Problem installing petsc on a Blue Gene/L

[Shi Jin]

Thank you very much.
I did 
1. ./configure --CC=mpixlc --FC=mpixlf77 --with-batch --download-f-blas-lapack=1
=================================================================================
    Since your compute nodes require use of a batch system or mpiexec you must:
 1) Submit ./conftest to 1 processor of your batch system or system you are    
    cross-compiling for; this will generate the file reconfigure.py            
 2) Run ./reconfigure.py (to complete the configure process).                  
=================================================================================
2.  mpirun -partition R001 -n 1 -mode vn  -cwd $PWD -exe $PWD/conftest
But it exited with error during the run. I see the output file
sjin at fen1 petsc-3.0.0-p0 $ cat reconfigure.py
#!/usr/bin/python

configure_options = [
 '--with-memcmp-ok',  '--sizeof_char=1',
  '--sizeof_void_p=4',
  '--sizeof_short=2',
  '--sizeof_int=4',
  '--sizeof_long=4',
  '--sizeof_long_long=8',
  '--sizeof_float=4',
  '--sizeof_double=8',
  '--sizeof_size_t=4',
 '--bits_per_byte=8',
  '--sizeof_MPI_Comm=4',
  '--sizeof_MPI_Fint=4',
sjin at fen1 petsc-3.0.0-p0 $

It is not complete and error must have happened after sizeof_MPI_Fint. The good news is that the sizeof(char) error is no longer there once we do the batch mode. I am wondering if there is a way to keep the conftest.c source and relevant header files (I think they are created temporarily and deleted after the built). This way, it would be fairly easy to figure out which part is having problem. 
Please help.
Thank you very much.
--
Shi Jin, PhD


--- On Mon, 12/29/08, Barry Smith <bsmith at mcs.anl.gov> wrote:

> From: Barry Smith <bsmith at mcs.anl.gov>
> Subject: Re: Problem installing petsc on a Blue Gene/L
> To: petsc-users at mcs.anl.gov
> Date: Monday, December 29, 2008, 10:34 AM
> Since the BlueGene is a batch system you need the additional
> option --with-batch and follow
> the directions.
> 
>    Barry
> 
> On Dec 29, 2008, at 4:34 AM, Shi Jin wrote:
> 
> > Hi there,
> > 
> > I have been trying to install petsc-3.0 on a Blue
> Gene/L system.
> > Here is what I used to configure:
> > ./configure --CC=blrts_xlc
> --CFLAGS="-I/bgl/BlueLight/ppcfloor/bglsys/include
> -qtune=440 -qarch=440d -qlist -qsource  -O3   
> -L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts
> -lmsglayer.rts -lrts.rts -ldevices.rts"
> --with-mpi-compilers=0 --with-fortran=0
> > 
> > I got an error as following:
> > TESTING: checkSizeof from
> config.types(/gpfs/bglscratch/pi/sjin/src/petsc-3.0.0-p0/config/BuildSystem/config/types.py:251)
> >
> *********************************************************************************
> >         UNABLE to CONFIGURE with GIVEN OPTIONS    (see
> configure.log for details):
> >
> ---------------------------------------------------------------------------------------
> > Unable to determine sizeof_char
> >
> *********************************************************************************
> > 
> > Here is the relevant configure.log part:
> > TEST checkSizeof from
> config.types(/gpfs/bglscratch/pi/sjin/src/petsc-3.0.0-p0/config/BuildSystem/config/types.py:251)
> > TESTING: checkSizeof from
> config.types(/gpfs/bglscratch/pi/sjin/src/petsc-3.0.0-p0/config/BuildSystem/config/types.py:251)
> >  Determines the size of type "typeName", and
> defines SIZEOF_"typeName" to be the size
> > Checking for size of type: char
> >          Pushing language C
> > sh: blrts_xlc -c -o conftest.o
> -I/bgl/BlueLight/ppcfloor/bglsys/include -qtune=440
> -qarch=440d -qlist -qsource  -O3   
> -L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts
> -lmsglayer.rts -lrts.rts -ldevices.rts -g  conftest.c
> > Executing: blrts_xlc -c -o conftest.o
> -I/bgl/BlueLight/ppcfloor/bglsys/include -qtune=440
> -qarch=440d -qlist -qsource  -O3   
> -L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts
> -lmsglayer.rts -lrts.rts -ldevices.rts -g  conftest.c
> > sh:
> >                      Pushing language C
> >                      Popping language C
> > sh: blrts_xlc  -o conftest  
> -I/bgl/BlueLight/ppcfloor/bglsys/include -qtune=440
> -qarch=440d -qlist -qsource  -O3   
> -L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts
> -lmsglayer.rts -lrts.rts -ldevices.rts -g  conftest.o
> > Executing: blrts_xlc  -o conftest  
> -I/bgl/BlueLight/ppcfloor/bglsys/include -qtune=440
> -qarch=440d -qlist -qsource  -O3   
> -L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts
> -lmsglayer.rts -lrts.rts -ldevices.rts -g  conftest.o
> > sh:
> > Executing: ./conftest
> > sh: ./conftest
> > Executing: ./conftest
> > sh:
> > ERROR while running executable: Could not execute
> './conftest':
> >
> *********************************************************************************
> >         UNABLE to CONFIGURE with GIVEN OPTIONS    (see
> configure.log for details):
> >
> ---------------------------------------------------------------------------------------
> > Unable to determine sizeof_char
> >
> *********************************************************************************
> >  File "./configure", line 217, in
> petsc_configure
> >    framework.configure(out = sys.stdout)
> >  File
> "/gpfs/bglscratch/pi/sjin/src/petsc-3.0.0-p0/config/BuildSystem/config/framework.py",
> line 884, in configure
> >    child.configure()
> >  File
> "/gpfs/bglscratch/pi/sjin/src/petsc-3.0.0-p0/config/BuildSystem/config/types.py",
> line 353, in configure
> >    map(lambda type: self.executeTest(self.checkSizeof,
> type), ['char','void *', 'short',
> 'int', 'long', 'long long',
> 'float', 'double', 'size_t'])
> >  File
> "/gpfs/bglscratch/pi/sjin/src/petsc-3.0.0-p0/config/BuildSystem/config/types.py",
> line 353, in <lambda>
> >    map(lambda type: self.executeTest(self.checkSizeof,
> type), ['char','void *', 'short',
> 'int', 'long', 'long long',
> 'float', 'double', 'size_t'])
> >  File
> "/gpfs/bglscratch/pi/sjin/src/petsc-3.0.0-p0/config/BuildSystem/config/base.py",
> line 97, in executeTest
> >    ret = apply(test, args,kargs)
> >  File
> "/gpfs/bglscratch/pi/sjin/src/petsc-3.0.0-p0/config/BuildSystem/config/types.py",
> line 275, in checkSizeof
> >    raise RuntimeError('Unable to determine
> '+typename)
> > 
> > Do you know what could be my possible cause of the
> error?
> > I wrote a simple C test code and was able to show that
> sizeof(char)=1. Is there a way to get the conftest.c code
> and try it out manually?
> > Thanks a lot.
> > 
> > --
> > Shi Jin, PhD
> > 
> > 
> > 
> >