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Monitor Panel |
The Monitor panel can be used to manage and monitor the progress of any Schrödinger computational job.
To open the Monitor panel, you can:
Choose Applications → Monitor Jobs in the main window.
Choose Tasks → Monitor Jobs in the main window.
Click the Monitor button in the job status window, which you open from the Job toolbar in an application panel.
Double-click a table row in the job status window.
Click the Jobs button in the status bar of the main window.
Click the job status icon in any workflow panel that has this icon.
The Monitor panel can be opened automatically when you start a job, by setting a preference to do so in the Jobs - Monitoring tab of the Preferences panel.
The Monitor panel is used for showing information on jobs, monitoring the progress of jobs, and managing jobs.
Only one job can be monitored at any given time. To monitor a job, double-click it in the table in the Jobs tab. The table row is colored blue, and the File tab is placed on top, so you can see the log file.
Monitoring a job is necessary for the job to be incorporated under the following circumstances:
Most jobs write information to a log file as the job progresses. This file is copied back periodically to the job submission directory, and is available to the Monitor panel. Some jobs copy back other files periodically, and these files can also be monitored. Some jobs (notably Jaguar and MacroModel) do structural monitoring, and the current structure is displayed in the Workspace as a scratch entry, and is updated while the job is being monitored.
When a job from the current project that is being monitored finishes, the results are automatically incorporated into the project using the settings that were active when the job was started. Once incorporation is complete the newly incorporated entries are selected in the project and the first of these is included in the Workspace. The job can then be removed from the list of jobs with the Delete button on the monitor panel.
The Monitor panel has a jobs table and two tabs. Below the table is a set of action buttons that can be applied to jobs.
The jobs table lists jobs started by the current user, using a tree format. The job information is taken from the job database for the user. This information is updated periodically.
To monitor a job, select the table row and click Monitor, or double-click the table row. The table row is highlighted in blue,and the File tab is placed on top with the log file displayed.
You can select multiple rows in the table with the usual shift-click and control-click actions, or you can select all rows by using the shortcut menu. If you select multiple rows, the Details and File tabs and the Monitor button are unavailable. You can apply an action to the selected jobs with the other action buttons. The actions are also available from the shortcut menu. You can also show and hide subjobs, using the "turner" in the parent job row.
You can sort the table rows by clicking in the heading of the column whose values you want to sort by. Subjobs are kept under the parent job during sorting, so the top-level jobs are sorted by the column values, then for each job, the subjobs are sorted.
The table cells have tooltips, which are displayed when you pause the pointer over the cell. The tooltips display the full content of the cell, except for the Status column, where an informative message describing the meaning of the status is displayed, and the Host column, where the host entry name from the hosts file is displayed.
| Job ID | ID by which the job is identified to Job Control. Jobs that have subjobs are displayed with a + or − symbol to the left of the ID. The + symbol indicates that the list is hidden; the − symbol indicates that the list is displayed. To display or undisplay the list, click the symbol. Subjob IDs are indented relative to the parent job ID. | |
| Name | Name of the job. The job name can be specified on the Job toolbar or in the Job Settings dialog box when you start a job from Maestro, or on the command line. Subjob job names are indented relative to the parent job name. | |
| Status | Job status. The status for subjobs is indented relative to the parent job status. See Job Status Descriptors below for information on the content of this column. | |
| Errs | Number of errors logged for this job. These errors are not necessarily fatal errors. Most of them are for tasks initiated by Job Control. You can view details of the errors by selecting the job record in the Details tab and viewing it in the File tab. | |
| Start Time | Time at which the job was started | |
| Host | Host to which the job was submitted or on which the job is running. This is the actual host name, such as the name of the machine or cluster node, not the name of the host entry in the hosts file. The host entry name is available in the tooltip for this cell and in the job summary (shown in the Details tab). | |
| Application | Name of the application being run (e.g. MacroModel). | |
| Project | Name of the project to which the job belongs. |
This menu allows you to choose the class of jobs that is displayed in the table. There are three options:
These buttons perform actions on the table or table rows. The buttons are spread over two rows in the panel.
Update the status of all running jobs.
Incorporate all jobs for the current project that are waiting for incorporation. This includes jobs whose incorporation method was set to Workspace. For these jobs, display of the structure in the Workspace is suppressed.
Clean up the job database. This action removes records for the
incorporated jobs and completed jobs that cannot be incorporated. The command
that is executed is $SCHRODINGER/jobcontrol -delete all.
Set preferences for job monitoring. Opens the Preferences panel at the Jobs – Monitoring tab.
Monitors the currently selected job. Switches to the File tab and by default displays the log file for the job. If the job includes structural monitoring the generated structures will be displayed in the Workspace.
Suspend the selected jobs. The jobs are not stopped, but they will take no CPU time and make no progress on the calculation.
Resume progress on the selected jobs, after they have been paused.
Stop the selected jobs at the next convenient stopping point. This point is defined by the application and allows a clean shutdown of the job, with return of the results up to the stopping point. This action is only available for some applications (MacroModel, Jaguar, Desmond). Some time may elapse before the job finally stops.
Force termination of the selected jobs as soon as possible. Subjobs are killed by the parent job to ensure a clean job termination. Note that it may not be possible to successfully incorporate the output from a killed job into the project.
[MacroModel conformational searches only] Instructs the program to print
the current results and write all the currently found structures to the
.out file. This button has no effect on any other type of job.
Delete the selected job from the job database and delete the associated files. If you delete a job that has subjobs, the subjobs are also deleted. When you click Delete, a dialog box is displayed with two options for cleaning up the job:
Create a postmortem report on each of the selected jobs. Opens the Create Postmortem dialog box in which you can choose options for information to go into the report (archive), and create reports for the jobs.
This tab shows details of the selected job. The job information is repeated in the Job Summary text area. The Files table lists all files associated with the job except for the structure files. When you select a file in the table, the file is displayed in the File tab. If you double-click a file, the File tab is displayed with the selected file. By default, the log file is selected. Gray rows in the table mark files that are not available for viewing.
The job record for the job is the last file in the list. This file shows details of the progress of the job and is useful for diagnosing errors.
The File tab displays the file that is selected in the Details tab. By default, this file is the log file for the job. The display is updated at regular intervals. When new text is added, the display scrolls to show any new text if the display is already at the end of the file. If the display is not at the end of the file when text is added, the display remains at the same location in the file, and you must scroll down to the end of the file to see the new text.
The status of a job can be one of the following descriptors:
| launched | Job submitted and a JobId assigned | |
| submitted | Job waiting to start on a batch queue | |
| started | Environment for job is being set up | |
| running | Job running | |
| paused | Job temporarily suspended | |
| exited | Job terminated and being cleaned up | |
| completed | Job terminated and cleaned up. Followed by the exit status (see below) | |
| incorporated | job output incorporated into Maestro project. Followed by the exit status (see below) | |
| stranded | job could not be reached by job control | |
| unreachable | machine running the job could not be reached by job control |
When the job status is completed or incorporated, it is followed by a colon and the exit status. The possible exit status values are:
| finished | Job finished successfully | |
| fizzled | Job failed before the program could be run | |
| stopped | Job stopped gracefully at user's request | |
| killed | Job was killed by a kill request | |
| died | Job failed during program execution |
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