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

Matthew Knepley knepley at gmail.com
Wed Jan 4 08:13:16 CST 2017 

On Wed, Jan 4, 2017 at 7:37 AM, Klaij, Christiaan <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
> *******************************************************************
>
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 <+31%20317%20493%20344> | C.Klaij at marin.nl |
> www.marin.nl
>
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> <http://www.marin.nl/web/News/News-items/MARIN-Report-119-highlighting-naval-research-projects.htm>
>
> ------------------------------
> *From:* Matthew Knepley <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>
> 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 | 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>
>> Sent: Tuesday, January 03, 2017 4:37 PM
>> To: Klaij, Christiaan
>> Cc: 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 | mailto:C.Klaij at marin.nl |
>> http://www.marin.nl
>> >
>> > MARIN news: http://www.marin.nl/web/News/N
>> ews-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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