[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: disk space requirement for mpich2 during PETSc library compilation
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@xxxxxxxxx> 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@xxxxxxxxxxx
> 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@xxxxxxxxx> 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.
>
>