[petsc-users] problems after glibc upgrade to 2.17-157

[Satish Balay]

The patch that Matt mentioned is in 'master' branch - so its not in
3.7.4. I've now added it to 'maint' branch - so it should be in next
petsc patch tarball [i.e 3.7.6] - whenever its released.

You can apply the patch to your current sources - that should tell us
the exact error you get with the intel compiler.

To workarround - you would still have to follow my suggestion [i.e
disable autodetect..]

Satish

On Tue, 3 Jan 2017, Klaij, Christiaan 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)
> 
> dr. ir. Christiaan Klaij | CFD Researcher | Research & Development
> MARIN | T +31 317 49 33 44 | C.Klaij at marin.nl<mailto:C.Klaij at marin.nl> | 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 <knepley at gmail.com>
> Sent: Tuesday, January 03, 2017 4:36 PM
> To: Klaij, Christiaan
> Cc: petsc-users at 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.Klaij at marin.nl<mailto:C.Klaij at 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/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:C.Klaij at marin.nl<mailto:C.Klaij at 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
> 
> 
>