BEAST2 on XSEDE (Restart) 2.3.2 Bayesian Evolutionary Analysis by Sampling Trees - run on XSEDE Remco Boukaert, Alexei Drummond, Andrew Rambaut, and Marc A. Suchard Bouckaert R, Heled J, Kühnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) "BEAST2: A software platform for Bayesian evolutionary analysis". PLOS Computational Biogogy 10(4): e1003537, 2014. doi:10.1371/journal.pcbi.1003537 Phylogeny / Alignment beast2_xsede_restart beast2_232 perl $which_beast2 == 32 perl "" 0 beast2_230 perl $which_beast2 == 30 perl "" 0 beast2_213 perl $which_beast2 == 13 perl "" 0 number_threads1 2 scheduler.conf perl !$is_partitioned perl "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" partitions_1 perl !$is_partitioned perl "-threads 1 " 3 number_threads2 2 scheduler.conf perl $nu_partitions == 2 perl "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=2\\n" partitions_2 perl $nu_partitions == 2 perl "-threads 2 " 4 number_threads3 2 scheduler.conf perl $nu_partitions > 2 && $nu_patterns < 1600 perl "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=2\\n" partitions_3 perl $nu_partitions > 2 && $nu_patterns < 1600 perl "-threads 2 " 4 number_threads3b 2 scheduler.conf perl $nu_partitions > 2 && $nu_patterns >= 1600 perl "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=3\\n" partitions_3b perl $nu_partitions > 2 && $nu_patterns >= 1600 perl "-threads 3" 4 infile Input File (must be in BEAST XML format) perl "-resume infile.xml" 99 infile.xml all_results * beagle_scaling Set the Beagle Scaling Parameter (the choice can affect performance) perl !$no_beagle perl "-beagle_SSE -beagle_scaling dynamic" 4 which_beast2 1 scheduler.conf Which BEAST2 Version? 32 30 13 32 Please choose a BEAST version perl !defined $value The job will run on 1 processors as configured. If it runs for the entire configured time, it will consume 1 x $runtime cpu hours perl !$is_partitioned The job will run on 2 processors as configured (jobs without BEAGLE run on a single processor. If it runs for the entire configured time, it will consume 2 x $runtime cpu hours perl $nu_partitions == 2 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 $nu_partitions > 2 && $nu_patterns < 1600 The job will run on 3 processors as configured. If it runs for the entire configured time, it will consume 3 x $runtime cpu hours perl $nu_partitions > 2 && $nu_patterns >= 1600 Estimate the maximum time your job will need to run. We recommend testimg 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. 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 testimg 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. nu_patterns 0 How many patterns does your data have? (use # chars if you arent sure) Please enter an integer greater than 1 for the number of patterns in your data set. perl $nu_patterns < 2 Please enter an integer greater than 1 for the number of patterns in your data set. perl !defined $nu_patterns This option will help the application determine how to run the job. Approximate is fine. The number of patterns can be fond in the Beauti file. You can use the number of characters if you aren't sure is_partitioned 0 My data set is partitioned 0 This option will help the application determine how to run the job nu_partitions 0 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 no_beagle Do not use Beagle 0 The Do not use Beagle option is intended only for cases when runs with Beagle fail. Runs without Beagle are slower and less efficient. perl $no_beagle == 1 4 This option is offered because sometimes a bug in the interface between BEAST and BEAGLE prevents a run from completing. Use this option if you wish to run a data set that has failed using the normal BEAST/BEAGLE implementation. Runs made this way are always slower, so use this option as a last resort. spec_seed Specify a seed for this run (by default a random seed is used) 0 4 This option allows the user to specify the random seed BEAST uses, so results can be compared between runs. seed_val Enter the seed value here perl $spec_seed perl "-seed $value" 12345 4 overwrite_logs Overwrite existing log files perl $value ? "-overwrite":"" 0 4 resume_logfile Select your log file perl beast.log 4 resume_treefile Select your tree file perl 4 resume_statefile Select your state file perl infile_altered.xml.state 4