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MrBayes 3.1.2 on ABE

MrBayes on ABE provides a familiar MrBayes interface, and submits jobs to ABE, a large NSF Teragrid Resource. The code used is a hybrid MrBayes, created by Alexandrous Stamatakis. Jobs on Abe can be run for up to 168 hours / 7 days.

How to use it: Submission to the TeraGrid requires the user to provide parameters that determine job priority in the queue, help identify the number of processors required, and set a time for job termination (whether the run is finished or not). First time users should view the primer on using TeraGrid resources here.

If you do not use a MrBayes block in your input file, most of the decisions are made automatically, depending on settings the user configures in the interface. Just enter the number of characters your matirx at the top of the form. The value you enter can be approximate, as long as it is pretty close.

If you submit an input file with a MrBayes block (which we recommend), configuring the run is slightly more complex, because the MrBayes block contains a lot of configuration information that the application does not yet “read”.

  1. Specify that your data set contains a MrBayes Block.
  2. Assure us that "autoclose = no" does not appear in the MrBayes block. If you include such a statement, you will cause an entire disk to fill with a single repeating line from your log file, crashing everyone else’s job in the process. Not a good use of resources.
  3. Third tell the application the values of nruns=  and nchains=  in your MrBayes block. (Guide to setting nruns= and nchains=) These values help us distribute the job across the correct number of processors and threads. The interface currently limits nruns*nchains to be <= 16. nruns*nchains must be a multiple of 2
  4. Enter the number of characters in your matrix.
  5. Tell the application if your MrBayes Block specifies one or more partitions * 

Disadvantages:The queue times on Teragrid resources vary according to traffic and according to the size of your job (shorter jobs typically have shorter queue waits). Sometimes TeraGrid resources go down for preventative maintenance or due to unforeseen circumstances. At present, this will cause your job to fail, and you will have to restart it. There is no restart capability at present.

Click this icon to check the traffic on TeraGrid: Teragrid Traffic  
Click this icon to check the Teragrid maintenance schedule: TeraGrid Calendar  

Known Issues:
MrBayes 3.1.2 has a known issue where the job can "runaway", creating a large log file, and making no progress. At present we beleive this is triggered by runs that have low generation counts (< 5,000 gens). We have tried to compensate for this by preventing users from submitting jobs less than 5,000 generations. Should you experience, or think you experienced a runaway job, please contact us. We expect this issue to be resolved in the next release of MrBayes (MB V 3.2.0).

The command string mcmcp is used in some local installations of MrBayes, but it cannot be used in the CIPRES Science Gateway. You must use the command mcmc ngen= xxxxx etc.
The command mcmcp ngen= xxxx will produce no results.

If there is a tool or a feature you need, let us know.