doc/en/hpc-howto.xml

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<title>High Performance Computing on Gentoo Linux</title>

<author title="Author">
  <mail link="marc@adelielinux.com">Marc St-Pierre</mail>
</author>
<author title="Author">
  <mail link="benoit@adelielinux.com">Benoit Morin</mail>
</author>
<author title="Assistant/Research">
  <mail link="jean-francois@adelielinux.com">Jean-Francois Richard</mail>
</author>
<author title="Assistant/Research">
  <mail link="olivier@adelielinux.com">Olivier Crete</mail>
</author>
<author title="Reviewer">
  <mail link="dberkholz@gentoo.org">Donnie Berkholz</mail>
</author>

<!-- No licensing information; this document has been written by a third-party
     organisation without additional licensing information.

     In other words, this is copyright adelielinux R&D; Gentoo only has
     permission to distribute this document as-is and update it when appropriate
     as long as the adelie linux R&D notice stays
-->

<abstract>
This document was written by people at the Adelie Linux R&amp;D Center
&lt;http://www.adelielinux.com&gt; as a step-by-step guide to turn a Gentoo
System into a High Performance Computing (HPC) system.
</abstract>

<version>1.6</version>
<date>2006-12-18</date>

<chapter>
<title>Introduction</title>
<section>
<body>

<p>
Gentoo Linux, a special flavor of Linux that can be automatically optimized
and customized for just about any application or need. Extreme performance,
configurability and a top-notch user and developer community are all hallmarks
of the Gentoo experience.
</p>

<p>
Thanks to a technology called Portage, Gentoo Linux can become an ideal secure
server, development workstation, professional desktop, gaming system, embedded
solution or... a High Performance Computing system. Because of its
near-unlimited adaptability, we call Gentoo Linux a metadistribution.
</p>

<p>
This document explains how to turn a Gentoo system into a High Performance
Computing system. Step by step, it explains what packages one may want to
install and helps configure them.
</p>

<p>
Obtain Gentoo Linux from the website <uri>http://www.gentoo.org</uri>, and
refer to the <uri link="/doc/en/">documentation</uri> at the same location to
install it.
</p>

</body>
</section>
</chapter>

<chapter>
<title>Configuring Gentoo Linux for Clustering</title>
<section>
<title>Recommended Optimizations</title>
<body>

<note>
We refer to the <uri link="/doc/en/handbook/">Gentoo Linux Handbooks</uri> in
this section.
</note>

<p>
During the installation process, you will have to set your USE variables in
<path>/etc/make.conf</path>. We recommended that you deactivate all the
defaults (see <path>/etc/make.profile/make.defaults</path>) by negating them in
make.conf. However, you may want to keep such use variables as x86, 3dnow, gpm,
mmx, nptl, nptlonly, sse, ncurses, pam and tcpd. Refer to the USE documentation
for more information.
</p>

<pre caption="USE Flags">
USE="-oss 3dnow -apm -arts -avi -berkdb -crypt -cups -encode -gdbm -gif gpm -gtk
-imlib -java -jpeg -kde -gnome -libg++ -libwww -mikmod mmx -motif -mpeg ncurses
-nls nptl nptlonly -oggvorbis -opengl pam -pdflib -png -python -qt3 -qt4 -qtmt
-quicktime -readline -sdl -slang -spell -ssl -svga tcpd -truetype -X -xml2 -xv
-zlib"
</pre>

<p>
Or simply:
</p>

<pre caption="USE Flags - simplified version">
USE="-* 3dnow gpm mmx ncurses pam sse tcpd"
</pre>

<note>
The <e>tcpd</e> USE flag increases security for packages such as xinetd.
</note>

<p>
In step 15 ("Installing the kernel and a System Logger") for stability
reasons, we recommend the vanilla-sources, the official kernel sources
released on <uri>http://www.kernel.org/</uri>, unless you require special
support such as xfs.
</p>

<pre caption="Installing vanilla-sources">
# <i>emerge -p syslog-ng vanilla-sources</i>
</pre>

<p>
When you install miscellaneous packages, we recommend installing the
following:
</p>

<pre caption="Installing necessary packages">
# <i>emerge -p nfs-utils portmap tcpdump ssmtp iptables xinetd</i>
</pre>

</body>
</section>
<section>
<title>Communication Layer (TCP/IP Network)</title>
<body>

<p>
A cluster requires a communication layer to interconnect the slave nodes to
the master node. Typically, a FastEthernet or GigaEthernet LAN can be used
since they have a good price/performance ratio. Other possibilities include
use of products like <uri link="http://www.myricom.com/">Myrinet</uri>, <uri
link="http://quadrics.com/">QsNet</uri> or others.
</p>

<p>
A cluster is composed of two node types: master and slave. Typically, your
cluster will have one master node and several slave nodes.
</p>

<p>
The master node is the cluster's server. It is responsible for telling the
slave nodes what to do. This server will typically run such daemons as dhcpd,
nfs, pbs-server, and pbs-sched. Your master node will allow interactive
sessions for users, and accept job executions.
</p>

<p>
The slave nodes listen for instructions (via ssh/rsh perhaps) from the master
node. They should be dedicated to crunching results and therefore should not
run any unnecessary services.
</p>

<p>
The rest of this documentation will assume a cluster configuration as per the
hosts file below. You should maintain on every node such a hosts file
(<path>/etc/hosts</path>) with entries for each node participating node in the
cluster.
</p>

<pre caption="/etc/hosts">
# Adelie Linux Research &amp; Development Center
# /etc/hosts

127.0.0.1       localhost

192.168.1.100   master.adelie master

192.168.1.1     node01.adelie node01
192.168.1.2     node02.adelie node02
</pre>

<p>
To setup your cluster dedicated LAN, edit your <path>/etc/conf.d/net</path>
file on the master node.
</p>

<pre caption="/etc/conf.d/net">
# Global config file for net.* rc-scripts

# This is basically the ifconfig argument without the ifconfig $iface
#

iface_eth0="192.168.1.100 broadcast 192.168.1.255 netmask 255.255.255.0"
# Network Connection to the outside world using dhcp -- configure as required for you network
iface_eth1="dhcp"
</pre>


<p>
Finally, setup a DHCP daemon on the master node to avoid having to maintain a
network configuration on each slave node.
</p>

<pre caption="/etc/dhcp/dhcpd.conf">
# Adelie Linux Research &amp; Development Center
# /etc/dhcp/dhcpd.conf

log-facility local7;
ddns-update-style none;
use-host-decl-names on;

subnet 192.168.1.0 netmask 255.255.255.0 {
        option domain-name "adelie";
        range 192.168.1.10 192.168.1.99;
        option routers 192.168.1.100;

        host node01.adelie {
                # MAC address of network card on node 01
                hardware ethernet 00:07:e9:0f:e2:d4;
                fixed-address 192.168.1.1;
        }
        host node02.adelie {
                # MAC address of network card on node 02
                hardware ethernet 00:07:e9:0f:e2:6b;
                fixed-address 192.168.1.2;
        }
}
</pre>

</body>
</section>
<section>
<title>NFS/NIS</title>
<body>

<p>
The Network File System (NFS) was developed to allow machines to mount a disk
partition on a remote machine as if it were on a local hard drive. This allows
for fast, seamless sharing of files across a network.
</p>

<p>
There are other systems that provide similar functionality to NFS which could
be used in a cluster environment. The <uri
link="http://www.openafs.org">Andrew File System
from IBM</uri>, recently open-sourced, provides a file sharing mechanism with
some additional security and performance features. The <uri
link="http://www.coda.cs.cmu.edu/">Coda File System</uri> is still in
development, but is designed to work well with disconnected clients. Many
of the features of the Andrew and Coda file systems are slated for inclusion
in the next version of <uri link="http://www.nfsv4.org">NFS (Version 4)</uri>.
The advantage of NFS today is that it is mature, standard, well understood,
and supported robustly across a variety of platforms.
</p>

<pre caption="Ebuilds for NFS-support">
# <i>emerge -p nfs-utils portmap</i>
# <i>emerge nfs-utils portmap</i>
</pre>

<p>
Configure and install a kernel to support NFS v3 on all nodes:
</p>

<pre caption="Required Kernel Configurations for NFS">
CONFIG_NFS_FS=y
CONFIG_NFSD=y
CONFIG_SUNRPC=y
CONFIG_LOCKD=y
CONFIG_NFSD_V3=y
CONFIG_LOCKD_V4=y
</pre>

<p>
On the master node, edit your <path>/etc/hosts.allow</path> file to allow
connections from slave nodes. If your cluster LAN is on 192.168.1.0/24,
your <path>hosts.allow</path> will look like:
</p>

<pre caption="hosts.allow">
portmap:192.168.1.0/255.255.255.0
</pre>

<p>
Edit the <path>/etc/exports</path> file of the master node to export a work
directory structure (/home is good for this).
</p>

<pre caption="/etc/exports">
/home/  *(rw)
</pre>

<p>
Add nfs to your master node's default runlevel:
</p>

<pre caption="Adding NFS to the default runlevel">
# <i>rc-update add nfs default</i>
</pre>

<p>
To mount the nfs exported filesystem from the master, you also have to
configure your salve nodes' <path>/etc/fstab</path>. Add a line like this
one:
</p>

<pre caption="/etc/fstab">
master:/home/  /home  nfs  rw,exec,noauto,nouser,async  0 0
</pre>

<p>
You'll also need to set up your nodes so that they mount the nfs filesystem by
issuing this command:
</p>

<pre caption="Adding nfsmount to the default runlevel">
# <i>rc-update add nfsmount default</i>
</pre>

</body>
</section>
<section>
<title>RSH/SSH</title>
<body>

<p>
SSH is a protocol for secure remote login and other secure network services
over an insecure network. OpenSSH uses public key cryptography to provide
secure authorization. Generating the public key, which is shared with remote
systems, and the private key which is kept on the local system, is done first
to configure OpenSSH on the cluster.
</p>

<p>
For transparent cluster usage, private/public keys may be used. This process
has two steps:
</p>

<ul>
  <li>Generate public and private keys</li>
  <li>Copy public key to slave nodes</li>
</ul>

<p>
For user based authentication, generate and copy as follows:
</p>

<pre caption="SSH key authentication">
# <i>ssh-keygen -t dsa</i>
Generating public/private dsa key pair.
Enter file in which to save the key (/root/.ssh/id_dsa): /root/.ssh/id_dsa
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /root/.ssh/id_dsa.
Your public key has been saved in /root/.ssh/id_dsa.pub.
The key fingerprint is:
f1:45:15:40:fd:3c:2d:f7:9f:ea:55:df:76:2f:a4:1f root@master

<comment>WARNING! If you already have an "authorized_keys" file,
please append to it, do not use the following command.</comment>

# <i>scp /root/.ssh/id_dsa.pub node01:/root/.ssh/authorized_keys</i>
root@master's password:
id_dsa.pub   100%  234     2.0MB/s   00:00

# <i>scp /root/.ssh/id_dsa.pub node02:/root/.ssh/authorized_keys</i>
root@master's password:
id_dsa.pub   100%  234     2.0MB/s   00:00
</pre>

<note>
Host keys must have an empty passphrase. RSA is required for host-based
authentication.
</note>

<p>
For host based authentication, you will also need to edit your
<path>/etc/ssh/shosts.equiv</path>.
</p>

<pre caption="/etc/ssh/shosts.equiv">
node01.adelie
node02.adelie
master.adelie
</pre>

<p>
And a few modifications to the <path>/etc/ssh/sshd_config</path> file:
</p>

<pre caption="sshd configurations">
# $OpenBSD: sshd_config,v 1.42 2001/09/20 20:57:51 mouring Exp $
# This sshd was compiled with PATH=/usr/bin:/bin:/usr/sbin:/sbin

# This is the sshd server system-wide configuration file. See sshd(8)
# for more information.

# HostKeys for protocol version 2
HostKey /etc/ssh/ssh_host_rsa_key
</pre>

<p>
If your application require RSH communications, you will need to emerge
net-misc/netkit-rsh and sys-apps/xinetd.
</p>

<pre caption="Installing necessary applicaitons">
# <i>emerge -p xinetd</i>
# <i>emerge xinetd</i>
# <i>emerge -p netkit-rsh</i>
# <i>emerge netkit-rsh</i>
</pre>

<p>
Then configure the rsh deamon. Edit your <path>/etc/xinet.d/rsh</path> file.
</p>

<pre caption="rsh">
# Adelie Linux Research &amp; Development Center
# /etc/xinetd.d/rsh

service shell
{
        socket_type     = stream
        protocol        = tcp
        wait            = no
        user            = root
        group           = tty
        server          = /usr/sbin/in.rshd
        log_type        = FILE /var/log/rsh
        log_on_success  = PID HOST USERID EXIT DURATION
        log_on_failure  = USERID ATTEMPT
        disable         = no
}
</pre>

<p>
Edit your <path>/etc/hosts.allow</path> to permit rsh connections:
</p>

<pre caption="hosts.allow">
# Adelie Linux Research &amp; Development Center
# /etc/hosts.allow

in.rshd:192.168.1.0/255.255.255.0
</pre>

<p>
Or you can simply trust your cluster LAN:
</p>

<pre caption="hosts.allow">
# Adelie Linux Research &amp; Development Center
# /etc/hosts.allow

ALL:192.168.1.0/255.255.255.0
</pre>

<p>
Finally, configure host authentication from <path>/etc/hosts.equiv</path>.
</p>

<pre caption="hosts.equiv">
# Adelie Linux Research &amp; Development Center
# /etc/hosts.equiv

master
node01
node02
</pre>

<p>
And, add xinetd to your default runlevel:
</p>

<pre caption="Adding xinetd to the default runlevel">
# <i>rc-update add xinetd default</i>
</pre>

</body>
</section>
<section>
<title>NTP</title>
<body>

<p>
The Network Time Protocol (NTP) is used to synchronize the time of a computer
client or server to another server or reference time source, such as a radio
or satellite receiver or modem. It provides accuracies typically within a
millisecond on LANs and up to a few tens of milliseconds on WANs relative to
Coordinated Universal Time (UTC) via a Global Positioning Service (GPS)
receiver, for example. Typical NTP configurations utilize multiple redundant
servers and diverse network paths in order to achieve high accuracy and
reliability.
</p>

<p>
Select a NTP server geographically close to you from <uri
link="http://www.eecis.udel.edu/~mills/ntp/servers.html">Public NTP Time
Servers</uri>, and configure your <path>/etc/conf.d/ntp</path> and
<path>/etc/ntp.conf</path> files on the master node.
</p>

<pre caption="Master /etc/conf.d/ntp">
# /etc/conf.d/ntpd

# NOTES:
#  - NTPDATE variables below are used if you wish to set your
#    clock when you start the ntp init.d script
#  - make sure that the NTPDATE_CMD will close by itself ...
#    the init.d script will not attempt to kill/stop it
#  - ntpd will be used to maintain synchronization with a time
#    server regardless of what NTPDATE is set to
#  - read each of the comments above each of the variable

# Comment this out if you dont want the init script to warn
# about not having ntpdate setup
NTPDATE_WARN="n"

# Command to run to set the clock initially
# Most people should just uncomment this line ...
# however, if you know what you're doing, and you
# want to use ntpd to set the clock, change this to 'ntpd'
NTPDATE_CMD="ntpdate"

# Options to pass to the above command
# Most people should just uncomment this variable and
# change 'someserver' to a valid hostname which you
# can acquire from the URL's below
NTPDATE_OPTS="-b ntp1.cmc.ec.gc.ca"

##
# A list of available servers is available here:
# http://www.eecis.udel.edu/~mills/ntp/servers.html
# Please follow the rules of engagement and use a
# Stratum 2 server (unless you qualify for Stratum 1)
##

# Options to pass to the ntpd process that will *always* be run
# Most people should not uncomment this line ...
# however, if you know what you're doing, feel free to tweak
#NTPD_OPTS=""

</pre>

<p>
Edit your <path>/etc/ntp.conf</path> file on the master to setup an external
synchronization source:
</p>

<pre caption="Master ntp.conf">
# Adelie Linux Research &amp; Development Center
# /etc/ntp.conf

# Synchronization source #1
server ntp1.cmc.ec.gc.ca
restrict ntp1.cmc.ec.gc.ca
# Synchronization source #2
server ntp2.cmc.ec.gc.ca
restrict ntp2.cmc.ec.gc.ca
stratum 10
driftfile /etc/ntp.drift.server
logfile /var/log/ntp
broadcast 192.168.1.255
restrict default kod
restrict 127.0.0.1
restrict 192.168.1.0 mask 255.255.255.0
</pre>

<p>
And on all your slave nodes, setup your synchronization source as your master
node.
</p>

<pre caption="Node /etc/conf.d/ntp">
# /etc/conf.d/ntpd

NTPDATE_WARN="n"
NTPDATE_CMD="ntpdate"
NTPDATE_OPTS="-b master"
</pre>

<pre caption="Node ntp.conf">
# Adelie Linux Research &amp; Development Center
# /etc/ntp.conf

# Synchronization source #1
server master
restrict master
stratum 11
driftfile /etc/ntp.drift.server
logfile /var/log/ntp
restrict default kod
restrict 127.0.0.1
</pre>

<p>
Then add ntpd to the default runlevel of all your nodes:
</p>

<pre caption="Adding ntpd to the default runlevel">
# <i>rc-update add ntpd default</i>
</pre>

<note>
NTP will not update the local clock if the time difference between your
synchronization source and the local clock is too great.
</note>

</body>
</section>
<section>
<title>IPTABLES</title>
<body>

<p>
To setup a firewall on your cluster, you will need iptables.
</p>

<pre caption="Installing iptables">
# <i>emerge -p iptables</i>
# <i>emerge iptables</i>
</pre>

<p>
Required kernel configuration:
</p>

<pre caption="IPtables kernel configuration">
CONFIG_NETFILTER=y
CONFIG_IP_NF_CONNTRACK=y
CONFIG_IP_NF_IPTABLES=y
CONFIG_IP_NF_MATCH_STATE=y
CONFIG_IP_NF_FILTER=y
CONFIG_IP_NF_TARGET_REJECT=y
CONFIG_IP_NF_NAT=y
CONFIG_IP_NF_NAT_NEEDED=y
CONFIG_IP_NF_TARGET_MASQUERADE=y
CONFIG_IP_NF_TARGET_LOG=y
</pre>

<p>
And the rules required for this firewall:
</p>

<pre caption="rule-save">
# Adelie Linux Research &amp; Development Center
# /var/lib/iptables/rule-save

*filter
:INPUT ACCEPT [0:0]
:FORWARD ACCEPT [0:0]
:OUTPUT ACCEPT [0:0]
-A INPUT -m state --state RELATED,ESTABLISHED -j ACCEPT
-A INPUT -p tcp -m tcp --dport 22 -j ACCEPT
-A INPUT -s 192.168.1.0/255.255.255.0 -i eth1 -j ACCEPT
-A INPUT -s 127.0.0.1 -i lo -j ACCEPT
-A INPUT -p icmp -j ACCEPT
-A INPUT -j LOG
-A INPUT -j REJECT --reject-with icmp-port-unreachable
COMMIT
*nat
:PREROUTING ACCEPT [0:0]
:POSTROUTING ACCEPT [0:0]
:OUTPUT ACCEPT [0:0]
-A POSTROUTING -s 192.168.1.0/255.255.255.0 -j MASQUERADE
COMMIT
</pre>

<p>
Then add iptables to the default runlevel of all your nodes:
</p>

<pre caption="Adding iptables to the default runlevel">
# <i>rc-update add iptables default</i>
</pre>

</body>
</section>
</chapter>

<chapter>
<title>HPC Tools</title>
<section>
<title>OpenPBS</title>
<body>

<p>
The Portable Batch System (PBS) is a flexible batch queueing and workload
management system originally developed for NASA. It operates on networked,
multi-platform UNIX environments, including heterogeneous clusters of
workstations, supercomputers, and massively parallel systems. Development of
PBS is provided by Altair Grid Technologies.
</p>

<pre caption="Installing openpbs">
# <i>emerge -p openpbs</i>
</pre>

<note>
OpenPBS ebuild does not currently set proper permissions on var-directories
used by OpenPBS.
</note>

<p>
Before starting using OpenPBS, some configurations are required. The files
you will need to personalize for your system are:
</p>

<ul>
  <li>/etc/pbs_environment</li>
  <li>/var/spool/PBS/server_name</li>
  <li>/var/spool/PBS/server_priv/nodes</li>
  <li>/var/spool/PBS/mom_priv/config</li>
  <li>/var/spool/PBS/sched_priv/sched_config</li>
</ul>

<p>
Here is a sample sched_config:
</p>

<pre caption="/var/spool/PBS/sched_priv/sched_config">
#
# Create queues and set their attributes.
#
#
# Create and define queue upto4nodes
#
create queue upto4nodes
set queue upto4nodes queue_type = Execution
set queue upto4nodes Priority = 100
set queue upto4nodes resources_max.nodect = 4
set queue upto4nodes resources_min.nodect = 1
set queue upto4nodes enabled = True
set queue upto4nodes started = True
#
# Create and define queue default
#
create queue default
set queue default queue_type = Route
set queue default route_destinations = upto4nodes
set queue default enabled = True
set queue default started = True
#
# Set server attributes.
#
set server scheduling = True
set server acl_host_enable = True
set server default_queue = default
set server log_events = 511
set server mail_from = adm
set server query_other_jobs = True
set server resources_default.neednodes = 1
set server resources_default.nodect = 1
set server resources_default.nodes = 1
set server scheduler_iteration = 60
</pre>

<p>
To submit a task to OpenPBS, the command <c>qsub</c> is used with some
optional parameters. In the example below, "-l" allows you to specify
the resources required, "-j" provides for redirection of standard out and
standard error, and the "-m" will e-mail the user at beginning (b), end (e)
and on abort (a) of the job.
</p>

<pre caption="Submitting a task">
<comment>(submit and request from OpenPBS that myscript be executed on 2 nodes)</comment>
# <i>qsub -l nodes=2 -j oe -m abe myscript</i>
</pre>

<p>
Normally jobs submitted to OpenPBS are in the form of scripts. Sometimes, you
may want to try a task manually. To request an interactive shell from OpenPBS,
use the "-I" parameter.
</p>

<pre caption="Requesting an interactive shell">
# <i>qsub -I</i>
</pre>

<p>
To check the status of your jobs, use the qstat command:
</p>

<pre caption="Checking the status of the jobs">
# <i>qstat</i>
Job id  Name  User   Time Use S Queue
------  ----  ----   -------- - -----
2.geist STDIN adelie 0        R upto1nodes
</pre>

</body>
</section>
<section>
<title>MPICH</title>
<body>

<p>
Message passing is a paradigm used widely on certain classes of parallel
machines, especially those with distributed memory. MPICH is a freely
available, portable implementation of MPI, the Standard for message-passing
libraries.
</p>

<p>
The mpich ebuild provided by Adelie Linux allows for two USE flags:
<e>doc</e> and <e>crypt</e>. <e>doc</e> will cause documentation to be
installed, while <e>crypt</e> will configure MPICH to use <c>ssh</c> instead
of <c>rsh</c>.
</p>

<pre caption="Installing the mpich application">
# <i>emerge -p mpich</i>
# <i>emerge mpich</i>
</pre>

<p>
You may need to export a mpich work directory to all your slave nodes in
<path>/etc/exports</path>:
</p>

<pre caption="/etc/exports">
/home  *(rw)
</pre>

<p>
Most massively parallel processors (MPPs) provide a way to start a program on
a requested number of processors; <c>mpirun</c> makes use of the appropriate
command whenever possible. In contrast, workstation clusters require that each
process in a parallel job be started individually, though programs to help
start these processes exist. Because workstation clusters are not already
organized as an MPP, additional information is required to make use of them.
Mpich should be installed with a list of participating workstations in the
file <path>machines.LINUX</path> in the directory
<path>/usr/share/mpich/</path>. This file is used by <c>mpirun</c> to choose
processors to run on.
</p>

<p>
Edit this file to reflect your cluster-lan configuration:
</p>

<pre caption="/usr/share/mpich/machines.LINUX">
# Change this file to contain the machines that you want to use
# to run MPI jobs on. The format is one host name per line, with either
#    hostname
# or
#    hostname:n
# where n is the number of processors in an SMP. The hostname should
# be the same as the result from the command "hostname"
master
node01
node02
# node03
# node04
# ...
</pre>

<p>
Use the script <c>tstmachines</c> in <path>/usr/sbin/</path> to ensure that
you can use all of the machines that you have listed. This script performs
an <c>rsh</c> and a short directory listing; this tests that you both have
access to the node and that a program in the current directory is visible on
the remote node. If there are any problems, they will be listed. These
problems must be fixed before proceeding.
</p>

<p>
The only argument to <c>tstmachines</c> is the name of the architecture; this
is the same name as the extension on the machines file. For example, the
following tests that a program in the current directory can be executed by
all of the machines in the LINUX machines list.
</p>

<pre caption="Running a test">
# <i>/usr/local/mpich/sbin/tstmachines LINUX</i>
</pre>

<note>
This program is silent if all is well; if you want to see what it is doing,
use the -v (for verbose) argument:
</note>

<pre caption="Running a test verbosively">
# <i>/usr/local/mpich/sbin/tstmachines -v LINUX</i>
</pre>

<p>
The output from this command might look like:
</p>

<pre caption="Output of the above command">
Trying true on host1.uoffoo.edu ...
Trying true on host2.uoffoo.edu ...
Trying ls on host1.uoffoo.edu ...
Trying ls on host2.uoffoo.edu ...
Trying user program on host1.uoffoo.edu ...
Trying user program on host2.uoffoo.edu ...
</pre>

<p>
If <c>tstmachines</c> finds a problem, it will suggest possible reasons and
solutions. In brief, there are three tests:
</p>

<ul>
  <li>
    <e>Can processes be started on remote machines?</e> tstmachines attempts
    to run the shell command true on each machine in the machines files by
    using the remote shell command.
  </li>
  <li>
    <e>Is current working directory available to all machines?</e> This
    attempts to ls a file that tstmachines creates by running ls using the
    remote shell command.
  </li>
  <li>
    <e>Can user programs be run on remote systems?</e> This checks that shared
    libraries and other components have been properly installed on all
    machines.
  </li>
</ul>

<p>
And the required test for every development tool:
</p>

<pre caption="Testing a development tool">
# <i>cd ~</i>
# <i>cp /usr/share/mpich/examples1/hello++.c ~</i>
# <i>make hello++</i>
# <i>mpirun -machinefile /usr/share/mpich/machines.LINUX -np 1 hello++</i>
</pre>

<p>
For further information on MPICH, consult the documentation at <uri
link="http://www-unix.mcs.anl.gov/mpi/mpich/docs/mpichman-chp4/mpichman-chp4.htm">http://www-unix.mcs.anl.gov/mpi/mpich/docs/mpichman-chp4/mpichman-chp4.htm</uri>.
</p>

</body>
</section>
<section>
<title>LAM</title>
<body>

<p>
(Coming Soon!)
</p>

</body>
</section>
<section>
<title>OMNI</title>
<body>

<p>
(Coming Soon!)
</p>

</body>
</section>
</chapter>

<chapter>
<title>Bibliography</title>
<section>
<body>

<p>
The original document is published at the <uri
link="http://www.adelielinux.com">Adelie Linux R&amp;D Centre</uri> web site,
and is reproduced here with the permission of the authors and <uri
link="http://www.cyberlogic.ca">Cyberlogic</uri>'s Adelie Linux R&amp;D
Centre.
</p>

<ul>
  <li><uri>http://www.gentoo.org</uri>, Gentoo Foundation, Inc.</li>
  <li>
    <uri link="http://www.adelielinux.com">http://www.adelielinux.com</uri>,
    Adelie Linux Research and Development Centre
  </li>
  <li>
    <uri link="http://nfs.sourceforge.net/">http://nfs.sourceforge.net</uri>,
    Linux NFS Project
  </li>
  <li>
    <uri link="http://www-unix.mcs.anl.gov/mpi/mpich/">http://www-unix.mcs.anl.gov/mpi/mpich/</uri>,
    Mathematics and Computer Science Division, Argonne National Laboratory
  </li>
  <li>
    <uri link="http://www.ntp.org/">http://ntp.org</uri>
  </li>
  <li>
    <uri link="http://www.eecis.udel.edu/~mills/">http://www.eecis.udel.edu/~mills/</uri>,
    David L. Mills, University of Delaware
  </li>
  <li>
    <uri link="http://www.ietf.org/html.charters/secsh-charter.html">http://www.ietf.org/html.charters/secsh-charter.html</uri>,
    Secure Shell Working Group, IETF, Internet Society
  </li>
  <li>
    <uri link="http://www.linuxsecurity.com/">http://www.linuxsecurity.com/</uri>,
    Guardian Digital
  </li>
  <li>
    <uri link="http://www.openpbs.org/">http://www.openpbs.org/</uri>,
    Altair Grid Technologies, LLC.
  </li>
</ul>

</body>
</section>
</chapter>

</guide>