MrBayes Restart on XSEDE 3.2.x Tree Inference Using Bayesian Analysis - run on XSEDE John P. Huelsenbeck and Fred Ronquist Huelsenbeck, J. P. and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755. Ronquist, F. and J. P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574. . Phylogeny / Alignment mrbayes_restart_xsede mbmpi_323 perl $run_version eq "3" perl "" 0 mbmpi_326 perl $run_version eq "6" perl "" 0 mpi_processes_conf 3 scheduler.conf perl "jobtype=mpi\\n" . "mpi_processes=" . $nchains_specified * $nruns_specified . "\\n" number_nodes_lt8 2 scheduler.conf perl ($nruns_specified * $nchains_specified) <= 8 perl "node_exclusive=0\\n" . "nodes=1\\n" number_nodes_gt8 2 scheduler.conf perl ($nruns_specified * $nchains_specified) > 8 perl "node_exclusive=1\\n" . "nodes=1\\n" infile Input File (must be in Nexus format) (-execute) paramfile.txt perl "execute infile.nex\\n" 2 infile.nex ALL_FILES * run_version I am restarting a checkpoint from 3 6 6 nruns_specified 1 My MrBayes Block specifies nruns= scheduler.conf 2 The values entered for nruns and nchains influence the number of cpu's that can be used in parallel. Please enter the value you specified for nruns in the MrBayes block of the Nexus file. If you didn't specify a value for nruns, please leave this field at its default value of 2. Please enter a value for nruns perl !$nruns_specified The value of nruns must be greater than 0 perl $nruns_specified < 1 nchains_specified 1 My MrBayes Block specifies nchains= scheduler.conf 4 The value entered for nruns and nchains influences the number of cpu's that can be used in parallel. Enter the value you specified for nchains in the MrBayes block of the nexus file. If you didn't specify a value for nchains, please leave this field at its default value of 4. Please enter value for nchains perl !$nchains_specified The value of nchains must be greater than 0 perl $nchains_specified < 1 nruns x nchains must be less than or equal to 16. perl ($nruns_specified * $nchains_specified > 16) nruns x nchains must be a multiple of 2 perl ((($nruns_specified * $nchains_specified) % 2) != 0) runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 0.5 The maximum hours to run must be less than 168 perl $runtime > 168.0 Please enter a positive number for the maximum runtime perl $runtime < 0 Please specify a maximum runtime perl !defined $runtime perl "runhours=$value\\n" The job will run on 2 processors as configured. If it runs for the entire configured time, it will consume 2 x $runtime cpu hours perl $nchains_specified * $nruns_specified == 2 The job will run on 4 processors as configured. If it runs for the entire configured time, it will consume 4 x $runtime cpu hours perl $nchains_specified * $nruns_specified == 4 The job will run on 6 processors as configured. If it runs for the entire configured time, it will consume 6 x $runtime cpu hours perl $nchains_specified * $nruns_specified == 6 The job will run on 8 processors as configured. If it runs for the entire configured time, it will consume 8 x $runtime cpu hours perl $nchains_specified * $nruns_specified == 8 The job will run on 16 processors as configured. If it runs for the entire configured time, it will consume 16 x $runtime cpu hours perl $nchains_specified * $nruns_specified > 8 Estimate the maximum time your job will need to run. We recommend testing initially with a < 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. upload_ckpfile 2 Choose the Checkpoint File (.ckp) infile.nex.ckp Please select the Checkpoint file to upload perl !defined $upload_ckpfile upload_mcmcfile 2 Choose the mcmc File (.mcmc) infile.nex.mcmc Please select the mcmc file to upload perl !defined $upload_mcmcfile upload_ssfile 2 Choose the Stepping Stone File (.ss) infile.ss num_tfiles 2 How many Sumt files do you wish to use? 1 1 2 3 4 5 6 7 8 upload_sumtfile1 2 Select Sumt File 1 (.t) infile.nex.run1.t Please select the first Sumt file to upload perl !defined $upload_sumtfile1 upload_sumtfile2 2 Select Sumt File 2 (.t) perl $num_tfiles > 1 infile.nex.run2.t Please select the second Sumt file to upload perl !defined $upload_sumtfile2 upload_sumtfile3 2 Select Sumt File 3 (.t) perl $num_tfiles > 2 infile.nex.run3.t Please select the third Sumt file to upload perl !defined $upload_sumtfile3 upload_sumtfile4 2 Select Sumt File 4 (.t) perl $num_tfiles > 3 infile.nex.run4.t Please select the fourth Sumt file to upload perl !defined $upload_sumtfile4 upload_sumtfile5 2 Select Sumt File 5 (.t) infile.nex.run5.t perl $num_tfiles > 4 Please select the fifth Sumt file to upload perl !defined $upload_sumtfile5 upload_sumtfile6 2 Select Sumt File 6 (.t) perl $num_tfiles > 5 infile.nex.run6.t Please select the sixth Sumt file to upload perl !defined $upload_sumtfile6 upload_sumtfile7 2 Select Sumt File 7 (.t) perl $num_tfiles > 6 infile.nex.run7.t Please select the seventh Sumt file to upload perl !defined $upload_sumtfile7 upload_sumtfile8 2 Select Sumt File 8 (.t) perl $num_tfiles > 7 infile.nex.run8.t Please select the eigth Sumt file to upload perl !defined $upload_sumtfile8 num_pfiles 2 How many Sump files do you wish to use? 1 1 2 3 4 upload_sumpfile1 2 Select Sump File 1 (.p) infile.nex.run1.p Please select the first Sump file for the run perl !defined $upload_sumpfile1 upload_sumpfile2 2 Select Sump File 2 (.p) perl $num_pfiles > 1 infile.nex.run2.p Please select the second Sump file to upload perl !defined $upload_sumpfile2 upload_sumpfile3 2 Select Sump File 3 (.p) perl $num_pfiles > 2 infile.nex.run3.p Please select the third Sump file to upload perl !defined $upload_sumpfile3 upload_sumpfile4 2 Select Sump File 4 (.p) perl $num_pfiles > 3 infile.nex.run4.p Please select the fourth Sump file to upload perl !defined $upload_sumpfile4