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

[Klaij, Christiaan]

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.

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.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

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