[petsc-users] Building Linux 32-bit PETSc lib

[Satish Balay]

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>
> > 
> >
>