RevBayes on ACCESS 1.2.5 Tree Inference Using Bayesian Analysis - run on XSEDE Sebastian Höhna, Michael J. Landis, Tracy A. Heath, Bastein Boussau, Nicholas Lartillot, Brian R. Moore, John P. Huelsenbeck, and Frederik Ronquist Höhna, S., Landis, M., Heath, T., Boussau, B., Lartillot, N., Moore, B. R. Huelsenbeck, J., Ronquist, F. 2016. RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language. Systematic Biology, 65:726-736. Phylogeny/Tree Inference revbayes_xsede revbayes_125 perl $which_revbayes eq "125" perl "" 0 revbayes_130 perl $which_revbayes eq "130" perl "" 0 mpi_processes_conf1 3 scheduler.conf perl !$scriptfile_specifies perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "mem=2G\\n" . "node_exclusive=0\\n" . "mpi_processes=1\\n" mpi_processes_conf1b 3 scheduler.conf perl $scriptfile_specifies && $specify_memory == 16 perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "mem=16G\\n" . "node_exclusive=0\\n" . "mpi_processes=8\\n" mpi_processes_conf1c 3 scheduler.conf perl $scriptfile_specifies && $specify_processes == 8 && $specify_memory == 32 perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "more_memory=2\\n" . "mem=32G\\n" . "node_exclusive=0\\n" . "mpi_processes=8\\n" mpi_processes_conf1d 3 scheduler.conf perl $scriptfile_specifies && $specify_processes == 8 && $specify_memory == 64 perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "more_memory=4\\n" . "mem=64G\\n" . "node_exclusive=0\\n" . "mpi_processes=8\\n" mpi_processes_conf1e 3 scheduler.conf perl $scriptfile_specifies && $specify_processes == 8 && $specify_memory == 128 perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "more_memory=8\\n" . "mem=128G\\n" . "node_exclusive=0\\n" . "mpi_processes=8\\n" mpi_processes_conf1f 3 scheduler.conf perl $scriptfile_specifies && $specify_processes == 8 && $specify_memory == 243 perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "more_memory=16\\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "mpi_processes=8\\n" mpi_processes_conf2a 3 scheduler.conf perl $scriptfile_specifies && $specify_processes == 16 && $specify_memory == 32 perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "mem=32G\\n" . "node_exclusive=0\\n" . "mpi_processes=16\\n" mpi_processes_conf2b 3 scheduler.conf perl $scriptfile_specifies && $specify_processes == 16 && $specify_memory == 64 perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "more_memory=2\\n" . "mem=64G\\n" . "node_exclusive=0\\n" . "mpi_processes=16\\n" mpi_processes_conf2c 3 scheduler.conf perl $scriptfile_specifies && $specify_processes == 16 && $specify_memory == 128 perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "more_memory=4\\n" . "mem=128G\\n" . "node_exclusive=0\\n" . "mpi_processes=16\\n" mpi_processes_conf2d 3 scheduler.conf perl $scriptfile_specifies && $specify_processes == 16 && $specify_memory == 243 perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "more_memory=8\\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "mpi_processes=16\\n" mpi_processes_conf3a 3 scheduler.conf perl $scriptfile_specifies && $specify_processes == 32 && $specify_memory == 64 perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "mem=64G\\n" . "node_exclusive=0\\n" . "mpi_processes=32\\n" mpi_processes_conf3b 3 scheduler.conf perl $scriptfile_specifies && $specify_processes == 32 && $specify_memory == 128 perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "more_memory=2\\n" . "mem=128G\\n" . "node_exclusive=0\\n" . "mpi_processes=32\\n" mpi_processes_conf3c 3 scheduler.conf perl $scriptfile_specifies && $specify_processes == 32 && $specify_memory == 243 perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "more_memory=4\\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "mpi_processes=32\\n" mpi_processes_conf4a 3 scheduler.conf perl $scriptfile_specifies && $specify_processes == 64 && $specify_memory == 128 perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "mem=128G\\n" . "node_exclusive=0\\n" . "mpi_processes=64\\n" mpi_processes_conf4b 3 scheduler.conf perl $scriptfile_specifies && $specify_processes == 64 && $specify_memory == 243 perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "more_memory=2\\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "mpi_processes=64\\n" mpi_processes_conf5a 3 scheduler.conf perl $scriptfile_specifies && $specify_processes == 128 && $specify_memory == 243 perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "mpi_processes=128\\n" infile Input File (must be in Nexus format) (-execute) revbayes_datafile.nex ALL_FILES * runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 168 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" Your file must call the data file from your script as ./revbayes_datafile.nex. Please adjust your file if necessary. perl defined $add_scriptfile The job will run on 1 processor as configured. If it runs for the entire configured time, it will consume 1 x $runtime cpu hours perl !$scriptfile_specifies 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 $scriptfile_specifies && $specify_memory == 16 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 $scriptfile_specifies && $specify_processes == 8 && $specify_memory == 32 The job will run on 32 processors as configured. If it runs for the entire configured time, it will consume 32 x $runtime cpu hours perl $scriptfile_specifies && $specify_processes == 8 && $specify_memory == 64 The job will run on 64 processors as configured. If it runs for the entire configured time, it will consume 64 x $runtime cpu hours perl $scriptfile_specifies && $specify_processes == 8 && $specify_memory == 128 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $scriptfile_specifies && $specify_processes == 8 && $specify_memory == 243 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 $scriptfile_specifies && $specify_processes == 16 && $specify_memory == 32 The job will run on 32 processors as configured. If it runs for the entire configured time, it will consume 32 x $runtime cpu hours perl $scriptfile_specifies && $specify_processes == 16 && $specify_memory == 64 The job will run on 64 processors as configured. If it runs for the entire configured time, it will consume 64 x $runtime cpu hours perl $scriptfile_specifies && $specify_processes == 16 && $specify_memory == 128 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $scriptfile_specifies && $specify_processes == 16 && $specify_memory == 243 The job will run on 32 processors as configured. If it runs for the entire configured time, it will consume 32 x $runtime cpu hours perl $scriptfile_specifies && $specify_processes == 32 && $specify_memory == 64 The job will run on 64 processors as configured. If it runs for the entire configured time, it will consume 64 x $runtime cpu hours perl $scriptfile_specifies && $specify_processes == 32 && $specify_memory == 128 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $scriptfile_specifies && $specify_processes == 32 && $specify_memory == 243 The job will run on 64 processors as configured. If it runs for the entire configured time, it will consume 64 x $runtime cpu hours perl $scriptfile_specifies && $specify_processes == 64 && $specify_memory == 128 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $scriptfile_specifies && $specify_processes == 64 && $specify_memory == 243 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $scriptfile_specifies && $specify_processes == 128 && $specify_memory == 243 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. which_revbayes Choose the RevBayes version you wish to run 125 130 130 Please select the RevBayes version to run perl !defined $which_revbayes add_scriptfile Select the scriptfile for your run scriptfile.txt Please select a scriptfile (will be called scriptfile.txt) perl !defined $add_scriptfile specify_inputfiles How many additional input molecular data files do you need? 0 1 2 3 4 add_datafile1 Select first additional datafile for your run (revbayes_datafile2.nex) perl $specify_inputfiles > 0 revbayes_datafile2.nex Please select a first additional datafile perl $specify_inputfiles > 0 && !defined $add_datafile1 add_datafile2 Select the second additional datafile for your run (revbayes_datafile3.nex) perl $specify_inputfiles > 1 revbayes_datafile3.nex Please select a second additional datafile (revbayes_datafile3.nex) perl $specify_inputfiles > 1 && !defined $add_datafile2 add_datafile3 Select the third additional datafile for your run (revbayes_datafile4.nex) perl $specify_inputfiles > 2 revbayes_datafile4.nex Please select the third additional datafile perl $specify_inputfiles > 2 && !defined $add_datafile3 add_datafile4 Select the fourth additional datafile for your run (revbayes_datafile5.nex) perl $specify_inputfiles > 3 revbayes_datafile5.nex Please select a fourth additional datafile perl $specify_inputfiles > 3 && !defined $add_datafile4 add_bindatafile Select a binary datafile for your run (morpho_datafile.nex) morpho_datafile.nex add_bindatafile2 Select a second binary datafile for your run (morpho_datafile2.nex) morpho_datafile2.nex add_scriptcontincharfile Select a continuous character file (it will be ./contchar.nex) 1 contchar.nex The continuous character file is used when you need to call a file specifying a continuous character file from your script. If you need to use this file, just make sure your script specifies the file location as ./contchar.nex add_auxfile Select a taxon name file (it will be ./tsvfile.txt) tsvfile.txt 1 The taxon name file is used when you need to call a file specifying taxon names from your script. If you need to use this file, just make sure your script specifies the file location as ./tsvfile.txt add_auxfile1 Select an auxiliary file (it will be ./auxfile1.txt) 1 auxfile1.txt Auxiliary files are used when you need to call a file from your script that is not specified above. If you need to use auxiliary files, just make sure your script specifies the file location as indicated in the prompt. add_auxfile2 Select an auxiliary file (it will be ./auxfile2.txt) 1 auxfile2.txt Auxiliary files are used when you need to call a file from your script that is not specified above. If you need to use auxiliary files, just make sure your script specifies the file location as indicated in the prompt. add_auxfile3 Select a taxon name file (it will be ./auxfile3.txt) 1 auxfile3.txt Auxiliary files are used when you need to call a file from your script that is not specified above. If you need to use auxiliary files, just make sure your script specifies the file location as indicated in the prompt. scriptfile_specifies My Scriptfile specifies mymcmc.run 1 specify_memory How much memory is required? 16 32 64 128 243 specify_processes How many processes do you wish to run? 8 16 32 64 128 Please specify your number of processes perl $specify_processes && !defined $specify_processes Please specify your memory requirement perl $specify_processes && !defined $specify_memory A run with 128 processes must use 243G of memory perl $specify_processes == 128 && $specify_memory < 243 A run with 64 processes must use 128G or 243G of memory perl $specify_processes == 64 && $specify_memory < 128 A run with 32 processes must use 64G of memory or more perl $specify_processes == 32 && $specify_memory < 64 A run with 16 processes must use at least 32G of memory perl $specify_processes == 16 && $specify_memory < 32