BEAST2 on ACCESS 2.7.6 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 beast2_266_cpua perl $which_beast2 == 66 && !$is_cloudeligible perl "" 0 beast2_273_cpua perl $which_beast2 > 69 && !$is_cloudeligible perl "" 0 beast2_266_cloud perl $which_beast2 == 66 && $is_cloudeligible perl "" 0 beast2_273_cloud perl $which_beast2 > 69 && $is_cloudeligible perl "" 0 beast2_252 perl $which_beast2 == 52 perl "" 0 partitions_145b perl $nu_partitions < 4 && $nu_patterns < 5000 && !$no_beagle && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "-threads 3 -instances 3 -beagle_SSE" 3 number_threads145b 2 scheduler.conf perl $nu_partitions < 4 && $nu_patterns < 5000 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "cpus-per-task=3\\n" . "mem=6G\\n" . "threads_per_process=3\\n" partitions_145d perl $nu_partitions < 4 && $nu_patterns > 4999 && $nu_patterns < 38000 && !$no_beagle && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "-threads 1 -instances 1 -beagle_GPU " 3 number_threads145d 2 scheduler.conf perl $nu_partitions < 4 && $nu_patterns > 4999 && $nu_patterns < 38000 && !$no_beagle && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "ChargeFactor=1.0\\n" . "gpu=1\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "mem=90G\\n" . "threads_per_process=1\\n" partitions_145e perl $nu_partitions < 4 && $nu_patterns > 37999 && $nu_patterns < 100000 && !$no_beagle && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "-threads 1 -instances 1 -beagle_GPU" 3 number_threads145e 2 scheduler.conf perl $nu_partitions < 4 && $nu_patterns > 37999 && $nu_patterns < 100000 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "ChargeFactor=1.0\\n" . "gpu=1\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "mem=90G\\n" . "threads_per_process=1\\n" partitions_145f perl $nu_partitions < 4 && $nu_patterns > 99999 && !$no_beagle && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "-threads 2 -instances 2 -beagle_GPU -beagle_order 1,2" 3 number_threads145f 2 scheduler.conf perl $nu_partitions < 4 && $nu_patterns > 99999 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "ChargeFactor=1.0\\n" . "gpu=2\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "mem=180G\\n" . "threads_per_process=1\\n" partitions_445a perl $nu_partitions > 3 && $nu_partitions < 18 && $nu_patterns < 1200 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "-threads 1 -instances 1 -beagle_SSE" 3 number_threads445a 2 scheduler.conf perl $nu_partitions > 3 && $nu_partitions < 18 && $nu_patterns < 1200 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "cpus-per-task=1\\n" . "mem=1G\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" partitions_445b perl $nu_partitions > 3 && $nu_partitions < 18 && $nu_patterns > 1199 && $nu_patterns < 5000 && !$no_beagle && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "-threads 3 -instances 1 -beagle_SSE " 3 number_threads445b 2 scheduler.conf perl $nu_partitions > 3 && $nu_partitions < 18 && $nu_patterns > 1199 && $nu_patterns < 5000 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "cpus-per-task=3\\n" . "mem=6G\\n" . "node_exclusive=0\\n" . "threads_per_process=3\\n" partitions_445c perl $nu_partitions > 3 && $nu_partitions < 18 && $nu_patterns > 4999 && $nu_patterns < 20000 && !$no_beagle && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "-threads 6 -instances 2 -beagle_SSE " 3 number_threads445c 2 scheduler.conf perl $nu_partitions > 3 && $nu_partitions < 18 && $nu_patterns > 4999 && $nu_patterns < 20000 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "cpus-per-task=6\\n" . "mem=12G\\n" . "threads_per_process=6\\n" partitions_445d perl $nu_partitions > 3 && $nu_partitions < 18 && $nu_patterns > 19999 && !$no_beagle && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "-threads 1 -instances 1 -beagle_GPU" 3 number_threads445d 2 scheduler.conf perl $nu_partitions > 3 && $nu_partitions < 18 && $nu_patterns > 19999 && !$no_beagle && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "ChargeFactor=1.0\\n" . "gpu=1\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "mem=92G\\n" . "threads_per_process=1\\n" partitions_2045e perl $nu_partitions > 17 && $nu_patterns < 8000 && !$no_beagle && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "-threads 2 -instances 1 -beagle_SSE " 3 number_threads2045e 2 scheduler.conf perl $nu_partitions > 17 && $nu_patterns < 8000 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "mem=4G\\n" . "cpus-per-task=1\\n" . "threads_per_process=2\\n" partitions_2045f perl $nu_partitions > 17 && $nu_patterns > 7999 && $nu_patterns < 14000 && !$no_beagle && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "-threads 3 -instances 1 -beagle_SSE " 3 number_threads2045f 2 scheduler.conf perl $nu_partitions > 17 && $nu_patterns > 7999 && $nu_patterns < 14000 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "mem=6G\\n" . "cpus-per-task=3\\n" . "threads_per_process=3\\n" partitions_2045g perl $nu_partitions > 17 && $nu_patterns > 13999 && $nu_patterns < 40000 && !$no_beagle && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "-threads 6 -instances 2 -beagle_SSE " 3 number_threads2045g 2 scheduler.conf perl $nu_partitions > 17 && $nu_patterns > 13999 && $nu_patterns < 40000 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "mem=12G\\n" . "cpus-per-task=6\\n" . "threads_per_process=6\\n" partitions_2045h perl $nu_partitions > 17 && $nu_patterns > 39999 && !$no_beagle && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "-threads 1 -instances 1 -beagle_GPU" 3 number_threads2045h 2 scheduler.conf perl $nu_partitions > 17 && $nu_patterns > 39999 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 perl "ChargeFactor=1.0\\n" . "gpu=1\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "mem=90G\\n" . "threads_per_process=1\\n" partitions_2045g1 perl !$datatype && !$snapp_analysis && !$path_sampling && $more_memory2 perl "-threads 12 -instances 1 -beagle_SSE " 3 number_threads2045e2 2 scheduler.conf perl !$datatype && !$snapp_analysis && !$path_sampling && $more_memory2 perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "mem=24G\\n" . "cpus-per-task=12\\n" . "threads_per_process=12\\n" partitions_prot145a perl $nu_partitions < 2 && $nu_patterns < 12000 && !$no_beagle && $datatype && !$snapp_analysis && !$path_sampling perl "-threads 1 -instances 1 -beagle_GPU " 3 number_threads_prot145a 2 scheduler.conf perl $nu_partitions < 2 && $nu_patterns < 12000 && !$no_beagle && $datatype && !$snapp_analysis && !$path_sampling perl "ChargeFactor=1.0\\n" . "gpu=1\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "mem=92G\\n" . "threads_per_process=1\\n" partitions_prot145b perl $nu_partitions < 2 && $nu_patterns > 11999 && !$no_beagle && $datatype && !$snapp_analysis && !$path_sampling perl "-threads 4 -instances 4 -beagle_GPU -beagle_order 1,2,3,4 " 3 number_threads_prot145b 2 scheduler.conf perl $nu_partitions < 2 && $nu_patterns > 11999 && !$no_beagle && $datatype && !$snapp_analysis && !$path_sampling perl "ChargeFactor=1.0\\n" . "gpu=4\\n" . "nodes=1\\n" . "node_exclusive=1\\n" . "mem=368G\\n" . "threads_per_process=4\\n" partitions_prot245a perl $nu_partitions > 1 && $nu_partitions < 40 && !$no_beagle && $datatype && !$snapp_analysis && !$path_sampling perl "-threads 1 -instances 1 -beagle_GPU " 3 number_threads_prot245a 2 scheduler.conf perl $nu_partitions > 1 && $nu_partitions < 40 && !$no_beagle && $datatype && !$snapp_analysis && !$path_sampling perl "ChargeFactor=1.0\\n" . "gpu=1\\n" . "nodes=1\\n" . "mem=92G\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" partitions_prot4045a perl $nu_partitions > 39 && !$no_beagle && $datatype && !$snapp_analysis && !$path_sampling perl "-threads 24 -instances 1 -beagle_SSE " 3 number_threads_prot4045a 2 scheduler.conf perl $nu_partitions > 39 && !$no_beagle && $datatype && !$snapp_analysis && !$path_sampling perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "cpus-per-task=24\\n" . "mem=46G\\n" . "node_exclusive=0\\n" . "threads_per_process=24\\n" snapp_notpath_threads perl $snapp_analysis && !$path_sampling perl "-threads 24 -instances 1 -beagle_SSE " 3 snapp_notpath_mem 2 scheduler.conf perl $snapp_analysis && !$path_sampling perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=46G\\n" . "cpus-per-task=24\\n" . "node_exclusive=0\\n" . "threads_per_process=24\\n" snapp_path_threads perl $snapp_analysis && $path_sampling && !$more_memory perl "-threads 25 -instances 1 -beagle_SSE " 3 snapp_path_mem 2 scheduler.conf perl $snapp_analysis && $path_sampling && !$more_memory perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=50G\\n" . "node_exclusive=0\\n" . "cpus-per-task=25\\n" . "threads_per_process=25\\n" snapp_path_threads_moremem perl $snapp_analysis && $path_sampling && $more_memory perl "-threads 25 -instances 1 -beagle_SSE " 3 snapp_path_moremem 2 scheduler.conf perl $snapp_analysis && $path_sampling && $more_memory perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=80G\\n" . "node_exclusive=0\\n" . "cpus-per-task=25\\n" . "threads_per_process=25\\n" path_notsnapp_threads perl $path_sampling && !$snapp_analysis perl "-threads 6 -instances 1 -beagle_SSE " 3 path_notsnapp_mem 2 scheduler.conf perl $path_sampling && !$snapp_analysis perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=11G\\n" . "node_exclusive=0\\n" . "cpus-per-task=6\\n" . "threads_per_process=6\\n" infile Input File (must be in BEAST XML format) perl "infile.xml" 99 infile.xml all_results * beagle_scaling Set the Beagle Scaling Parameter (the choice can affect performance) perl !$no_beagle && $which_beast2 > 40 perl " -beagle_scaling dynamic" 4 which_beast2 1 scheduler.conf Which BEAST2 Version? 70 66 70 Please choose a BEAST version perl !defined $value Datasets prepared using BEAUTI below version 2.6.x will fail with 2.7.x; datasets are not forward compatible between major releases perl $which_beast2 >= 70 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 >= 1 && $nu_partitions < 4 && $nu_patterns < 5000 && !$no_beagle && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 The job will run on 10 processors and 1 gpu as configured. If it runs for the entire configured time, it will consume 20 x $runtime cpu hours perl $nu_partitions >= 1 && $nu_partitions < 4 && $nu_patterns > 4999 && $nu_patterns < 100000 && !$no_beagle && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 The job will run on 20 processors and 2 gpu as configured. If it runs for the entire configured time, it will consume 40 x $runtime cpu hours perl $nu_partitions >= 1 && $nu_partitions < 4 && $nu_patterns > 99999 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 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 $nu_partitions > 3 && $nu_partitions < 18 && $nu_patterns < 1200 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 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 > 3 && $nu_partitions < 18 && $nu_patterns > 1199 && $nu_patterns < 5000 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 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 $nu_partitions > 3 && $nu_partitions < 18 && $nu_patterns > 4999 && $nu_patterns < 20000 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 The job will run on 10 processors and one gpu as configured. If it runs for the entire configured time, it will consume 23 x $runtime cpu hours perl $nu_partitions > 3 && $nu_partitions < 18 && $nu_patterns > 19999 && !$no_beagle && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 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 > 17 && $nu_patterns < 8000 && !$no_beagle && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 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 > 17 && $nu_patterns > 7999 && $nu_patterns < 14000 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 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 $nu_partitions > 17 && $nu_patterns > 13999 && $nu_patterns < 40000 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 The job will run on 10 processors and 1 GPU as configured. If it runs for the entire configured time, it will consume 20 x $runtime cpu hours perl $nu_partitions > 17 && $nu_patterns > 39999 && !$datatype && !$snapp_analysis && !$path_sampling && !$more_memory2 The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x $runtime cpu hours perl !$datatype && !$snapp_analysis && !$path_sampling && $more_memory2 The job will run on 10 processors and 1 gpu as configured. If it runs for the entire configured time, it will consume 23 x $runtime cpu hours perl $nu_partitions == 1 && $nu_patterns < 12000 && !$no_beagle && $datatype && !$snapp_analysis && !$path_sampling The job will run on 40 processors and four gpus as configured. If it runs for the entire configured time, it will consume 92 x $runtime cpu hours perl $nu_partitions == 1 && $nu_patterns > 11999 && !$no_beagle && $datatype && !$snapp_analysis && !$path_sampling The job will run on 10 processors and one gpu as configured. If it runs for the entire configured time, it will consume 23 x $runtime cpu hours perl $nu_partitions > 1 && $nu_partitions < 40 && !$no_beagle && $datatype && !$snapp_analysis && !$path_sampling 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 $nu_partitions > 39 && !$no_beagle && $datatype && !$snapp_analysis && !$path_sampling The job will run on 25 processors as configured. If it runs for the entire configured time, it will consume 25 x $runtime cpu hours perl $snapp_analysis && $path_sampling && !$more_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 $snapp_analysis && $path_sampling && $more_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 $snapp_analysis && !$path_sampling The job will run on 6 processors as configured. If it runs for the entire configured time, it will consume 6 x $runtime cpu hours perl !$snapp_analysis && $path_sampling 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. runtime 1 scheduler.conf Maximum Hours to Run (up to 168 hours) 0.5 The maximum runtime for a non-gpu job must be less than 168 hours perl $runtime > 168.0 && $which_beast2 < 42 The maximum runtime for a non-gpu job must be less than 168 hours perl $runtime > 168.0 && $snapp_analysis The maximum runtime for a non-gpu job must be less than 168 hours perl $runtime > 168.0 && $nu_partitions >= 1 && $nu_partitions < 4 && $nu_patterns < 5000 && !$datatype && !$snapp_analysis && !$path_sampling The maximum runtime for a gpu job must be less than 120 hours perl $runtime > 120.0 && $nu_partitions >= 1 && $nu_partitions < 4 && $nu_patterns > 4999 && !$datatype && !$snapp_analysis && !$path_sampling The maximum runtime for this job must be less than 168 hours perl $runtime > 168.0 && $nu_patterns < 20000 && $nu_partitions > 3 && $nu_partitions < 18 && !$datatype && !$snapp_analysis && !$path_sampling The maximum runtime for a gpu job must be less than 120 hours perl $runtime > 120.0 && $nu_patterns > 19999 && $nu_partitions > 3 && $nu_partitions < 18 && !$datatype && !$snapp_analysis && !$path_sampling The maximum runtime for this job must be less than 168 hours perl $runtime > 168.0 && $nu_partitions > 17 && !$datatype && !$snapp_analysis && !$path_sampling The maximum runtime for a gpu job must be less than 120 hours perl $runtime > 120.0 && $nu_partitions < 40 && $datatype && !$snapp_analysis && !$path_sampling The maximum runtime for a non-gpu job must be less than 168 hours perl $runtime > 168.0 && $nu_partitions > 39 && $datatype && !$snapp_analysis && !$path_sampling The maximum runtime for this job must be less than 168 hours perl $runtime > 168.0 && ($snapp_analysis || $path_sampling) 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? (if you dont know, make a short run and find this in the output) 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 $nu_patterns This option will help the application determine how to run the job. Approximate is fine. The number of patterns can be found in the Beauti file. You can make a quick pre-run, and the number of patterns and partitions will be obvious in the output, if you aren't sure nu_partitions 0 How many partitions does your data set have? perl !$snapp_analysis && !$path_sampling Please enter the number of partitions. perl !$snapp_analysis && !$path_sampling && !defined $nu_partitions The number of partitions must be greater than 0. perl !$snapp_analysis && !$path_sampling && $nu_partitions < 1 This option will help the application determine how to run the job path_sampling 0 This is a Path Sampling analysis For Path Sampling, your input data must specify: rootdir \= ./tmp/step, where the .\/ is required. The actual directory names given (tmp/step in this example) are arbitary, and can be anything linux accepts perl $path_sampling Because of the details of their data management, Path Sampling jobs cannot be restarted using the CIPRES restart mechanism. perl $path_sampling This option will help the application determine how to run the job more_memory2 I need more memory for DNA run that doesn't use Path Sampling/SNAPP perl !$snapp_analysis && !$path_sampling && !$datatype This option will help the application determine how to run the job more_memory I need more memory for a Path Sampling/SNAPP analysis perl $snapp_analysis || $path_sampling This option will help the application determine how to run the job snapp_analysis 0 This is a SNAPP (or SNAPPER) analysis This option will help the application determine how to run the job datatype 0 The matrix contains amino acids Protein sequences require a slightly different configuration than DNA sequences. 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 $value ? "-overwrite":"" 0 4 restart perl ($value) ? "-resume" : "" 4 is_cloudeligible perl "" 0 4