I've downloaded the tarball on October 24th:
$ ls -lh petsc-lite-3.7.4.tar.gz -rw-r--r-- 1 cklaij domain users 8.4M Oct 24 11:07 petsc-lite-3.7.4.tar.gz (no direct internet access on cluster) dr. ir. Christiaan Klaij | CFD Researcher | Research & Development MARIN | T +31 317 49 33 44 | [email protected]<mailto:[email protected]> | www.marin.nl<http://www.marin.nl> [LinkedIn]<https://www.linkedin.com/company/marin> [YouTube] <http://www.youtube.com/marinmultimedia> [Twitter] <https://twitter.com/MARIN_nieuws> [Facebook] <https://www.facebook.com/marin.wageningen> MARIN news: Modelling natural transition on hydrofoils for application in underwater gliders<http://www.marin.nl/web/News/News-items/Modelling-natural-transition-on-hydrofoils-for-application-in-underwater-gliders-1.htm> ________________________________ From: Matthew Knepley <[email protected]> Sent: Tuesday, January 03, 2017 4:36 PM To: Klaij, Christiaan Cc: [email protected] Subject: Re: [petsc-users] problems after glibc upgrade to 2.17-157 On Tue, Jan 3, 2017 at 9:04 AM, Klaij, Christiaan <[email protected]<mailto:[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<tel:%2B31%20317%2049%2033%2044> | mailto:[email protected]<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
