1.8c Restart a PhyloBayes MPI run on XSEDE Nicolas Lartillot, Thomas Lepage, and Samuel Blanquart Nicolas Lartillot, Thomas Lepage, and Samuel Blanquart. 2009. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25(17) 2286–2288. Lartillot, N., Rodrigue, N., Stubbs, D., Richer, J. 2013. PhyloBayes MPI. Phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Systematic Biology. Phylogeny / Alignment phylobayes_xsede_restart invocation1 perl "PBMultiRun_expanse.bash" 0 dna_conf1 3 scheduler.conf perl $datatype ne "PROTEIN" && $num_sites < 2000 perl "jobtype=mpi\\n" . "workflow_type=mpi_complex\\n" . "cpus-per-task=1\\n" . "nodes=1\\n" . "mem=92G\\n" . "node_exclusive=0\\n" . "mpi_processes=48\\n" dna_conf2 3 scheduler.conf perl $datatype ne "PROTEIN" && $num_sites > 1999 perl "jobtype=mpi\\n" . "workflow_type=mpi_complex\\n" . "cpus-per-task=1\\n" . "nodes=1\\n" . "mem=123G\\n" . "node_exclusive=0\\n" . "mpi_processes=64\\n" prot_conf1 3 scheduler.conf perl $datatype eq "PROTEIN" && $num_sites < 1000 perl "jobtype=mpi\\n" . "workflow_type=mpi_complex\\n" . "cpus-per-task=1\\n" . "nodes=1\\n" . "mem=123G\\n" . "node_exclusive=0\\n" . "mpi_processes=64\\n" prot_conf2 3 scheduler.conf perl $datatype eq "PROTEIN" && $num_sites > 999 perl "jobtype=mpi\\n" . "workflow_type=mpi_complex\\n" . "cpus-per-task=1\\n" . "mem=186G\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "mpi_processes=96\\n" infile Input Data (relaxed phylip format) 41 infile.phy ALL_FILES * runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 0.5 perl "remove_mv2_param=1\\n" . "runhours=$value\\n" 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 The job will run on 48 cores as configured. If it runs for the entire configured time, it will consume 48 x $runtime core (cpu) hours perl $datatype ne "PROTEIN" && $num_sites < 2000 The job will run on 64 cores as configured. If it runs for the entire configured time, it will consume 64 x $runtime core (cpu) hours perl $datatype ne "PROTEIN" && $num_sites > 1999 The job will run on 64 cores as configured. If it runs for the entire configured time, it will consume 64 x $runtime core (cpu) hours perl $datatype eq "PROTEIN" && $num_sites < 1000 The job will run on 96 cores as configured. If it runs for the entire configured time, it will consume 96 x $runtime core (cpu) hours perl $datatype eq "PROTEIN" && $num_sites > 999 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. set_chains 4 perl "-N 2" num_sites Number of sites in the data set Please specify the number of sites (columns) in your data set. perl !defined $num_sites You can make a quick run and find this value in the stderr file. datatype My data set contains DNA DNA PROTEIN Amino acids unk other Please specify the type of data. perl !defined $datatype acceptdiffval 10 Maximum \maxdiff" value to accept. perl "--ACCEPTDIFF $value" 0.1 Please specify the Maximum "maxdiff" value to accept. The manual says 0.3 is "acceptable" and 0.1 is "very good." perl !defined $acceptdiffval end_of_wrapper 40 perl "" chainparamfile1 Select the first chain.param file to restart 41 chain0.param Please select the first chain.param file perl !defined $chainparamfile1 If you used the -s option during your first run, please do not select your chain.chain files here, these will fail. chainparamfile2 Select the second chain.param file 41 chain1.param Please select the second chain.param file perl !defined $chainparamfile2 chaintreefile1 Select the first chain.treelist file to restart 41 chain0.treelist Please select the first chain.treelist file perl !defined $chaintreefile1 chaintreefile2 Select the second chain.treelist file 41 chain1.treelist Please select the second chain.treelist file perl !defined $chaintreefile2 chaintracefile1 Select the first chain.trace file to restart 41 chain0.trace Please select the first chain.trace file perl !defined $chaintracefile1 chaintracefile2 Select the second chain.trace file 41 chain1.trace Please select the second chain.trace file perl !defined $chaintracefile2 chainmonfile1 Select the first chain.monitor file to restart 41 chain0.monitor Please select the first chain.monitor file perl !defined $chainmonfile1 chainmonfile2 Select the second chain.monitor file 41 chain1.monitor Please select the second chain.monitor file perl !defined $chainmonfile2