On Tue, Jan 3, 2017 at 9:04 AM, Klaij, Christiaan <[email protected]> wrote:
> > I've been using petsc-3.7.4 with intel mpi and compilers, > superlu_dist, metis and parmetis on a cluster running > SL7. Everything was working fine until SL7 got an update where > glibc was upgraded from 2.17-106 to 2.17-157. > I cannot see the error in your log. We previously fixed a bug with this error reporting: https://bitbucket.org/petsc/petsc/commits/32cc76960ddbb48660f8e7c667e293c0ccd0e7d7 in August. Is it possible that your PETSc is older than this? Could you apply that patch, or run the configure with 'master'? My guess is this is a dynamic library path problem, as it always is after upgrades. Thanks, Matt > This update seemed to have broken (at least) parmetis: the > standalone binary gpmetis started to give a segmentation > fault. The core dump shows this: > > Core was generated by `gpmetis'. > Program terminated with signal 11, Segmentation fault. > #0 0x00002aaaac6b865e in memmove () from /lib64/libc.so.6 > > That's when I decided to recompile, but to my surprise I cannot > even get past the configure stage (log attached)! > > ************************************************************ > ******************* > UNABLE to EXECUTE BINARIES for ./configure > ------------------------------------------------------------ > ------------------- > Cannot run executables created with FC. If this machine uses a batch system > to submit jobs you will need to configure using ./configure with the > additional option --with-batch. > Otherwise there is problem with the compilers. Can you compile and run > code with your compiler 'mpif90'? > See http://www.mcs.anl.gov/petsc/documentation/faq.html#libimf > ************************************************************ > ******************* > > Note the following: > > 1) Configure was done with the exact same options that worked > fine before the update of SL7. > > 2) The intel mpi and compilers are exactly the same as before the > update of SL7. > > 3) The cluster does not require a batch system to run code. > > 4) I can compile and run code with mpif90 on this cluster. > > 5) The problem also occurs on a workstation running SL7. > > Any clues on how to proceed? > Chris > > > dr. ir. Christiaan Klaij | CFD Researcher | Research & Development > MARIN | T +31 317 49 33 44 | mailto:[email protected] | http://www.marin.nl > > MARIN news: http://www.marin.nl/web/News/News-items/Comparison-of- > uRANS-and-BEMBEM-for-propeller-pressure-pulse-prediction.htm > > -- 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
