WebMO

Legacy documentation This page describes a service provided by a retired ACENET system. Most ACENET services are currently provided by national systems, for which please visit https://docs.computecanada.ca.

Introduction

WebMO is a web-based interface for computational chemistry packages which features automatic input generation, in browser molecule building (or you can import a molecule from many file formats), easy job submission and much more. When a job completes you can visualize the data in your browser, and download the results to your computer. Currently we have support for NWChem, GAMESS, Q-Chem and Gaussian.

To gain access to Gaussian through WebMO you must visit the page of that package and follow the instructions to get added to the group with permissions to use it. In addition to this, to use the Gaussian WebMO interface you must sign up for NQS (follow instructions on that page).

If you want to use NWChem through WebMO, then currently only an older version of NWChem 5.1 is available, which requires users to accept the NWChem license, thus please follow the instructions on the NWChem page to get added to the group with permission to use NWChem 5.1. More recent versions of NWChem, which are distributed under an open source license, cannot be accessed via the WebMO interface.

You can find WebMO for ACENET at https://webmo.ace-net.ca

Applying for a WebMO account

• Apply for an ACENET Account
• Please contact support asking to be added to the WebMO group

If you have been asked to use WebMO for class purposes your instructor may register your entire class at once, in which case you don't need to contact support separately. Follow the instructions your instructor provides and you will be sent a group password via email. Class instructors, please see the Roster registration for WebMO and NQS page.

• After you receive your group password:
  • Go to the ACENET WebMO site
  • Sign in with your ACENET credentials
  • Enter the group password when prompted [One time only]
• You can now submit jobs using the WebMO interface

User guide

New Users to WebMO

Any users new to using the WebMO interface should read their very useful User Guide, and after read the changes ACENET made as it will affect your WebMO experience.

If you wish to use the Gaussian or NWChem interfaces of Webmo please visit the pages of those packages and follow the instructions to get added to the unix group required to use those packages. Otherwise you will not have an option to use either of these interfaces. In addition, to use the Gaussian webmo interface you must sign up for no quota scratch.

ACENET Changes and Warnings

There are a number of changes that had to be made to get WebMO to work with ACENET's systems and to adhere to our policies

• There are two new values to the job submission screen: h_rt and h_vmem. Please refer to ACENET's User Guide to learn why.
• The jobs are run and the input and output stored in your scratch space /home/${USER}/scratch/webmo.
• Some intermediate files associated with each job are stored in the webmo scratch space, /home/webmo/scratch/UserName.
• The files in /home/webmo/scratch/UserName will have to be cleaned occasionally.
  • Periodically as /home/webmo/scratch/ begins to fill up, files older than 4 months may be removed at the discretion of the technical staff.
  • When this happens the affected jobs will vanish from the WebMO graphical interface.
  • Files in /home/${USER}/scratch/webmo will be unaffected.
• The files in /home/webmo/scratch/ are visible to all users within the webmo group. Therefore, it is not recommended that you use WebMO if you have sensitive data. Instead, ssh to the ACENET machines and use command-line tools for job preparation and submission.
• Sometimes there is a disk writing delay and you will not be able to see your output right away. Just wait a few minutes and you will be able to see it soon. This causes some jobs to appear failed for a short time, but this status will clear promptly.

Known Issues

Jobs are "failing" immediately

Jobs within WebMO are being erroneously marked as Failed although they are actually running. Once a job finishes, it's status will change from Failed to Complete.
Please check your job status with the qstat command after logging on to placentia.ace-net.ca via SSH (see the User Guide). Once the WebMO job no longer shows up in the output of qstat, it can be actually considered as failed.
Looking at the "Raw Output" file from the allegedly Failed job (in the Actions column of the Job Manager table) can also reveal either reveal an error message - in which case the job would be actually failed - or if the output looks normal and after reloading more output is being appended, the job is still running.

Q-Chem no longer supported

We were not able to integrate our Q-Chem 3.x version with WebMO 17. Q-Chem will therefore not be available as a backend for WebMO until further notice.

Supported Browsers

With the upgrade to WebMO 17, the Java browser-plugin is no longer required as the molecule viewer and -builder are based on HTML5. It should be possible to use WebMO with any modern web browser (e.g. Google Chrome, Firefox, Safari, Microsoft Edge).

Importing z-matrices generated by Molden: Z-matrices that are created using Molden and saved as Gaussian input files give the error

GaussianFormat not recognized

when imported into WebMO. This is due to Molden adding a space in the otherwise blank line between the molecule specification and variable definition parts of the z-matrix. To see this space, open the file using a text editor and ask it to show the hidden characters. In vi, this is done with

set list

Remove the space, then try to import the molecule into WebMO.

If you know of any additional issues with WebMO please email support.

Upcoming WebMO features for ACENET

• Email notification for completed/failed jobs.