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

Tue Jan 3 09:46:39 CST 2017

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>

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________________________________
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

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