schrodinger.application.desmond.multisimstartup module¶

Multisim startup script.

This will launch the driver: chorus_multijob.py.

class schrodinger.application.desmond.multisimstartup.Help(app_name)¶

Bases: object

VERSION = 'multisim v4.0.0'¶

SHORT_USAGE = "\nMultisim workflow program\n\nUsage:\n* To run a new job:\n _APPLICATION_NAME_ [<options>] {-m <file>.msj} {<file>.cms|<file>.mae}\n\n* To restart a previous job:\n _APPLICATION_NAME_ [<options>] {-RESTART <multisim_checkpoint_file>}\n You normally also need to specify the '-d' option.\n\nFrequently used options:\n -m <input_file> input .msj file defining the basic workflow\n -d <input_file> stage data file from the previous job and usually with\n the .tgz suffix. This option should be used only in\n restarting a job with multisim checkpoint file.\n -c <input_file> set configuration parameters for a family of stages.\n -o <output_file> output .cms or .mae file. This file can be incorporated\n into Maestro.\n -maxjob <number> maximum number of simultaneous subjobs (default is 1)\n -mode {umbrella} run in non-default execution mode. Currently, there is\n only 1 valid value: umbrella. In umbrella mode, subjobs\n will run on the nodes allocated to the main job.\n -notify <email_addr> send a notification email when this job terminates.\n -nopref ignore the multisim preference file.\n -probe probe a checkpoint file and quit.\n -JOBNAME <job_name> name of this multisim job\n -HOST <host_name> host machine to run the multisim main job (default is\n localhost)\n -SUBHOST <host_name> host machine to run subjobs\n -RESTART <input_file> restart a previous job from its multisim checkpoint file.\n\n -h [<topic>] show help and quit. User can optionally specify a topic\n for help. Valid topics are the following: @all, @doc,\n @<flag> (where <flag> represents the flag of any valid\n option, e.g. @-help), @examples, and @deprecated.\n For more detail see help of the '@-help' topic.\n"¶

LONG_USAGE = "\nMultisim workflow program\n\nUsage:\n* To run a new job:\n _APPLICATION_NAME_ [<options>] {-m <file>.msj} {<file>.cms|<file>.mae}\n\n* To restart a previous job:\n _APPLICATION_NAME_ [<options>] {-RESTART <multisim_checkpoint_file>}\n You normally also need to specify the '-d' option.\n\nI/O options:\n -i <input file> input structure file in the .cms or .mae format\n (This option has been DEPRECATED, please specify the\n .cms or .mae file without the -i flag in the future)\n -m <input_file> input .msj file defining the basic workflow\n -RESTART <input_file> multisim checkpoint file for restarting a job.\n -r <input file> multisim checkpoint file for restarting a job.\n (This option has been DEPRECATED, please use -RESTART\n instead in the future)\n -d <input_file> stage data file from the previous job and usually with\n the .tgz suffix. This option should be used only in\n restarting a job with multisim checkpoint file.\n -c <input_file> set configuration parameters for a family of stages.\n -ADD_FILE <input_file> Additional input file to copy to the working directory\n of this multisim job\n -ALT_DIR <directory> Alternative directory where to look for input files\n -o <output_file> output .cms or .mae file. This file can be incorporated\n into Maestro.\n\nWorkflow options:\n -m <input_file> input .msj file defining the basic workflow\n -c <input_file> set configuration parameters for a family of stages.\n -set <string> modify the basic workflow defined by the .msj file.\n\nJob options:\n -JOBNAME <job_name> name of this multisim job\n -HOST <host_name> host machine to run the multisim main job (default is\n localhost)\n -SUBHOST <host_name> host machine to run subjobs\n -host <host_name> host machine to run subjobs.\n (This option has been DEPRECATED, please use -SUBHOST\n instead in the future)\n -RETRIES <number> maximum times to retry failed subjobs (default is 3).\n -max_retries <number> maximum times to retry failed subjobs (default is 3).\n (This option has been DEPRECATED, please use -RETRIES\n instead in the future)\n -TMPDIR <dir> specify a tmpdir setting for this job\n -WAIT do not return until the job completes.\n -SAVE return zip archive of job directory at job completion.\n -NICE run the job at reduced priority.\n -maxjob <number> maximum number of simultaneous subjobs (default is 1)\n -mode {umbrella} run in non-default execution mode. Currently, there is\n only 1 valid value: umbrella. In umbrella mode, subjobs\n will run on the nodes allocated to the main job.\n -max-walltime <number> number of seconds to run the job and then checkpoint.\n\nOther options:\n -description <text> job description to print to the log\n -notify <email_addr> send a notification email when this job terminates.\n -nopref ignore the multisim preference file.\n -probe probe a checkpoint file and quit.\n -quiet light log information (default)\n -verbose heavy log information\n -debug turn on multisim debug mode.\n -DEBUG turn on both multisim and jobcontrol debug modes.\n -v, -version show the program's version and exit.\n\n -h, -help, -HELP [<topic>]\n show help and quit. User can optionally specify a topic\n for help. Valid topics are the following: @all, @doc,\n @<flag> (where <flag> represents the flag of any valid\n option, e.g. @-help), @example, and @deprecated.\n For more detail see help of the '@-help' topic.\n"¶

TOPIC = {'@-ADD_FILE': '\nIf your workflow needs additional input files to run, you can specify these\ninput files after the -ADD_FILE flag. You can repeat the -ADD_FILE flag multiple\ntimes with each one followed by one file so to include all necessary files. All\nthe input files will be automatically copied to the host of the main job.\nNormally, you do not need to use this option since multisim can do a pretty good\njob in figuring out the necessary input files as mentioned in either the command\nor the .msj file.', '@-ALT_DIR': '\nWhen multisim looks for a file with relative path name, it will search the\ncurrent directory by default. To let multisim also search other directories,\nuser can specify the directories with this option. The searching order will be\nthe current directory first, then user-specified directories. You can set the\n-ALT_DIR option multiple times to specify multiple search directories.', '@-DEBUG': '\nTurn on both multisim and jobcontrol debug modes.', '@-HELP': '\nLet multisim show online help and then quit. Aliases of the -HELP flag are:\n-help and -h. A value can be optionally given after the flag to specify a\nparticular topic for help. If no value is given, multisim will show concise help\nfor the most frequently used options. Valid values (or topics) are the following:\n @all - Show concise help of all valid options.\n @doc - Show detailed help of all valid options.\n @<flag> - Show detailed help of the <flag> option, e.g. @-h.\n @examples - Show a few command examples.\n @deprecated - Show a list of deprecated options.', '@-HOST': '\nSpecify the host machine to run the multisim main job. If this option is\nomitted, the default host will be localhost. The main job normally requires\nonly 1 processor to run. In some cases (for example, when you run the job in the\numbrella mode -- see the help of the -mode option), you want the main job to\nrun on more than 1 processor. For such cases, you can explicitly request the\nnumber of processors for the main job using the host syntax:\n<hostname>:<number_of_processors>, e.g., -HOST robin_para:8. Note that you\nshould use a parallel queue if you want the main job to gain multiple\nprocessors on a queued host.', '@-JOBNAME': '\nThe value after the flag specifies the name of this multisim job. If this\noption is omitted, multisim will automatically generate a unique job name using\nyour username, current date and time. The automatic name is after the pattern\n<username><yyyymmdd>T<hhmmss>, e.g., bgates20101120T193036.', '@-LOCAL': "\nIf you want to run main job in the local directory, you can add this option to\nyour command. Note that the local directory must be accessible on the host of\nthe main job, otherwise your job will fail. For this reason, this option is\nused most times when the main job's host is localhost. Also note that this\noption affects the main job only.", '@-NICE': '\nLet the multisim job run at reduced priority.', '@-RESTART': '\nThe value after the -RESTART flag should specify a multisim checkpoint file for\nrestarting a job. You can explicitly specify the restarting stage using the\nsyntax: <multisim_checkpoint_file>:<stage_number>. The restarted stage must be\neither a previously completed stage or the interrupted stage. If the restarting\nstage is not explicitly specified, multisim will restart the job from the\ninterruption point. The restarted job will run, following the previous workflow.\nIf you want it to follow an altered workflow, you can specify the workflow via\nthe -m option.', '@-RETRIES': '\nSpecify the maximum times to retry failed subjobs. By default, multisim retries\nfor at most 3 times.', '@-SAVE': '\nLet jobcontrol return the zip archive of this job directory at the job\ncompletion.', '@-SUBHOST': '\nSpecify the default host machine to run subjobs. Unless a stage has explicitly\nset a different host to run its subjobs, subjobs will run on the machine\nspecified via the -SUBHOST option. This option does not support the\n<hostname>:<number_of_processors> syntax. In umbrella mode, this option will be\nignored, and so the compute host should be specified using the -HOST option.', '@-TMPDIR': '\nThe value after the flag should specify a scratch dir where this multisim job\nwill run.', '@-USER': '\nUse a different username to launch the job. This option has been DEPRECATED, and\nthis feature will likely be removed in future releases. Please try not to use\nthis option any more.', '@-WAIT': '\nWith this option the launch command will not finish/return until this job\nterminates.', '@-c': '\nIn general, the value after the -c flag should specify a configuration file,\nwhere the settings will affect a family of stages of the basic workflow (as\ndefined by the .msj file). Only Desmond stage family is supported so far. So the\nvalue after the -c flag currently must specify a Desmond front-end .cfg file.\nThe settings from the configuration file will effect unless the same settings\nare explicitly mentioned in the stages.', '@-d': '\nThis option should be used only for restarting a job from multisim\ncheckpoint file. The value after the -d flag must specify a stage-data file\nproduced by the previous job. Stage-data files usually have a .tgz extension.\nIn a restarted job if the stages to run will read the files of the previous\nstages, you need to specify the stage-data files of these previous stages\nusing the -d option. The -d option can be specified multiple times to include\nall needed stage-data files.', '@-debug': '\nTurn on multisim debug mode -- multisim will print not only normal log\ninformation but also degugging information.', '@-description': '\nThis value after the flag should be a text, which will be printed to the\nmain log file. If the text contains spaces, then it must be quoted.', '@-h': '\nLet multisim show online help and then quit. Aliases of the -h flag are: -HELP\nand -help. A value can be optionally given after the flag to specify a\nparticular topic for help. If no value is given, multisim will show concise help\nfor the most frequently used options. Valid values (or topics) are the following:\n @all - Show concise help of all valid options.\n @doc - Show detailed help of all valid options.\n @<flag> - Show detailed help of the <flag> option, e.g. @-h.\n @examples - Show a few command examples.\n @deprecated - Show a list of deprecated options.', '@-help': '\nLet multisim show online help and then quit. Aliases of the -help flag are:\n-HELP and -h. A value can be optionally given after the flag to specify a\nparticular topic for help. If no value is given, multisim will show concise help\nfor the most frequently used options. Valid values (or topics) are the following:\n @all - Show concise help of all valid options.\n @doc - Show detailed help of all valid options.\n @<flag> - Show detailed help of the <flag> option, e.g. @-h.\n @examples - Show a few command examples.\n @deprecated - Show a list of deprecated options.', '@-host': '\nThis option has been deprecated. The -host flag is temporarily an alias of\n-SUBHOST. See the help for the latter for detail. Please try not to use this\nflag, use -SUBHOST instead.', '@-i': '\nThe value after the -i flag should specify a structure input file (either .mae\nor .cms file). This option has been deprecated. You can specify the structure\ninput file without the -i flag.', '@-m': '\nThe value after the -m flag should specify a .msj file that defines the basic\nworkflow for this multisim job. The .msj file must be specified for a new job,\nbut it is optional for restarting a job from multisim checkpoint file. The\nbasic workflow defined by the .msj file can be altered using the -set and -c\noptions.', '@-max-walltime': '\nThe number of seconds to run the job before automatically checkpointing.\nIf this is part of a subjob, it will request that the main job automatically\nrestart this job. This can be useful for running on a resource that limits\njobs to a certain run time.', '@-max_retries': '\nThis option has been deprecated. The -max_retries flag is temporarily an alias\nof -RETRIES. See the help for the latter for detail. Please try not to use this\nflag, use -RETRIES instead.', '@-maxjob': "\nSet the maximum number of simultaneously active subjobs. Active jobs are those\nin the waiting or running state. Any non-negative integer is a valid value for\nthis option. The default value is 1, which means at any moment of the main\njob's life time there is at most 1 active subjob, and only when this subjob is\ncompleted will another subjob be launched. Value 0 is also a valid value, but\nits exact semantics depends on multisim mode (see help of the -mode option). In\nthe default mode, value 0 means that the number of simulataneously active\nsubjobs is unlimited. If you run subjobs on a cluster with a queuing system, you\nprobably want to use 0 in the default mode. In the 'umbrella' mode, value 0 is\nequivalent to 1.", '@-mode': '\nMultisim will run in a predefined but nondefault mode. Only one nondefault mode\nis supported so far: umbrella. You can activate this mode by adding\n"-mode umbrella" (without quotes) in your command.\nThe umbrella mode will let all subjobs run on the nodes allocated to the main\njob, which avoids submitting the subjobs into the queueing system and thus the\nwaiting time. The umbrella mode ignores the -SUBHOST option, so specify the\ncompute host using the -HOST option.', '@-nopref': '\nUser can customize default values of certain options in the\n$HOME/.schrodinger/multisim_preference file. This -nopref switch causes multisim\nto ignore this file.', '@-notify': '\nThe value after the flag should be an email address. When the main job\nterminates multisim will send an email (with multisim log file attached) to the\nemail address. You can repeat the option multiple times to specify more than one\nemail addresses.', '@-o': '\nThe value after the -o flag specifies the output structure file name. If an\noutput structure is produced, it will be written to the file with the specified\nfilename. If no structure will be produced, the -o option will have no effect.', '@-probe': "\nProbe a checkpoint file and quit. The value after the flag should specify a\nmultisim checkpoint file. Multisim will show the previous job's state as\nrecorded in the checkpoint file. In addition, multisim will indicate whether\nthe checkpoint file is compatible (and thus restartable) with the current\nversion of multisim.", '@-quiet': '\nWith this option multisim will print minimum amount of information to the main\nlog file. This is the default log level.', '@-r': '\nThis option has been deprecated. The -r flag is temporarily an alias of\n-RESTART. See the help for the -RESTART option for detail. Please try not to\nuse this flag, use -RESTART instead.', '@-set': '\nThis option enables you to mutate the basic workflow through the command line\ninterface. For example, if you want to change the value of stage 3\'s time\nparameter, you can include this setting in your command:\n -set "stage[3].time=2.0"\n. You can repeat the -set flag multiple times to include all workflow\nmutations.', '@-v': "\nShow the program's version and then quit. The -version flag is an alias of the\n-v flag.", '@-verbose': '\nWith this option multisim will print a heavy amount of information to the main\nlog file.', '@-version': "\nShow the program's version and then quit. The -v flag is an alias of the\n-version flag.", '@deprecated': "\nThe following options have been deprecated in this release and will be removed\nin the future:\n -r Use -RESTART instead.\n -i Specify the input structure file without the '-i' flag.\n -host Use -SUBHOST instead.\n -max_retries Use -RETRIES instead.", '@examples': '_APPLICATION_NAME_ -JOBNAME my_ligand -m my_protocol.msj my_structure.cms\n\nLaunch a new job with the name of \'my_ligand\'. The input structure file is\nmy_structure.cms, and the workflow is defined by the my_protocol.msj file.\n\n\n_APPLICATION_NAME_ -JOBNAME "my ligand" -m my_protocol.msj my_structure.cms\n\nSimilar to the above example, but note the space and the quotes in the value of\nthe \'-JOBNAME\' option.\nIn general, if a value has spaces in it, the value needs to be quoted.\n\n\n_APPLICATION_NAME_ -JOBNAME my_ligand_restart -RESTART my_ligand-multisim_checkpoint -d my_ligand-6.tgz\n\nRestart a previous job using multisim checkpoint file. The job will be restarted\nfrom the point where the previous job was interrupted. You usually need to\nprovide the data file of the stage prior to the interrupted one. In this example,\nwe assume the previous job was interrupted at stage 7, so we specify the -d option\nwith the my_ligand_6.tgz file.\n\n\n_APPLICATION_NAME_ -JOBNAME my_ligand_restart -RESTART my_ligand-multisim_checkpoint:5 -d my_ligand-4.tgz\n\nRestart a previous job using multisim checkpoint file. The job will be restarted\nfrom stage 5 (which should be either completed or be the point where the previous\njob was interrupted).\n'}¶

__init__(app_name)¶

print_version()¶

Prints version information.

print_help(topic=None)¶

Print help information.

class schrodinger.application.desmond.multisimstartup.Startup(argv, orig_argv=None)¶

Bases: object

APPLICATION_NAME = '$SCHRODINGER/utilities/multisim'¶

SCRIPT = 'chorus_multijob.py'¶

class Help(app_name)¶

Bases: object

LONG_USAGE = "\nMultisim workflow program\n\nUsage:\n* To run a new job:\n _APPLICATION_NAME_ [<options>] {-m <file>.msj} {<file>.cms|<file>.mae}\n\n* To restart a previous job:\n _APPLICATION_NAME_ [<options>] {-RESTART <multisim_checkpoint_file>}\n You normally also need to specify the '-d' option.\n\nI/O options:\n -i <input file> input structure file in the .cms or .mae format\n (This option has been DEPRECATED, please specify the\n .cms or .mae file without the -i flag in the future)\n -m <input_file> input .msj file defining the basic workflow\n -RESTART <input_file> multisim checkpoint file for restarting a job.\n -r <input file> multisim checkpoint file for restarting a job.\n (This option has been DEPRECATED, please use -RESTART\n instead in the future)\n -d <input_file> stage data file from the previous job and usually with\n the .tgz suffix. This option should be used only in\n restarting a job with multisim checkpoint file.\n -c <input_file> set configuration parameters for a family of stages.\n -ADD_FILE <input_file> Additional input file to copy to the working directory\n of this multisim job\n -ALT_DIR <directory> Alternative directory where to look for input files\n -o <output_file> output .cms or .mae file. This file can be incorporated\n into Maestro.\n\nWorkflow options:\n -m <input_file> input .msj file defining the basic workflow\n -c <input_file> set configuration parameters for a family of stages.\n -set <string> modify the basic workflow defined by the .msj file.\n\nJob options:\n -JOBNAME <job_name> name of this multisim job\n -HOST <host_name> host machine to run the multisim main job (default is\n localhost)\n -SUBHOST <host_name> host machine to run subjobs\n -host <host_name> host machine to run subjobs.\n (This option has been DEPRECATED, please use -SUBHOST\n instead in the future)\n -RETRIES <number> maximum times to retry failed subjobs (default is 3).\n -max_retries <number> maximum times to retry failed subjobs (default is 3).\n (This option has been DEPRECATED, please use -RETRIES\n instead in the future)\n -TMPDIR <dir> specify a tmpdir setting for this job\n -WAIT do not return until the job completes.\n -SAVE return zip archive of job directory at job completion.\n -NICE run the job at reduced priority.\n -maxjob <number> maximum number of simultaneous subjobs (default is 1)\n -mode {umbrella} run in non-default execution mode. Currently, there is\n only 1 valid value: umbrella. In umbrella mode, subjobs\n will run on the nodes allocated to the main job.\n -max-walltime <number> number of seconds to run the job and then checkpoint.\n\nOther options:\n -description <text> job description to print to the log\n -notify <email_addr> send a notification email when this job terminates.\n -nopref ignore the multisim preference file.\n -probe probe a checkpoint file and quit.\n -quiet light log information (default)\n -verbose heavy log information\n -debug turn on multisim debug mode.\n -DEBUG turn on both multisim and jobcontrol debug modes.\n -v, -version show the program's version and exit.\n\n -h, -help, -HELP [<topic>]\n show help and quit. User can optionally specify a topic\n for help. Valid topics are the following: @all, @doc,\n @<flag> (where <flag> represents the flag of any valid\n option, e.g. @-help), @example, and @deprecated.\n For more detail see help of the '@-help' topic.\n"¶

SHORT_USAGE = "\nMultisim workflow program\n\nUsage:\n* To run a new job:\n _APPLICATION_NAME_ [<options>] {-m <file>.msj} {<file>.cms|<file>.mae}\n\n* To restart a previous job:\n _APPLICATION_NAME_ [<options>] {-RESTART <multisim_checkpoint_file>}\n You normally also need to specify the '-d' option.\n\nFrequently used options:\n -m <input_file> input .msj file defining the basic workflow\n -d <input_file> stage data file from the previous job and usually with\n the .tgz suffix. This option should be used only in\n restarting a job with multisim checkpoint file.\n -c <input_file> set configuration parameters for a family of stages.\n -o <output_file> output .cms or .mae file. This file can be incorporated\n into Maestro.\n -maxjob <number> maximum number of simultaneous subjobs (default is 1)\n -mode {umbrella} run in non-default execution mode. Currently, there is\n only 1 valid value: umbrella. In umbrella mode, subjobs\n will run on the nodes allocated to the main job.\n -notify <email_addr> send a notification email when this job terminates.\n -nopref ignore the multisim preference file.\n -probe probe a checkpoint file and quit.\n -JOBNAME <job_name> name of this multisim job\n -HOST <host_name> host machine to run the multisim main job (default is\n localhost)\n -SUBHOST <host_name> host machine to run subjobs\n -RESTART <input_file> restart a previous job from its multisim checkpoint file.\n\n -h [<topic>] show help and quit. User can optionally specify a topic\n for help. Valid topics are the following: @all, @doc,\n @<flag> (where <flag> represents the flag of any valid\n option, e.g. @-help), @examples, and @deprecated.\n For more detail see help of the '@-help' topic.\n"¶

TOPIC = {'@-ADD_FILE': '\nIf your workflow needs additional input files to run, you can specify these\ninput files after the -ADD_FILE flag. You can repeat the -ADD_FILE flag multiple\ntimes with each one followed by one file so to include all necessary files. All\nthe input files will be automatically copied to the host of the main job.\nNormally, you do not need to use this option since multisim can do a pretty good\njob in figuring out the necessary input files as mentioned in either the command\nor the .msj file.', '@-ALT_DIR': '\nWhen multisim looks for a file with relative path name, it will search the\ncurrent directory by default. To let multisim also search other directories,\nuser can specify the directories with this option. The searching order will be\nthe current directory first, then user-specified directories. You can set the\n-ALT_DIR option multiple times to specify multiple search directories.', '@-DEBUG': '\nTurn on both multisim and jobcontrol debug modes.', '@-HELP': '\nLet multisim show online help and then quit. Aliases of the -HELP flag are:\n-help and -h. A value can be optionally given after the flag to specify a\nparticular topic for help. If no value is given, multisim will show concise help\nfor the most frequently used options. Valid values (or topics) are the following:\n @all - Show concise help of all valid options.\n @doc - Show detailed help of all valid options.\n @<flag> - Show detailed help of the <flag> option, e.g. @-h.\n @examples - Show a few command examples.\n @deprecated - Show a list of deprecated options.', '@-HOST': '\nSpecify the host machine to run the multisim main job. If this option is\nomitted, the default host will be localhost. The main job normally requires\nonly 1 processor to run. In some cases (for example, when you run the job in the\numbrella mode -- see the help of the -mode option), you want the main job to\nrun on more than 1 processor. For such cases, you can explicitly request the\nnumber of processors for the main job using the host syntax:\n<hostname>:<number_of_processors>, e.g., -HOST robin_para:8. Note that you\nshould use a parallel queue if you want the main job to gain multiple\nprocessors on a queued host.', '@-JOBNAME': '\nThe value after the flag specifies the name of this multisim job. If this\noption is omitted, multisim will automatically generate a unique job name using\nyour username, current date and time. The automatic name is after the pattern\n<username><yyyymmdd>T<hhmmss>, e.g., bgates20101120T193036.', '@-LOCAL': "\nIf you want to run main job in the local directory, you can add this option to\nyour command. Note that the local directory must be accessible on the host of\nthe main job, otherwise your job will fail. For this reason, this option is\nused most times when the main job's host is localhost. Also note that this\noption affects the main job only.", '@-NICE': '\nLet the multisim job run at reduced priority.', '@-RESTART': '\nThe value after the -RESTART flag should specify a multisim checkpoint file for\nrestarting a job. You can explicitly specify the restarting stage using the\nsyntax: <multisim_checkpoint_file>:<stage_number>. The restarted stage must be\neither a previously completed stage or the interrupted stage. If the restarting\nstage is not explicitly specified, multisim will restart the job from the\ninterruption point. The restarted job will run, following the previous workflow.\nIf you want it to follow an altered workflow, you can specify the workflow via\nthe -m option.', '@-RETRIES': '\nSpecify the maximum times to retry failed subjobs. By default, multisim retries\nfor at most 3 times.', '@-SAVE': '\nLet jobcontrol return the zip archive of this job directory at the job\ncompletion.', '@-SUBHOST': '\nSpecify the default host machine to run subjobs. Unless a stage has explicitly\nset a different host to run its subjobs, subjobs will run on the machine\nspecified via the -SUBHOST option. This option does not support the\n<hostname>:<number_of_processors> syntax. In umbrella mode, this option will be\nignored, and so the compute host should be specified using the -HOST option.', '@-TMPDIR': '\nThe value after the flag should specify a scratch dir where this multisim job\nwill run.', '@-USER': '\nUse a different username to launch the job. This option has been DEPRECATED, and\nthis feature will likely be removed in future releases. Please try not to use\nthis option any more.', '@-WAIT': '\nWith this option the launch command will not finish/return until this job\nterminates.', '@-c': '\nIn general, the value after the -c flag should specify a configuration file,\nwhere the settings will affect a family of stages of the basic workflow (as\ndefined by the .msj file). Only Desmond stage family is supported so far. So the\nvalue after the -c flag currently must specify a Desmond front-end .cfg file.\nThe settings from the configuration file will effect unless the same settings\nare explicitly mentioned in the stages.', '@-d': '\nThis option should be used only for restarting a job from multisim\ncheckpoint file. The value after the -d flag must specify a stage-data file\nproduced by the previous job. Stage-data files usually have a .tgz extension.\nIn a restarted job if the stages to run will read the files of the previous\nstages, you need to specify the stage-data files of these previous stages\nusing the -d option. The -d option can be specified multiple times to include\nall needed stage-data files.', '@-debug': '\nTurn on multisim debug mode -- multisim will print not only normal log\ninformation but also degugging information.', '@-description': '\nThis value after the flag should be a text, which will be printed to the\nmain log file. If the text contains spaces, then it must be quoted.', '@-h': '\nLet multisim show online help and then quit. Aliases of the -h flag are: -HELP\nand -help. A value can be optionally given after the flag to specify a\nparticular topic for help. If no value is given, multisim will show concise help\nfor the most frequently used options. Valid values (or topics) are the following:\n @all - Show concise help of all valid options.\n @doc - Show detailed help of all valid options.\n @<flag> - Show detailed help of the <flag> option, e.g. @-h.\n @examples - Show a few command examples.\n @deprecated - Show a list of deprecated options.', '@-help': '\nLet multisim show online help and then quit. Aliases of the -help flag are:\n-HELP and -h. A value can be optionally given after the flag to specify a\nparticular topic for help. If no value is given, multisim will show concise help\nfor the most frequently used options. Valid values (or topics) are the following:\n @all - Show concise help of all valid options.\n @doc - Show detailed help of all valid options.\n @<flag> - Show detailed help of the <flag> option, e.g. @-h.\n @examples - Show a few command examples.\n @deprecated - Show a list of deprecated options.', '@-host': '\nThis option has been deprecated. The -host flag is temporarily an alias of\n-SUBHOST. See the help for the latter for detail. Please try not to use this\nflag, use -SUBHOST instead.', '@-i': '\nThe value after the -i flag should specify a structure input file (either .mae\nor .cms file). This option has been deprecated. You can specify the structure\ninput file without the -i flag.', '@-m': '\nThe value after the -m flag should specify a .msj file that defines the basic\nworkflow for this multisim job. The .msj file must be specified for a new job,\nbut it is optional for restarting a job from multisim checkpoint file. The\nbasic workflow defined by the .msj file can be altered using the -set and -c\noptions.', '@-max-walltime': '\nThe number of seconds to run the job before automatically checkpointing.\nIf this is part of a subjob, it will request that the main job automatically\nrestart this job. This can be useful for running on a resource that limits\njobs to a certain run time.', '@-max_retries': '\nThis option has been deprecated. The -max_retries flag is temporarily an alias\nof -RETRIES. See the help for the latter for detail. Please try not to use this\nflag, use -RETRIES instead.', '@-maxjob': "\nSet the maximum number of simultaneously active subjobs. Active jobs are those\nin the waiting or running state. Any non-negative integer is a valid value for\nthis option. The default value is 1, which means at any moment of the main\njob's life time there is at most 1 active subjob, and only when this subjob is\ncompleted will another subjob be launched. Value 0 is also a valid value, but\nits exact semantics depends on multisim mode (see help of the -mode option). In\nthe default mode, value 0 means that the number of simulataneously active\nsubjobs is unlimited. If you run subjobs on a cluster with a queuing system, you\nprobably want to use 0 in the default mode. In the 'umbrella' mode, value 0 is\nequivalent to 1.", '@-mode': '\nMultisim will run in a predefined but nondefault mode. Only one nondefault mode\nis supported so far: umbrella. You can activate this mode by adding\n"-mode umbrella" (without quotes) in your command.\nThe umbrella mode will let all subjobs run on the nodes allocated to the main\njob, which avoids submitting the subjobs into the queueing system and thus the\nwaiting time. The umbrella mode ignores the -SUBHOST option, so specify the\ncompute host using the -HOST option.', '@-nopref': '\nUser can customize default values of certain options in the\n$HOME/.schrodinger/multisim_preference file. This -nopref switch causes multisim\nto ignore this file.', '@-notify': '\nThe value after the flag should be an email address. When the main job\nterminates multisim will send an email (with multisim log file attached) to the\nemail address. You can repeat the option multiple times to specify more than one\nemail addresses.', '@-o': '\nThe value after the -o flag specifies the output structure file name. If an\noutput structure is produced, it will be written to the file with the specified\nfilename. If no structure will be produced, the -o option will have no effect.', '@-probe': "\nProbe a checkpoint file and quit. The value after the flag should specify a\nmultisim checkpoint file. Multisim will show the previous job's state as\nrecorded in the checkpoint file. In addition, multisim will indicate whether\nthe checkpoint file is compatible (and thus restartable) with the current\nversion of multisim.", '@-quiet': '\nWith this option multisim will print minimum amount of information to the main\nlog file. This is the default log level.', '@-r': '\nThis option has been deprecated. The -r flag is temporarily an alias of\n-RESTART. See the help for the -RESTART option for detail. Please try not to\nuse this flag, use -RESTART instead.', '@-set': '\nThis option enables you to mutate the basic workflow through the command line\ninterface. For example, if you want to change the value of stage 3\'s time\nparameter, you can include this setting in your command:\n -set "stage[3].time=2.0"\n. You can repeat the -set flag multiple times to include all workflow\nmutations.', '@-v': "\nShow the program's version and then quit. The -version flag is an alias of the\n-v flag.", '@-verbose': '\nWith this option multisim will print a heavy amount of information to the main\nlog file.', '@-version': "\nShow the program's version and then quit. The -v flag is an alias of the\n-version flag.", '@deprecated': "\nThe following options have been deprecated in this release and will be removed\nin the future:\n -r Use -RESTART instead.\n -i Specify the input structure file without the '-i' flag.\n -host Use -SUBHOST instead.\n -max_retries Use -RETRIES instead.", '@examples': '_APPLICATION_NAME_ -JOBNAME my_ligand -m my_protocol.msj my_structure.cms\n\nLaunch a new job with the name of \'my_ligand\'. The input structure file is\nmy_structure.cms, and the workflow is defined by the my_protocol.msj file.\n\n\n_APPLICATION_NAME_ -JOBNAME "my ligand" -m my_protocol.msj my_structure.cms\n\nSimilar to the above example, but note the space and the quotes in the value of\nthe \'-JOBNAME\' option.\nIn general, if a value has spaces in it, the value needs to be quoted.\n\n\n_APPLICATION_NAME_ -JOBNAME my_ligand_restart -RESTART my_ligand-multisim_checkpoint -d my_ligand-6.tgz\n\nRestart a previous job using multisim checkpoint file. The job will be restarted\nfrom the point where the previous job was interrupted. You usually need to\nprovide the data file of the stage prior to the interrupted one. In this example,\nwe assume the previous job was interrupted at stage 7, so we specify the -d option\nwith the my_ligand_6.tgz file.\n\n\n_APPLICATION_NAME_ -JOBNAME my_ligand_restart -RESTART my_ligand-multisim_checkpoint:5 -d my_ligand-4.tgz\n\nRestart a previous job using multisim checkpoint file. The job will be restarted\nfrom stage 5 (which should be either completed or be the point where the previous\njob was interrupted).\n'}¶

VERSION = 'multisim v4.0.0'¶

__init__(app_name)¶

print_help(topic=None)¶

Print help information.

print_version()¶

Prints version information.

__init__(argv, orig_argv=None)¶

print_version()¶

print_usage(i_argv=None, text=None)¶

get_launcher()¶

launch(env=None)¶: Create and launch multisim job

schrodinger.application.desmond.multisimstartup.get_input_files(cmd)¶: Returns registered multisim input files

schrodinger.application.desmond.multisimstartup.get_licenses(cmd)¶: Get the licenses being used in the given multisim command :param cmd: the multisim command :type cmd: List[str] :return: the licenses being used :rtype: list[str]

schrodinger.application.desmond.multisimstartup.backup_files(jobname: str)¶

Backs-up the primary output files from multisim into a new backup directory

Only creates the backup directory if one of the files exists