This tool allows you to organize and manipulate calculations in Ecce. By invoking other tools from the Calculation Manager, you can plan, submit, and monitor a large number of calculations, as well as examine and manipulate the results.
The Calculation Manager window depicts calculations within projects, much as the Microsoft Windows Explorer depicts files within folders on a personal computer. A project is a container that may include calculations and other projects. A calculation represents a single computational run (including restarts).
The Calculation Manager window is split into three panes. The left pane displays the project tree. The right pane or project workspace lists the contents of the current project (the project selected in the project tree). The bottom pane or message area displays information about current operations.
Selecting a calculation in the Calculation Manager provides a means to manipulate the parameters and results of that calculation. When the Calculation Manager is opened and displays the last-used project area, the project tree automatically scrolls the project into view in the tree.
Names of projects displayed above the message area show the name of the data server in URL format rather than just the path to the calculation.
Click on the Calculation Manager icon in the Ecce Gateway. If the Calculation Manager is already running, this will bring its window to the front. To start a separate instance of the Calculation Manager in a separate window, shift-click on the icon.
The following items briefly describe elements of the Calculation Manager window.
The Calculation Manager's optional toolbar provides one-click editing and movement around the project tree. To show/hide the toolbar, use the Option menu's Show Toolbar option.
|Copy the currently selected calculation or project|
|Paste a copied calculation or project into the currently selected folder|
|Delete the currently selected calculation or project|
Interrupt the current Copy/Paste/Delete/Navigation operation--helpful if the server hangs or if you change your mind during a long operation such as copying a large project hierarchy. The stop sign icon turns red when one of these server operations is under way. Otherwise the Interrupt button is inactive (grayed out).
|Project Tree Navigation Buttons|
|Find project or calculation name(s) that contains a specified case-sensitive string of characters (same as the Find option on the Calculation menu). This prototype searching capability can be slow when performed over many projects and calculations. To cancel a Find operation, use the Interrupt button.|
|Back to the previously selected project--helpful when you switch between projects that are widely separated in the project tree|
|Up one level in the project tree from the currently selected folder|
|Forward to a previously selected project (after using the Back button)|
The project tree (left pane) of the Calculation Manager window shows a hierarchy of folders that represent projects or collections of projects. You always have access to projects stored in the "share" folder or in your own folder, which is located within the "user" folder. Access to other project folders may require additional authentication.
A single calculation can be moved by dragging it to a destination project folder in the tree view. The Calculation Manager supports copy-and-paste or drag-and-drop operations across data servers or authentication realms. This is useful to move data from one server to another (for sites using multiple data servers) or to copy data to the share area for others to view.
The project workspace (right pane) of the window lists the contents of the folder selected in the project tree. To show the contents of a project folder, click on the project name or folder icon in the project treeor double-click on the project name or icon in the right pane.
When the selected project contains calculations, the workspace lists each calculation by name in a table of calculation properties with other descriptors such as the "Creation Date" and the "Application" (computational code).
|How to...||Manage Projects and Calculations|
Icons in the workspace indicate the "Type" of item and some other calculation properties.
|Descriptor||Icons||What the Icons Mean|
|Type||Project folder for containing calculations and subprojects|
|Ecce calculation (not associated with an application)|
|State|| Calculation run state icons indicate (by their shape and color)
the preparation or processing state of Ecce calculations--such as "created"
or "running" or "completed."
|Reviewed||Check mark in the Reviewed column indicates that the calculation has been reviewed in the Calculation Viewer.|
|Check mark for these properties indicates that an annotation or citation has been created for the calculation.|
You can customize the appearance of the workspace to suit your purpose:
|How to...||Display Calculation Properties|
|Customize the Calculation Manager Display|
|Tip: Open any menu from the keyboard by using the Alt+underlined letter combination (for example, Alt+h opens the Help menu). Then select a menu option by pressing the letter that corresponds to the option.|
The Calculation menu enables you to create, import, and delete calculations as well as create and delete projects.
|New Calculation||Create a new calculation within the currently selected project. If no project is selected, this option will appear disabled on the menu.|
|New Project||Create a new project folder for containing calculations or other new subprojects. The new project appears as a folder in the current project workspace.|
|Import Calculation||Import a previously run calculation that was generated outside of the Ecce user interface.|
|Delete||Delete the selected project or calculation (and all associated files and directories) from the project tree and workspace.|
|Find||Find project or calculation name(s) that contains a specified case-sensitive string of characters. This prototype searching capability can be slow when performed over many projects and calculations. To cancel a Find operation, use the Interrupt button.|
|Quit||Close the Calculation Manager window.
The Edit menu enables you to perform various cut and paste operations on the item currently selected in the project workspace of the Calculation Manager window.
|Duplicate|| Make a duplicate of a project or calculation and place it at the same
level in the project tree as the original item. The Duplicate operation
reproduces the input files of calculations but NOT the output files of any
finished calculations: if a project contains finished calculations, the
duplicated project will contain similar calculations that are ready to run.
|Duplicate Setup with Last Geometry|| Duplicate the inputs of a completed geometry optimization calculation
(as above), but use the chemical system geometry from the final step of
the selected calculation.
|Copy||Copy a project or calculation into the cut/paste buffer for pasting into another project.|
|Paste||Insert a copied item into the currently selected project.|
|Annotation...||Bring up the UNIX default editor in order to enter/edit/view text in a special file that is associated with a given project or calculation. This Annotation option is the only way to access this information. The only way to remove an annotation is to delete all annotation text.|
|Citation...||Bring up the UNIX default editor in order to enter/edit/view a literature citation that is associated with the selected item. The only way to remove a citation is to delete all citation text.|
|Preferences...||Open the Preferences window for customizing the appearance and operation of the Calculation Manager. Options include the selection and order of calculation properties displayed and the formats for date and time. Use the Access Control tab to selectively grant read or read-write access to other users for project data you own. By default only the owner of the data has read-write access. The access permissions you set remain in effect until you change them.|
The menu includes items for controlling how the tree hierarchy is sorted along with some display and operating options previously found within the Calculation Manager's Preferences window. Click on a toggle button to turn the option on or off .
|Change Access Control...||
Open the Access Control dialog window to specify which Ecce users may have access to the contents of your project folders. You may grant access only to project folders that you have created. This window contains two fields for entering user names to grant access to the project folder that is currently open and displayed in the Calculation Manager: one field for "read-only" access and one field for "read/write" access.
To grant access to all Ecce users, enter the keyword ALL instead of specific user names. To deny access to a project, just leave the fields blank.
|Sort Tree by>||Sort the project tree by Name, Name (in reverse), Date, Date (in reverse), None (no sort order).|
|Confirm Deletes||Mark this option to see a confirmation dialog each time you delete projects or calculations.|
|Confirm Resets||Mark this option to see a confirmation dialog each time you reset a calculation.|
|Show Toolbar||Mark this option to show the Calculation Manager's option tool bar of
editing and navigation buttons--including an Interrupt button for
interrupting server operations that are unexpectedly long.
|Show Run State Legend||Mark this option to show the legend of calculation run state icons across
the middle of the Calculation Manager:
|Use Fixed "Type" and "Name" Columns||Mark this option to maintain the Type and Name columns at a fixed position on the left side of the properties table in the Calculation Manager.|
The Run Management menu provides options for monitoring or halting the progress of a running calculation, resetting a calculation for a modifed run, and cleaning up files created by the calculation.
|tail -f on Output File...||Open an xterm window that shows the contents of the output file for the selected calculation so that you can monitor its progress in real time as it runs. The output file scrolls in the window as the calculation runs.|
|shell in Calculation Run Directory...||Open an xterm window into the scratch directory (on the machine that is running the calculation) where Ecce stores temporary files during processing. With the proper knowledge of UNIX and the computational code, you can monitor what is happening.|
|Manage Files...||Opens a window which shows a list of the files on either the Ecce data server or the compute server. You can View or Remove files at either location, or Copy specific files from the compute server to the Ecce data server.|
|Terminate Calculation||Kill a submitted or running calculation--or abort a calculation import in progress. Ecce may take half a minute to confirm that the job is terminated and display the killed (coffin) icon for that calculation.|
|Check Job Monitoring||Check whether job monitoring has failed for any calculations in the currently displayed folder. This detects errors that could not be caught by the monitoring process and reports them in the message area. Use this option if calculations seem to be hung in the submitted or running states.|
|Reconnect Job Monitoring||Re-establish the job monitoring process for a submitted or running calculation so that information displayed in the Calculation Manager is updated correctly. Use this option when job monitoring terminates before your calculation completes, which is usually indicated by the Monitor Error icon for the calculation.|
|Reset to Rerun||Reset the selected calculation to the "ready" state and delete any data associated with previous runs, including all output properties and files on the run machine.|
|Reset for Restart||Reset the selected calculation to the "ready" state so that
it can be restarted from Ecce. (Only the Ecce calculation state is changed.
No chemical system properties or output files are deleted, and the input
file remains the same.) After selecting "Reset for Restart"
and before launching the calculation again, you must manually edit
the calculation input file, specifying whatever "restart" keyword
and supporting inputs are necessary for the current code.)
|Reset State>||Set the selected calculation to one of these run states:
Mark as Reviewed
|Manually specify a selected calculation as either "reviewed"
or "unreviewed" in the Calculation Viewer. Any calculation that
has been opened and reviewed in the Calculation Viewer is automatically
marked as reviewed.
|Cleanup Run Directory Files||Remove both the calculation and scratch directories from the machine where
the selected calculation was run.
|View Run Log...||Open a window that shows a log of messages generated by the system during the calculation processing--sometimes a useful tool for "debugging" a run. Run logs are in XML (extended markup language) format.|
The Tools menu provides access to a variety of tools that can operate on calculations.
|Builder...||Start the chemical system Builder tool using the chemical system from the currently selected calculation. (Or if the chemical system is not yet specified for the calculation, use the Builder to create or choose a chemical system.)|
|Calculation Editor... >||Start the default Calculation Editor tool for editing inputs to the currently
selected calculation--or open a specific Calculation Editor from a submenu
of computational code options:
If the calculation IS aready associated with a different code, Ecce first prompts to confirm whether to change the code for the calculation. Calculations that are in a read-only state (such as submitted, running, or completed calculations) are not switchable between computational codes.
|Basis Set Tool...||
Start the Basis Set tool for assistance in specifying a basis set for the currently selected calculation.
|Job Launcher...||Start the Job Launcher tool for submitting a ready calculation to a computer for processing.|
|Calculation Viewer...||Start the Calculation Viewer tool for the currently selected calculation. This tool summarizes all information for a calculation and can display graphic visualizations of such things as the chemical system, molecular orbitals, or a set of vibrational normal modes.|
|View Input File...||View the contents of the input file for the currently selected calculation.|
|View Output File...||View the contents of the output file for the currently selected (and completed) calculation.|
|Help on this tool||Show online help information for this tool or window.|
|Support|| Display a form for providing support requests to your onsite Ecce representative
or adminstrator about problems, questions, or other comments.
Each calculation within a project in the Calculation Manager can be marked by a small colored icon that indicates the state of the calculation by the icon color and shape. The legend shows the icons associated with each of the nine possible calculation run states. You can hide the legend by opening the Options menu and unmarking Show Run State Legend.
The nine calculation states are defined as follows:
|Created||Calculation is in preparation and has been saved on Ecce's data server.|
|Ready||Calculation is defined and ready for submission to a machine.|
|Submitted||Calculation has been submitted for processing on a machine.|
|Running||Calculation is currently being processed on the designated machine.|
|Completed||Processing is complete.|
|Imported||Calculation results were imported from an external source such as the code output results of a calculation processed outside of Ecce.|
|Killed||Processing has been canceled (coffin icon).
See also ... Terminate Calculation in the Run Mgmt menu.
|Incomplete||Processing did not complete successfully.|
|Monitor Error||Calculation monitoring has failed or encountered errors after 25 attempts to restart and continue monitoring. When a calculation has this state, open the Run Mgmt menu and use View Run Log to identify the problem by scanning for an error at the end of the run log.|
|System Error||Job has failed during monitoring due to the current status of the machine (such as a machine being taken off the network for maintenance).|
The colors shown here are the Ecce default colors. You can modify these run state colors for your own use by using the Preferences option from the Ecce Gateway.
|How to...||Set Color Preferences|
At the bottom of the window is a footer that displays the following status information:
|More about...||Items in the Ecce Window Footer.|
|Ecce Online Help
Revised: May 5, 2004