schrodinger.application.desmond.starter.ui.multisim module

Multisim command line UI

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.desmond.starter.ui.multisim.Help(app_name)

Bases: object

LONG_USAGE = "\nMultisim workflow program\n\nUsage:\n* To run a new job:\n _APPLICATION_NAME_ [<options>] -m <workflow.msj> <data-files...>\n\n* To restart a previous job:\n _APPLICATION_NAME_ [<options>] -RESTART <multisim-checkpoint-file>\n Usually you need to specify the '-d' option to supply the stage data for the\n workflow to restart.\n\nI/O options:\n -m <FILE> input .msj file defining the basic workflow\n -RESTART <FILE> multisim checkpoint file for restarting a job.\n -d <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 <FILE> set configuration parameters for a family of stages.\n -ADD_FILE <FILE> additional input file to copy to the working directory\n of this multisim job\n -ALT_DIR <DIR> alternative directory where to look for input files\n -o <FILE> output .cms or .mae file. This file can be incorporated\n into Maestro.\n \nWorkflow options: \n -m <FILE> input .msj file defining the workflow\n -c <FILE> set configuration parameters for a family of stages.\n -cpu <NUMBER> number of CPUs for each subjob. For Desmond subjobs,\n this can be a string indicating the CPU topology for\n each replica, e.g., '2 2 2'.\n -set <STRING> modify the basic workflow defined by the .msj file.\n\nJob options:\n -JOBNAME <NAME> name of this multisim job\n -HOST <NAME> host machine to run the multisim master job (default is\n localhost)\n -SUBHOST <NAME> host machine to run subjobs\n -RETRIES <NUMBER> maximum times to retry failed subjobs (default is 3).\n -LOCAL run master job in the local directory.\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 -NOJOBID run the job without jobcontrol.\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 master job.\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., @-cpu, @-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 <workflow.msj> <data-files...>\n\n* To restart a previous job:\n _APPLICATION_NAME_ [<options>] -RESTART <multisim-checkpoint-file>\n Usually you need to specify the '-d' option to supply the stage data for the\n workflow to restart.\n\nFrequently used options:\n -m <FILE> input .msj file defining the basic workflow\n -d <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 <FILE> set configuration parameters for a family of stages.\n -o <FILE> output .cms or .mae file. This file can be incorporated\n into Maestro.\n -cpu <NUMBER> number of CPUs for each subjob. For Desmond subjobs,\n this can be a string indicating the CPU topology for\n each replica, e.g., '2 2 2'.\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 master job.\n -notify <EMAIL_ADDR> send a notification email when this job terminates.\n -probe probe a checkpoint file and quit.\n -JOBNAME <NAME> name of this multisim job\n -HOST <NAME> host machine to run the multisim master job (default is\n localhost)\n -SUBHOST <NAME> host machine to run subjobs\n -RESTART <FILE> restart a previous job with this multisim checkpoint\n 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., @-cpu, @-help), @examples, and @deprecated.\n For more detail see help of the '@-help' topic.\n"

TOPIC = {'@-SAVE': '\nLet jobcontrol return the zip archive of this job directory at the job\ncompletion.', '@-version': "\nShow the program's version and then quit. The -v flag is an alias of the\n-version flag.", '@-verbose': '\nWith this option multisim will print a heavy amount of information to the master\nlog file.', '@-LOCAL': "\nIf you want to run master 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 master job, otherwise your job will fail. For this reason, this option is\nused most times when the master job's host is localhost. Also note that this\noption affects the master job only.", '@-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.', '@-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 master\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.\nNote that the maximum number of CPUs that could be used is <cpu> x <maxjob>, and\nin case of Desmond jobs, it is <cpu> x <number-of-replica> x <maxjob>.", '@-RETRIES': '\nSpecify the maximum times to retry failed subjobs. By default, multisim retries\nfor at most 3 times.', '@-HOST': '\nSpecify the host machine to run the multisim master job. If this option is\nomitted, the default host will be localhost. The master 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 master job to\nrun on more than 1 processor. For such cases, you can explicitly request the\nnumber of processors for the master 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 master job to gain multiple\nprocessors on a queued host.', '@-quiet': '\nWith this option multisim will print minimum amount of information to the master\nlog file. This is the default log level.', '@-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.', '@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 -m my_protocol.msj -cpu "2 2 1" my_structure.cms\n\nLaunch a new job with customized processor topology. Note that for the \'-cpu\'\noption, we specify a triplet with the numbers separated by spaces, and because\nthe value has spaces, we need to quote it.\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', '@-debug': '\nTurn on multisim debug mode -- multisim will print not only normal log\ninformation but also degugging information.', '@-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 master 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.', '@-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.', '@-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.', '@-WAIT': '\nWith this option the launch command will not finish/return until this job\nterminates.', '@-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., @-cpu, @-h.\n @examples - Show a few command examples.\n @deprecated - Show a list of deprecated options.', '@-NOJOBID': '\nWith this option the multisim job will run without under jobcontrol.', '@-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.', '@-TMPDIR': '\nThe value after the flag should specify a scratch dir where this multisim job\nwill run.', '@-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.', '@-cpu': '\nThe value after the -cpu flag specifies the processors for subjobs, depending on\nhow the particular type of stages interpretates the -cpu option and whether it\nhas multiple processor support. The value should be either a single integer or a\nquoted integer triplet (e.g., "2 2 2" (with quotes)). The latter form is accepted\nby Desmond stages.', '@-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 master\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.', '@-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.', '@deprecated': '\nNo deprectaed features so far.', '@-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.', '@-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.', '@-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., @-cpu, @-h.\n @examples - Show a few command examples.\n @deprecated - Show a list of deprecated features.', '@-notify': '\nThe value after the flag should be an email address. When the master 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.', '@-v': "\nShow the program's version and then quit. The -version flag is an alias of the\n-v flag.", '@-DEBUG': '\nTurn on both multisim and jobcontrol debug modes.', '@-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.", '@-NICE': '\nLet the multisim job run at reduced priority.', '@-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., @-cpu, @-h.\n @examples - Show a few command examples.\n @deprecated - Show a list of deprecated options.', '@-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.', '@-description': '\nThis value after the flag should be a text, which will be printed to the\nmaster log file. If the text contains spaces, then it must be quoted.'}

VERSION = 'multisim v3.8.5.19'

print_help(topic=None)

• Print help information.

print_version()

• Prints version information.

class schrodinger.application.desmond.starter.ui.multisim.UI(argv, extra_options=[])

Bases: object

APPLICATION_NAME = '$SCHRODINGER/utilities/multisim'

class Help(app_name)

Bases: object

LONG_USAGE = "\nMultisim workflow program\n\nUsage:\n* To run a new job:\n _APPLICATION_NAME_ [<options>] -m <workflow.msj> <data-files...>\n\n* To restart a previous job:\n _APPLICATION_NAME_ [<options>] -RESTART <multisim-checkpoint-file>\n Usually you need to specify the '-d' option to supply the stage data for the\n workflow to restart.\n\nI/O options:\n -m <FILE> input .msj file defining the basic workflow\n -RESTART <FILE> multisim checkpoint file for restarting a job.\n -d <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 <FILE> set configuration parameters for a family of stages.\n -ADD_FILE <FILE> additional input file to copy to the working directory\n of this multisim job\n -ALT_DIR <DIR> alternative directory where to look for input files\n -o <FILE> output .cms or .mae file. This file can be incorporated\n into Maestro.\n \nWorkflow options: \n -m <FILE> input .msj file defining the workflow\n -c <FILE> set configuration parameters for a family of stages.\n -cpu <NUMBER> number of CPUs for each subjob. For Desmond subjobs,\n this can be a string indicating the CPU topology for\n each replica, e.g., '2 2 2'.\n -set <STRING> modify the basic workflow defined by the .msj file.\n\nJob options:\n -JOBNAME <NAME> name of this multisim job\n -HOST <NAME> host machine to run the multisim master job (default is\n localhost)\n -SUBHOST <NAME> host machine to run subjobs\n -RETRIES <NUMBER> maximum times to retry failed subjobs (default is 3).\n -LOCAL run master job in the local directory.\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 -NOJOBID run the job without jobcontrol.\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 master job.\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., @-cpu, @-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 <workflow.msj> <data-files...>\n\n* To restart a previous job:\n _APPLICATION_NAME_ [<options>] -RESTART <multisim-checkpoint-file>\n Usually you need to specify the '-d' option to supply the stage data for the\n workflow to restart.\n\nFrequently used options:\n -m <FILE> input .msj file defining the basic workflow\n -d <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 <FILE> set configuration parameters for a family of stages.\n -o <FILE> output .cms or .mae file. This file can be incorporated\n into Maestro.\n -cpu <NUMBER> number of CPUs for each subjob. For Desmond subjobs,\n this can be a string indicating the CPU topology for\n each replica, e.g., '2 2 2'.\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 master job.\n -notify <EMAIL_ADDR> send a notification email when this job terminates.\n -probe probe a checkpoint file and quit.\n -JOBNAME <NAME> name of this multisim job\n -HOST <NAME> host machine to run the multisim master job (default is\n localhost)\n -SUBHOST <NAME> host machine to run subjobs\n -RESTART <FILE> restart a previous job with this multisim checkpoint\n 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., @-cpu, @-help), @examples, and @deprecated.\n For more detail see help of the '@-help' topic.\n"

TOPIC = {'@-SAVE': '\nLet jobcontrol return the zip archive of this job directory at the job\ncompletion.', '@-version': "\nShow the program's version and then quit. The -v flag is an alias of the\n-version flag.", '@-verbose': '\nWith this option multisim will print a heavy amount of information to the master\nlog file.', '@-LOCAL': "\nIf you want to run master 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 master job, otherwise your job will fail. For this reason, this option is\nused most times when the master job's host is localhost. Also note that this\noption affects the master job only.", '@-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.', '@-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 master\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.\nNote that the maximum number of CPUs that could be used is <cpu> x <maxjob>, and\nin case of Desmond jobs, it is <cpu> x <number-of-replica> x <maxjob>.", '@-RETRIES': '\nSpecify the maximum times to retry failed subjobs. By default, multisim retries\nfor at most 3 times.', '@-HOST': '\nSpecify the host machine to run the multisim master job. If this option is\nomitted, the default host will be localhost. The master 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 master job to\nrun on more than 1 processor. For such cases, you can explicitly request the\nnumber of processors for the master 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 master job to gain multiple\nprocessors on a queued host.', '@-quiet': '\nWith this option multisim will print minimum amount of information to the master\nlog file. This is the default log level.', '@-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.', '@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 -m my_protocol.msj -cpu "2 2 1" my_structure.cms\n\nLaunch a new job with customized processor topology. Note that for the \'-cpu\'\noption, we specify a triplet with the numbers separated by spaces, and because\nthe value has spaces, we need to quote it.\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', '@-debug': '\nTurn on multisim debug mode -- multisim will print not only normal log\ninformation but also degugging information.', '@-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 master 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.', '@-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.', '@-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.', '@-WAIT': '\nWith this option the launch command will not finish/return until this job\nterminates.', '@-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., @-cpu, @-h.\n @examples - Show a few command examples.\n @deprecated - Show a list of deprecated options.', '@-NOJOBID': '\nWith this option the multisim job will run without under jobcontrol.', '@-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.', '@-TMPDIR': '\nThe value after the flag should specify a scratch dir where this multisim job\nwill run.', '@-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.', '@-cpu': '\nThe value after the -cpu flag specifies the processors for subjobs, depending on\nhow the particular type of stages interpretates the -cpu option and whether it\nhas multiple processor support. The value should be either a single integer or a\nquoted integer triplet (e.g., "2 2 2" (with quotes)). The latter form is accepted\nby Desmond stages.', '@-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 master\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.', '@-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.', '@deprecated': '\nNo deprectaed features so far.', '@-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.', '@-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.', '@-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., @-cpu, @-h.\n @examples - Show a few command examples.\n @deprecated - Show a list of deprecated features.', '@-notify': '\nThe value after the flag should be an email address. When the master 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.', '@-v': "\nShow the program's version and then quit. The -version flag is an alias of the\n-v flag.", '@-DEBUG': '\nTurn on both multisim and jobcontrol debug modes.', '@-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.", '@-NICE': '\nLet the multisim job run at reduced priority.', '@-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., @-cpu, @-h.\n @examples - Show a few command examples.\n @deprecated - Show a list of deprecated options.', '@-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.', '@-description': '\nThis value after the flag should be a text, which will be printed to the\nmaster log file. If the text contains spaces, then it must be quoted.'}

VERSION = 'multisim v3.8.5.19'

print_help(topic=None)

• Print help information.

print_version()

• Prints version information.

print_usage(i_argv=None, text=None)

Prints the online help and then quits.

print_version()

Prints the version of the application and then quits.

schrodinger.application.desmond.starter.ui.multisim.ui(argv)