General Usage of Hydra - Revision history

Homa: added physical memory limit option

2015-10-10T22:12:56Z

added physical memory limit option

← Older revision		Revision as of 17:12, 10 October 2015
Line 18:		Line 18:
	# ### maximum wall time		# ### maximum wall time
	#PBS -l walltime=[dd:hh:mm:ss]		#PBS -l walltime=[dd:hh:mm:ss]

			# ### maximum physical memory required (use 'kb', 'mb', or 'gb')
			#PBS -l mem=512mb

	# ### number of nodes and processors per node		# ### number of nodes and processors per node

Administrator at 19:13, 10 June 2014

2014-06-10T19:13:16Z

← Older revision		Revision as of 14:13, 10 June 2014
Line 12:		Line 12:
	#PBS -N [name_of_job]		#PBS -N [name_of_job]

	# ### mail for ~~begin/~~end/abort		# ### mail for end/abort
	#PBS -m ea		#PBS -m ea
	#PBS -M [email_address]		#PBS -M [email_address]

Wzhwei at 22:54, 9 June 2014

2014-06-09T22:54:44Z

← Older revision		Revision as of 17:54, 9 June 2014
Line 72:		Line 72:
	qstat -u [username]		qstat -u [username]
	</pre>		</pre>
	where <tt>[username]</tt> is your own ~~user name~~. This command will show the status of your own jobs.		where <tt>[username]</tt> is your own username. This command will show the status of your own jobs.
	</ul>		</ul>

Wzhwei at 22:54, 9 June 2014

2014-06-09T22:54:08Z

← Older revision		Revision as of 17:54, 9 June 2014
Line 7:		Line 7:
	<li>Example of job.pbs file		<li>Example of job.pbs file
	<pre>		<pre>
	### AUTOMATICALLY GENERATED BATCH FILE		### AUTOMATICALLY GENERATED BATCH FILE

	# ### name of job		# ### name of job
Line 54:		Line 54:

	<tt>[queue_name]</tt>		<tt>[queue_name]</tt>
	~~You~~ ~~can~~ ~~submit~~ ~~your~~ ~~jobs~~ on fast ~~nodes~~ or default ~~nodes~~.		There are two options for queue name: fast or default.

	<tt>[job_location]</tt>		<tt>[job_location]</tt>

Wzhwei at 22:53, 9 June 2014

2014-06-09T22:53:20Z

← Older revision		Revision as of 17:53, 9 June 2014
Line 17:		Line 17:

	# ### maximum wall time		# ### maximum wall time
	#PBS -l walltime=30:00:00:00		#PBS -l walltime=[dd:hh:mm:ss]

	# ### number of nodes and processors per node		# ### number of nodes and processors per node
	#PBS -l nodes=1:ppn=1		#PBS -l nodes=1:ppn=1

	# # ### queue		# ### queue
	###PBS -q [~~queue~~]		#PBS -q [queue_name]

	# ### indicates that job should not rerun if it fails		# ### indicates that job should not rerun if it fails
Line 52:		Line 52:
	<tt>[dd:hh:mm:ss]</tt>		<tt>[dd:hh:mm:ss]</tt>
	This is the maximum allowed running time for your job. dd: days; hh: hours; mm: minutes; ss: seconds.		This is the maximum allowed running time for your job. dd: days; hh: hours; mm: minutes; ss: seconds.

			<tt>[queue_name]</tt>
			You can submit your jobs on fast nodes or default nodes.

	<tt>[job_location]</tt>		<tt>[job_location]</tt>

Wzhwei at 22:50, 9 June 2014

2014-06-09T22:50:46Z

← Older revision		Revision as of 17:50, 9 June 2014
Line 10:		Line 10:

	# ### name of job		# ### name of job
	#PBS -N [~~name_~~]		#PBS -N [name_of_job]

	# ### mail for begin/end/abort		# ### mail for begin/end/abort
	#PBS -m ea		#PBS -m ea
	#PBS -M ~~zonghuiroot@gmail.com~~		#PBS -M [email_address]

	# ### maximum ~~cpu~~ time		# ### maximum wall time
	####PBS -l cput=5000:00:00
	#PBS -l walltime=30:00:00:00		#PBS -l walltime=30:00:00:00

Line 24:		Line 23:

	# # ### queue		# # ### queue
	###PBS -q ~~fast~~		###PBS -q [queue]

	# ### indicates that job should not rerun if it fails		# ### indicates that job should not rerun if it fails
Line 38:		Line 37:
	#PBS -S /bin/bash		#PBS -S /bin/bash

			cd /home/[job_location]
	cd /home/zonghui/Scratch/Multi_chain/Double_length_DNA_experiment/ppa12.peg5_cr_5_double_ka_4/ppa.cat12.pegcat2.peg5
	#mpirun -np 2 /opt/lammps/lmp2013_mpi -in input.dat

	time /opt/lammps/lmp2013 < input.dat		time /opt/lammps/lmp2013 < input.dat

	#/home/wei/Install/lammps/current/src/lmp_suse_linux < input.dat

	if [ $? -eq 0 ] ; then		if [ $? -eq 0 ] ; then
Line 49:		Line 44:
	fi		fi
	</pre>		</pre>
	<tt>[~~job_location~~]</tt>		<tt>[name_of_job]</tt>
	This is the ~~address~~ of the ~~folder~~ ~~where~~ ~~your~~ ~~input~~ ~~file~~ is ~~located~~.		This is the name of the job that will be showed in the queue.

		⚫	<tt>[email_address]</tt>
		⚫	This is the email address you used to receive the system notice when job begins, aborted or ended.

	<tt>[dd:hh:mm:ss]</tt>		<tt>[dd:hh:mm:ss]</tt>
	This is the maximum allowed running time for your job. dd: days; hh: hours; mm: minutes; ss: seconds.		This is the maximum allowed running time for your job. dd: days; hh: hours; mm: minutes; ss: seconds.

⚫	<tt>[email_address]</tt>
⚫	This is the email address you used to receive the system notice when job begins, aborted or ended.

	<tt>[job_location]</tt>		<tt>[job_location]</tt>
Line 64:		Line 59:
	<li>Submit jobs		<li>Submit jobs
	<pre>		<pre>
	~~msb~~ job.~~mbs~~		qsub job.pbs
	</pre>		</pre>
	<li>Check job status		<li>Check job status
	<pre>		<pre>
			qstat
	showq
	</pre>		</pre>
	show all jobs		show status of all jobs.
	<pre>		<pre>
	qstat		qstat -u [username]
	</pre>		</pre>
			where <tt>[username]</tt> is your own user name. This command will show the status of your own jobs.
	show your own jobs
	</ul>		</ul>

Wzhwei: Created page with "

Example of job.pbs file

  ### AUTOMATICALLY GENERATED BATCH FILE  # ### name of job #PBS -N [name_]  # ### mail for begi..."

2014-06-09T22:44:21Z

Created page with "<ul> <li>Login <pre> ssh hydra </pre> </li> <li>Example of job.pbs file <pre> ### AUTOMATICALLY GENERATED BATCH FILE # ### name of job #PBS -N [name_] # ### mail for begi..."

New page

<ul>
<li>Login
<pre>
ssh hydra
</pre>
</li>
<li>Example of job.pbs file
<pre>
### AUTOMATICALLY GENERATED BATCH FILE

# ### name of job
#PBS -N [name_]

# ### mail for begin/end/abort
#PBS -m ea
#PBS -M zonghuiroot@gmail.com

# ### maximum cpu time
####PBS -l cput=5000:00:00
#PBS -l walltime=30:00:00:00

# ### number of nodes and processors per node
#PBS -l nodes=1:ppn=1

# # ### queue
###PBS -q fast

# ### indicates that job should not rerun if it fails
#PBS -r n

# ### stdout and stderr merged as stderr
#PBS -j eo

# ### write stderr to file
#PBS -e log.err

# ### the shell that interprets the job script
#PBS -S /bin/bash

cd /home/zonghui/Scratch/Multi_chain/Double_length_DNA_experiment/ppa12.peg5_cr_5_double_ka_4/ppa.cat12.pegcat2.peg5
#mpirun -np 2 /opt/lammps/lmp2013_mpi -in input.dat

time /opt/lammps/lmp2013 < input.dat

#/home/wei/Install/lammps/current/src/lmp_suse_linux < input.dat

if [ $? -eq 0 ] ; then
touch COMPLETED
fi
</pre>
<tt>[job_location]</tt>
This is the address of the folder where your input file is located.

<tt>[dd:hh:mm:ss]</tt>
This is the maximum allowed running time for your job. dd: days; hh: hours; mm: minutes; ss: seconds.

<tt>[email_address]</tt>
This is the email address you used to receive the system notice when job begins, aborted or ended.

<tt>[job_location]</tt>
This is the address of the folder where your input file is located.

</li>
<li>Submit jobs
<pre>
msb job.mbs
</pre>
<li>Check job status
<pre>
showq
</pre>
show all jobs
<pre>
qstat
</pre>
show your own jobs
</ul>

General Usage of Hydra - Revision history

Homa: added physical memory limit option

Administrator at 19:13, 10 June 2014

Wzhwei at 22:54, 9 June 2014

Wzhwei at 22:54, 9 June 2014

Wzhwei at 22:53, 9 June 2014

Wzhwei at 22:50, 9 June 2014

Wzhwei: Created page with " Login ssh hydra Example of job.pbs file ### AUTOMATICALLY GENERATED BATCH FILE # ### name of job #PBS -N [name_] # ### mail for begi..."

Wzhwei: Created page with "

Login
ssh hydra

Example of job.pbs file
### AUTOMATICALLY GENERATED BATCH FILE # ### name of job #PBS -N [name_] # ### mail for begi..."