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MrBayes 3.2.1 on XSEDE Restart Interface (BETA release)

MrBayes 3.2.1 supports checkpointing, which makes it possible to restart a run that has terminated unexpectedly, or that has reached the end of the maximum allowed run time without converging. The MrBayes 3.2.1 on XSEDE Restart Interface makes it possible for users to take advantage of this feature. The current interface is admittedly fragile, but it does make it possible to access the restart capability. We plan to improve the functionality of the interface in the near future.

To use the restart capability, please us the following steps exactly:

  1. Open the results pane for a MrBayes job that you wish to restart. Confirm that the results list includes a checkpoint (.ckp) file (it is possible for a job to terminate so early this file is not created, and it is also possible to turn checkpointing off via the MrBayes block. Please see the MrBayes 3.2.1 manual for more details.)

  2. Identify all of the files that will be required for a restart run. These are <filename>.ckp, <filename>.mcmc, and infile.nex and any file with the format <filename>.run<number>.t, or <filename>.run<number>.p,
    where <filename> is either infile.nex (default) or any string specified by the command filename= in your Nexus block.

  3. One at a time, click the hyperlink for <filename>.ckp. When the file display page opens, look at the top of the page for the button "Save to Current Folder". Click that link. You will be prompted to specify the name of the file. Name the infile.nex.ckp, and submit.

  4. Repeat this process for each file, including <filename>.mcmc, and all files with the format <filename>.run<number>.t, or <filename>.run<number>.p. Be sure to preserve the numbers of the .t and .p files. So for example, <filename>.run1.t would become infile.nex.run1.t, and so forth.

  5. Once this process is complete, download the infile.nex file to your local machine. You must modify the file in two ways. First, in the mcmc command set in the MrBayes block, add the statement append=yes. Next, remove any filenames=<filename> commands in the MrBayes block.

  6. Upload the modified infile.nex to your work area.

  7. Now configure the job using the Restart Interface. Create a new Job. Select the modified infile.nex as the input file. Select the MrBayes 3.2.1 Restart as the Tool.

  8. Open the parameter pane, and select the files required for the restart, including infile.nex.ckp, infile.nex.mcmc, and any .t and .p files, such as infile.nex.run1.p, infile.nex.run1.t, etc

  9. Save the parameters, and start the run.

  10. Once the run begins, you will see in the "intermediate results" that two sets files will appear for each file you uploaded. For example, there will be an infile.nex.mcmc and an infile.nex.mcmc~ file. The file with the tilde (~) after it is a file created as part of the new run. The file without the tilde will be the file you uploaded, with the restart information appended to it.

We apologize for this very cumbersome process, but we wanted to expose this capability as soon as possible. We should have something more elegant in place in a few weeks.

Known Issues: No known issues at present.

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