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WebMO

Table of Contents

Introduction

WebMO is a Web-frontend for computational Chemistry. It allows users for  editing of input data, visualization of results of the computations, and running/managing batch jobs in an unified way for several Computational Chemistry codes (Gaussian, GAMESS-US, PSI4, VASP, Quantum Espresso etc.). WebMO also allows for some degree of project organization by keeping a database of "archives" containing results of completed jobs, and for some portability between systems (for example, Westgrid and AceNET) as these "archives" can be downloaded from and uploaded to different WebMO installations.

Restrictions / License Information

Westgrid had purchased a single, academic WebMO Enterprise license for the Grex cluster. Access to WebMO on Grex is open for all the academic ComputeCanada users. The access to individual computational interfaces (such as Gaussian and VASP) that are available to be used with WebMO is subject to the usual Westgrid software policies. That is, to be able to run Gaussian or VASP jobs from WebMO portal, users would have to be eligible, and to apply for access to these codes just like if them were using the codes in a stand-alone, manual submission batch mode.

Running Instructions

These are not really "Running Instructions" as WebMO is not a separate code but a Web-service. Rather, how to run Computational Chemistry jobs from within the WebMO portal.

The address of WebMO on Grex is https://grexapps.westgrid.ca/webmo/cgi-bin/login.cgi ; no special registration is required, users' Westgrid login and password has to be used to log in. Presently the following interfaces are available and fully functional:

    • Gaussian (Gaussian 09 E.01) (note that Gaussian on Grex was updated from D.01!)
    • PSI (PSI4 beta 5)
    • NWChem (NWchem 6.6)

Usage of the WebMO is described here: http://www.webmo.net/tour/index.html . Note that WebMO on Grex was modified to integrate it with our TORQUE batch queuing system. For the available interfaces, we recommend to set proper values for maximum wall-time (in hh:mm:ss format) and maximim memory (in Megabytes, only the integer value without specifying the units) the jobs would require. These values are to be set in the "Advanced" tab of the JobManager's "Job Options" dialog. Unlike some other systems (most importantly, AceNET) on Grex, the "Node properties" field of this dialog must be left blank. When importing job archives from the other systems, the options in the "Advanced" tab have to be doublechecked as they might inherit the values/formats from the other system that might make job submission fail.

Computational jobs submitted from WebMO on Grex obey the same limits and access rules as the regular TORQUE jobs. For instance, Gaussian jobs can have walltime limits up to 21 day, and all other jobs up to 7 days; Gaussian and VASP calculations are available only to the members of wg-gauss and wg-vasp5 groups (even though the corresponding interfaces are visible for all the users, jobs submitted by non-members of these groups would not execute). The best practices as described by corresponding Computational Chemistry software pages (for example, recommended memory limits and numbers of CPUs per job) also for the most part apply for the jobs with these interfaces submitted by WebMO.

UPDATE: The recent Java update on the client side, to JRE 8u31 created a problem with loading WebMO browser applet. The problem is that Java fails to confirm validity of the SSL certificate for https://grexapps.westgrid.ca and fails to load the Editor applet.To work around it, either Java should be rolled back to pre-8u31 version, or, for the new Java, OCSP certificate relocation check should be disabled. For more information contact support@westgrid.ca

UPDATE1: The above update might not be actual anymore with the recent WebMO 16 as installed on Grex in Dec. 2015.

System Grex
Version 16.0