[petsc-users] problems after glibc upgrade to 2.17-157
Klaij, Christiaan
C.Klaij at marin.nl
Wed Jan 4 08:53:30 CST 2017
So how would I do that? Does LIBS=<string> accept spaces in the string? Something like this perhaps:
LIBS="-L/cm/shared/apps/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64_lin -lifcore"
But I'm starting to believe that my intel install is somehow broken. I'm getting these intel compilers from rpm's provided by our cluster vendor. On a workstation I can try yum remove and install of the intel packages. Not so easy on a production cluster. Is this worth a try? Or will it just copy/paste the same broken (?) stuff in the same place?
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 3:13 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 7:37 AM, Klaij, Christiaan <C.Klaij at marin.nl<mailto:C.Klaij at marin.nl>> wrote:
I've tried with:
--LIBS=/cm/shared/apps/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64_lin/libifcore.a -lstdc++\\
This is likely connected to the problem below, but I would have to see the log.
but that doesn't seem to make a difference.
With the option --with-cxx=0 the configure part does work(!), but then I get
**************************ERROR*************************************
Error during compile, check Linux-x86_64-Intel/lib/petsc/conf/make.log
Send it and Linux-x86_64-Intel/lib/petsc/conf/configure.log to petsc-maint at mcs.anl.gov<mailto:petsc-maint at mcs.anl.gov>
*******************************************************************
Here is the problem:
CLINKER /projects/developers/cklaij/ReFRESCO/Dev/trunk/Libs/build/petsc-3.7.4/Linux-x86_64-Intel/lib/libpetsc.so.3.7.4
ld: /cm/shared/apps/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64_lin/libifcore.a(for_init.o): relocation R_X86_64_32 against `.rodata.str1.4' can not be used when making a shared object; recompile with -fPIC
/cm/shared/apps/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64_lin/libifcore.a: could not read symbols: Bad value
Clearly there is something wrong with the compiler install.
However, can you put a libifcore.so in LIBS instead?
Matt
See the attached log files.
Chris
dr. ir. Christiaan Klaij | CFD Researcher | Research & Development
MARIN | T +31 317 49 33 44<tel:+31%20317%20493%20344> | 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<mailto:knepley at gmail.com>>
Sent: Wednesday, January 04, 2017 1:43 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 4:32 AM, Klaij, Christiaan <C.Klaij at marin.nl<mailto:C.Klaij at marin.nl>> wrote:
Satish,
I tried your suggestion:
--with-clib-autodetect=0 --with-fortranlib-autodetect=0 --with-cxxlib-autodetect=0 LIBS=LIBS=/path_to/libifcore.a
I guess I don't really need "LIBS= " twice (?) so I've used this line:
LIBS=/cm/shared/apps/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64_lin/libifcore.a
Unfortunately, this approach also fails (attached log):
Ah, this error is much easier:
Executing: mpif90 -o /tmp/petsc-3GfeyZ/config.compilers/conftest -fPIC -g -O3 /tmp/petsc-3GfeyZ/config.compilers/conftest.o /tmp/petsc-3GfeyZ/config.compilers/cxxobj.o /tmp/petsc-3GfeyZ/config.compilers/confc.o -ldl /cm/shared/apps/intel/compilers_and_libraries_2016.3.210/linux/compiler/lib/intel64_lin/libifcore.a
Possible ERROR while running linker: exit code 256
stderr:
/tmp/petsc-3GfeyZ/config.compilers/cxxobj.o:(.gnu.linkonce.d.DW.ref.__gxx_personality_v0+0x0): undefined reference to `__gxx_personality_v0'
Intel as lazy writing its C++ compiler, so it uses some of g++. If you want to use C++, you will need to add -lstdc++ to your LIBS variable (I think).
Otherwise, please turn it off using --with-cxx=0.
Thanks,
Matt
*******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
-------------------------------------------------------------------------------
Fortran could not successfully link C++ objects
*******************************************************************************
There are multiple libifcore.a in the intel compiler lib: one in intel64_lin and one in intel64_lin_mic. Tried both, got same error.
Chris
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
MARIN news: http://www.marin.nl/web/News/News-items/Comparison-of-uRANS-and-BEMBEM-for-propeller-pressure-pulse-prediction.htm
________________________________________
From: Satish Balay <balay at mcs.anl.gov<mailto:balay at mcs.anl.gov>>
Sent: Tuesday, January 03, 2017 4:37 PM
To: Klaij, Christiaan
Cc: 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
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<tel:%2B31%20317%2049%2033%2044> | mailto:C.Klaij at marin.nl<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
>
>
--
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
--
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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