NAMD - Revision history

Mhanby@uab.edu at 19:53, 31 October 2016

2016-10-31T19:53:22Z

← Older revision		Revision as of 19:53, 31 October 2016
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	First, create the working directory for the job. You can create any directory to run your job. It is recommended that the job directory be on the scratch (i.e. lustre filesystem) instead of your home directory.		First, create the working directory for the job. You can create any directory to run your job. It is recommended that the job directory be on the scratch (i.e. lustre filesystem) instead of your home directory.

	The ${USER_SCRATCH} variable expands to /scratch/~~user/USERNAME~~, where ~~USERNAME~~ is your cheaha account name.		The ${USER_SCRATCH} variable expands to /data/scratch/$USER, where $USER is your cheaha account name.

	<pre>		<pre>
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	Copy the directory "apoa1" from the local host to a remote host's directory "NAMD"		Copy the directory "apoa1" from the local host to a remote host's directory "NAMD"
	<pre>		<pre>
	$ scp -r apoa1 USERNAME@cheaha.uabgrid.uab.edu:/scratch~~/user~~/USERNAME/jobs/NAMD		$ scp -r apoa1 USERNAME@cheaha.uabgrid.uab.edu:/data/scratch/USERNAME/jobs/NAMD
	</pre>		</pre>

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	outputtiming 20		outputtiming 20

	outputname /scratch~~/user~~/USERNAME/jobs/NAMD/output		outputname /data/scratch/USERNAME/jobs/NAMD/output

	</pre>		</pre>

Mhanby@uab.edu at 19:38, 22 May 2013

2013-05-22T19:38:14Z

← Older revision		Revision as of 19:38, 22 May 2013
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	First, create the working directory for the job. You can create any directory to run your job. It is recommended that the job directory be on the scratch (i.e. lustre filesystem) instead of your home directory.		First, create the working directory for the job. You can create any directory to run your job. It is recommended that the job directory be on the scratch (i.e. lustre filesystem) instead of your home directory.

	The ${~~UABGRID_SCRATCH~~} variable expands to /~~lustre~~/~~scratch~~/USERNAME, where USERNAME is your cheaha account name.		The ${USER_SCRATCH} variable expands to /scratch/user/USERNAME, where USERNAME is your cheaha account name.

	<pre>		<pre>
	$ mkdir -p ${~~UABGRID_SCRATCH~~}/jobs/NAMD		$ mkdir -p ${USER_SCRATCH}/jobs/NAMD
	$ cd ${~~UABGRID_SCRATCH~~}/jobs/NAMD		$ cd ${USER_SCRATCH}/jobs/NAMD
	</pre>		</pre>

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	Copy the directory "apoa1" from the local host to a remote host's directory "NAMD"		Copy the directory "apoa1" from the local host to a remote host's directory "NAMD"
	<pre>		<pre>
	$ scp -r apoa1 USERNAME@cheaha.uabgrid.uab.edu:/~~lustre~~/~~scratch~~/USERNAME/jobs/NAMD		$ scp -r apoa1 USERNAME@cheaha.uabgrid.uab.edu:/scratch/user/USERNAME/jobs/NAMD
	</pre>		</pre>

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	outputtiming 20		outputtiming 20

	outputname /~~lustre~~/~~scratch~~/USERNAME/jobs/NAMD/output		outputname /scratch/user/USERNAME/jobs/NAMD/output

	</pre>		</pre>
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	# Ready ...		# Ready ...
	#		#
	cd ${~~UABGRID_SCRATCH~~}/jobs/NAMD		cd ${USER_SCRATCH}/jobs/NAMD
	export MYFILE=apoa1		export MYFILE=apoa1

Mhanby@uab.edu: /* NAMD Versions */

2012-08-17T14:42:19Z

NAMD Versions

← Older revision		Revision as of 14:42, 17 August 2012
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	namd/namd-2.7		namd/namd-2.7
	namd/namd-2.8		namd/namd-2.8
			namd/namd-2.9
	</pre>		</pre>

Tanthony@uab.edu: added category MD

2012-04-04T14:58:34Z

added category MD

← Older revision		Revision as of 14:58, 4 April 2012
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	[[Category:~~NAMD~~]][[Category:~~Software~~]]		[[Category:Software]][[Category:Molecular Dynamics]]

Tanthony@uab.edu: added category software

2012-04-04T14:09:51Z

added category software

← Older revision		Revision as of 14:09, 4 April 2012
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	[[Category:NAMD]]		[[Category:NAMD]][[Category:Software]]

Mhanby@uab.edu at 21:43, 8 March 2012

2012-03-08T21:43:05Z

← Older revision		Revision as of 21:43, 8 March 2012
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	#!/bin/bash		#!/bin/bash
	#$ -S /bin/bash		#$ -S /bin/bash
			#
			# Example NAMD job submission script can be found here:
			# https://docs.uabgrid.uab.edu/wiki/NAMD#Submitting_NAMD_jobs_to_Cheaha
			#
	# Execute from the current working directory		# Execute from the current working directory
	#$ -cwd		#$ -cwd

Mhanby@uab.edu at 21:41, 8 March 2012

2012-03-08T21:41:04Z

← Older revision		Revision as of 21:41, 8 March 2012
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	These instructions provide an example of how to create and submit a NAMD job on [[Cheaha]].		These instructions provide an example of how to create and submit a NAMD job on [[Cheaha]].

	First, create the working directory for the job~~- Replace 'USERNAME' with the account associated username on Cheaha~~.		First, create the working directory for the job. You can create any directory to run your job. It is recommended that the job directory be on the scratch (i.e. lustre filesystem) instead of your home directory.
	You can create any directory to run your job. It is recommended that the job directory be on the scratch (i.e. lustre filesystem) instead of ~~the user~~ home directory.
			The ${UABGRID_SCRATCH} variable expands to /lustre/scratch/USERNAME, where USERNAME is your cheaha account name.

	<pre>		<pre>
	$ mkdir -p ~~/lustre/scratch/USERNAME~~/jobs/NAMD		$ mkdir -p ${UABGRID_SCRATCH}/jobs/NAMD
	$ cd ~~/lustre/scratch/USERNAME~~/jobs/NAMD		$ cd ${UABGRID_SCRATCH}/jobs/NAMD
	</pre>		</pre>


	Next, Copy all the files required for NAMD to the working directory.		Next, Copy all the files required for NAMD to the working directory.
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	#		#
	#$ -pe namd* 32		#$ -pe namd* 32
			#
	# Load the appropriate module(s)		# Load the appropriate module(s)
	. /etc/profile.d/modules.sh		. /etc/profile.d/modules.sh
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	#$ -l vf=1G		#$ -l vf=1G
	#		#
	~~# Single precision~~

	~~# The $NSLOTS variable is set automatically by SGE to match the number of~~
	~~# slots requests~~

	~~export CHARMRUN_NAMD_DIR=/share/apps/namd/NAMD_2.8b1_Linux-x86_64-ibverbs~~

	#		#
	########## Do Not Edit This Section ##########		########## Do Not Edit This Section ##########
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	# Prepare nodelist file for charmrun ...		# Prepare nodelist file for charmrun ...
	#		#
			# The scheduler provides several variables, two of which we are using here:
			# $NSLOTS - This contains the number of cpu slots requested by the -pe namd*
			# $TMPDIR - This is a temporary directory used by the scheduler for this job
			# we use it to build the charmlist machine file for charmrun
	echo "Got ${NSLOTS} slots."		echo "Got ${NSLOTS} slots."
	echo "group main" > ${TMPDIR}/charmlist		echo "group main" > ${TMPDIR}/charmlist
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	export MYFILE=apoa1		export MYFILE=apoa1

			# The variable ${CHARMRUN_NAMD_DIR} is automatically set by the
			# "module load namd/namd-2.8" command above and points to the installation
			# directory for NAMD
	${CHARMRUN_NAMD_DIR}/charmrun ${CHARMRUN_NAMD_DIR}/namd2 ++nodelist ${TMPDIR}/charmlist +p ${NSLOTS} ${MYFILE}.namd > ${MYFILE}.out		${CHARMRUN_NAMD_DIR}/charmrun ${CHARMRUN_NAMD_DIR}/namd2 ++nodelist ${TMPDIR}/charmlist +p ${NSLOTS} ${MYFILE}.namd > ${MYFILE}.out

Mhanby@uab.edu: /* Submitting NAMD jobs to Cheaha */

2012-03-08T21:27:12Z

Submitting NAMD jobs to Cheaha

← Older revision		Revision as of 21:27, 8 March 2012
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	#		#
	########## Do Not Edit This Section ##########		########## Do Not Edit This Section ##########
	## ~~20120302 - MJH - Are~~ these variables ~~really needed~~, ~~or just an artifact~~		## NAMD requires these variables, otherwise it will try to use rsh
	## of ~~a previous job script? I don~~'t ~~think NAMD uses any of these variables~~		## instead of ssh, which won't work on cheaha
	#		#
	~~# The version of MPICH to use, transport protocol & a trick to delete cleanly~~
	~~# running MPICH jobs ...~~
	#
	~~#$ -v MPIR_HOME=/opt/lam/intel/bin~~
	#$ -v P4_RSHCOMMAND=rsh		#$ -v P4_RSHCOMMAND=rsh
	#$ -v MPICH_PROCESS_GROUP=no		#$ -v MPICH_PROCESS_GROUP=no

Mhanby@uab.edu: changed references of "-pe namd2" to "-pe namd*", use the wildcard in examples when an application has multiple PEs available

2012-03-08T21:17:33Z

changed references of "-pe namd2" to "-pe namd*", use the wildcard in examples when an application has multiple PEs available

← Older revision		Revision as of 21:17, 8 March 2012
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	* -N - job name		* -N - job name
	* -M - user email		* -M - user email
	* -pe ~~namd2~~ numberOfProcessors (-pe ~~namd2~~ 32 - run the code in parallel on 32 processors on the ~~Sipsey~~ nodes of ~~Cheaha~~)		* -pe namd* numberOfProcessors (-pe namd* 32 - run the code in parallel on 32 processors on the Cheaha compute nodes. The * wildcard instructs the scheduler to use any of the namd parallel environments and should always be used for NAMD jobs unless you really know what you are doing)
	* -l vf to the maximum memory needed for each task		* -l vf to the maximum memory needed for each task
	* cd to the current working directory where the job data is stored		* cd to the current working directory where the job data is stored
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	#$ -m be		#$ -m be
	#		#
	#$ -pe ~~namd2~~ 32		#$ -pe namd* 32
	# Load the appropriate module(s)		# Load the appropriate module(s)
	. /etc/profile.d/modules.sh		. /etc/profile.d/modules.sh

Mhanby@uab.edu: /* Submitting NAMD jobs to Cheaha */

2012-03-02T17:24:06Z

Submitting NAMD jobs to Cheaha

← Older revision		Revision as of 17:24, 2 March 2012
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	#$ -cwd		#$ -cwd
	#		#
	# Job runtime (~~24 hours~~)		# Job runtime (1 hour, at 55 minutes NAMD will be notified to shut down)
	#$ -l h_rt=1:00:00,s_rt=0:55:00		#$ -l h_rt=1:00:00,s_rt=0:55:00
	#$ -j y		#$ -j y
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	#		#
	########## Do Not Edit This Section ##########		########## Do Not Edit This Section ##########
			## 20120302 - MJH - Are these variables really needed, or just an artifact
			## of a previous job script? I don't think NAMD uses any of these variables
	#		#
	# The version of MPICH to use, transport protocol & a trick to delete cleanly		# The version of MPICH to use, transport protocol & a trick to delete cleanly
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	#$ -v MPICH_PROCESS_GROUP=no		#$ -v MPICH_PROCESS_GROUP=no
	#$ -v CONV_RSH=ssh		#$ -v CONV_RSH=ssh
	#		##############################################

	# Prepare nodelist file for charmrun ...		# Prepare nodelist file for charmrun ...
	#		#
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	awk '{print "host " $1}' ${TMPDIR}/machines >> ${TMPDIR}/charmlist		awk '{print "host " $1}' ${TMPDIR}/machines >> ${TMPDIR}/charmlist
	cat ${TMPDIR}/charmlist		cat ${TMPDIR}/charmlist
	#
	########## Edit The ~~Filename~~ ##########		########## Edit The Directory and MYFILE ##########
	#
	# Ready ...		# Ready ...
	#		#
			cd ${UABGRID_SCRATCH}/jobs/NAMD
	cd ~~/lustre/scratch/USERNAME~~/jobs/NAMD


	export MYFILE=apoa1		export MYFILE=apoa1

			${CHARMRUN_NAMD_DIR}/charmrun ${CHARMRUN_NAMD_DIR}/namd2 ++nodelist ${TMPDIR}/charmlist +p ${NSLOTS} ${MYFILE}.namd > ${MYFILE}.out
	${CHARMRUN_NAMD_DIR}/charmrun ${CHARMRUN_NAMD_DIR}/namd2 ++nodelist
	${TMPDIR}/charmlist +p ${NSLOTS} ${MYFILE}.namd > ${MYFILE}.out

	</pre>		</pre>