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Release Notes

ECCE Version 1.3 Release Notes

The intent of this document is to provide information specific to the Version 1.3 release of ECCE. This includes a description of all known significant errors with workarounds, if any. A brief description of new features and significant bug fixes is followed by information about any patches applied since the initial release of V1.3. For issues not pertaining to a specific version of ECCE please check this document and the ECCE FAQ before contacting ecce-support@emsl.pnl.gov.

Known bugs in V1.3

  1. If you submit a job to mpp1 and it takes longer than 24 hours to start running, ecce will consider the job to have failed due to a timeout.
  2. Changes to values in Job Launcher text entry fields may not be used for a launch under certain circumstances.
  3. Geometries not parsed for Gaussian-94 molecules without Standard orientation.
  4. Gaussian-94 MP4 and MP5 generated input files not correct.
  5. Drag from builder can cause the builder to die.

What's new or fixed in V1.3?

  1. ECCE is now decoupled from the EMSL environment.
  2. Communication to compute servers such as for launching jobs and file transfer now uses the Secure Shell package (ssh/scp) and the standard UNIX rsh/rcp.
  3. Mulliken charges are now displayed as a color spectrum on the atoms.
  4. Gaussian 94 is supported on the mpp.
  5. The Molecular Orbital algorithm has been re-implemented.
  6. The database selection dialog has been replaced.
  7. The builder now supports 10 coordinate atoms.
  8. Performance of importing large molecules is vastly improved.
  9. The builder now has an Undo option which allows you to undo up to 10 operations.
  10. The restriction to only launch jobs on the local machine as the current user has been removed.
  11. Communication to compute servers for launching jobs is now more reliable and consistent.
  12. Local machine passwords are no longer required because of the removal of rexec for remote communications.
  13. Local and remote job launches are now handled analgously.
  14. The Manage Files dialog no longer erroneously duplicates listing entries.
  15. The meaning of "scratch" and "calculation" directories in the launcher have been changed.
  16. Problems running a calculation after using the "Reset for Restart" menu item have been fixed.
  17. Less overhead to the oc_client and oc_server process that collect data from running jobs.
  18. Additional properties are now parsed for NWChem runs.
  19. NWChem IRIntensity values for DFT Vibrational runs are converted into km/mol units.
  20. The list of properties displayed in the Calculation Browser has been limited.
  21. Limited the number of properties that can be displayed in the Visual Clipboard by the Calculation Browser.
  22. When selecting a DFT Orbital basis set, ecce now grabs only the charge fitting set by default.
  23. Startup time for the Calculation Editor has been significantly reduced.
  24. To use old databases they must have their schema migrated.
  25. To run gaussian in parrallel on the mpp, you must have a proper .rhosts file on the compute machine.
  26. Several changes have been made in the Calculation Editor so that the default values appearing in the Calculation Editor menus match those listed in the current NWChem documentation.
  27. Only selected instances of certain properties are returned from the server to be stored in the database.
  28. Speed of transferring files from server to client at the end of a calculation is improved.
  29. The log files for the oc_client and oc_server programs are now removed by default if there are no errors.
  30. Job priority in Job Launcher has changed wording and is now handled properly.

Known Problems

  1. If you submit a job to mpp1 and it takes longer than 24 hours to start running, ecce will consider the job to have failed due to a timeout.
  2. Changes to values in Job Launcher text entry fields may not be used for a launch under certain circumstances. If the time limit, priority reduction, or number of nodes on a parallel machine is changed and then the launch button is immediately hit the new value may not be used for the launch even though it is shown in the interface. This happens when the mouse pointer is moved outside the typein field before the new value is entered and then the new value is typed in. This is actually a bug with all numeric text entry fields in ecce. However in other instances the value change will be recognized when the user performs another operation in the interface that forces input focus from the numeric field. With the Launcher the immediate action of doing a launch never causes focus to leave the last numeric field changed so the change isn't recognized.
  3. For any Gaussian-94 calculations, ecce will not parse geometry steps if they are not put into the output file in Standard orientation. This will happen in certain cases such as symmetric tops and atomic systems where only the Input orientation is output by Gaussian. For the same reasons, these calculations cannot currently be imported. If you encounter a case like this, please contact ecce-support@emsl for assistance with importing the results.
  4. Gaussian-94 MP4 and MP5 generated input files not correct.
    Gaussian-94 input files generated by ecce have the keywords Density Pop=(NOAB) in order to get the orbital occupations for displaying MOs. However, this causes the following error:
    5. Post-SCF densities or gradients only with
    Real MP2, MP3, MP4SDQ, CI, CCD, and QCI.
    The work-around is to use Final Edit in the Calculation Editor to modify the kewords to read: Density=HF Pop=(NOAB). If you do this, be aware that the orbitals are the HF orbitals and not the MP orbitals.
  5. Drag from builder can cause the builder to die.
    There is a bug that can corrupt memory and result in the builder exiting when you drag a molecule out of the builder. This will be fixed in V1.4. To avoid the problem, start the builder in the context of a calculation and use the File/Save menu item rather than using the drag functionality.

What's new or fixed in V1.3?

  1. ECCE is now decoupled from the EMSL environment and is able to be ftp'ed to other sites.
  2. Communication to compute servers such as for launching jobs and file transfer now uses the Secure Shell package (ssh/scp) and the standard UNIX rsh/rcp. The selection of which remote shell program to use is done on a machine-by-machine basis using the regmachine administration script. The use of rsh/rcp is only recommended for those platforms that don't support ssh or inside networks protected by firewalls where rsh/rcp usage meets local security requirements. The EMSL IBM SP2, NWMPP1, will now only support ssh for remote communication.
  3. Mulliken charges are now displayed as a color spectrum on the atoms. This allows you to see where the charges are accumulating. Mulliken shell charges are also available if provided by the computational code. NWChem provides them but Gaussian does not.
  4. Gaussian 94 is supported on the mpp. In addition, you can run it with multiple nodes on any multi-node system. If you are going to use Gaussian94 on the mpp, you must have a correct .rhosts file.
  5. The Molecular Orbital algorithm has been re-implemented. Theresa Windus can provide more info about this. Glyphs are not available since they are still implemented using the old algorithm.
  6. The database selection dialog has been replaced. Implemented file system selection capability into the database selection dialog so that the various database levels could be traversed.
  7. The builder now supports 10 coordinate atoms.
  8. Performance of importing large molecules is vastly improved. You can new read in a 5000-10,000atom system in 10-30 seconds. This is useful mainly for making color hardcopies or gif images.
  9. The builder now has an Undo option which allows you to undo up to 10 operations.
  10. The restriction to only launch jobs on the local machine as the current user has been removed. In order to launch as a different user on the same machine ssh or rsh must be available and configured.
  11. Communication to compute servers for launching jobs is now more reliable and consistent. Previous problems with random failures during the validation before jobs were actually submitted have been resolved due to a more robust design of the remote communications.
  12. Local machine passwords are no longer required because of the removal of rexec for remote communications. Further if used by the site, DCE authentication is automatically handled through ssh password authentication.
  13. Local and remote job launches are now handled analgously so that the calculation directory is no longer the same directory as the UNIX project tree directory for local launches.
  14. The Manage Files dialog no longer erroneously duplicates listing entries as it used to under a few circumstances.
  15. The meaning of "scratch" and "calculation" directories in the launcher have been changed and are certainly less confusing. The scratch directory is taken as is and turned over to the code you are running. For NWChem that means the scratch_dir keyword. For Gaussian94 it is the GAUSS_SCRDIR. The calculation directory is still a path prefix. However the final path will be much shorter than before. What gets appended now is "/Ecce/<dbname>/<calculation manager path>. This guarantees a unique run directory.
  16. Problems running a calculation after using the "Reset for Restart" menu item have been fixed.
  17. There is significantly less overhead to the oc_client and oc_server process that collect data from running jobs. This is primarily due to the fact that ecce now has the capability to grab selected instances of a property from the output file. The greatest impact is from the fact that ecce now only grabs the first and last MO set rather than grabbing the MOs from every step.
  18. Additional properties are now parsed for NWChem runs and available for viewing in the Calculation Browser and/or the Calculation Viewer. The additional properties availalbe include scalar energy values (e.g. Correlation, Coulomb, Exchange), mulliken shell charges, and alpha/beta MO's.
  19. NWChem IRIntensity values for DFT Vibrational runs are converted into km/mol units to match Gaussian output displayed in ECCE.
  20. The list of properties displayed in the Calculation Browser has been limited to include only those that are either a scalar or that can be displayed in the Visual Clipboard.
  21. Limited the number of properties that can be displayed in the Visual Clipboard by the Calculation Browser to avoid application crashes due to graphics memory limitations.
  22. When selecting a DFT Orbital basis set, ecce now grabs only the charge fitting set by default. You may still specify that the exchange fitting set in the Basis Set Tool but it is no longer the default behavior.
  23. Startup time for the Calculation Editor has been significantly reduced.
  24. Databases created with previous versions are incompatable with the current version of ecce. To use old databases, created with previous versions, they must have their schema migrated. Databases are migrated by an ecce developer upon request by an ecce user.
  25. To run gaussian in parrallel on the mpp, you must have a proper .rhosts file on the compute machine.
  26. Several changes have been made in the Calculation Editor so that the default values appearing in the Calculation Editor menus match those listed in the current NWChem documentation. If the default values are selected, ECCE does not include any directive in the NWChem input file it creates, so NWChem uses its own defaults. Thus, calculations run prior to these changes using the ECCE defaults have actually been run with the NWChem defaults. For those cases where there is a difference, the ECCE values are incorrect, and the calculations have actually used the defaults used in the NWChem users manual. Specific changes are listed below.

    SCF: The default values for Level Shift Size and New Level Shift After have been changed to 20.0 and 0.5 to match the defaults in the NWChem directive LEVEL PCG.

    DFT: The default value of the Gradient convergence threshold has been changed to 5.e-4, and the default Damping Percentage has been set 70. The Atomic Grid Cutoff has been set to 12 and the Coulomb Screening Tolerance has been set to 1.e-10.

    The Gradient field in the SCF convergence window is grayed out when the convergence algorithm is set to Iterative SCF. For this algorithm, the gradients are irrelevant. The energy and density convergence options have been enabled for the DFT calculations.

    MP2: The default number of iterations in the SCF calculation has been set to 20.

    CC: The default number of iterations in the SCF calculation has been set to 20. The Delta Energy options now writes out the NWChem directive in the correct format if a non-default value is used.

    For both the CC and MP2 calculations, the correct frozen core and virtual core defaults are now calculated whenever the reset button is hit.

    STEPPER: The correct default value of 1.e-4 for the Gradient convergence is used. This will change to 8.e-4 (the same as for DRIVER) when the next release of NWChem becomes available and both DRIVER and STEPPER will be using the same convergence criteria (at present they are slightly different).
  27. Only selected instances of certain properties (e.g., the first and last molecular orbital vectors) are returned from the server to be stored in the database. Formerly, all instances were returned.

  28. Speed of transferring files from server to client at the end of a calculation is improved.
  29. The log files for the oc_client and oc_server programs are now removed by default if there are no errors.
  30. Job priority in Job Launcher has changed wording and is now handled properly. Previously all jobs submitted to workstations were invoked with the "nice" command using the value specified in the Job Priority field. This automatically lowered the priority and thus increased the time it took to complete the job. The field has now been renamed "Priority Reduction" to imply that setting the value can only result in less CPU time being given. Further it is now possible to leave the field empty (the default) meaning that the job will be run at normal priority (the top priority possible) without being "niced." It was not valid to leave this field empty in previous versions of the Launcher so that unfavorably adjusting the priority was unavoidable.