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

Qin Lu lu_qin_2000 at yahoo.com
Thu Jan 9 15:32:41 CST 2014 

Can I specify the what version of Hypre to download? Do I need to use --with-hypre=1 and specify --with-hypre-dir? It will be nice if you may point me to a sample setting of configure options using --download-hypre.
 
Thanks,
Qin



On Thursday, January 9, 2014 3:07 PM, Matthew Knepley <knepley at gmail.com> wrote:
  
On Thu, Jan 9, 2014 at 3:05 PM, Qin Lu <lu_qin_2000 at yahoo.com> wrote:

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?

It will build it from source.

   Matt

 
>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>
>> > 
>> >
>> 
>
>
>    


-- 
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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