disk space requirement for mpich2 during PETSc library compilation

[Ben Tay]

Hi,

I've tried to use the shared version of mpich2 which I installed seperately
(due to above problem) with PETSc. The command is

./config/configure.py --with-fc=/lsftmp/g0306332/inter/fc/bin/ifort
--with-blas-lapack-dir=/lsftmp/g0306332/inter/mkl/
--with-mpi-dir=/lsftmp/g0306332/mpich2-l32 --with-x=0 --with-shared

During the test, this error msg was shown:

gcc -c -fPIC -Wall -Wwrite-strings -g3
-I/nas/lsftmp/g0306332/petsc-2.3.2-p8-I/nas/lsftmp/g0306332/petsc-
2.3.2-p8/bmake/linux-mpich2 -I/nas/lsftmp/g0306332/petsc-2.3.2-p8/include
-I/lsftmp/g0306332/mpich2-l32/include
-D__SDIR__="src/snes/examples/tutorials/" ex19.c
gcc -fPIC -Wall -Wwrite-strings -g3  -o ex19
ex19.o-Wl,-rpath,/nas/lsftmp/g0306332/petsc-
2.3.2-p8/lib/linux-mpich2
-L/nas/lsftmp/g0306332/petsc-2.3.2-p8/lib/linux-mpich2
-lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc
-Wl,-rpath,/lsftmp/g0306332/mpich2-l32/lib -L/lsftmp/g0306332/mpich2-l32/lib
-lmpich -lnsl -laio -lrt -Wl,-rpath,/lsftmp/g0306332/inter/mkl/lib/32
-L/lsftmp/g0306332/inter/mkl/lib/32 -lmkl_lapack -lmkl_def -lguide -lvml
-lpthread -lm -Wl,-rpath,/usr/lib/gcc-lib/i386-pc-linux/3.2.3
-L/usr/lib/gcc-lib/i386-pc-linux/3.2.3
-Wl,-rpath,/usr/lib/gcc-lib/i386-pc-linux/3.2.3/../../..
-L/usr/lib/gcc-lib/i386-pc-linux/3.2.3/../../.. -ldl -lgcc_eh
-Wl,-rpath,"/usr/lib/gcc-lib/i386-pc-linux/3.2.3"
-Wl,-rpath,"/usr/lib/gcc-lib/i386-pc-linux/3.2.3/../../.."
-Wl,-rpath,/lsftmp/g0306332/inter/fc/lib -L/lsftmp/g0306332/inter/fc/lib
-Wl,-rpath,/usr/lib/gcc-lib/i386-pc-linux/3.2.3/
-L/usr/lib/gcc-lib/i386-pc-linux/3.2.3/
-Wl,-rpath,/usr/lib/gcc-lib/i386-pc-linux/3.2.3/../../../
-L/usr/lib/gcc-lib/i386-pc-linux/3.2.3/../../../ -lifport -lifcore -limf -lm
-lipgo -lirc -lgcc_s -lirc_s -Wl,-rpath,/usr/lib/gcc-lib/i386-pc-linux/3.2.3
-Wl,-rpath,/usr/lib/gcc-lib/i386-pc-linux/3.2.3/../../.. -lm
-Wl,-rpath,/usr/lib/gcc-lib/i386-pc-linux/3.2.3
-L/usr/lib/gcc-lib/i386-pc-linux/3.2.3
-Wl,-rpath,/usr/lib/gcc-lib/i386-pc-linux/3.2.3/../../..
-L/usr/lib/gcc-lib/i386-pc-linux/3.2.3/../../.. -ldl -lgcc_eh -ldl
/nas/lsftmp/g0306332/petsc-2.3.2-p8/lib/linux-mpich2/libpetsc.so: undefined
reference to `mpi_conversion_fn_null_'
collect2: ld returned 1 exit status

Then I tried to my fortran example.

I realised that if I compile using ifort (using command similar to "make
ex1f", there is no problem but the result shown that 4 processors are
running 4 *individual* codes.

I then tried to use the mpif90 in the mpich2 directory. compiling was ok but
during linking the error was:

 /lsftmp/g0306332/mpich2-l32/bin/mpif90  -fPIC -g   -o ex2f ex2f.o
-Wl,-rpath,/nas/lsftmp/g0306332/petsc-2.3.2-p8/lib/linux-mpich2
-L/nas/lsftmp/g0306332/petsc-2.3.2-p8/lib/linux-mpich2 -lpetscksp -lpetscdm
-lpetscmat -lpetscvec -lpetsc    -Wl,-rpath,/lsftmp/g0306332/mpich2-l32/lib
-L/lsftmp/g0306332/mpich2-l32/lib -lmpich -lnsl -laio -lrt
-Wl,-rpath,/lsftmp/g0306332/inter/mkl/lib/32
-L/lsftmp/g0306332/inter/mkl/lib/32 -lmkl_lapack -lmkl_def -lguide -lvml
-lpthread -lm -Wl,-rpath,/usr/lib/gcc-lib/i386-pc-linux/3.2.3
-L/usr/lib/gcc-lib/i386-pc-linux/3.2.3
-Wl,-rpath,/usr/lib/gcc-lib/i386-pc-linux/3.2.3/../../..
-L/usr/lib/gcc-lib/i386-pc-linux/3.2.3/../../.. -ldl -lgcc_eh
-Wl,-rpath,"/usr/lib/gcc-lib/i386-pc-linux/3.2.3"
-Wl,-rpath,"/usr/lib/gcc-lib/i386-pc-linux/3.2.3/../../.."
-Wl,-rpath,/lsftmp/g0306332/inter/fc/lib -L/lsftmp/g0306332/inter/fc/lib
-Wl,-rpath,/usr/lib/gcc-lib/i386-pc-linux/3.2.3/
-L/usr/lib/gcc-lib/i386-pc-linux/3.2.3/
-Wl,-rpath,/usr/lib/gcc-lib/i386-pc-linux/3.2.3/../../../
-L/usr/lib/gcc-lib/i386-pc-linux/3.2.3/../../../ -lifport -lifcore -limf -lm
-lipgo -lirc -lgcc_s -lirc_s -Wl,-rpath,/usr/lib/gcc-lib/i386-pc-linux/3.2.3
-Wl,-rpath,/usr/lib/gcc-lib/i386-pc-linux/3.2.3/../../.. -lm
-Wl,-rpath,/usr/lib/gcc-lib/i386-pc-linux/3.2.3
-L/usr/lib/gcc-lib/i386-pc-linux/3.2.3
-Wl,-rpath,/usr/lib/gcc-lib/i386-pc-linux/3.2.3/../../..
-L/usr/lib/gcc-lib/i386-pc-linux/3.2.3/../../.. -ldl -lgcc_eh -ldl
/lsftmp/g0306332/inter/fc/lib/libifcore.so.5: undefined reference to
`__clog10q'
/lsftmp/g0306332/inter/fc/lib/libifcore.so.5: undefined reference to
`__cexp10q'
/lsftmp/g0306332/inter/fc/lib/libifcore.so.5: undefined reference to
`__csqrtq'
/lsftmp/g0306332/inter/fc/lib/libifcore.so.5: undefined reference to
`__ccoshq'
/lsftmp/g0306332/inter/fc/lib/libifcore.so.5: undefined reference to
`__ctanhq'
/lsftmp/g0306332/inter/fc/lib/libifcore.so.5: undefined reference to
`__ccosq'
/lsftmp/g0306332/inter/fc/lib/libifcore.so.5: undefined reference to
`__clogq'
/lsftmp/g0306332/inter/fc/lib/libifcore.so.5: undefined reference to
`__csinhq'
/lsftmp/g0306332/inter/fc/lib/libifcore.so.5: undefined reference to
`__ctanq'
/lsftmp/g0306332/inter/fc/lib/libifcore.so.5: undefined reference to
`__cpowq'
/lsftmp/g0306332/inter/fc/lib/libifcore.so.5: undefined reference to
`__exp10q'
/lsftmp/g0306332/inter/fc/lib/libifcore.so.5: undefined reference to
`__cexpq'
/lsftmp/g0306332/inter/fc/lib/libifcore.so.5: undefined reference to
`__cabsq'
/lsftmp/g0306332/inter/fc/lib/libifcore.so.5: undefined reference to
`__fabsq'
/lsftmp/g0306332/inter/fc/lib/libifcore.so.5: undefined reference to
`__csinq'
/lsftmp/g0306332/inter/fc/lib/libifcore.so.5: undefined reference to
`__ldexpq'
/lsftmp/g0306332/inter/fc/lib/libifcore.so.5: undefined reference to
`__frexpq'


So what is wrong? I am a novice in mpi so I hope someone can give some
advice. Thank you.

PS: Has the "make clean" on MPICH been updated on
BuildSystem/config/packages/MPI.py?


On 1/13/07, Ben Tay <zonexo at gmail.com> wrote:
>
> Thanks Barry & Aron.
>
> I've tried to install mpich2 on a scratch directory and it finished in a
> short while.
>
>
>  On 1/13/07, Barry Smith <bsmith at mcs.anl.gov> wrote:
> >
> >
> > Ben,
> >
> > This is partially our fault. We never run "make clean" on MPICH after
> > the
> > install so there are lots of .o and .a files lying around. I've updated
> > BuildSystem/config/packages/MPI.py to run make clean after the install.
> >
> >   Barry
> >
> > On Sat, 13 Jan 2007, Aron Ahmadia wrote:
> >
> > > Hi Ben,
> > >
> > > My PETSc install on an OS X machine requires about 343 MB of space,
> > > about 209 MB of which is MPICH.  Unfortunately this has the potential
> > > of exceeding 500 MB temporarily I believe as the make process
> > > generates a lot of object files during the software build.
> > >
> > > I think what you want to do is compile and install your own copy of
> > > MPICH (using a scratch directory or whatever tools you have at your
> > > disposal), then use the --with-mpi-dir=/location/to/mpich/install
> > > argument into configure.
> > >
> > > I've never staged a PETSc build on a machine with an extremely limited
> > > quota, the developers might have some suggestions on how to do this.
> > >
> > > ~A
> > >
> > > On 1/13/07, Ben Tay <zonexo at gmail.com> wrote:
> > > > Hi,
> > > >
> > > > I am trying to compile PETSc with mpi using --download-mpich=1 in
> > linux. The
> > > > command is
> > > >
> > > >
> > > >
> > > > ./config/configure.py
> > > > --with-fc=/lsftmp/g0306332/inter/fc/bin/ifort
> > > > --with-blas-lapack-dir=/lsftmp/g0306332/inter/mkl/
> > > > --download-mpich=1 --with-x=0 --with-shared
> > > >
> > > > It displays:
> > > >
> > > >
> > =================================================================================
> > > > Running configure on MPICH; this may take several
> > > > minutes
> > > >
> > =================================================================================
> > > >
> > =================================================================================
> > > > Running make on MPICH; this may take several
> > > > minutes
> > > >
> > =================================================================================
> > > >
> > > > then it says disk quota exceeded. I've about 450mb free space, which
> > is all
> > > > filled up when the error shows. May I know how much disk space is
> > required?
> > > >
> > > > Also can I compile just mpich on a scratch directory and then moved
> > it to
> > > > the PETSc externalpackages directory? Or do I have to compile
> > everything
> > > > (including PETSc) on a scratch directory and moved it my my
> > directory?
> > > >
> > > > thank you.
> > >
> > >
> >
> >
>
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