ExaBayes on XSEDE 1.5 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_nodes == 1 && $num_procs < 24 perl "jobtype=mpi\\n" . "mpi_processes=$num_procs\\n" . "node_exclusive=0\\n" . "nodes=1\\n" number_threads1b 2 scheduler.conf perl $num_nodes == 1 && $num_procs == 24 perl "jobtype=mpi\\n" . "mpi_processes=$num_procs\\n" . "node_exclusive=1\\n" . "nodes=1\\n" number_threads2 2 scheduler.conf perl $num_procs > 24 perl "jobtype=mpi\\n" . "mpi_processes=$num_procs\\n" . "node_exclusive=1\\n" . "nodes=2\\n" num_procs Enter the number of processes you need (required) perl "mpirun -np $num_procs /projects/ps-ngbt/opt/comet/exabayes/exabayes-1.5/exabayes" 1 Please enter the number of mpi processes perl !defined $num_procs The number of mpi processes must be less than or equal to 24 perl $num_nodes == 1 && $num_procs > 24 The number of mpi processes must be less than or equal to 48 perl $num_nodes == 2 && $num_procs > 48 The job will run on $num_procs processors as configured. If it runs for the entire configured time, it will consume $num_procs x $runtime cpu hours perl $num_procs < 24 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_nodes == 1 && $num_procs == 24 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_procs > 24 num_nodes Enter the number of nodes 1 2 1 Please select the number of nodes perl !defined $num_nodes 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" 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 nu_partitions How many partitions does your data have? perl $is_partitioned Please enter an integer greater than 1 for the number of partitions. If you have just one partition, please uncheck the box that says "My data set is partitioned" perl $is_partitioned && $nu_partitions < 2 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 perl !defined $seed_val num_indanalyses Number of independent analyses perl "-R $value" 6 num_coupledchains Number of coupled chains perl "-C $value" 6 output_name Provide a name for output files perl (defined $value ) ? "-n $value":"" 12 mode_type Select the memory mode 0 1 2 3 perl (defined $value ) ? "-M $value":"" 13