[petsc-users] SLEPc Build Error

[Eda Oktay]

================================================================================
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/
> >
>
>
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