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

[Satish Balay]

Do you have similar issues with gnu compilers?

It must be some incompatibility with intel compilers with this glibc change.

>>>>>>>>>
          compilers: Check that C libraries can be used from Fortran
                      Pushing language FC
                      Popping language FC
                      Pushing language FC
                      Popping language FC
                          Pushing language FC
                          Popping language FC
**** Configure header /tmp/petsc-rOjdnN/confdefs.h ****
<<<<<<<<<<

Thre is a bug in configure [Matt?] that eats away some of the log - so
I don't see the exact error you are getting.

If standalone micc/mpif90 etc work - then you can try the following additional options:

--with-clib-autodetect=0 --with-fortranlib-autodetect=0 --with-cxxlib-autodetect=0 LIBS=LIBS=/path_to/libifcore.a

[replace "path_to" with the correct path to the ifort lubifcore.a library]

Note: I have a RHEL7 box with this glibc - and I don't see this issue.

>>>>
-bash-4.2$ cat /etc/redhat-release 
Red Hat Enterprise Linux Server release 7.3 (Maipo)
-bash-4.2$ rpm -q glibc
glibc-2.17-157.el7_3.1.x86_64
glibc-2.17-157.el7_3.1.i686
-bash-4.2$ mpiicc --version
icc (ICC) 17.0.0 20160721
Copyright (C) 1985-2016 Intel Corporation.  All rights reserved.

-bash-4.2$ 
<<<<

Satish

On Tue, 3 Jan 2017, Klaij, Christiaan 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.
> 
> 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
> 
>