Petsc and ISSM compile error: _METIS_PartMeshNodal

johannesbondzio

Dear all,

I have trouble reinstalling ISSM for the first time since a longer while on my system (mac, 64 bit). I had to configure PETSC using --with-shared-libraries=0, otherwise the compilation would fail. The hint used here didn't help. Then with PETSC compiled I attempted to compile ISSM, but ran into the following error:

ld: targeted OS version does not support use of thread local variables in _METIS_PartMeshNodal for architecture x86_64

collect2: ld returned 1 exit status

make: *** Error 1

I guess it has to do with the faulty PETSC compilation. Any suggestions which flags to set there?

Best, Johannes

johannesbondzio

Hello again,

an update to the above issue. The error was due to a faulty compiler used.

I updated Xcode to version 5.1 (this might not have helped solving the issue, but I mention it for completeness). Then I had to recompile MPICH3.0 with the "real" gcc (version 4.8) from macports. Apple Xcode's gcc is a llvm one, and does apparently not work for Petsc 3.5. (Mathieu recommended to compile the current version of Petsc while I’m at it). After compiling MPICH, I reconfigured Petsc without fblaslapack, as suggested by the Petsc maintainers, but no other tweaks had to be applied as Petsc's make was then using the mpicc/mpicxx from MPICH, which ran as a charm.

During Petsc make install I had to reset $PETSC_DIR to $ISSM_DIR/externalpackages/petsc/src, as it was set to $ISSM_DIR/externalpackages/petsc/install during an earlier sourcing of etc/environment.sh which lead to an error.

ISSM itself then compiled only with Apple's own cc/gcc. I might come back to that later.

Best,

Johannes