Module jobcontrol

Return a list of Jobs in the database.

The query can be "all" or "active"; otherwise, raises an Exception.

Run a process under job control and return a Job object. For a process to be under job control, it must print a valid JobId: line to stdout. If such a line isn't printed, a RuntimeError will be raised.

The cmd argument should be a list of command arguments (including the executable) as expected by the subprocess module.

If the executable is present in $SCHRODINGER or $SCHRODINGER/utilities, an absolute path does not need to be specified.

Parameters:

• print_output (bool) - Determines if the output from jlaunch is printed to the terminal or not. Output will be logged (to stderr by default) if Python or JobControl debugging is turned on or if there is a launch failure, even if 'print_output' is False.
• expandvars (bool) - If True, any environment variables of the form $var or ${var} will be expanded with their values by the os.path.expandvars function.

Raises:

• RuntimeError - If there is a problem launching the job (e.g., no JobId gets printed). If running within Maestro, an error dialog will first be shown to the user.

A function to clean up the command passed to launch_job.

Parameters:

• cmd (list of strings) - A command in a form that can be passed to subprocess.Popen.
• expandvars (bool) - If True, any environment variables of the form $var or ${var} will be expanded with their values by the os.path.expandvars function.

Returns:

The command to be launched

A convenience function to see if we're running under job control. If so, return a _Backend object. Otherwise, return None.

Return the runtime path for the input file 'pathname'.

If the pathname is of a type that job control will not copy to the job directory or no runtime file can be found, returns the original path name.

Return the name of the schrodinger.hosts file last used by get_hosts(). The file is found using the standard search path ($SCHRODINGER_HOSTS, local dir, $HOME/.schrodinger, $SCHRODINGER).

Return the pathname for the schrodinger.hosts file installed in the most recent previous installation directory we can find.

If a root pathname is passed in, previous installations are searched for there. Otherwise, we look in the standard install locations.

Return a list of all Hosts in the schrodinger.hosts file. After this is called, get_hostfile() will return the pathname for the schrodinger.hosts file that was used.

Return a list of the given Host objects re-ordered to satisfy the
conditions that,
1. the localhost entry (if any) is first, and
2. any entry used as a base entry is defined before it's used.
Otherwise, the input order is preserved.

Return a Host object for the named host. If the host is not found, we return a Host object with the provided name and details that match localhost. This matches behavior that jobcontrol uses.

Convert a hosts string (Ex: "galina:1 monica:4") to a list of tuples. First value of each tuple is the host, second value is # of cpus.

Converts a hosts list (Ev: [ ('host1',1), ('host2', 10) ] ) to a string. Output example: "host1:1,host2:10"

Return a list of (host, ncpu) tuples corresponding to the host list that is specified on the command line.

This function is meant to be called by scripts that are running under a toplevel job control script but are not running under jlaunch.

The host list is determined from the following sources:

1. SCHRODINGER_NODELIST
2. JOBHOST (if only a single host is specified)
3. "localhost" (if no host is specified)

If no SCHRODINGER_NODELIST is present in the environment, None is returned.

Return a list of (host, ncpu) tuples corresponding to the host list as determined from the SCHRODINGER_NODEFILE.

This function is meant to be called from scripts that are running under jlaunch (i.e. backend scripts).

Returns None if SCHRODINGER_NODEFILE is not present in the environment.

Derive the number of jobs from the specified host list.
This function is useful to determine number of subjobs if user didn't
specified the '-NJOBS' option.

@type host_list: String
                 or
                 List of tuples
@param host_list: String of hosts along with optional number of cpus
                  or
                  List of tuples consist of hosts along with optional
                  number of cpus

If host list is not specified then it uses get_command_line_host_list() to
determine njobs, else uses the user provided host list.

Please note: the host_list can be passes as string or as a list of tuples.
    For example: for -GLIDE_HOST "host1 host2:4" host_list would become
        [('host1', None), ('host2', 4)]

__doc__

Value:

""" Core job control for python. There are currently four major sections of this module - "Job database ," "Job launching," "Job backend," and "Job hosts." The job database sect ion deals with getting info about existing Jobs, the job launching section ...

jobid_re

Value:

re.compile(r"^JobId:\s+(\S+)", re.IGNORECASE | re.MULTILINE)

entry_fields

Value:

["name", "base", "host", "nodelist", "user", "queue", "qargs", "schrod inger", "proxyhost", "proxyport", "proxyexec", "tmpdir", "shareddir", "env", "processors", "processors_per_node", "parallel", "ngpu", "gpgpu ", "maestrocontrols", "walltime", "memory", "accountcodes"]

field_sortkey

Value:

dict([(k, v) for(v, k) in enumerate(entry_fields)])