Difference between revisions of "MPI"

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** MPICH-1 runs a background process for each application process: 0, 0b, 1, 1b, ..., therefore, attach to the first ones.
 
** MPICH-1 runs a background process for each application process: 0, 0b, 1, 1b, ..., therefore, attach to the first ones.
  
== Profiling ==
+
== Profiling ==
[http://www.bsc.es/plantillaA.php?cat_id=488 Paraver] by Barcelona Supercomputing Center is a "a flexible performance visualization and analysis tool"
+
 
 +
[http://www.bsc.es/computer-sciences/performance-tools/paraver/general-overview Paraver] by Barcelona Supercomputing Center is a "a flexible performance visualization and analysis tool"  
 +
 
 +
[http://www.bsc.es/computer-sciences/performance-tools/downloads Download here] and [http://www.bsc.es/computer-sciences/performance-tools/documentation tutorials 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):
 +
 
 +
<source lang="bash">#!/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=${EXTRAE_HOME}/lib/libmpitrace.so
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## Run the desired program
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$*</source>
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Using the standard extrae.xml supplied with the package.
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  mpirun -np 3 ~/bin/trace.sh ./executable
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 +
Files created: ''TRACE.mpits, TRACExxxxxx.mpit''
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 +
On head node run:
 +
 
 +
  mpi2prv -f TRACE.mpits -e ./executable -o output_tracefile.prv
 +
 
 +
On local machine open ''output_tracefile.prv'' with paraver

Latest revision as of 23:01, 16 July 2012

Documentation

Implementations

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 here and tutorials 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