MacroModel Reference Manual - ISP

Chapter 2: Running MacroModel2.3.3.2 External DistributionExternal distribution of MacroModel jobs supports serial calculations including serial MCMM,LMCS, LMC2, MCMM-LMCS MCMM-LMC2, SPMC, MBAE, and CGEN conformational searches.Since processing each input structure in these calculations is inherently independent of theother structures, the collection of input structures can be broken down in to smaller sets andprocessed by separate MacroModel runs using bmin. This could be done by the user manuallyor by a custom script. The para_bmin utility is provided to carry out this task. The para_bminjobs use the same input files as the corresponding non-distributed calculation and do notrequire that customized schrodinger.hosts files be made up when jobs are run on differentcollections of processors or hosts.To launch a distributed job, enter the following command in a terminal window:$SCHRODINGER/para_bmin [options] jobnamereplacing jobname with the stem of the input file name (not needed if the -TEST or -HELPoptions are specified) and including any of the options listed in Table 2.2. The standard JobControl options are also supported—see Section 2.3 of the Job Control Guide. Additionaldiagnostic options, which do not run the job but provide information, are also given in thesection mentioned.Table 2.2. Options for the para_bmin command.Option-HELP | -help | -h-HOSTFILE hostfilename-INTERVAL time-LOCAL-GZIP-JOBCTS maxctsjob-NJOBS number-OUTPUT_ORG optionDescriptionPrint the para_bmin command syntax, options, and their definitions,and exit.The name of the hosts file to use for this run. The default is theschrodinger.hosts file found by Job Control.The maximum time in seconds for updating the monitoring files.Do not use a temporary directory keep the files. Keep files in thelocal directory.Compress output structure files.Ensure that each subjob has no more than this many structures toprocess. Default: 100.Divide the overall job into this many subjobs.Produce more than one output structure file. If option isBY_SUBJOB produce one output file for each subjob. Otherwisecreate a new directory called option and create separate output filesfor each input structure within this new directory. Automaticallysets -LOCAL if a new directory is created.MacroModel 9.7 Reference Manual 23