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

Wed Jan 4 07:21:25 CST 2017

Our sysadmin says that SL7 does not provide the debug version of glibc.

Chris

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: Wednesday, January 04, 2017 1:40 PM
To: Klaij, Christiaan
Cc: petsc-users; Satish Balay
Subject: Re: [petsc-users] problems after glibc upgrade to 2.17-157

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