[petsc-users] make check error?

[Matthew Knepley]

On Tue, Apr 6, 2021 at 5:13 PM Bhamidipati, Vikram <
vikram.bhamidipati at swri.org> wrote:

> From configure.log and also my make check command I receive error message
> due to my Lapack libraries depending on older version of gfortran compared
> to petsc libraries. I am copy+pasting make check output:
>
>
>
>
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> Running check examples to verify correct installation
>
> Using PETSC_DIR=/home/vbhamidipati/petsc/petsc and
> PETSC_ARCH=arch-linux-c-debug
>
> *******************Error detected during compile or
> link!*******************
>
> See http://www.mcs.anl.gov/petsc/documentation/faq.html
>
> /home/vbhamidipati/petsc/petsc/src/snes/tutorials ex19
>
>
> *********************************************************************************
>
> mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
> -fstack-protector -fvisibility=hidden -g3  -Wall -Wwrite-strings
> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector
> -fvisibility=hidden -g3    -I/home/vbhamidipati/petsc/petsc/include
> -I/home/vbhamidipati/petsc/petsc/arch-linux-c-debug/include     ex19.c
> -Wl,-rpath,/home/vbhamidipati/petsc/petsc/arch-linux-c-debug/lib
> -L/home/vbhamidipati/petsc/petsc/arch-linux-c-debug/lib
> -Wl,-rpath,/usr/lib64/mpich-3.2/lib -L/usr/lib64/mpich-3.2/lib
> -Wl,-rpath,/opt/rh/devtoolset-8/root/usr/lib/gcc/x86_64-redhat-linux/8
> -L/opt/rh/devtoolset-8/root/usr/lib/gcc/x86_64-redhat-linux/8
> -Wl,-rpath,/opt/rh/devtoolset-8/root/usr/lib64
> -L/opt/rh/devtoolset-8/root/usr/lib64
> -Wl,-rpath,/opt/rh/devtoolset-8/root/usr/lib
> -L/opt/rh/devtoolset-8/root/usr/lib -lpetsc -llapack -lblas -lpthread -lm
> -lX11 -lstdc++ -ldl -lmpifort -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s
> -lquadmath -lstdc++ -ldl -o ex19
>
> /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld:
> warning: libgfortran.so.3, needed by /lib/../lib64/liblapack.so, may
> conflict with libgfortran.so.5
>
> /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld:
> warning: libgfortran.so.3, needed by /lib/../lib64/liblapack.so, may
> conflict with libgfortran.so.5
>
> C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process
>
> C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes
>
> *******************Error detected during compile or
> link!*******************
>
> See http://www.mcs.anl.gov/petsc/documentation/faq.html
>
> /home/vbhamidipati/petsc/petsc/src/snes/tutorials ex5f
>
> *********************************************************
>
> mpif90 -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -g   -Wall
> -ffree-line-length-0 -Wno-unused-dummy-argument -g
> -I/home/vbhamidipati/petsc/petsc/include
> -I/home/vbhamidipati/petsc/petsc/arch-linux-c-debug/include     ex5f.F90
> -Wl,-rpath,/home/vbhamidipati/petsc/petsc/arch-linux-c-debug/lib
> -L/home/vbhamidipati/petsc/petsc/arch-linux-c-debug/lib
> -Wl,-rpath,/usr/lib64/mpich-3.2/lib -L/usr/lib64/mpich-3.2/lib
> -Wl,-rpath,/opt/rh/devtoolset-8/root/usr/lib/gcc/x86_64-redhat-linux/8
> -L/opt/rh/devtoolset-8/root/usr/lib/gcc/x86_64-redhat-linux/8
> -Wl,-rpath,/opt/rh/devtoolset-8/root/usr/lib64
> -L/opt/rh/devtoolset-8/root/usr/lib64
> -Wl,-rpath,/opt/rh/devtoolset-8/root/usr/lib
> -L/opt/rh/devtoolset-8/root/usr/lib -lpetsc -llapack -lblas -lpthread -lm
> -lX11 -lstdc++ -ldl -lmpifort -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s
> -lquadmath -lstdc++ -ldl -o ex5f
>
> /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld:
> warning: libgfortran.so.3, needed by /lib/../lib64/liblapack.so, may
> conflict with libgfortran.so.5
>
> /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld:
> warning: libgfortran.so.3, needed by /lib/../lib64/liblapack.so, may
> conflict with libgfortran.so.5
>
> /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld:
> warning: libgfortran.so.3, needed by /lib/../lib64/liblapack.so, may
> conflict with libgfortran.so.5
>
> /opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/ld:
> warning: libgfortran.so.3, needed by /lib/../lib64/liblapack.so, may
> conflict with libgfortran.so.5
>
> Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process
>
> Completed test examples
>
>
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
>
>
> Is this OK? Or should I replace Lapack libraries and rebuild petsc?
>

This should be fine.

  Thanks,

     Matt


> Thanks,
>
> Vikram
>
> ---------------------------------------------------
>
> Vikram Bhamidipati
>
> Senior Research Engineer
>
> Computational Material Integrity Section
>
> Materials Engineering Department
>
> Mechanical Engineering Division
>
> Ph: (210) 522-2576
>
-- 
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/ <http://www.cse.buffalo.edu/~knepley/>
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