On Wed, Jan 4, 2017 at 3:16 AM, Klaij, Christiaan <[email protected]> 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:[email protected] | 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 <[email protected]> > Sent: Tuesday, January 03, 2017 5:00 PM > To: Matthew Knepley > Cc: Klaij, Christiaan; [email protected] > 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
