree,
     ^
In file included from ../../../bibc/utilitai/superlu_wrapper.c:39:0:
/usr/include/superlu/slu_ddefs.h:160:16: note: declared here
extern void    dgstrf (superlu_options_t*, SuperMatrix*,

I don't know which superlu version is needing to compile and install. Or can I try to use another version of Petsc, not 3.9.4 ? In superlu_wrapper.c there is if block

#ifdef _HAVE_PETSC
#include "slu_ddefs.h"

Last edited by AlexKaz (2021-06-18 16:54:43)

AlexKaz

Member

Registered: 2016-06-18

Posts: 7

Re: something wrong with superlu

I have solved problem after compilation superlu 5.2.1 from official repo. My distro manager can download and install only v4.3.