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To Generate Conformers in a Background Process

 You can generate conformers either interactively or as a background task. The advantages of running conformer generation as a background process are that you can run Catalyst interactively on the same machine, although somewhat more slowly, and also you can schedule long running jobs for times when the host machine is not required for an interactive session. For information about background processes, choose from the following topics:

To Set Up a Conformer Generation Background Process

 You can set up conformer generation to run on your local machine, or on another machine on the network for which you have an appropriate software license. If you select more than one compound on the shelf before you select the Generate Conformational Model command, Catalyst generates conformers for each selected compound.

If you want the background job to run now on your current machine:

  1. Select Run As Background Process on the Generate Conformational Model dialog box.

  2. Complete the Generate Conformational Model dialog box and then select the Generate button.

    If you want to specify a specific host or time for the background job to run, set up parameters for the job as follows:

  1. In the Generate Conformational Model dialog box, select the Run as Background Process button, and then select the Job Options button. The Job Options dialog box is displayed with several default parameters. (If a warning dialog box tells you that there might not be enough tokens, see "When You Set Up a Background Process" under "What Happens if There Are Not Enough Tokens?")

    The Job Options dialog box allows you to choose whether to run the background process on your own machine or a different one on the network, to specify a directory to store the generated data in, and to set the time at which the background process is to start. The default values are displayed.

  2. Fill in the text boxes as follows:

    Process Name. Catalyst displays a unique default name for the process, but you can change it. Left-click in the text box to make it active, press the Back Space and Delete keys to remove unwanted characters, and type in your name for the background process.

    Local Directory. Catalyst creates a new subdirectory of your current directory and gives it the name in this text box. If you select Remotely on, Catalyst also creates a subdirectory for the specified Remote Directory and gives it the same name. Catalyst places all the files necessary for running the background process and then stores the results in the local directory on the host machine. Change the name if you want a different designation.

    Start Time . You can specify a time for the process to begin either by entering a starting time or selecting a process name in the Queue After scroll list. To specify a start time, enter the value as a time, optionally followed by a date.

    Format for start time. You can give the time either as an hour or as an hour and minutes. Give just the hour as a one- or two-digit number. Give the time in hours and minutes as a four-digit number. You can also separate the hours and minutes by a colon, using as many digits as needed. You can optionally add am or pm following the time. If you do not do so, the time is assumed to be in 24-hour clock time. You can also give the time as now, noon, or midnight.

    Format for date. The date is optional. If you do not give it, Catalyst interprets the date to be the next time the specified time occurs. The date can be any month and day combination, a day of the week, today, or tomorrow. Both the month and the day of the week can be spelled out in full, or given as a three-letter abbreviation. The month and day are not case sensitive; that is, you can type either upper- or lowercase characters when you specify months and days.

    Queue After. To schedule a background process to run after a previously scheduled background job has finished, select it by clicking on its name in the Queue After scroll list. If you do not select a process name in the Queue After list, Catalyst will run the job at the time you specify in the Start Time text box. The Queue After scroll list shows each job that has been scheduled to start at a particular time and which has no job scheduled to run after it. It does not list scheduled jobs that already have jobs scheduled to follow them. You can use the scroll bar to see scheduled jobs that are not visible. To set the correct scheduling, the correct process must be selected and highlighted in the Queue After list when you left-click on the OK button at the end of the setup process. (When a task is properly selected to queue after another job, any time entered in the Start Time text box is ignored.) To deselect a selected process in the Queue After list, click on the blank space at the end of the scroll list.

    Locally. To run the background process on your machine, select Locally. This is the default.

    Remotely on. If you want the background process to run on another machine on your network (and have an additional Catalyst license for it), select Remotely on. Running on a remote host requires that you have access permission to the remote machine and that the Catalyst software has been installed or is available via NFS (Network File System) on that machine.

    Remote Host. If you select Remotely on, enter the name of the remote host machine in this text box by selecting from the scroll list or by typing.

    Remote Directory. If you select Remotely on, enter the name of the directory for Catalyst to create on the remote host (if you want it to be different from the default). Catalyst places all the files necessary for running the background process and storing the results in this directory.

  3. Select OK to complete the background setup procedure. The Job Options dialog box disappears.

  4. Complete the Generate Conformational Model dialog box and then select the Generate button.

What Happens When Catalyst Sets Up to Run a Background Process

 When you elect to generate conformers in the background, selecting Generate causes Catalyst to gray out and display the cursor as a clock symbol to indicate that it is preparing the system for the background process. Catalyst creates a local directory on the host machine and places in it the files necessary to run the job. When the preparation is finished, an Alert message informs you that everything is ready for the background process. If there is a problem in setting up the task, Alert messages describe what is wrong.

Select the Acknowledged button to dismiss the alert box. At the specified time, the background process starts automatically. If you specify now as the start time, the background process begins within a minute or so (depending on system load) on the appropriate machine. See "When a Background Process Starts" under "What Happens if There Are Not Enough Tokens?" for additional information.

Quitting Catalyst When a Background Process Is Scheduled or Running

After setting up a background process, you can exit Catalyst and even log off your machine. That is, terminating your Catalyst session or logging out does not terminate the background process, nor does the background process require you to be logged on or to have an active Catalyst session for it to run as scheduled.

If you are generating conformers, you can retrieve the results of the conformer generation process as long as your current Stockroom contains the compounds for which the conformers were generated. This means that after you set up the background process, you must save your StockroomDB (which contains the molecules for which conformers are being generated).

For more information, select a topic:

Monitoring Background Processes and Retrieving the Generated Results

 When the background generation process has finished, you must retrieve the data to bring the generated conformers into your Catalyst session. When the background process has finished and you have retrieved the results and saved your StockroomDB, or if the process could not finish successfully and it "died," you should clean up the files associated with it. Catalyst also has facilities for viewing the progress of the background process, and you can cancel a running process.

For more information, select from the list on the following page.

To View the Status and Log File of a Background Process

 To view the status of a background process, do the following:

  1. Select the Process Information command from the Data menu in the Stockroom or any lab to open the Process Control dialog box. It displays a list of all background processes that are scheduled, have started, are waiting for a token to become available, have finished, have failed, have had their data collected and brought into Catalyst, and which have not yet had their files cleaned up (deleted). The list includes the unique name for each process, its status, its type, and the name of the remote host, if the process was to run remotely. The status of a process can be one of the following:

    You can view the log file for any process after it has started. The log file gives information about the progress of the process.

  2. To see the log file for a particular process, click on the name of the process in the Process Control dialog box so that the name is selected and highlighted.

  3. Select the Show Process Log button to open a window displaying a snapshot of the log file for the background process. The log file records a commentary on the progress of the background process. When the process has completed successfully, Done! is the last entry in the log file. If the process is still running, select the Show Process Log button again for an updated log file.

  4. To print a copy of the log file, type in the name of the printer, and then select the Print button. If you want a printed copy, you must do this before you select Clean Process Data, which removes all of the files from the directory.

To Collect the Results of a Background Process

 When you run a background process to generate conformers, you must retrieve the results in order to view them or use them in Catalyst. To collect the results of a background process, do the following:

  1. In the lab in which you have your compounds and want to keep the results, select the Process Information command from the Data menu.

    The Process Control dialog box is displayed.

  2. In the dialog box, left-click on the name of the process whose results you want to collect.

  3. Select the Collect Process Data button. If the process was for conformer generation, Catalyst retrieves the conformers and automatically saves them with the appropriate molecule in the current session.

If the current Catalyst session does not contain the compound for which the conformers were generated, a dialog box appears warning you that the compound does not exist. If you have previously exported this molecule, you can import it and try collecting the process data again.

If you have already retrieved process data, Catalyst displays a box advising you that it has been collected. It also prompts you to select the Collect Process Data button if you want to retrieve the data for conformer generation again. You might want to collect data more than once if, for example, you collected it in a previous session, and then did not save the StockroomDB before exiting Catalyst.

After collecting and saving the results of a background process, you should clean up the files that were created for the process with the Clean Process Data command, as described in "To Remove the Files Associated with a Background Process." For more information on using conformers or hypotheses, select from

To Cancel a Running Process

 You can cancel a background process that is currently running as follows:

  1. Select the Process Information command from the Data menu in the Stockroom to open the Process Control dialog box.

  2. In the dialog box, left-click on the name of the process that you want to cancel, so that it is selected and highlighted.

  3. Select the Cancel Running Process button. You can cancel a queued, registered, or running process. A dialog box warns you that the process will be terminated.

  4. Select Yes in the dialog box to proceed with the cancellation. Catalyst cancels the job and updates the Process Control dialog box to show the status of the process as DIED. You will still need to clean up process data to remove the files associated with it, as described in "To Remove the Files Associated with a Background Process.

To Remove the Files Associated with a Background Process

 When you set up a background process, Catalyst creates new directories and files to hold the results of the background process. To free up disk space use the Clean Process Data button to delete all files and their associated directories created by a background process, both locally and on any remote machines, for the following cases:

  1. Select the Process Information command from the Data menu in the Stockroom to open the Process Control dialog box.

  2. In the dialog box, left-click on the name of the process that you want to clean up so that it is selected and highlighted.

  3. Select the Clean Process Data button. Catalyst removes both the directories and files associated with the selected background process. When the cleanup is finished, the name of the selected process disappears from the Process Control dialog box.


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Last updated April 16, 1996 at 12:04pm PDT.
Copyright © 1999, Molecular Simulations Inc. All rights reserved.