CCP4i: Graphical User Interface
	Running a Job

Run Modes

Running Jobs Remotely/Later/In Batch

How Jobs are Run

Run Modes

Jobs can be run from the Run menubutton at the bottom of task interfaces or from the ReRun Job interface. There are three modes of running a job:

Run Now

the task is run 'in background' - you can continue using the interface while the job is running and can exit the interface without interrupting the job.

Run & View Com File

displays the command line and command file for the CCP4 program. You can edit the command file. This could be useful if you want to use an option not included in the Interface (but please let us know if there is something useful missing).

Run Remote/Batch/Later

options to run a script on a remote machine (using the Unix system rsh command) and/or to start at a later time (using the system at command). And, if this is supported by your local system, to submit the job to a batch queue. See Running Jobs Remotely/Later/In Batch.

Running Jobs Remotely/Later/In Batch

Selecting this mode will bring up a window with a menu option to select whether to run the job remotely, or later, or submit to batch. Not all of these options will necessarily appear - it depends on your local setup which is defined in the file $CCP4I_top/etc/resources.def and can be edited using the Configure Interface option at the bottom of the menu on the right hand side of the Main Window.

The job is run remotely using the rsh command - this will only work for Unix machines on the same network which can see the same file system.

Delayed jobs are run using the at command and the time input should be in a format suitable for at. A subset of suitable formats is:

now

run the job now

now + n units

where n is an integer and units is: minutes, hours or days.

HH:MM

run the job at the time in hours and minutes of a 24-hour clock.

HH:MM Day

where Day is the full name of a day of the week.

HH:MM Month Day

where Month is a three-letter abbreviation of the month and Day is a number.

The status of the job reported in the Job List will be:

ON_HOLD

for jobs not yet started on the local machine.

RUNNING

once job is started.

REMOTE

for jobs waiting to run or running on a remote machine or in batch.

Note that the usual mechanism by which jobs report their status to the main Interface, does not work across machines. To overcome this, the Interface will periodically check on the contents of the log file and if the usual termination statement is not present, it will assume the task is still runnning. This means there may be a short delay (less than a minute) before the termination is reported. Another possibility to consider if a job appears to have taken a very long time is that the script running on the remote machine has failed but the termination may not be written to the log.

The View Files from Job option to View Log File will list a log file being generated on a remote machine.

How Jobs are Run

You do NOT NEED to know what follows but you may be interested or it may help in figuring out any problems.

A run script called (project_name)_(job_number)_(task_name).run (e.g. insulin_32_refmac.run), which runs the CCP4 programs, is created in the TEMPORARY directory. This file is written in the Tcl/Tk scripting language and is put together from three components:

• the parameters from the task interface
• a script appropriate for each task, which is copied from $CCP4I_top/scripts/taskname.script
• header and termination script, added to control communication with the main Interface program and to ensure a clean termination of the run script

This script is run as an independent process - it uses the Tk send command to send updates on progress back to the main interface.
N.B. The installation of the Tcl/Tk must be correct for this to work (see Installation notes). The progress is recorded in the status column in the Job List.

As the task runs, the output is listed to a log file (project_name)_(job_number)_(task_name).log
(i.e. same root name but different file extension to the run file). The output from all the programs run will be concatenated into this file. For some tasks there may also be some extra output from the run script.

The run file could potentially be run external to the Interface with either of the commands:

ccp4i -r[un] run_file [-debug]

ccp4ish run_file

The only obvious differences between these are:

• the ccp4i -r version will update the job status (i.e. STARTED/FINISHED) in the Job List window, but the ccp4ish will not.
• the ccp4i -debug option will give stack listings for the errors which cause the ERROR status.

To run each individual CCP4 program, the script creates a temporary file which contains the command input. This is put in a file rather than simply streamed to the program, because of limitations running on VMS. If you are running the Run&View Com File mode, the script will pause here to display the com file and the run command line. You can edit either of these before continuing.

To run the job on a remote machine or in batch, the Interface creates a short .com file in the TEMPORARY directory. This will have the name of the run script with an extra extension .com. The com file contains the following:

setup_ccp4
/y/programs/ccp4i/bin/ccp4ish $SCRATCH/test_1_refmac.run

The first line is the command to setup CCP4 and the second line is the full path name of the CCP4i program and the name of the run file. This com file will not work if the path name for either the CCP4i directory or the TEMPORARY directory are different on the remote machine.