Mrbayes-software - Revision history

Charliep: /* Cairo */

2008-01-31T05:29:54Z

Cairo

← Older revision		Revision as of 05:29, 31 January 2008
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	=== Cairo ===		=== Cairo ===
	Copy and paste these commands, replacing the name of the MrBayes input file with your own, in ~~to a file~~. The <code>vi</code> and <code>emacs</code> editors are both available on the Cairo nodes.		Copy and paste these commands into a file, replacing the name of the MrBayes input file with your own (<code>Hybrid_Bayesian.txt</code> in this example). The <code>vi</code> and <code>emacs</code> editors are both available on the Cairo nodes.

	<code>		<code>
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	lamwipe # stops LAM (if it's running)		lamwipe # stops LAM (if it's running)
	lamboot -v lambhosts.def # starts LAM with the hosts listed in lambhosts.def <br>		lamboot -v lambhosts.def # starts LAM with the hosts listed in lambhosts.def <br>
	mpirun -np 4 /cluster/cairo/bin/mb # starts mb on four cores <br>		mpirun -np 4 /cluster/cairo/bin/mb Hybrid_Bayesian.txt < /dev/null > Hybrid_Baye
			sian.log# starts mb on four cores <br>
	lamwipe # stops LAM <br>		lamwipe # stops LAM <br>
	</code>		</code>

Charliep at 05:18, 31 January 2008

2008-01-31T05:18:09Z

← Older revision		Revision as of 05:18, 31 January 2008
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	The CCG supports MrBayes on the Cairo (PowerPC) and BobSCEd (quad core Xeon) clusters. The software is installed in <code>/cluster/{cairo, bobsced}/bin/mb</code>. Both versions are built with the Message Passing Interface (MPI) libraries enabling parallel runs using up to 4 cores. Scaling beyond 4 tasks is limited by the software's architecture. One way around this limitation is to break your large runs into groups of 4.		The CCG supports MrBayes on the Cairo (PowerPC) and BobSCEd (quad core Xeon) clusters. The software is installed in <code>/cluster/{cairo, bobsced}/bin/mb</code>. Both versions are built with the Message Passing Interface (MPI) libraries enabling parallel runs using up to 4 cores. Scaling beyond 4 tasks is limited by the software's architecture. One way around this limitation is to break your large runs into groups of 4.

	~~<b>N.B.</b> Currently MrBayes is only available on Cairo, the BobSCEd version is being upgraded.~~

	Both versions of MrBayes, Cairo and BobSCEd, are built with the LAM MPI libraries. While this improves the performance of MrBayes somewhat over other MPI bindings it does make the running of parallel jobs slightly more complicated.		Both versions of MrBayes, Cairo and BobSCEd, are built with the LAM MPI libraries. While this improves the performance of MrBayes somewhat over other MPI bindings it does make the running of parallel jobs slightly more complicated.
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	=== Cairo ===		=== Cairo ===

	Copy and paste these commands, replacing the name of the MrBayes input file with your own, in to a file. The <code>vi</code> and <code>emacs</code> editors are both available on the Cairo nodes.		Copy and paste these commands, replacing the name of the MrBayes input file with your own, in to a file. The <code>vi</code> and <code>emacs</code> editors are both available on the Cairo nodes.

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	You will also need a <code>lam-hosts.def</code> file listing the cluster nodes you want to run your jobs on. Remember that the node you start the job on (<code>c4</code> in this example) must be listed in the <code>lam-hosts.def</code> file.		You will also need a <code>lam-hosts.def</code> file listing the cluster nodes you want to run your jobs on. Remember that the node you start the job on (<code>c4</code> in this example) must be listed in the <code>lam-hosts.def</code> file.

			<code>
			c4 cpu=2 <br>
			c5 cpu=2 <br>
			</code>

			Once these two files and your MrBayes input file are ready you can run job in the background with the command:
	are ~~You~~ can run ~~the script file~~ in the background with the command:

	<code>		<code>
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	</code>		</code>

	~~Sample script~~		There are sample scripts and MrBayes input files in <code>/cluster/home/charliep/mb-test-cairo</code>. Note near the end of the MrBayes input file <code>Hybrid_Bayesian.txt</code>, the <code>mcmcp</code> command has an option for <code>nchains</code>, this should be set to 4 in your input file per the information above.

	~~watching with ps~~		You can use the <code>top</code> command to see if your program is running. 'q' exits <code>top</code>. The data set and analysis described in <code>Hybrid_Bayesian.txt</code> takes about N days to run on 4 Cairo cores.


	~~Other useful commands:~~
	~~$ lamnodes # displays~~ the ~~hosts~~ in ~~your LAM world~~




	~~Sample command lines~~

	=== BobSCEd ===		=== BobSCEd ===
			<b>N.B.</b> Currently MrBayes is only available on Cairo, the BobSCEd version is being upgraded.

Charliep at 04:50, 31 January 2008

2008-01-31T04:50:21Z

← Older revision		Revision as of 04:50, 31 January 2008
Line 1:		Line 1:
	The CCG supports MrBayes on the Cairo (PowerPC) and BobSCEd (quad core Xeon) clusters. The software is installed in <code>/cluster/{cairo, bobsced}/bin/mb</code>. Both versions are built with the Message Passing Interface (MPI) libraries enabling parallel runs using up to 4 cores. Scaling beyond 4 tasks is limited by the software's architecture. One way around this limitation is to break your large runs into groups of 4.		The CCG supports MrBayes on the Cairo (PowerPC) and BobSCEd (quad core Xeon) clusters. The software is installed in <code>/cluster/{cairo, bobsced}/bin/mb</code>. Both versions are built with the Message Passing Interface (MPI) libraries enabling parallel runs using up to 4 cores. Scaling beyond 4 tasks is limited by the software's architecture. One way around this limitation is to break your large runs into groups of 4.

			<b>N.B.</b> Currently MrBayes is only available on Cairo, the BobSCEd version is being upgraded.

			Both versions of MrBayes, Cairo and BobSCEd, are built with the LAM MPI libraries. While this improves the performance of MrBayes somewhat over other MPI bindings it does make the running of parallel jobs slightly more complicated.

			The difference between LAM and other MPI bindings is that you need to start the LAM world before running the parallel program, and then shut it down when the parallel program is complete. The simplest way to accomplish this is with a small shell script.

			=== Cairo ===

			Copy and paste these commands, replacing the name of the MrBayes input file with your own, in to a file. The <code>vi</code> and <code>emacs</code> editors are both available on the Cairo nodes.

			<code>
			!#/bin/bash <br>
			lamwipe # stops LAM (if it's running)
			lamboot -v lambhosts.def # starts LAM with the hosts listed in lambhosts.def <br>
			mpirun -np 4 /cluster/cairo/bin/mb # starts mb on four cores <br>
			lamwipe # stops LAM <br>
			</code>

			You will also need a <code>lam-hosts.def</code> file listing the cluster nodes you want to run your jobs on. Remember that the node you start the job on (<code>c4</code> in this example) must be listed in the <code>lam-hosts.def</code> file.



			are You can run the script file in the background with the command:

			<code>
			c4$ nohup ./this-run.sh & <br>
			</code>

			Sample script

			watching with ps


			Other useful commands:
			$ lamnodes # displays the hosts in your LAM world




	Sample command lines		Sample command lines

			=== BobSCEd ===

Charliep at 02:43, 30 January 2008

2008-01-30T02:43:50Z

New page

The CCG supports MrBayes on the Cairo (PowerPC) and BobSCEd (quad core Xeon) clusters. The software is installed in <code>/cluster/{cairo, bobsced}/bin/mb</code>. Both versions are built with the Message Passing Interface (MPI) libraries enabling parallel runs using up to 4 cores. Scaling beyond 4 tasks is limited by the software's architecture. One way around this limitation is to break your large runs into groups of 4.

Sample command lines