===== linpack =====
Benchmark tool

===== nis =====

todo: 
  * set hostname and domainname
  * firewall for nis/nfs server

Some good setup info:
[[http://penguin.triumf.ca/recipes/nis-auto/index.html]]

==== nis client ====
  # hostname (does it need the fqdn?)
  # domainname (make sure it is set)
  # domainname setup (to set it to 'setup')
  # ypdomainname (same, but from yp tools)
  # portmap (should be running)
edit /etc/yp.conf and add to the end:

<file>
  domain setup server G4-cluster01.setup.lan
</file>

Create /var/yp if it does not exist
  mkdir /var/yp

edit /etc/nsswitch.conf

<file>
...

passwd:     files nis
shadow:     files nis
group:      files nis

...

automount:  files nis

...
</file>

To start the NIS client, otherwise known as ypbind:
  # service ypbind start
To test:
  # rpcinfo -p localhost
Output similar to:
<file>
       program vers proto   port
        100000    2   tcp    111  portmapper
        100000    2   udp    111  portmapper
        100007    2   udp    758  ypbind
        100007    1   udp    758  ypbind
        100007    2   tcp    761  ypbind
        100007    1   tcp    761  ypbind
</file>
  # rpcinfo -u localhost ypbind
Output similar to:
<file>
        program 100007 version 1 ready and waiting 
        program 100007 version 2 ready and waiting
</file>
  # ypcat passwd
Should output the yp users in password file.

Start ypbind
  chkconfig ypbind on
  service ypbind start

==== nis server ====
install:
  # yum install ypserv
already installed (add if not already installed):
  yp-tool 
  ypbind

edit /etc/yp.conf as above

add normal unix users, then
  # /usr/lib/yp/ypinit -m

option: on slaves yp servers (not all clients)
  # ypinit -s G4-cluster01.setup.lan

Check the nis server:
  # rpcinfo -u localhost ypserv
  program 100004 version 1 ready and waiting
  program 100004 version 2 ready and waiting

If not running,
  # service ypserv start

To update the map (don't use ypinit -m):
  (update users)
  # cd /var/yp
  # make
  
To allow password changes:
  # rpc.yppasswdd
  # rpc.yppasswdd -e chfn -e chsh (to allow changing of full name and login shell)

/etc/ypsecurenets
<file>
# allow connections from local host -- necessary
host 127.0.0.1
# same as 255.255.255.255 127.0.0.1
#
# allow connections from any host
# on the 192.168.2.0 network
255.255.255.0   192.168.2.0
</file>

start services on boot
  chkconfig ypserv on
  chkconfig ypbind on
  chkconfig ypxfrd on
  chkconfig yppasswdd on


===== nfs =====
  * edit /etc/exports
<file>
/home \
        G4-cluster01.setup.lan(rw,sync,no_root_squash) \
        G4-cluster02.setup.lan(rw,sync,no_root_squash) \
        G4-cluster03.setup.lan(rw,sync,no_root_squash) \
        G4-cluster04.setup.lan(rw,sync,no_root_squash)

/usr \
        G4-cluster01.setup.lan(rw,sync,no_root_squash) \
        G4-cluster02.setup.lan(rw,sync,no_root_squash) \
        G4-cluster03.setup.lan(rw,sync,no_root_squash) \
        G4-cluster04.setup.lan(rw,sync,no_root_squash)


</file>
  
  * Add to startup services

  chkconfig portmap on
  chkconfig nfs on

  * Start the nfs server

  portmap
  service nfs start

  * Reload any nfs changes to /etc/exports

  exportfs -ra

===== auto mount =====
====if not using automount, add to /etc/fstab====
  G4-cluster01:/home      /home                   nfs     defaults        0 0

====If using automount, on master:====

/etc/auto.master
  /home auto.home
/etc/auto.home
  steve    G4-cluster01.setup.lan:/home/&
or
  *        G4-cluster01.setup.lan:/home/&
/etc/nsswitch
  automount:  files nis
Then update the database if yp is already running:
  cd /var/yp
  make


===== mpi =====
[[mpi]]
===== openmp =====
[[http://www.linux-mag.com/id/4609|openmp in 30 minutes]]

===== system monitoring =====
[[http://www.redhat.com/docs/manuals/linux/RHL-9-Manual/admin-primer/s1-resource-rhlspec.html|Red Hat Linux-Specific Information]]
[[http://www.redhat.com/cluster_suite/|Red Hat Cluster Suite]]
===== batch system =====

Also refer to the Parallel Matlab section

https://www.aoe.vt.edu/~stedwar1/Steve/doku/dokuwiki-2009-02-14/doku.php?id=aoe:matlab

====pbs====
[[http://euler.phys.cmu.edu/cluster/pbs.html]]

  qsub
  showq
  checkjob

notes from Shinpaugh:

openpbs -> torque

A free version of Moab is maui

To submit your job to the queuing system use the command qsub:

    qsub ./JobScript.sh

This will return your job name of the form xxxx.queueserver.  Example: 4567.admin01

To remove a job from the queue, or stop a running job, use the command `qdel <job_number>`.  Example:  qdel 4567

To see status information about your job, you can use:

        `qstat -f <job_number>`     which is a Torque command that will provide detailed information about the job.
        `showstart  <job_number>`     which is a Moab command that will tell you expected start and finish times.
         and `checkjob -v <job_number>`     which is a Moab command that will provide detailed information about the job.

NOTE:  The Moab commands may report an error of the form "ERROR:  cannot locate job '<job name>' if the scheduler has not yet picked up the newly submitted job.  If so, just a wait a minute and try again.

When your job has finished running, any outputs to stdout or stderr will be placed in the files .o and .e. These 2 files will be in the directory that you submitted the job from.

To find information about all your queued or running jobs you can use the commands `qstat` and `showq`.  The `qstat` command without a <job name> argument will show all ithaca jobs from the Torque resource manager's perspective.  The `showq` command without arguments will show all of the running jobs on all ARC systems from the Moab scheduler's perspective .  If you wish to only view ithaca jobs with showq, use `showq -p ITHACA`.  NOTE: Users generally find showq to be more useful that qstat.

==== High Availability Cluster ====
http://olex.openlogic.com/wazi/2011/ensure-high-availability-with-centos-6-clustering/