RevBayes on ACCESS 1.2.1 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_111 perl $which_revbayes eq "111" perl "" 0 revbayes_121 perl $which_revbayes eq "121" perl "" 0 mpi_processes_conf1 3 scheduler.conf perl !$more_memory && !$stillmore_memory perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "mem=" . ($nchains_specified * $nruns_specified * 2) . "G\\n" . "node_exclusive=0\\n" . "mpi_processes=" . $nchains_specified * $nruns_specified . "\\n" mpi_processes_conf1b 3 scheduler.conf perl $more_memory && !$stillmore_memory perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "more_memory=16\\n" . "mem=" . ($nchains_specified * $nruns_specified * 8 ) . "G\\n" . "node_exclusive=0\\n" . "mpi_processes=" . $nchains_specified * $nruns_specified . "\\n" mpi_processes_conf1c 3 scheduler.conf perl $stillmore_memory perl "jobtype=mpi\\n" . "cpus-per-task=1\\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "mpi_processes=" . $nchains_specified * $nruns_specified . "\\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" 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 111 121 121 nruns_specified 1 My parameter file 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 $nruns_specified < 1 nchains_specified 1 My parameter file specifies nchains= scheduler.conf 4 The value entered for nruns and nchains influences the number of cpu's that can be used in parallel. Enter the value you specified for nchains in the RevBayes parameter file. If you didn't specify a value for nchains, please leave this field at its default value of 4. Please enter value for nchains perl !$nchains_specified The value of nchains must be greater than 0 perl $nchains_specified < 1 The value for nchains must be 1 or greater. The recommended value is at least 4. 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) 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 2 processors as configured. If it runs for the entire configured time, it will consume 2 x $runtime cpu hours perl ($nchains_specified * $nruns_specified == 2) && !$more_memory 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 * $nruns_specified == 4) && !$more_memory 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 * $nruns_specified == 6 ) && !$more_memory 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 * $nruns_specified == 8 ) && !$more_memory The job will run on 10 processors as configured. If it runs for the entire configured time, it will consume 10 x $runtime cpu hours perl ($nchains_specified * $nruns_specified == 10 ) && !$more_memory The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x $runtime cpu hours perl ($nchains_specified * $nruns_specified == 12 ) && !$more_memory The job will run on 14 processors as configured. If it runs for the entire configured time, it will consume 14 x $runtime cpu hours perl ($nchains_specified * $nruns_specified == 14 ) && !$more_memory 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 * $nruns_specified == 16 ) && !$more_memory 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 == 2 ) && $more_memory && !$stillmore_memory 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 == 4 ) && $more_memory && !$stillmore_memory The job will run on 24 processors as configured. If it runs for the entire configured time, it will consume 24 x $runtime cpu hours perl ($nchains_specified * $nruns_specified == 6 ) && $more_memory && !$stillmore_memory The job will run on 32 processors as configured. If it runs for the entire configured time, it will consume 32 x $runtime cpu hours perl ($nchains_specified * $nruns_specified == 8 ) && $more_memory && !$stillmore_memory The job will run on 40 processors as configured. If it runs for the entire configured time, it will consume 40 x $runtime cpu hours perl ($nchains_specified * $nruns_specified == 10 ) && $more_memory && !$stillmore_memory The job will run on 48 processors as configured. If it runs for the entire configured time, it will consume 48 x $runtime cpu hours perl ($nchains_specified * $nruns_specified == 12 ) && $more_memory && !$stillmore_memory The job will run on 56 processors as configured. If it runs for the entire configured time, it will consume 56 x $runtime cpu hours perl ($nchains_specified * $nruns_specified == 14 ) && $more_memory && !$stillmore_memory The job will run on 64 processors as configured. If it runs for the entire configured time, it will consume 64 x $runtime cpu hours perl ($nchains_specified * $nruns_specified == 16 ) && $more_memory && !$stillmore_memory 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 $stillmore_memory 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_datafile2.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. more_memory I need more memory 0 1 stillmore_memory I need way more memory 0 1