Class Manager

Set up the manager.

:Arguments:
  *statedir*
      directory component under the remote scratch dir (should
      be different for different jobs)  [basename(CWD)]
  *prefix*
      identifier for job names [MD]

Overrides: object.__init__

scp dirname to host.

:Arguments: dirname to be transferred :Returns: return code from scp

scp *filename* to host in *dirname*.

:Arguments: filename and dirname to be transferred to :Returns: return code from scp

``scp -r`` *dirname* from host into *targetdir*

:Arguments:

• *dirname*: dir to download
• *checkfile*: raise OSError/ENOENT if *targetdir/dirname/checkfile* was not found
• *targetdir*: put *dirname* into this directory

:Returns: return code from scp

Find *checkfile* locally if possible.

If *checkfile* is not found in *dirname* then it is transferred from the remote host.

If needed, the trajectories are concatenated using :meth:`Manager.cat`.

:Returns: local path of *checkfile*

Concatenate parts of a run in *dirname*.

Always uses :func:`gromacs.cbook.cat` with *resolve_multi* = 'guess'.

.. Note:: The default is to immediately delete the original files
          (*cleanup* = ``True``).

:Keywords:
   *dirname*
      directory to work in
   *prefix*
      prefix (deffnm) of the files [md]
   *cleanup* : boolean
      if ``True``, remove all used files [``True``]

Submit job remotely on host.

This is the most primitive implementation: it just runs the commands :

  cd remotedir && qsub qscript

on :attr:`Manager._hostname`. *remotedir* is *dirname* under :attr:`Manager._scratchdir` and *qscript* defaults to the queuing system script hat was produced from the template :attr:`Manager._qscript`.

Check status of remote job by looking into the logfile.

Report on the status of the job and extracts the performance in ns/d if
available (which is saved in :attr:`Manager.performance`).

:Arguments:
  - *dirname*
  - *logfilename* can be a shell glob pattern [md*.log]
  - *silent* = True/False; True suppresses log.info messages

:Returns: ``True`` is job is done, ``False`` if still running
          ``None`` if no log file found to look at

.. Note:: Also returns ``False`` if the connection failed.

.. Warning:: This is an important but somewhat  **fragile** method. It
             needs to be improved to be more robust.

Check status of remote job by looking into the logfile.

Report on the status of the job and extracts the performance in ns/d if
available (which is saved in :attr:`Manager.performance`).

:Arguments:
  - *dirname*
  - *logfilename* can be a shell glob pattern [md*.log]
  - *silent* = True/False; True suppresses log.info messages

:Returns: ``True`` is job is done, ``False`` if still running
          ``None`` if no log file found to look at

.. Note:: Also returns ``False`` if the connection failed.

.. Warning:: This is an important but somewhat  **fragile** method. It
             needs to be improved to be more robust.

Check status of remote job by looking into the logfile.

Report on the status of the job and extracts the performance in ns/d if
available (which is saved in :attr:`Manager.performance`).

:Arguments:
  - *dirname*
  - *logfilename* can be a shell glob pattern [md*.log]
  - *silent* = True/False; True suppresses log.info messages

:Returns: ``True`` is job is done, ``False`` if still running
          ``None`` if no log file found to look at

.. Note:: Also returns ``False`` if the connection failed.

.. Warning:: This is an important but somewhat  **fragile** method. It
             needs to be improved to be more robust.

Calculate how many dependent (chained) jobs are required.

Uses *performance* in ns/d (gathered from :meth:`get_status`) and job max
*walltime* (in hours) from the class unless provided as keywords.

   n = ceil(runtime/(performance*0.99*walltime)

:Keywords:
   *runtime*
       length of run in ns
   *performance*
       ns/d with the given setup
   *walltime*
       maximum run length of the script (using 99% of it), in h

:Returns: *n*  or 1 if walltime is unlimited

Wait until the job associated with *dirname* is done.

Super-primitive, uses a simple while ... sleep for *seconds* delay

:Arguments:
  *dirname*
      look for log files under the remote dir corresponding to *dirname*
  *seconds*
      delay in *seconds* during re-polling

Set up position restraints run and transfer to host.

*kwargs* are passed to :func:`gromacs.setup.MD_restrained`

Set up production and transfer to host.

:Arguments:

• *jobnumber*: 1,2 ...
• *struct* is the starting structure (default from POSRES run but that is just a guess);
• kwargs are passed to :func:`gromacs.setup.MD`

log_RE

Regular expression used by :meth:`Manager.get_status` to parse the logfile from :program:`mdrun`.

Value:

re.compile(r'(?x)Run\stime\sexceeded\s+(?P<exceeded>.*)\s+hours,\swill \sterminate\sthe\srun|Performance:\s*(?P<performance>[\s\d\.]+)\n|(?P< completed>Finished\smdrun\son\snode)')