ExaBayes on XSEDE 1.5.1 Bayesian Evolutionary Analysis by Sampling Trees - run on XSEDE Aberer, A. J., Kobert, K., and Stamatakis, A. Aberer, A. J., Kobert, K., and Stamatakis, A. (2014) ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era. Molecular Biology and Evolution 31, 2553-2556 Phylogeny / Alignment exabayes_xsede exabayes_15 perl "" 0 number_threads1 2 scheduler.conf perl $num_patterns < 4000 perl "jobtype=mpi\\n" . "mpi_processes=24\\n" . "mem=46G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" number_threads2 2 scheduler.conf perl $num_patterns > 3999 && $num_patterns < 25000 perl "jobtype=mpi\\n" . "mpi_processes=48\\n" . "mem=92G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" number_threads3 2 scheduler.conf perl $num_patterns > 24999 perl "jobtype=mpi\\n" . "mpi_processes=128\\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "nodes=1\\n" infile Input File (must be in relaxed Phylip format) perl "-f infile.phy" 5 infile.phy all_results * runtime 1 scheduler.conf Maximum Hours to Run (up to 168 hours) 0.5 The maximum hours to run must be less than 168 perl $runtime > 168.0 The maximum hours to run must be greater than 0.05 perl $runtime < 0.05 perl "runhours=$value\\n" 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 $num_patterns < 4000 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 $num_patterns < 25000 && $num_patterns > 3999 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 $num_patterns > 24999 Estimate the maximum time your job will need to run. We recommend testing initially with a < 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. datatype Specify the datatype (required if there is no partitioning) perl !$is_partitioned DNA PROT perl "-m $value" Please select a datatype perl !defined $datatype && !$is_partitioned config_file 12 Select configuration file (optional) pise defined $config_file ? "-c config.nex":"" config.nex This option will help the application determine how to run the job is_partitioned My data set is partitioned 0 num_patterns How many patterns does your data have? Please enter an integer greater than 1 for the number of patterns. perl !defined $num_patterns This option will help the application determine how to run the job model_file Select a partition file for the alignment 7 perl (defined $value) ? "-q part.txt":"" part.txt Please select a partition file perl $is_partitioned && !defined $model_file seed_val Enter a seed value here perl "-s $value" 6 Please specify a seed value, this is required perl !defined $seed_val num_indanalyses Number of independent analyses perl "-R $value" 2 6 num_coupledchains Number of chains to be run in parallel (-C) perl "-C $value" Advisory only: The value for C cannot be larger than numCoupledChains perl defined $value && defined $config_file 6 output_name Provide a name for output files (-n) perl (defined $value ) ? "-n $value":"" 12 Please enter a name for the output files perl !defined $output_name mode_type Select the memory mode 0 1 2 3 perl (defined $value ) ? "-M $value":"" 13 run_consense Use consense to compute consensus trees from sets of trees perl ($value) ? "&& exabayes_consense_wrapper_1.5.0":"" 80 use_MRE Use MRE for the threshold perl ($value) ? "-b MRE ":"" 81 specify_threshold Specify a threshold for the consensus tree perl $run_consense && !$use_MRE perl ($value) ? "-b $value ":"" Please choose a consensus threshold value less than 100 perl $specify_threshold > 100 Please choose a consensus threshold value greater than or equal to 50 perl $specify_threshold < 50 Please choose MRE or specify a Threshold perl !defined $specify_threshold && !$use_MRE 81 specify_burnin Specify burnin value for consensus trees perl $run_consense perl (defined $value) ? "-b $value":"" 0.25 82 specify_nf perl $run_consense perl "-f *topologies.* -n $output_name" 82