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

[Matthew Knepley]

On Wed, Jan 4, 2017 at 3:16 AM, Klaij, Christiaan <C.Klaij at marin.nl> wrote:

> Well, a bit clearer perhaps. It seems the relevant ERROR is on
> line 31039. So I did this case by hand using the compile and link
> lines from the log, then run it in gdb:
>
> $ pwd
> /tmp/petsc-Q0URwQ/config.setCompilers
> $ ls
> confdefs.h  conffix.h  conftest  conftest.F  conftest.o
> $ gdb
> GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-80.el7
> Copyright (C) 2013 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.
> html>
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
> and "show warranty" for details.
> This GDB was configured as "x86_64-redhat-linux-gnu".
> For bug reporting instructions, please see:
> <http://www.gnu.org/software/gdb/bugs/>.
> (gdb) file conftest
> Reading symbols from /tmp/petsc-Q0URwQ/config.
> setCompilers/conftest...done.
> (gdb) run
> Starting program: /tmp/petsc-Q0URwQ/config.setCompilers/conftest
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x00002aaaae32f65e in ?? ()
> Missing separate debuginfos, use: debuginfo-install
> glibc-2.17-157.el7.x86_64
> (gdb) bt
> #0  0x00002aaaae32f65e in ?? ()
> #1  0x00002aaaaaab7675 in _dl_relocate_object ()
>    from /lib64/ld-linux-x86-64.so.2
> #2  0x00002aaaaaaae792 in dl_main () from /lib64/ld-linux-x86-64.so.2
> #3  0x00002aaaaaac1e36 in _dl_sysdep_start () from
> /lib64/ld-linux-x86-64.so.2
> #4  0x00002aaaaaaafa31 in _dl_start () from /lib64/ld-linux-x86-64.so.2
> #5  0x00002aaaaaaac1e8 in _start () from /lib64/ld-linux-x86-64.so.2
> #6  0x0000000000000001 in ?? ()
> #7  0x00007fffffffd4e2 in ?? ()
> #8  0x0000000000000000 in ?? ()
> (gdb)
>
> Does this make any sense to you?


No. It looks like there is something deeply wrong with the dynamic loader.
You might  try

  debuginfo-install glibc-2.17-157.el7.x86_64

as it says so that we can see the stack trace. Considering that the error
happens inside of

  _dl_sysdep_start () from /lib64/ld-linux-x86-64.so.2

I am guessing that it is indeed connected to your upgrade of glibc. Since
it only happens when
you are not using compiler libraries, I think your compiler has pointers
back to old things in the
OS. I would recommend either a) using GNU as Satish says, or b)
reinstalling the whole compiler
suite.

I will look at the new problem when not using compiler libraries.

  Thanks,

    Matt


>
>
> 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/Software-seminar-
> in-Shanghai-for-the-first-time-March-28.htm
>
> ________________________________________
> From: Klaij, Christiaan
> Sent: Wednesday, January 04, 2017 9:26 AM
> To: Matthew Knepley; petsc-users; Satish Balay
> Subject: Re: [petsc-users] problems after glibc upgrade to 2.17-157
>
> So I've applied the patch to my current 3.7.4 source, the new
> configure.log is attached. It's slightly larger but not much
> clearer too me...
>
> Chris
> ________________________________________
> From: Satish Balay <balay at mcs.anl.gov>
> Sent: Tuesday, January 03, 2017 5:00 PM
> To: Matthew Knepley
> Cc: Klaij, Christiaan; petsc-users at mcs.anl.gov
> Subject: Re: [petsc-users] problems after glibc upgrade to 2.17-157
>
> On Tue, 3 Jan 2017, Matthew Knepley wrote:
>
> > Or get the new tarball when it spins tonight, since Satish has just
> > added the fix to maint.
>
> We don't spin 'maint/patch-release' tarballs everynight. Its every 1-3
> months - [partly depending upon the number of outstanding patches - or
> their severity]
>
> -rw-r--r-- 1 petsc pdetools 23194357 Jan  1 10:41 petsc-3.7.5.tar.gz
> -rw-r--r-- 1 petsc pdetools 23189526 Oct  2 22:06 petsc-3.7.4.tar.gz
> -rw-r--r-- 1 petsc pdetools 23172670 Jul 24 12:22 petsc-3.7.3.tar.gz
> -rw-r--r-- 1 petsc pdetools 23111802 Jun  5  2016 petsc-3.7.2.tar.gz
> -rw-r--r-- 1 petsc pdetools 23113397 May 15  2016 petsc-3.7.1.tar.gz
> -rw-r--r-- 1 petsc pdetools 22083999 Apr 25  2016 petsc-3.7.0.tar.gz
>
> Satish
>



-- 
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
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