MPI

Documentation

• http://www.mpi-forum.org/docs/docs.html

Implementations

• LAM
• MPICH
• OpenMPI
• MPICH2

Manual installation

Install in separate subfolder $HOME/SUBDIR, because you may need some MPI implementations (see Libraries)

Tips & Tricks

• For safe consecutive communications create new context, for example:

int communication_operation(MPI_Comm comm) {
MPI_Comm newcomm;
MPI_Comm_dup(comm, &newcomm);
... // work with newcomm
MPI_Comm_free(&newcomm);
}

Mind the overhead of MPI_Comm_dup and MPI_Comm_free.

• If you are having trouble with the multi-homed nature of the HCL Cluster, check here

Debugging

• Add the following code:

int rank;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
if (!rank)
  getc(stdin);
MPI_Barrier(MPI_COMM_WORLD);

• Compile your code with -g option
• Run parallel application
• Attach to process(es) from GDB
  • MPICH-1 runs a background process for each application process: 0, 0b, 1, 1b, ..., therefore, attach to the first ones.

Profiling

Paraver by Barcelona Supercomputing Center is a "a flexible performance visualization and analysis tool"

Download from here. Use Extrae to create trace files.

Configered and installed extrae on Grid5000 with:

./configure --prefix=$HOME --with-papi=$HOME --with-mpi=/usr --enable-openmp --with-unwind=$HOME --without-dyninst
make; make install

Create trace.sh (modified from example extrae file):

#!/bin/bash
export EXTRAE_HOME=$HOME
export EXTRAE_CONFIG_FILE=$HOME/bin/extrae.xml
export LD_LIBRARY_PATH=${EXTRAE_HOME}/lib:@sub_MPI_HOME@/lib:@sub_PAPI_HOME@/lib:@sub_UNWIND_HOME@/lib:$LD_LIBRARY_PATH
export LD_PRELOAD=${EXTRAE_HOME}/lib/libmpitrace.so

## Run the desired program
$*

Using the standard extrae.xml supplied with the package.

 mpirun -np 3 ~/bin/trace.sh ./executable

Files created: TRACE.mpits, TRACExxxxxx.mpit

On head node run:

 mpi2prv -f TRACE.mpits -e ./executable -o output_tracefile.prv

On local machine open output_tracefile.prv with paraver