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.kl...@marin.nl<mailto:c.kl...@marin.nl> | www.marin.nl<http://www.marin.nl> [LinkedIn]<https://www.linkedin.com/company/marin> [YouTube] <http://www.youtube.com/marinmultimedia> [Twitter] <https://twitter.com/MARIN_nieuws> [Facebook] <https://www.facebook.com/marin.wageningen> MARIN news: Modelling natural transition on hydrofoils for application in underwater gliders<http://www.marin.nl/web/News/News-items/Modelling-natural-transition-on-hydrofoils-for-application-in-underwater-gliders-1.htm> ________________________________ From: Matthew Knepley <knep...@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.kl...@marin.nl<mailto:c.kl...@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.kl...@marin.nl<mailto:c.kl...@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 <ba...@mcs.anl.gov<mailto:ba...@mcs.anl.gov>> Sent: Tuesday, January 03, 2017 5:00 PM To: Matthew Knepley Cc: Klaij, Christiaan; petsc-users@mcs.anl.gov<mailto:petsc-users@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
