[petsc-users] Building Linux 32-bit PETSc lib
Qin Lu
lu_qin_2000 at yahoo.com
Thu Jan 9 15:05:00 CST 2014
Is the linker ld compitable with Intel compilers?
If I use --download-hypre=1, will it download the 32-bit Hypre lib that is consistent with my MPI lib and my PETSc lib built with Intel compilers?
Thanks,
Qin
On Thursday, January 9, 2014 11:43 AM, Satish Balay <balay at mcs.anl.gov> wrote:
Well the compiler [ld] doesn't appear to like the hypre library you built.
What do you have for:
file /d/dev01/qlu/Lib/hypre-2.8.0b/LINUX_32/lib/libHYPRE.a
Why not use --download-hypre=1 ?
Satish
On Thu, 9 Jan 2014, Qin Lu wrote:
> Now it got new problem later in configure: it does not like the Hypre lib :"Possible ERROR while running linker: ld: skipping incompatible /d/dev01/qlu/Lib/hypre-2.8.0b/LINUX_32/lib/libHYPRE.a when searching for -lHYPRE". Please see the attached log file for details.
>
> I built the Hypre-2.8.0b using the same Intel compilers as PETSc.
>
> Thanks for any ideas,
> Qin
>
>
>
> On Thursday, January 9, 2014 9:25 AM, Qin Lu <lu_qin_2000 at yahoo.com> wrote:
>
> Thanks a lot for pointing out the problem. Configure passed it after I set the path of libirc.so.
>
> Regards,
> Qin
>
>
>
> On Wednesday, January 8, 2014 4:25 PM, Satish Balay <balay at mcs.anl.gov> wrote:
>
> > ('Linux', 'houhpclc01', '2.6.18-308.4.1.el5', '#1 SMP Tue Apr 17 17:08:10 EDT 2012', 'i686', 'i686')
>
> the machine appears to to be running 32bit linux - so I'm not sure why it has a 64bit libirc.so
>
> [and the paths linker is referencing to are 32bit library paths]
>
> The workarround to try [for intel compilers] is:
>
> --with-clib-autodetect=0 --with-fortranlib-autodetect=0 --with-cxxlib-autodetect=0 LIBS="-Bstatic -lifcore -Bdynamic"
>
> Satish
>
>
> The On Wed, 8 Jan 2014, Barry Smith wrote:
>
> >
> > Here is how icc is linking a C main program:
> >
> > ld --eh-frame-hdr -dynamic-linker /lib/ld-linux.so.2 -m elf_i386 -o /tmp/petsc-3SW45q/config.compilers/conftest -L/apps/compilers/intel/Compiler/11.1/056/lib/ia32
> -L/usr/lib/gcc/i386-redhat-linux/4.1.2/ -L/usr/lib/gcc/i386-redhat-linux/4.1.2/../../../ -L/lib/ -L/usr/lib /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crt1.o /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crti.o /usr/lib/gcc/i386-redhat-linux/4.1.2/crtbegin.o /tmp/petsc-3SW45q/config.compilers/conftest.o -ldl -Bstatic -limf -lsvml -Bdynamic -lm -Bstatic -lipgo -ldecimal -Bdynamic -lgcc_s -lgcc -Bstatic -lirc -Bdynamic -lc -lgcc_s -lgcc -Bstatic -lirc_s -Bdynamic -ldl -lc /usr/lib/gcc/i386-redhat-linux/4.1.2/crtend.o /usr/lib/gcc/i386-redhat-linux/4.1.2/../../../crtn.o
> >
> > Since PETSc uses C if you use Fortran it needs to link against this same stuff with the intel Fortran linker. We try to rationalize the above list and get
> >
> > Libraries needed to link C code with another linker: ['-ldl', '-L/apps/compilers/intel/Compiler/11.1/056/lib/ia32',
> '-L/usr/lib/gcc/i386-redhat-linux/4.1.2', '-limf', '-lsvml', '-lipgo', '-ldecimal', '-lgcc_s', '-lirc', '-lirc_s', '-L/apps/compilers/intel/Compiler/11.1/056/lib/ia32', '-L/usr/lib/gcc/i386-redhat-linux/4.1.2’]
> >
> > So when it uses ifort to link something it uses
> >
> > /apps/compilers/intel/Compiler/11.1/056/bin/ia32/ifort -o /tmp/petsc-3SW45q/config.setCompilers/conftest -O3 /tmp/petsc-3SW45q/config.setCompilers/conftest.o -ldl -L/apps/compilers/intel/Compiler/11.1/056/lib/ia32 -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -limf -lsvml -lipgo -ldecimal -lgcc_s -lirc -lirc_s -L/apps/compilers/intel/Compiler/11.1/056/lib/ia32 -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -ldl
> >
> > which when running the code results in
> >
> > ERROR while running executable: Could not execute
> "/tmp/petsc-3SW45q/config.setCompilers/conftest":
> > /tmp/petsc-3SW45q/config.setCompilers/conftest: error while loading shared libraries: libirc.so: wrong ELF class: ELFCLASS64
> >
> > Because the -Bstatic are stripped from the link line the wrong libirc.so gets picked up by the linker resulting in the runtime error.
> >
> > I’ve seen these perverse icc link lines mess things up before but don’t remember a solution. Satish must remember!
> >
> > Is there a reason to use the 32bit version? Have you tried using the 64 bit compilers ? Generally I don’t think there is a reason to use 32bit now a days.
> >
> > Barry
> >
> >
> >
> >
> >
> >
> > On Jan 8, 2014, at 3:21
> PM, Qin Lu <lu_qin_2000 at yahoo.com> wrote:
> >
> > > Hello,
> > >
> > > I am trying to build a Linux 32-bit PETSc lib. I first built python-2.7.5 in a 32-bit Linux workstation without problem, then used this python to configure PETSc-3.4.2 with Intel C/C++/Fortran compilers, it got the following error:
> > >
> > > =============================================================================== TESTING: checkCLibraries from
> config.compilers(config/BuildSystem/config/compilers.py:161) *******************************************************************************
> > > 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 C/C++ (and maybe Fortran) compilers?
> > > See http://www.mcs.anl.gov/petsc/documentation/faq.html#libimf
> > > *******************************************************************************
> > >
> > > It seems that a test program built with the given Intel ifort does not run. But I have built another program using ifort in the same workstation and it runs fine.
> > >
> > > Please see the attached configure.log file for details.
> > >
> > > Thanks for your suggestions!
> > >
> > > Regards,
> > > Qin
> > >
> > >
> > >
> <configure.log>
> >
> >
>
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