On Sat, 1 Nov 2008, Saswata Hier-Majumder wrote: > Greetings, > I am new to petsc and not sure how to interpret the result I get when running > petsc example codes (bratu problem and hello world) in an SGI Altix 1300 > cluster. Any help will be greatly appreciated! > > I compile the petsc code using a makefile that came with the petsc > distribution, submit the job to the queue using pbspro, and run using mpirun. > The solution returned by running the bratu problem > ($PETSC_DIR/src/snes/examples/tutorials/ex5f90.F) looks correct, but I am > not sure if petsc is using all processors supplied to it by mpirun. > MPI_COMM_SIZE always returns a size of 1 and MPI_COMM_RANK always returns rank > 0, when I call these routines from inside my code, despite using a command > like > > mpirun -n 16 -machinefile $PBS_NODEFILE myexecutable.exe > > in my submit shell script. > > I get similar results when I run hello world with Petsc. It prints 16 lines > displaying rank=0 and size=1, when run with 16 processors. Run just with mpi, > helloworld prints the size and ranks as expected, i.e. 16 different lines with > size 16 and ranks from 0 to 15. > > Am I correct in assuming that petsc is somehow not able use the version of > mpirun implemented in vltmpi? I reran the petsc using the install shell > script given below, but it did not help > > export PETSC_DIR=$PWD > ./config/configure.py --with-mpi-dir=/opt/vltmpi/OPENIB/mpi.icc.rsh/bin
This should be --with-mpi-dir=/opt/vltmpi/OPENIB/mpi.icc.rsh Configure should print a summary of compilers being used. [it should be /opt/vltmpi/OPENIB/mpi.icc.rsh/bin/mpicc etc..] If you can use /opt/vltmpi/OPENIB/mpi.icc.rsh/bin/mpicc & mpirun with a sample MPI test code and run it parallelly - then you should be able to do the exact same thing with PETSc examples [using the same tools] Satish > make all test > > Sash Hier-Majumder > >
