Editing HPC High Processing Cluster in BITS PILANI (section)

=<center>'''INSTALLATION OF MPI(MESSAGE PASSING INTERFACE)'''</center>=

The MPI mpich2 can be downloaded from [http://www.mpich.org/static/tarballs/1.2/mpich2-1.2.tar.gz http://www.mpich.org/static/tarballs/1.2/mpich2-1.2.tar.gz]

1. Unpack the tar ﬁle. 

 tar -zxvf mpich2-1.2.tar.gz

2. Choose an installation directory (the default is /usr/local/bin): 


 mkdir /home/wolf/mpich2-install
 cd /home/wolf/mpich2-install/mpich2-install
 ./configure --prefix=/home/wolf/mpich2-install/ 2>&1 | tee c.txt
 make 2>&1 | tee m.txt
 make check
 make install 2>&1 | tee mi.txt 

Set the enviroment variable for user “wolf” in /home/wolf/.bash_profile 

Add following lines. 

 MPICH2=/home/wolf/mpich2-install/bin/
 PATH=$PATH:$HOME/bin:$MPICH2/bin 

2.MPICH2, uses an external process manager for scalable startup of large MPI jobs. The default process manager is called MPD, which is a ring of daemons on the machines where you will run your MPI programs. 

For security reasons, mpd looks in your home directory for a ﬁle named .mpd.conf containing the line in home directory. So create this file as follows 

 cd $HOME 
 touch .mpd.conf 
 chmod 600 .mpd.conf 

add a line 

 <nowiki>secretword=<anysecretword> </nowiki>

we used “redhat123” as secretword in our case. 

3.The ﬁrst sanity check consists of bringing up a ring of one mpd on the local machine, testing one mpd command, and bringing the “ring” down. 

 mpd &
 mpdtrace
 mpdallexit


The output of mpdtrace should be the hostname of the machine you 

are running on. The mpdallexit causes the mpd daemon to exit 

4.Now we will bring up a ring of mpd’s on a set of machines. Create a ﬁle consisting of a list of machine names, one per line. Name this ﬁle .mpd.hosts in home directory of user wolf. These hostnames will be used as targets for ssh so include full domain names if necessary. Check that you can reach these machines with ssh without entering a password. You can test by doing. 

 Ssh node1 –l wolf 

# Start the daemons on (some of) the hosts in the ﬁle mpd.hosts 

 <nowiki>mpdboot -n <number to start> -f mpd.hosts </nowiki>

The number to start can be less than 1 + number of hosts in the ﬁle,but cannot be greater than 1 + the number of hosts in the ﬁle. One mpd is always started on the machine where mpdboot is run, and is counted in the number to start, whether or not it occurs in the ﬁle. By default, mpdboot will only start one mpd per machine even if the machine name appears in the hosts ﬁle multiple times. 

 mpdboot -n 5 -f mpd.hosts 

This will start the cluster. 

 mpdtrace 

This command will show you the nodes in the cluster like below 

ibm-39.bits.ac

ibm-40.bits.ac

== PREPERATION OF SLAVE NODE(IBM-40) ==
a. beowulf and wolf user were created as in master node 

b. Edit file /home/wolf/.bash_pofile 

 export LAMRSH='ssh -x' 
 ssh-agent 
 MPICH2=/home/wolf/mpich2-install/mpich2 
 PATH=$HOME/bin:$MPICH2/bin 

Make /linuxeda directory 

 mkdir /linuxeda 

This file have all the binaries and need to rsync with all when changes occurred.

 chmod 770 /linuxeda 

All home directories are in lvm mode name and location 

/staff :This Home directory is for 2 node IBM HPC.

/projects:This Home directory is for 2 node IBM HPC.

/ugassignments:This Home directory is for 9 node Sunfire HPC.

/pgassignments:This Home directory is for 9 node Sunfire HPC.

Following entry is made in /etc/exports file 

 /staff <nowiki>* (rw,no_root_squash,sync) </nowiki>
 /projects <nowiki>* (rw,no_root_squash,sync) </nowiki>
 /ugassignments<nowiki>* (rw,no_root_squash,sync) </nowiki>
 /pgassignments<nowiki>* (rw,no_root_squash,sync) </nowiki>
 <nowiki># service nfs start ; chkconfig nfs on</nowiki>

c. Reboot all the nodes. 

d. login as wolf users and install MPI as described above in MPI installation section above.

'''Note''': Firewall should be disabled in all nodes as MPI uses randoms ports each time it is started. 

 “mpdboot -n 2 -f mpd.hosts”  ** command should be executed as wolf user from master node. This will start mpd daemon in slave nodes **

Now we will run an MPI job, using the mpiexec command as specified in the MPI-2 standard.

As part of the build process for MPICH2, a simple program to compute the value of ''pi ''by numerical integration is created in the mpich2-1.2/examples directory. If the current directory is the top level MPICH2 build directory, then you can run this program with


 mpiexec -n 2 ./examples/cpi


The cpi example will tell you which hosts it is running on.