ECCE Version 1.4.1 Release Notes

The intent of this page is to provide information specific to Version 1.4.1 of ECCE. If you are not familiar with the ECCE V1.4 Release Notes please start there because it is a larger scale release.

Release Notes for Previous Versions

What's new? Known bugs What's fixed?

What's new?

Support for NQE machines.
Telnet/ftp remote launches.
Globus remote launches.
Selection of remote communications shell.
Gaussian 98 has been registered.
Property (trajectory) import formats.
Property import format EcceImport0.1.
Property import format EcceImport0.2.
Calculation Viewer Improvements.
The Calculation Manager Edit menu has several new menu items.
New Visual Cues in Calculation Manager.
Open Remote Shell...button on Configure Machine window.
Scratch directory fields no longer have drop-down lists.
For advanced users there is a new environment variable ECCE_ALLOW_ANY_FS.
Manage Files dialog does remote to local file transfers.
(Site Administration) ECCE directory tree has been restructured for non-AFS file system support and simplified installation.
(Site Administration) Installation and configuration are now automated with scripts.

Known bugs

See also the ECCE V1.4 Release Notes for V1.4.1 bugs.

Failed Gaussian 94 geometry optimizations in Calculation Viewer.
Gaussian calculation import problems.
Cartesian vs. spherical coordinates for Gaussian calculations.
ECCE from a PC using Exceed3D

What's fixed?

Gaussian 94 registration fixes.
Changes to .cshrc/.mycshrc for compute servers.
ECCE job submission scripts have been revamped.
Importing of Gaussian output files.
Gaussian ECP basis set coefficients no longer zero.
Drag and drop in the Calculation Manager.
Duplicate option in the Calculation Manager now copies the input file.
Chemical System display in the Calculation Viewer.
Launches no longer interruptable after submission.
The "progress/interrupt" dialog.
Reset for restart run status recognition.

What's new? Top

ECCE now supports launching of jobs to NQE/NQS machines. This has been tested under a variety of NQE/NQS configurations including mulliken, mcurie.nersc.gov, and t3e.osc.edu. For NQE/NQS machines that are configured to select the queue based on the requested number of nodes and specified time limit, the Job Launcher will not show all queues. Instead it will display the maximum number of nodes any queue supports and the maximum time limit any queue supports.

In order to properly support NQE/NQS, the Job Launcher interface now includes a field for setting memory limits. It also displays and validates the maximum wall time.

Telnet in conjunction with ftp, has been integrated into ECCE for job launches. Use of telnet is only recommended when ssh is not available because ssh offers much better security. However, telnet is preferred over rsh because it does do password authentication instead of relying solely on .rhosts files. When telnet is specified as the remote shell in the Machine Configuration dialog, ftp is automatically used for file transfer. It is also possible to use ftp in conjunction with remote shells such as ssh (the remote shell is listed as ssh/ftp in the Machine Configuration dialog.) This is useful when the regular remote copy command (scp in this example) is not working for some reason. Again, ftp is not as secure as scp and is not the preferred file transfer command. The use of telnet requires potential changes to your .login environment files for those machines launching ECCE jobs via telnet on. A telnet session initiated from ECCE cannot have any interactive prompts such as for the type of display, window manager, etc. Suppressing prompts is done by conditionalizing the code in .login to only be executed when the $TERM environment variable is not set to either "ecce_telnet" or "ECCE_TELNET". Both lower and upper case comparisons are necessary due to machines changing the case of an environment variable values regardless of how they are originally set. The .login changes will have no impact on regular interactive telnet sessions you start outside of ECCE. An EMSL machine .login file that has been modified for launching ECCE jobs using telnet would look like this dependent on the commands within the outer if statement:
```
if ($TERM != 'ecce_telnet' && $TERM != 'ECCE_TELNET') then
  source /msrc/share/setup/v3.0/login

  # Setup X environment
  source $EMSL_DEFAULTS/Xsetup
endif
```

Globus has been integrated into ECCE for job launches. Globus, out of Argonne National Laboratory, supports LoadLeveler with and without the Maui Scheduler, NQE and NQS queueing systems at this time. Because of the extra administration necessary to setup Globus users for remote authentication it is only recommended that those familiar with Globus attempt launches with it. For a compute server configured to use Globus all remote communications to that machine occur via the globusrun command including the Manage Files window, opening remote shells, file transfer, etc. Thus if a machine only supports Globus and not ssh, rsh, or telnet then ECCE will still be functional. At this time there are no queuing systems that ECCE does not support without the benefit of Globus. The installation, administration, and configuration of Globus are the responsibility of the party wishing to use it with ECCE. For more information on the Globus project, see http://www.globus.org.

The Configure Machine window now allows you to select the remote communications shell to use when more than one is available. The possible shells are rsh, ssh, ssh/ftp, telnet, and Globus dependent upon which are supported by the machine. Changing the remote shell to Globus grays out the login name field because it is only possible to launch as a different user by changing the globusmap authentication file on the target machine. The label on the password field also changes to pass phrase to reflect that authentication is not done using regular login passwords. The Job Launcher's main window also has a remote shell option menu allowing the configured remote shell to be overridden for an individual launch.

For machines where Gaussian 98 is installed and working (does not work under Solaris 2.5.1 and not installed on mpp1) it is supported through ECCE. Other than a couple minor issues it is registered identically to Gaussian 94. If you find differences in how input files should be generated within ECCE between Gaussian 94 and Gaussian 98 please send mail to ecce-support@emsl.pnl.gov

The calculation import dialog (in the Calculation Manager) now supports two new property (including trajectory) import formats - EcceImport0.1 and EcceImport0.2. As you can see by the version numbers, this is very preliminary work and should be regarded as prototype functionality. Formats for these files are described in detail in the following release notes. Note that the EcceImport0.1 format is the same as the EcceImport format in the 1.4 release of ECCE.

EcceImport formats provide an input option for users with molecule structure files having multiple conformations or configurations. This is typical of molecular dynamics trajectories. Each configuration frame can be visualized in the Calculation Viewer in a way similar to geometry optimizations from NWChem or Gaussian Electronic Structure codes. Current formats have limited input options for properties which correlate with configuration. Extensions can be added upon user request. Requests for things already supported in ECCE (e.g., normal modes, Mulliken charge, and molecular orbitals) can be defined and added quickly. Properties involving statistical analyses could be added if there is enough interest.

The import functionality has been tested with molecular systems larger than normally handled by ECCE. For example, 100 configurations of 800 atoms for up to 400 configurations. Performance of ECCE with 100 configurations is reasonable, yet, load times get to be rather long with 400 configurations. The larger the total number of atoms (#atoms * #configurations), the longer it will take to load and render when you "open" the Geometry Trace window.

Files for import have relatively simple format requirements. Each configuration consists of a block of data in XYZ format enclosed in curly braces preceded with the keyword 'Geometry'. XYZ format begins with the number of atoms followed by the molecule name on the next line. Each subsequent line starts with an atom symbol followed by the X, Y, and Z coordinates for the atom. In general, you do not have to be cautious about white space but we have not performed extensive testing on this issue. Case DOES matter! Be sure to spell the keywords properly as there is no validity checking of the data. Atoms can be superimposed or have nonsensical bond lengths.

For import format EcceImport0.1 only one keyword is available, Geometry. Each block of XYZ data must be enclosed in:

Geometry {
}

Here is a sample file of three ethane geometries:

Geometry {
8
Ethane
C   -0.537090    0.148330   -0.000410
C    0.965490    0.079930    0.000250
H   -0.900450    1.054480   -0.502500
H   -0.979670   -0.711650   -0.519840
H   -0.942390    0.156680    1.019810
H    1.409980    0.944880    0.509490
H    1.329880   -0.820590    0.511890
H    1.370610    0.061380   -1.019850
}

Geometry {
8
Ethane
C   -1.537090    0.148330   -0.000410
C    0.965490    0.079930    0.000250
H   -0.900450    1.054480   -0.502500
H   -0.979670   -0.711650   -0.519840
H   -0.942390    0.156680    1.019810
H    1.409980    0.944880    0.509490
H    0.329880   -0.820590    0.511890
}

Geometry {
8
Ethane
C   -0.537090    0.148330   -0.000410
C    0.965490    0.079930    0.000250
H   -0.900450    1.054480   -0.502500
H   -0.979670   -0.711650   -0.519840
H   -0.942390    0.156680    1.019810
H    1.409980    0.944880    0.509490
H    2.329880   -0.820590    0.511890
}

Import format EcceImport0.2 recognizes several scalar properties which vary with geometry step in a molecular dynamics simulation. These keywords include:

Time
TotalEnergy
Kinetic Energy
Potential Energy
Temperature
Pressure

EcceImport

End

EcceImport



Time 1
TotalEnergy   -74.998
Geometry {
8
Ethane
C   -0.537090    0.148330   -0.000410
C    0.965490    0.079930    0.000250
H   -0.900450    1.054480   -0.502500
H   -0.979670   -0.711650   -0.519840
H   -0.942390    0.156680    1.019810
H    1.409980    0.944880    0.509490
H    1.329880   -0.820590    0.511890
H    1.370610    0.061380   -1.019850
}



Time 2
TotalEnergy   -74.875
Geometry {
8
Ethane
C   -1.537090    0.148330   -0.000410
C    0.965490    0.079930    0.000250
H   -0.900450    1.054480   -0.502500
H   -0.979670   -0.711650   -0.519840
H   -0.942390    0.156680    1.019810
H    1.409980    0.944880    0.509490
H    0.329880   -0.820590    0.511890
         }



Time 3
TotalEnergy   -74.869
Geometry {
8
Ethane
C   -0.537090    0.148330   -0.000410
C    0.965490    0.079930    0.000250
H   -0.900450    1.054480   -0.502500
H   -0.979670   -0.711650   -0.519840
H   -0.942390    0.156680    1.019810
H    1.409980    0.944880    0.509490
H    2.329880   -0.820590    0.511890
}



End

The Calculation Viewer has new functionality added in several places. The geometry trace interface now has a button labeled "XYZ..." that allows you to look at the coordinates of the current step. The normal modes interface has several new features and has improved functionality.

A "Swap Sign of Displacement" toggle allows you to change the direction of the displacement when displaying normal modes as vectors or animations. As the name implies, the normal mode displacement is either added or subtracted from the atomic coordinates. The effect is to change the vector direction or the initial animation direction.
The scale factor in the slide bar above the graphics window of the viewer has been changed to be the value by which the normal mode displacement is multiplied. The initial value is set to unity. Once adjusted, you may need to click on the slide bar background to return the value to 1.0. Alternatively, displaying another property, such as the Chemical System, then redisplaying the normal modes, resets the slide bar to unity.
An "Actual Displacement" option for the animation display forces all animation steps in the same direction. This allows you to produce geometries along a vibration mode displaced by a specific number of steps. A drag box has been added so you can capture the displaced geometry for a new calculation. This may be useful when applied to an imaginary frequency obtained during geometry minimization. By stopping the animation at a displaced geometry, you can start a new geometry optimization from the distorted structure, which may actually converge to a minimum energy structure.

The Calculation Manager Edit menu has several new menu items :

  Reset to Rerun
  Reset to Completed
  Reset to Failed

The Calculation Manager has two new visual cues displayed as icons next to the run state icon: one to indicate which calculations have annotations or citations and one to indicate which completed calculations have not yet been reviewed. Under the View menu item, there are toggles to control whether or not either or both of these will be displayed. By default, they are off so the icons will not be displayed regardless of whether annotations/citations exist and the reviewed state. These settings are saved as user preferences.

If you turn on the toggle "Annotation/Citation Icons", an icon with a text symbol will be displayed with each calculation that has either an annotation or citation. Note that to delete an annotation or citation, edit it and delete all the text.
If you turn on the toggle "Processed Icons", an icon will be displayed with each calculation that has not yet been "processed." Initially the definition of "processed" means that it has been reviewed in the Calculation Viewer. Under the Calculation menu in the Calculation Manager there are menu items to manually mark or unmark a calculation as processed. All calculations that have been run with previous releases of ECCE will be initially considered "unprocessed."

Below the login name and password fields on the Configure Machine window there is now a button labeled "Open Remote Shell..." This lets you create an xterm shell on that machine for determining appropriate calculation and scratch directories. It can be used immediately after entering the login name and password before saving the configuration. With the remote xterm you can use a "df -k" command to see what disks are available and have free space. Then you may want to cd to some of those disks checking write permissions or creating directories for your calculation and scratch directories.

The scratch directory input fields in the Configure Machine and Job Launcher windows are now regular text entry fields similiar to the calculation directory fields. The drop-down lists, or combo boxes were discarded because of the difficulty in determining and maintaining reasonable choices for scratch directories by ECCE administrators. Note that a scratch directory is not required. Leaving this field empty results in the calculation directory being used for scratch files if necessary. The new "Open Remote Shell..." button on the Configure Machine window also helps address this issue.

For advanced users there is a new environment variable ECCE_ALLOW_ANY_FS. If you set this before invoking ECCE, the Job Launcher will no longer prevent you from running jobs in NFS. Despite the name, it still prevents the use of AFS and DFS. This capability is being provided primarily because of problems with piofs on mpp1. The drawback to using NFS with ECCE jobs is that the job monitoring may not provide file update notifications in a timely manner or at all. The results are two-fold:

The calculation may finish long before ECCE captures and stores the data.
ECCE may time-out waiting for data and set the state to "failed." The timeout period is currently 1 hour.

The Manage Files dialog available from the Run Mgmt menu in the Calculation Manager has a new function button. When viewing the remote calculation directory a "Copy to Local" button is enabled. Selecting one or more files from the list and selecting this button copies the files from the calculation directory to the local directory. The main purpose of this feature is to provide a convenient way for the user to transfer output files back when the automatic copy fails as has been known to happen.

The ECCE release directory tree has been restructured so multiple platforms may be installed on any file system under a single client directory. Previously directories had to be modified by hand when installing multiple platforms using NFS. Only a single client installation is now required, eliminating local ECCE installations on each client host. Servers still require local installations. If configuration files need to be modified by hand, all files that may need to be edited have been moved to a central directory: $ECCE_HOME/siteconfig.

Instead of hand extracting and editing multiple files, the entire installation process has been automated as much as possible with three scripts: install_ecce, install_ecce_server, and config_ecce. Information that is not provided on the command line by these scripts is prompted for interactively. The "-h" option gives the usage of each script.

Known bugs Top

Failed geometry optimizations using Gaussian 94 may give some strange looking results when viewed in the Calculation Viewer. In particular, the configurations that appear when looking at the Mulliken population analysis, geometry trace, or dipole moment may be significantly different from the geometry that appears when the tool is first brought up. The problem occurs because Gaussian 94 puts out an extra geometry relative to the number of energies. This is not ordinarily a problem, since the last two geometries for a calculation that exits normally are the same, but it can create problems if the geometry optimization fails. This is particularly true if the last geometry in the optimization is significantly different from the previous geometry. So far, this only appears noticeable for semi-empirical calculations.

Import functionality is not always successful at correctly identifying the theory and runtype for Gaussian 94 and Gaussian 98 output files. If this occurs the Calculation Viewer will not display the correct total energy. There may be other problems related to the improper identification of theories and runtypes. These problems are also exhibited in previous ECCE releases.

When importing a Gaussian output file that has no basis functions of d or higher, the Gaussian output file indicates that there are 5 d functions and 7 f functions, like a spherical calculation. This happens even if the cartesian radio button in the Basis Set Tool has been selected before running the calculation. If the calculation is run and its output file is then imported, the radio button for spherical coordinates will be shown as selected reflecting that Gaussian has picked up the 5 d functions and 7 f functions characteristic of a spherical calculation. This produces an inconsistency where the radio button in the Basis Set Tool for cartesian coordinates is selected in a calculation ran using ECCE but in an imported calculation the radio button for spherical coordinates is selected. (NOTE: For calculations with only s and p functions spherical and cartesian coordinates are the same so having the spherical or cartesian coordinate radio buttons selected makes no difference.)

If you run ECCE from a PC using Exceed3D, you will not be able to generate images at your desktop. We have tested versions 6.0 and 6.1 and neither of them work. If you need access to a Unix box to generate the images, the machines in the Visualization labe can be used. Send account requests to mscf-consulting@emsl.

What's fixed? Top

Gaussian 94 vibration calculations have been completely registered and the vibration and geometry optimization plus vibration runtypes should run correctly. The availability of analytic and numerical first and second derivatives should be correctly reflected in the details menu and the results should be correct when viewed in the Calculation Viewer.

Problems in the Calculation Viewer that appear for CCD and CISD theories for geometry optimization runtypes have been corrected. For these theories, too many energy points were appearing for each geometry step.

You no longer need to source ECCE's runtime_setup script from your .cshrc or .mycshrc file for machines that you only launch to and do not run ECCE applications, such as mpp1. However, you are now responsible for insuring that scp, secure copy, is in your $PATH for those machines you launch to where ssh is used as the remote communications shell including mpp1. The path to scp for EMSL users is /msrc/apps/bin.

ECCE job submission scripts have been revamped. This was mainly done to allow for more customization. The main benefit to existing users is that the name of the script reflects the calculation name (submit__calcname>) so that any e-mail notification messages sent by Maui/LoadLeveler are uniquely identified. Previously all scripts were named "submit".

In addition, the submit script now appends a few lines of ecce Job Launching information to the end of the output file. This information can be useful in trying to figure out why a calculation was considered "failed" or "unconverged". In addition, on mpp1, a few lines of "refund" information is appended to the output file. Send all requests for refunds to mscf-consulting@emsl.

Scripts for importing Gaussian output files into ECCE are working again. A modified data structure for enabling the use of exchange fitting, charge fitting, and dft fitting basis sets caused the importing of Gaussian output files to work improperly. This error was found and corrected for V1.4.1. However, the import does not identify the basis set name for standard basis sets. All imported basis sets come in with the generic name ecce.gbs.

ECCE was allowing ECP basis set coefficients with a value of zero to be written into Gaussian input files. This was due to our basis set library being stored in NWChem format and converted to Gaussian format when an input file is generated. Some NWChem functions have zero values for coefficients as a place holder with the corresponding exponent being applied to another coefficient. These coefficients are now discarded for Gaussian input file generation.

Drag and Drop in the Calculation Manager (CTRL- Middle Mouse Button) now copies the entire calculation or project (including output properties and files). This mechanism can be used to merge the work of several people into one database or simply to reorganize your own work across multiple databases.

The Duplicate option in the Calculation Manager now copies the input file in addition to the calculation setup. This is useful if you have used Final Edit to customize the input file and want to rerun the calculation without losing your edits. As long as you don't make further changes to the calculation, the input file will not be regenerated.

The Chemical System display in the Calculation Viewer shows the last step for optimizations or the starting geometry if there are no steps. While this has always been the case, in previous versions, the display did not update automatically when an optimization was running. Now it will refresh with the new last step.

In V1.4 it was possible to abort a launch by hitting the stop sign icon in the Job Launcher and have the launch be aborted after submission, but before the "oc_client" has started. The oc_client stores properties parsed from the output file into the database. Thus aborting a launch after the calculation has been submitted but before the oc_client has started means the job still runs but that no results will be shown. This is no longer possible because it is very unlikely the user would intentionally want this to occur.

When importing calculations, the "progress/interrupt" dialog was occasionally not refreshed or not dismissed. This problem has been fixed.

Previously a queued job that was restarted would immediately go into the running state according to the run state legend even though it was actually still waiting in the queue. In order to fix this the previous output file is renamed with ".old" for an extension. If there are multiple restarts then each output file is appended to the same ".old" file.

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