[petsc-users] SLEPc Build Error

Tue Mar 19 07:15:34 CDT 2019

What is the output of 'make check' in $PETSC_DIR ?

> El 19 mar 2019, a las 13:02, Eda Oktay <eda.oktay at metu.edu.tr> escribió:
> 
> Without slepc, I configured petsc succesfully. Then I installed slepc with following steps:
> 
> export PETSC_ARCH=arch-linux2-c-debug
> export PETSC_DIR=/home/slurm_local/e200781/petsc-3.10.4
> export SLEPC_DIR=/home/slurm_local/e200781/slepc-3.10.2
> cd slepc-3.10.2
> ./configure
> 
> However, I still get the error:
> 
> Checking environment... done
> Checking PETSc installation... 
> ERROR: Unable to link with PETSc
> ERROR: See "arch-linux2-c-debug/lib/slepc/conf/configure.log" file for details
> 
> Where the configure.log is:
> 
> ================================================================================
> Starting Configure Run at Tue Mar 19 14:57:21 2019
> Configure Options: 
> Working directory: /home/slurm_local/e200781/slepc-3.10.2
> Python version:
> 2.7.9 (default, Sep 25 2018, 20:42:16) 
> [GCC 4.9.2]
> make: /usr/bin/make
> PETSc source directory: /home/slurm_local/e200781/petsc-3.10.4
> PETSc install directory: /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug
> PETSc version: 3.10.4
> PETSc architecture: arch-linux2-c-debug
> SLEPc source directory: /home/slurm_local/e200781/slepc-3.10.2
> SLEPc version: 3.10.2
> ================================================================================
> Checking PETSc installation...
> #include "petscsnes.h"
> int main() {
> Vec v; Mat m; KSP k;
> PetscInitializeNoArguments();
> VecCreate(PETSC_COMM_WORLD,&v);
> MatCreate(PETSC_COMM_WORLD,&m);
> KSPCreate(PETSC_COMM_WORLD,&k);
> return 0;
> }
> /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/bin/mpicc -o checklink.o -c -fPIC  -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g3   -I/home/slurm_local/e200781/petsc-3.10.4/include -I/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/include    `pwd`/checklink.c
> /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/bin/mpicc -fPIC  -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g3  -o checklink checklink.o  -Wl,-rpath,/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib -L/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib -Wl,-rpath,/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib -L/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9 -L/usr/lib/gcc/x86_64-linux-gnu/4.9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lpetsc -lopenblas -lparmetis -lmetis -lm -lX11 -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lstdc++ -ldl
> /usr/bin/ld: warning: libmpi.so.0, needed by /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/libopenblas.so, may conflict with libmpi.so.40
> /usr/bin/ld: warning: libmpi.so.0, needed by /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/libopenblas.so, may conflict with libmpi.so.40
> /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/libpetsc.so: undefined reference to `MatPartitioningParmetisSetRepartition'
> /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/libpetsc.so: undefined reference to `MatPartitioningCreate_Parmetis'
> collect2: error: ld returned 1 exit status
> makefile:2: recipe for target 'checklink' failed
> make: *** [checklink] Error 1
> 
> ERROR: Unable to link with PETSc
> 
> Jose E. Roman <jroman at dsic.upv.es>, 19 Mar 2019 Sal, 14:08 tarihinde şunu yazdı:
> There seems to be a link problem with PETSc.
> Suggest re-configuring without the option --download-slepc
> Then, after building PETSc, try 'make check' to make sure that PETSc is built correctly. Then install SLEPc afterwards.
> Jose
> 
> 
> > El 19 mar 2019, a las 11:58, Eda Oktay <eda.oktay at metu.edu.tr> escribió:
> > 
> > ================================================================================
> > Starting Configure Run at Tue Mar 19 11:53:05 2019
> > Configure Options: --prefix=/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug
> > Working directory: /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/externalpackages/git.slepc
> > Python version:
> > 2.7.9 (default, Sep 25 2018, 20:42:16) 
> > [GCC 4.9.2]
> > make: /usr/bin/make
> > PETSc source directory: /home/slurm_local/e200781/petsc-3.10.4
> > PETSc install directory: /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug
> > PETSc version: 3.10.4
> > PETSc architecture: arch-linux2-c-debug
> > SLEPc source directory: /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/externalpackages/git.slepc
> > SLEPc install directory: /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug
> > SLEPc version: 3.10.1
> > ================================================================================
> > Checking PETSc installation...
> > #include "petscsnes.h"
> > int main() {
> > Vec v; Mat m; KSP k;
> > PetscInitializeNoArguments();
> > VecCreate(PETSC_COMM_WORLD,&v);
> > MatCreate(PETSC_COMM_WORLD,&m);
> > KSPCreate(PETSC_COMM_WORLD,&k);
> > return 0;
> > }
> > make[2]: Entering directory '/tmp/slepc-2F1MtJ'
> > /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/bin/mpicc -o checklink.o -c -fPIC  -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g3   -I/home/slurm_local/e200781/petsc-3.10.4/include -I/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/include    `pwd`/checklink.c
> > /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/bin/mpicc -fPIC  -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g3  -o checklink checklink.o  -Wl,-rpath,/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib -L/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib -Wl,-rpath,/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib -L/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9 -L/usr/lib/gcc/x86_64-linux-gnu/4.9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lpetsc -lopenblas -lparmetis -lmetis -lm -lX11 -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lstdc++ -ldl
> > /usr/bin/ld: warning: libmpi.so.0, needed by /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/libopenblas.so, may conflict with libmpi.so.40
> > /usr/bin/ld: warning: libmpi.so.0, needed by /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/libopenblas.so, may conflict with libmpi.so.40
> > /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/libpetsc.so: undefined reference to `MatPartitioningParmetisSetRepartition'
> > /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/libpetsc.so: undefined reference to `MatPartitioningCreate_Parmetis'
> > collect2: error: ld returned 1 exit status
> > makefile:2: recipe for target 'checklink' failed
> > make[2]: *** [checklink] Error 1
> > make[2]: Leaving directory '/tmp/slepc-2F1MtJ'
> > 
> > ERROR: Unable to link with PETSc
> > 
> > 
> > Jose E. Roman <jroman at dsic.upv.es>, 19 Mar 2019 Sal, 13:49 tarihinde şunu yazdı:
> > Correction: the correct path is $PETSC_DIR/$PETSC_ARCH/externalpackages/git.slepc/$PETSC_ARCH/lib/slepc/conf/configure.log
> > 
> > 
> > 
> > > El 19 mar 2019, a las 11:46, Jose E. Roman via petsc-users <petsc-users at mcs.anl.gov> escribió:
> > > 
> > > And what is in $SLEPC_DIR/arch-linux2-c-debug/lib/slepc/conf/configure.log ?
> > > Jose
> > > 
> > >> El 19 mar 2019, a las 11:41, Eda Oktay via petsc-users <petsc-users at mcs.anl.gov> escribió:
> > >> 
> > >> This is slepc.log:
> > >> 
> > >> Checking environment... done
> > >> Checking PETSc installation... 
> > >> ERROR: Unable to link with PETSc
> > >> ERROR: See "arch-linux2-c-debug/lib/slepc/conf/configure.log" file for details
> > >> 
> > >> 
> > >> 
> > >> Matthew Knepley <knepley at gmail.com>, 19 Mar 2019 Sal, 13:36 tarihinde şunu yazdı:
> > >> On Tue, Mar 19, 2019 at 6:31 AM Eda Oktay via petsc-users <petsc-users at mcs.anl.gov> wrote:
> > >> Hello,
> > >> 
> > >> I am trying to install PETSc with following configure options:
> > >> 
> > >> ./configure --download-openmpi --download-openblas --download-slepc --download-cmake --download-metis --download-parmetis
> > >> 
> > >> Compilation is done but after the following command, I got an error:
> > >> 
> > >> make PETSC_DIR=/home/slurm_local/e200781/petsc-3.10.4 PETSC_ARCH=arch-linux2-c-debug all
> > >> 
> > >> *** Building slepc ***
> > >> **************************ERROR*************************************
> > >> Error building slepc. Check arch-linux2-c-debug/lib/petsc/conf/slepc.log
> > >> 
> > >> We need slepc.log
> > >> 
> > >>  Thanks,
> > >> 
> > >>     Matt
> > >> 
> > >> ********************************************************************
> > >> /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/petsc/conf/petscrules:46: recipe for target 'slepcbuild' failed
> > >> make[1]: *** [slepcbuild] Error 1
> > >> make[1]: Leaving directory '/home/slurm_local/e200781/petsc-3.10.4'
> > >> **************************ERROR*************************************
> > >>  Error during compile, check arch-linux2-c-debug/lib/petsc/conf/make.log
> > >>  Send it and arch-linux2-c-debug/lib/petsc/conf/configure.log to petsc-maint at mcs.anl.gov
> > >> ********************************************************************
> > >> makefile:30: recipe for target 'all' failed
> > >> make: *** [all] Error 1
> > >> 
> > >> How can I fix the problem?
> > >> 
> > >> Thank you,
> > >> 
> > >> Eda
> > >> 
> > >> 
> > >> -- 
> > >> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
> > >> -- Norbert Wiener
> > >> 
> > >> https://www.cse.buffalo.edu/~knepley/
> > > 
> > 
> 