On Tue, Jan 3, 2017 at 9:46 AM, Klaij, Christiaan <c.kl...@marin.nl> wrote:
> 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) > That is missing the fix. You can insert those few lines: https://bitbucket.org/petsc/petsc/commits/32cc76960ddbb48660f8e7c667e293 c0ccd0e7d7 Or get the new tarball when it spins tonight, since Satish has just added the fix to maint. Thanks, Matt > dr. ir. Christiaan Klaij | CFD Researcher | Research & Development > MARIN | T +31 317 49 33 44 <+31%20317%20493%20344> | c.kl...@marin.nl | > www.marin.nl > > [image: LinkedIn] <https://www.linkedin.com/company/marin> [image: > YouTube] <http://www.youtube.com/marinmultimedia> [image: Twitter] > <https://twitter.com/MARIN_nieuws> [image: 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 <knep...@gmail.com> > *Sent:* Tuesday, January 03, 2017 4:36 PM > *To:* Klaij, Christiaan > *Cc:* petsc-users@mcs.anl.gov > *Subject:* Re: [petsc-users] problems after glibc upgrade to 2.17-157 > > On Tue, Jan 3, 2017 at 9:04 AM, Klaij, Christiaan <c.kl...@marin.nl> > 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/32cc76960ddbb48660f8e7c667e293 > c0ccd0e7d7 > > 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:c.kl...@marin.nl | >> 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 > > -- 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