= Some Notes from MPICH2 Installation Guide =

== Offical [http://www.mcs.anl.gov/research/projects/mpich2/documentation/files/mpich2-doc-user.pdf User's Guide] ==

 * MPICH2 test examples - cpi
   * in Offical [http://www.mcs.anl.gov/research/projects/mpich2/documentation/files/mpich2-doc-user.pdf User's Guide]
{{{
mpd &
cd /home/you/mpich2-installed/examples
mpiexec -n 3 cpi
mpdallexit
}}}
   * in Debian environment
{{{
jazz@bio-cluster-12:~$ mpd &
[1] 3551
jazz@bio-cluster-12:~$ mpiexec -n 3 /usr/share/mpich2/examples/cpi
Process 1 of 3 is on bio-cluster-12
Process 2 of 3 is on bio-cluster-12
Process 0 of 3 is on bio-cluster-12
pi is approximately 3.1415926544231318, Error is 0.0000000008333387
wall clock time = 0.001213
jazz@bio-cluster-12:~$ mpdallexit
}}}
 * Compiling and Linking
   * 4.3 Special Issues for C++
     * Some users may get error messages such as
{{{
SEEK_SET is #defined but must not be for the C++ binding of MPI
}}}
     * The problem is that both stdio.h and the MPI C++ interface use SEEK SET, SEEK CUR, and SEEK END. This is really a bug in the MPI-2 standard. You can try adding following definition to the command line
{{{
-DMPICH_IGNORE_CXX_SEEK
}}}

 * 5.1 Standard mpiexec
   * Currently, MPICH2 does not fully support calling the dynamic process routines from MPI-2 (e.g., '''MPI_Comm_spawn''' or '''MPI_Comm_accept''') from processes that are not started with mpiexec.
   * Note: this might be the reason why we encounter R-MPI '''mpi.spawn.Rslaves()''' problem.

 * 5.3.1 Basic mpiexec arguments for MPD
   * You can use mpiexec to run non-MPI programs as well. This is sometimes useful in making sure all the machines are up and ready for use. Useful examples include
{{{
mpiexec -n 10 hostname
mpiexec -n 10 printenv
}}}

 * 5.3.2 Other Command-Line Arguments to mpiexec for MPD
   * This section describe ''machinefile'' format to specifying '''hosts''', '''number of processes''' and '''interface host name'''(ifhn)
   * i.e, ${hostname}:${number of processors} ifhn=${name of network interface}
{{{
# comment line
hosta
hostb:2
hostc   ifhn=hostc-gige
hostd:4 ifhn=hostd-gige
}}}

 * 5.7.1 MPD in the PBS environment
   * One way to convert the node file to the MPD format is as follows:
{{{
sort $PBS_NODEFILE | uniq -C | awk ’{ printf(”%s:%s”, $2, $1); }’ > mpd.nodes
}}}

 * 
{{{
tty1: 

jazz@bio-cluster-12:~$ mpiexec -n 2 /home/jazz/demo1
This is machine 0 of 2  name = bio-cluster-12
This is machine 1 of 2  name = bio-cluster-08

=================================================================
tty2: 

jazz@bio-cluster-12:~$ mpdlistjobs
jobid    = 4@bio-cluster-12_48909
jobalias =
username = jazz
host     = bio-cluster-12
pid      = 3619
sid      = 3618
rank     = 0
pgm      = /home/jazz/demo1

jobid    = 4@bio-cluster-12_48909
jobalias =
username = jazz
host     = bio-cluster-08
pid      = 6187
sid      = 6186
rank     = 1
pgm      = /home/jazz/demo1
}}}

== Offical [http://www.mcs.anl.gov/research/projects/mpich2/documentation/files/mpich2-doc-install.pdf Installer's Guide] ==

== [http://www.clustertech.com/cpe-eval/doc/mpich2instguide.pdf MPICH2 Installation and Configuration Guide] ==