= 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
}}}

 * 6.1 MPD
   * '''mpdlistjobs''' lists the jobs that the mpd’s are running. Jobs are identified by the name of the mpd where they were submitted and a number.
   * '''mpdsigjob''' delivers a signal to the named job. Signals are specified by name or number.
{{{
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
}}}
 * 7.1 gdb via mpiexec
   * If there are no gdb installed in your system, you might have following error message:
{{{
jazz@bio-cluster-12:~$ mpiexec -gdb -n 2 /home/jazz/demo1
0: Traceback (most recent call last):
0:   File "/usr/bin/mpdgdbdrv.py", line 78, in ?
0:     write(gdb_sin_fileno,'handle SIGUSR1 nostop noprint\n')
0: OSError: [Errno 32] Broken pipe
1: Traceback (most recent call last):
1:   File "/usr/bin/mpdgdbdrv.py", line 75, in ?
1:     write(gdb_sin_fileno,'set confirm off\n')
1: OSError: [Errno 32] Broken pipe
}}}
   * After install gdb, you can use gdb to debug your MPICH2 program.
{{{
jazz@bio-cluster-12:~$ sudo apt-get install gdb
jazz@bio-cluster-12:~$ mpiexec -gdb -n 2 /home/jazz/demo1
1: Traceback (most recent call last):
1:   File "/usr/bin/mpdgdbdrv.py", line 75, in ?
1:     write(gdb_sin_fileno,'set confirm off\n')
1: OSError: [Errno 32] Broken pipe
0:  (gdb) l
0:  4    * History:
0:  5    *   2008-04-09 BETA
0:  6    *   2008-06-25 增加顯示主機名稱功能
0:  7   */
0:  8
0:  9   #include <stdio.h>
0:  10  #include <unistd.h>
0:  11  #include "mpi.h"
0:  12  int main (int argc, char **argv)
0:  13  {
0:  (gdb)
}}}
   * You can attach to a running job with ''-gdba'' option, where <jobid> comes from '''mpdlistjobs'''.
{{{
mpiexec -gdba <jobid>
}}}


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

 * 4 Choosing the Communication Device
   * ch3:sock This is the default communication method. It uses sockets for all communications between processes.
   * ch3:ssm This method uses sockets between nodes and shared memory within a node.
   * ch3:shm This method only uses shared memory and only works within a single SMP. It does not support the MPI dynamic process routines such as MPI Comm spawn.
   * ch3:nemesis This method is our new, high performance method. It supports sockets, shared memory, and Myrinet-GM at present.
   * Most installations should use either the '''ch3:ssm''' or '''ch3:sock''' methods. If you need __'''multi-threaded MPI'''__, you must __'''use ch3:sock'''__ in this release. If you have __'''a cluster of SMPs and do not need a multi-threaded MPI'''__, then select __'''ch3:ssm'''__. If you are interested in trying out our highest-performance device, and need neither threads nor the dynamic process routines from MPI, then you can use ch3:nemesis.
 * 5.1.5 Running MPD on multi-homed systems
{{{
n1% mpd --ifhn=192.168.1.1 &
}}}

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