On Wed, Jan 4, 2017 at 4:32 AM, Klaij, Christiaan <c.kl...@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.kl...@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 <ba...@mcs.anl.gov> > Sent: Tuesday, January 03, 2017 4:37 PM > To: Klaij, Christiaan > Cc: petsc-users@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.kl...@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