Linux trick: installing OpenPBS

These are the steps to install OpenPBS on a linux cluster. The following refers to version 2.3.16.

Download and unpack the distribution. Run configure with the appropriate options: default settings are to install the package in /usr/local (and in particular /usr/local/bin and /usr/local/sbin; this should be fine for our purposes); to have the working directory (PBS_HOME) in /usr/spool/pbs; to have fifo as the scheduler. Configure with --with-scp (for all things to run smoothly, root on the server should be able to ssh into the execution hosts without password, and vice versa).

Patches needed with gcc 3.2.2 (before configuring); in buildutils/makedepend-sh, modify the eval $CPP… command at line 576 to include grep -v ">$" | \ after grep -v "$s\$" | \. Modify src/lib/Liblog/pbs_log.c by adding #include at the top. Same for src/server/svr_connect.c.

Cd into doc and make install to install the man pages.

Make and make install. If you have mounted /usr/local on other machines for access to Server/Executable/Client applications you may need to change permissions on /usr/local/sbin/pbs_mom. Each slave will also need a minimal pbs_mom directory structure. Copy buildutils/pbs_mkdirs from the source directory to the execution hosts, then on each of them run

sh pbs_mkdirs mom
sh pbs_mkdirs aux
sh pbs_mkdirs default

In order, run pbs_server, pbs_sched, pbs_mom (they are in /usr/local/sbin). The first time only, start pbs_server with the -t create option.

Before starting the Moms, you need to create the config file PBS_HOME/mom_priv/config, containing (assuming your pbs server is tweedledee)

$logevent 0x1ff
$clienthost tweedledee

Update [20040207]: Rajarshi Guha suggests adding also

$clienthost tweedledee.caltech.edu
$max_load 2.0
$ideal_load 1.0
$usecp tweedledee.caltech.edu:/home /home

where the first line is the fully qualified hostname of the server, the second and the third indicate the load above which a mom will not take a job (and the load that it will wait to have before taking new jobs, after refusing one), and the last line directs the moms to copy log files with cp (over NFS, assuming it's available) in case scp does not work. This config should go also to all the execution hosts. When this is done, start pbs_mom on all the hosts.

Update [20040207]: When everything is started, run qmgr and setup some options:

set s managers=root@tweedledee.caltech.edu
set s acl_hosts=tweedledee.caltech.edu
set s query_other_jobs=true
create q standard queue_type=e
set q standard resources_min.cput=1,resources_max.cput=12:00:00
set q standard resources_default.cput=30:00
set q standard enabled=true, started=true
set s scheduling=true

Next, still in qmgr, add all the nodes with

create node node-1
create node node-2
…

Update [20040207]: I like to have scripts in /usr/local/bin that execute a command and copy a file over the cluster: they would look something like

for host in ‘cat /usr/spool/PBS/server_priv/nodes`; do
        echo -n "$host "
        ssh $host "$*"
done

and

for host in `cat /usr/spool/PBS/server_priv/nodes`; do
        echo -n "$host "
        scp $1 $host:$2
done

[You’ll probably need to change permissions on the nodes file.] Now you're good to go!

Jan 03, 2006

openpbs (/linuxtricks)
2006-01-03, 14:43 [edit]


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© M. Vallisneri 2012 — last modified on 2010/01/29

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