Hi, Maybe there is a problem with the output-to-screen buffer. A not very uncommon problem if you use a job-scheduler. Try to add unbuffer (if it is available in your system) in your script file and see if it improves.
More information regarding unbuffer can be found here http:// expect.nist.gov/example/unbuffer.man.html With best regards, Shaman Mahmoudi On Jan 16, 2007, at 8:56 AM, Ben Tay wrote: > Hi Pan, > > I also got very big library files if I use PETSc with mpich2. > > Btw, I have tried several options but I still don't understand why > I can't get mpi to work with PETSc. > > The 4 processors are running together but each running its own code. > > I just use > > integer :: nprocs,rank,ierr > > call PetscInitialize(PETSC_NULL_CHARACTER,ierr) > > call MPI_Comm_rank(PETSC_COMM_WORLD,rank,ierr) > > call MPI_Comm_size(PETSC_COMM_WORLD,nprocs,ierr) > > print *, rank, nprocs > > call PetscFinalize(ierr) > > > The answers I get is 0,1 repeated 4 times instead of 0,4 1,4 2,4 3,4. > > I'm using my school's server's mpich and it work if I just compile > in pure mpi. > > Btw, if I need to send the job to 4 processors, I need to use a > script file: > > #BSUB -o std-output > #BSUB -q linux_parallel_test > #BSUB -n 4 > /usr/lsf6/bin/mpijob_gm /opt/mpich/myrinet/intel/bin/mpirun a.out > > I wonder if the problem lies here... > > > Thank you. > > > > > On 1/16/07, li pan <li76pan at yahoo.com> wrote: > I did try to download and install petsc2.3.2, but end > up with error: mpich can not be download & installed, > please install mpich for windows manually. > In the homepage of mpich2, I didn't choose the version > for windows but the source code version. And compiled > it by myself. Then, I gave the --with-mpi-dir="install > dir". Petsc was configured, and now it's doing "make". > One interesting thing is, I installed petsc in linux > before. The mpi libraries were very large > (libmpich.a==60 mb). But this time in cygwin it was > only several mbs. > > best > > pan > > > --- Ben Tay <zonexo at gmail.com> wrote: > > > hi, > > > > i install PETSc using the following command: > > > > ./config/configure.py --with-vendor-compilers=intel > > --with-gnu-compilers=0 > > > --with-blas-lapack-dir=/lsftmp/g0306332/inter/mkl/lib/32 > > --with-mpi-dir=/opt/mpich/intel/ --with-x=0 > > --with-shared > > > > then i got: > > > > Compilers: > > > > C Compiler: /opt/mpich/intel/bin/mpicc > > -fPIC -g > > Fortran Compiler: /opt/mpich/intel/bin/mpif90 > > -I. -fPIC -g -w90 -w > > Linkers: > > Shared linker: /opt/mpich/intel/bin/mpicc > > -shared -fPIC -g > > Dynamic linker: /opt/mpich/intel/bin/mpicc > > -shared -fPIC -g > > PETSc: > > PETSC_ARCH: linux-mpif90 > > PETSC_DIR: /nas/lsftmp/g0306332/petsc-2.3.2-p8 > > ** > > ** Now build and test the libraries with "make all > > test" > > ** > > Clanguage: C > > Scalar type:real > > MPI: > > Includes: ['/opt/mpich/intel/include'] > > PETSc shared libraries: enabled > > PETSc dynamic libraries: disabled > > BLAS/LAPACK: > > -Wl,-rpath,/lsftmp/g0306332/inter/mkl/lib/32 > > -L/lsftmp/g0306332/inter/mkl/lib/32 -lmkl_lapack > > -lmkl_ia32 -lguide > > > > i ran "make all test" and everything seems fine > > > > /opt/mpich/intel/bin/mpicc -c -fPIC -g > > > -I/nas/lsftmp/g0306332/petsc-2.3.2-p8-I/nas/lsftmp/g0306332/petsc- > > 2.3.2-p8/bmake/linux-mpif90 > > -I/nas/lsftmp/g0306332/petsc-2.3.2-p8/include > > -I/opt/mpich/intel/include > > -D__SDIR__="src/snes/examples/tutorials/" ex19.c > > /opt/mpich/intel/bin/mpicc -fPIC -g -o ex19 > > ex19.o-Wl,-rpath,/nas/lsftmp/g0306332/petsc- > > 2.3.2-p8/lib/linux-mpif90 > > > -L/nas/lsftmp/g0306332/petsc-2.3.2-p8/lib/linux-mpif90 > > -lpetscsnes -lpetscksp -lpetscdm -lpetscmat > > -lpetscvec -lpetsc > > -Wl,-rpath,/lsftmp/g0306332/inter/mkl/lib/32 > > -L/lsftmp/g0306332/inter/mkl/lib/32 -lmkl_lapack > > -lmkl_ia32 -lguide > > -lPEPCF90 -Wl,-rpath,/opt/intel/compiler70/ia32/lib > > -Wl,-rpath,/opt/mpich/intel/lib > > -L/opt/mpich/intel/lib -Wl,-rpath,-rpath > > -Wl,-rpath,-ldl -L-ldl -lmpich > > -Wl,-rpath,/opt/intel/compiler70/ia32/lib > > -Wl,-rpath,/opt/intel/compiler70/ia32/lib > > -L/opt/intel/compiler70/ia32/lib > > -Wl,-rpath,/usr/lib -Wl,-rpath,/usr/lib -L/usr/lib > > -limf -lirc -lcprts -lcxa > > -lunwind -ldl -lmpichf90 -lPEPCF90 > > -Wl,-rpath,/opt/intel/compiler70/ia32/lib > > -L/opt/intel/compiler70/ia32/lib -Wl,-rpath,/usr/lib > > -L/usr/lib -lintrins > > -lIEPCF90 -lF90 -lm -Wl,-rpath,\ -Wl,-rpath,\ -L\ > > -ldl -lmpich > > -Wl,-rpath,/opt/intel/compiler70/ia32/lib > > -L/opt/intel/compiler70/ia32/lib > > -Wl,-rpath,/usr/lib -L/usr/lib -limf -lirc -lcprts > > -lcxa -lunwind -ldl > > /bin/rm -f ex19.o > > C/C++ example src/snes/examples/tutorials/ex19 run > > successfully with 1 MPI > > process > > C/C++ example src/snes/examples/tutorials/ex19 run > > successfully with 2 MPI > > processes > > Fortran example src/snes/examples/tutorials/ex5f run > > successfully with 1 MPI > > process > > Completed test examples > > > > I then tried to run my own parallel code. It's a > > simple code which prints > > the rank of each processor. > > > > If I compile the code using just mpif90 test.F(using > > just mpif.h) > > > > I get 0,1,2,3 (4 processors). > > > > however, if i change the code to use petsc.h etc > > ie. > > > > > > program ns2d_c > > > > implicit none > > > > > > #include "include/finclude/petsc.h" > > #include "include/finclude/petscvec.h" > > #include "include/finclude/petscmat.h" > > #include "include/finclude/petscksp.h" > > #include "include/finclude/petscpc.h" > > #include "include/finclude/petscmat.h90" > > > > integer,parameter :: size_x=8,size_y=4 > > > > integer :: > > ierr,Istart_p,Iend_p,Ntot,Istart_m,Iend_m,k > > > > PetscMPIInt nprocs,rank > > > > > > > > > > call PetscInitialize(PETSC_NULL_CHARACTER,ierr) > > > > call > > MPI_Comm_rank(PETSC_COMM_WORLD,rank,ierr) > > > > call > > MPI_Comm_size(PETSC_COMM_WORLD,nprocs,ierr) > > > > end program ns2d_c > > > > > > > > i then rename the filename to ex2f.F and use "make > > ex2f" > > > > the result I get is something like 0,0,0,0. > > > > > > > > Why is this so? > > > > Thank you. > > > > > > > ______________________________________________________________________ > ______________ > Never Miss an Email > Stay connected with Yahoo! Mail on your mobile. Get started! > http://mobile.yahoo.com/services?promote=mail > > -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20070116/1248853c/attachment.htm>
