Difference between revisions of "Mrbayes-software"
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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. | ||
| + | |||
| + | 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. | ||
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| + | === 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 === | ||
Revision as of 00:50, 31 January 2008
The CCG supports MrBayes on the Cairo (PowerPC) and BobSCEd (quad core Xeon) clusters. The software is installed in /cluster/{cairo, bobsced}/bin/mb. 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.
N.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 vi and emacs editors are both available on the Cairo nodes.
!#/bin/bash
lamwipe # stops LAM (if it's running)
lamboot -v lambhosts.def # starts LAM with the hosts listed in lambhosts.def
mpirun -np 4 /cluster/cairo/bin/mb # starts mb on four cores
lamwipe # stops LAM
You will also need a lam-hosts.def file listing the cluster nodes you want to run your jobs on. Remember that the node you start the job on (c4 in this example) must be listed in the lam-hosts.def file.
are You can run the script file in the background with the command:
c4$ nohup ./this-run.sh &
Sample script
watching with ps
Other useful commands:
$ lamnodes # displays the hosts in your LAM world
Sample command lines
