libISSMCore.so: undefined references

zrashed

I am trying to compile the latest svn ISSM version on my ubuntu 18.04 machine and I am running into issues at the make stage. I installed the required packages in the following order: autotools -> mpich(3.0) -> cmake -> petsc(3.6, I had to add "-download-cmake=1 \" to the install-3.6-linux64.sh script because I was getting an error to do with cmake and installing metis during the petsc installation)->m1qn3->triangle. After this I moved on to configuration and used the following config file.

configure.sh
./configure \ --prefix=$ISSM_DIR \ --with-matlab-dir="/usr/local/MATLAB/R2020a" \ --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ --with-mpi-include="$ISSM_DIR/externalpackages/mpich/install/include" \ --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/7/ -lgfortran" \ --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -l$ --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \ --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install/" \ --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install/" \ --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \ --with-numthreads=2
After this I make and I run into the following errors:
sudo -E make make all-recursive make[1]: Entering directory '/usr/local/issm/trunk' Making all in src make[2]: Entering directory '/usr/local/issm/trunk/src' Making all in c make[3]: Entering directory '/usr/local/issm/trunk/src/c' CXXLD issm.exe ./.libs/libISSMCore.so: undefined reference tozgesv'
./.libs/libISSMCore.so: undefined reference to _gfortran_cpu_time_8' ./.libs/libISSMCore.so: undefined reference togfortran_transfer_integer_write'
./.libs/libISSMCore.so: undefined reference to _gfortran_st_open' ./.libs/libISSMCore.so: undefined reference togfortran_os_error'
./.libs/libISSMCore.so: undefined reference to _gfortran_transfer_character_write' ./.libs/libISSMCore.so: undefined reference togfortran_runtime_error_at'
./.libs/libISSMCore.so: undefined reference to _gfortran_runtime_error' ./.libs/libISSMCore.so: undefined reference togfortran_internal_unpack'
./.libs/libISSMCore.so: undefined reference to _gfortran_internal_pack' ./.libs/libISSMCore.so: undefined reference togfortran_st_write_done'
./.libs/libISSMCore.so: undefined reference to _gfortran_pow_c8_i4' ./.libs/libISSMCore.so: undefined reference togfortran_transfer_real_write'
./.libs/libISSMCore.so: undefined reference to _gfortran_stop_string' ./.libs/libISSMCore.so: undefined reference togfortran_st_write'
collect2: error: ld returned 1 exit status
Makefile:4429: recipe for target 'issm.exe' failed
make[3]: *** [issm.exe] Error 1
make[3]: Leaving directory '/usr/local/issm/trunk/src/c'
Makefile:462: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/usr/local/issm/trunk/src'
Makefile:583: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/usr/local/issm/trunk'
Makefile:480: recipe for target 'all' failed
make: *** [all] Error 2
`
I have tried changing the FORTRANLIB = -L/usr/lib/gcc/x86_64-linux-gnu/ -lgfortran but that didn't change anything and the same error was produced. I think this has to do with the gcc libraries as I have multiple folders under "/usr/lib/gcc/x86_64-linux-gnu/#" with their being a folder for 6,6.5,7,7.5,8 and only versions 7,7.5 are nonempty folders. Any ideas how to progress from here?

justinquinn

zrashed Yes, I agree with the approach Mathieu suggested: let the system + Autotools work out the best copy to use by removing "7/" from the path. That said, each of these should define those symbols, in my experience. However, perhaps,

_gfortran_cpu_time_8

provides a clue? Assuming that implies version 8 of gcc, changing "7/" to "8" in the path would most likely fix it.

mathieumorlighem

Hi,

could you try changing the option

--with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/7/ -lgfortran" \
to
--with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/ -lgfortran" \

if that does not work, we are going to need to figure out which fortran library defines these symbols...
Best
Mathieu

zrashed

Thanks! I changed
--with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/7/ -lgfortran" \
to
--with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/ -lgfortran" \

and after re-configuring and making I am not encountering that error anymore. But now I am receiving this error
` CXXLD libISSMCore.la

*** Warning: Linking the shared library libISSMCore.la against the
*** static library /usr/local/issm/trunk/externalpackages/m1qn3/install/libm1qn3.a is not portable!

*** Warning: Linking the shared library libISSMCore.la against the
*** static library /usr/local/issm/trunk/externalpackages/m1qn3/install/libddot.a is not portable!
/usr/bin/ld: cannot find -lmpi
/usr/bin/ld: cannot find -lmpicxx
/usr/bin/ld: cannot find -lmpifort
collect2: error: ld returned 1 exit status
Makefile:4029: recipe for target 'libISSMCore.la' failed
make[3]: *** [libISSMCore.la] Error 1
make[3]: Leaving directory '/usr/local/issm/trunk/src/c'
Makefile:462: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/usr/local/issm/trunk/src'
Makefile:583: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/usr/local/issm/trunk'
Makefile:480: recipe for target 'all' failed
make: *** [all] Error 2
`

mathieumorlighem

zrashed ok almost there! I think you need to change your --mpi-XX options because you installed the newest version of PETSc: try these
--with-mpi-include=$ISSM_DIR/externalpackages/petsc/install/include \
--with-mpi-libflags="-L$ISSM_DIR/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort"\
(we use the mopish provided by petsc, not the one in external packages)
Mathieu

zrashed

mathieumorlighem
It looks like I had accidentally removed a backslash in the --with mpi line so I am not getting that anymore and it's back to the fortran errors.
Here is my current config file:
#! /bin/sh ./configure \ --prefix=$ISSM_DIR \ --with-matlab-dir="/usr/local/MATLAB/R2020a" \ --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ --with-mpi-include="$ISSM_DIR/externalpackages/petsc/install/include" \ --with-mpi-libflags="-L$ISSM_DIR/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/ -lgfortran" \ --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \ --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install/" \ --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install/" \ --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \ --with-numthreads=2

and here is the error I am receiving
CXXLD libISSMModules.la ar:u' modifier ignored since D' is the default (seeU')
CXX main/issm-issm.o
CXXLD issm.exe
./.libs/libISSMCore.so: undefined reference to zgesv_' ./.libs/libISSMCore.so: undefined reference togfortran_cpu_time_8'
./.libs/libISSMCore.so: undefined reference to _gfortran_transfer_integer_write' ./.libs/libISSMCore.so: undefined reference togfortran_st_open'
./.libs/libISSMCore.so: undefined reference to _gfortran_os_error' ./.libs/libISSMCore.so: undefined reference togfortran_transfer_character_write'
./.libs/libISSMCore.so: undefined reference to _gfortran_runtime_error_at' ./.libs/libISSMCore.so: undefined reference togfortran_runtime_error'
./.libs/libISSMCore.so: undefined reference to _gfortran_internal_unpack' ./.libs/libISSMCore.so: undefined reference togfortran_internal_pack'
./.libs/libISSMCore.so: undefined reference to _gfortran_st_write_done' ./.libs/libISSMCore.so: undefined reference togfortran_pow_c8_i4'
./.libs/libISSMCore.so: undefined reference to _gfortran_transfer_real_write' ./.libs/libISSMCore.so: undefined reference to_gfortran_stop_string'
./.libs/libISSMCore.so: undefined reference to _gfortran_st_write' collect2: error: ld returned 1 exit status Makefile:4429: recipe for target 'issm.exe' failed make[3]: *** [issm.exe] Error 1 make[3]: Leaving directory '/usr/local/issm/trunk/src/c' Makefile:462: recipe for target 'all-recursive' failed make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory '/usr/local/issm/trunk/src' Makefile:583: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/usr/local/issm/trunk' Makefile:480: recipe for target 'all' failed make: *** [all] Error 2

justinquinn

zrashed Can you try,

--with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/8 -lgfortran"

Basically, we're trying to find the copy of libgfortran that PETSc was linked against.

zrashed

justinquinn Hi Justin,

I've tried setting --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/8 -lgfortran" but I still receive the same errors as earlier. Is there a direct way of finding the copy of libgfortran which PETSc is linked against?

justinquinn

zrashed Yes, sorry: I should have suggested this before. You should be able to run,

ldd $ISSM_DIR/externalpackages/petsc/install/lib/libpetsc.so | grep libgfortran

Let me know if that works (it may be that the dynamic loader picks up a different copy, in which case we'll have to dig further).

zrashed

Ok executing the command yields this.
libgfortran.so.4 => /usr/lib/x86_64-linux-gnu/libgfortran.so.4 (0x00007f8d16436000). Wouldn't this mean that the following should work?
--with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/ -lgfortran"

justinquinn

zrashed Ideally, but the linker may be doing something different than the loader. So, let's try,

--with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/libgfortran.so.4

zrashed

Hmmm, still the same error. It looks like the link is to /usr/lib/x86_64-linux-gnu/libgfortran.so.4, but I have been searching in /usr/lib/gcc/x86_64-linux-gnu/. Could that be the issue here?

justinquinn

zrashed Ah, yes, good catch. Although, one would think that those would be the same (perhaps even a symbolic link from from one to the other). But, yes, try that other path out.

zrashed

This is odd... I've tried recompiling a couple times and now I'm running into cannot find -lmpi,lmpicxx,lmpifort errors again. Nothing was else was changed but here is the current config file I'm using.
#! /bin/sh ./configure \ --prefix=$ISSM_DIR \ --with-matlab-dir="/usr/local/MATLAB/R2020a" \ --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ --with-mpi-include="$ISSM_DIR/externalpackages/petsc/install/include" \ --with-mpi-libflags="-L$ISSM_DIR/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \ --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/ -lgfortran" \ --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \ --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install/" \ --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install/" \ --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \ --with-numthreads=2
And from the Makefile,
MPIINCL = -I/usr/local/issm/trunk/externalpackages/petsc/install/include MPILIB = -L/usr/local/issm/trunk/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort FORTRANLIB = -L/usr/lib/x86_64-linux-gnu/ -lgfortran

justinquinn

zrashed First, let's make sure we're using this, to eliminate as many variables as possible,

--with-fortran-lib="-L/usr/lib/x86_64-linux-gnu/libgfortran.so.4

because the paths in the configuration and Makefile are different. Also, just to be clear, you are not manually generating a Makefile, right (it's being generated automatically by running configure)? You can check that indeed the MPICH libraries exist with ls $ISSM_DIR/externalpackages/petsc/install/lib/libmpi*. If they are not there, then I would suggest running $ISSM_DIR/externalpackages/petsc; rm -rf ./install; ./install-3.12-linux.sh, reconfiguring, and recompiling.

zrashed

justinquinn Thanks for all the help, I have everything working now! I had to change the mpi directory to mpich and look for fortran library in "-L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran". After making and installing I ran into an issue with matlab and an invalid MEX-file, to fix that I had to create a symbolic link to matlab in /usr/bin. This was my final config file that I used. Thanks again!

#! /bin/sh ./configure \ --prefix=$ISSM_DIR \ --with-matlab-dir="/usr/local/MATLAB/R2020a" \ --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \ --with-mpi-include="$ISSM_DIR/externalpackages/mpich/install/include" \ --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpi -lmpicxx -lmpifort" \ --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \ --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \ --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \ --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install/" \ --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install/" \ --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \ --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran" \ --with-numthreads=2

justinquinn

zrashed No worries! Glad you got it working. Please let us know if you run into any further issues.