Technology Report pubs.acs.org/jchemeduc
Web-Based Job Submission Interface for the GAMESS Computational Chemistry Program M. J. Perri* and S. H. Weber Department of Chemistry, Sonoma State University, Rohnert Park, California 94928, United States S Supporting Information *
ABSTRACT: A Web site is described that facilitates use of the free computational chemistry software: General Atomic and Molecular Electronic Structure System (GAMESS). Its goal is to provide an opportunity for undergraduate students to perform computational chemistry experiments without the need to purchase expensive software.
KEYWORDS: Upper-Division Undergraduate, Physical Chemistry, Computer-Based Learning, Internet/Web-Based Learning, Computational Chemistry
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possess. Running jobs on the client’s computers works well for short calculations (on the order of minutes), but jobs involving complex molecules or high level basis sets can take hours to run and the student has to either place the “Do not touch” sign on a department computer, blocking access to others, or leave their computer on while running the calculation, oftentimes slowing it to a crawl. If a job running on a department computer crashes, then the student will not find out until the next day, causing loss of valuable time. Other available Web-based software include the following: WebMO,14 a Web-based interface for GAMESS or other computational programs, but the free version is limited to submissions on a single computer. The Molecule Calculator15 and WebMTA16 allow students to do calculations directly in a Web interface, but available computational methods and basis sets are limited to those provided by the authors. GAMESS supports a much larger range of basis sets, density functional theory, excited state calculations, transition state searches, and reaction path following at the expense of ease of use.
omputational Chemistry experiments are an important component of a well-rounded Chemistry curriculum,1−8 but are not always included in a department’s offering. Many suites of commercial software are available if the department can afford the cost. This approach is straightforward, but students are limited to using the software on the department’s computers. Some packages require additional cost to upgrade, leaving departments with outdated versions that lack the newest computational techniques. Free software packages, such as the General Atomic and Molecular Electronic Structure System9,10 (GAMESS), allow anyone with access to a personal computer to perform research quality calculations with the latest techniques. We have created a Web interface to facilitate students’ use of GAMESS and other free software for computational chemistry. The interface manages the most time-consuming and difficult part of computational chemistrythe calculation itself. Students create input files for a job on either their personal computer, a department’s, or library’s computer, and then submit this job to the Web interface. The Web interface assigns the job to compute nodes, computers with the GAMESS computational software installed. The compute nodes perform the calculations and the student can download the results from the Web interface when the calculation is finished. The Web interface displays the job’s progress while it is running, and if the calculation fails (which happens often), the interface displays troubleshooting tips based on the error experienced. Other software is currently available to aid students running computations. Free software is available to manage GAMESS and run jobs solely on the student’s or a department’s computer such as Facio,11 Gabedit,12 and Molden.13 GAMESS can also be run directly from the command line on the student’s computer, but this requires more computer knowledge than most students © XXXX American Chemical Society and Division of Chemical Education, Inc.
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WEB SITE SOFTWARE The Web site runs on a University-operated Web server (chemcompute.sonoma.edu) running Linux. The front end uses the Apache HTTP Server17 to serve the static pages. The job submission, job status parsing, and downloading of output files is handled using Bottle,18 a python Web framework. Python scripts are used to monitor for incoming files, to automatically submit jobs, and to monitor output files. Currently, the Web site is available for all to use, but due to the limited computing resources, it may be configured to
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dx.doi.org/10.1021/ed5004228 | J. Chem. Educ. XXXX, XXX, XXX−XXX
Journal of Chemical Education
Technology Report
students from using others’ results. The output file is a text file and can be visualized by a number of programs. In our laboratories, we use MacMolPlt, which is available for both Mac and Windows computers. This software is run on the student’s, departments, or library’s computers and enables visualization of molecular geometry, molecular orbitals, vibrational mode animations, calculated spectroscopic frequencies and reports the molecule’s total energy.
require a password. Please contact the corresponding author if you would like to use the Web site in your class.
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JOB SUBMISSION
Input File Creation
Students start by using a free software package, such as Avogadro19,20 or MacMolPlt,21 to draw a molecule and generate a GAMESS input file by choosing their run type, basis set, and other options. This first step is performed locally on the student’s or department’s computers. These packages are usable even on library computers because they do not require administrator privileges to install. The GAMESS input file is a small text file and contains all parameters and atomic coordinates for the computational job.
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USE IN PHYSICAL CHEMISTRY LAB The procedure outlined was used in our physical chemistry laboratory. Previously, we had used a single license commercial software package. This limited students to running on only one computer in groups of two or three. This situation led to a typical outcome: one dominant student took charge while others sat back and watched. A test run was conducted in our senior integrated lab. With the use of the free software and Web-based job submission, eight students worked individually over the course of three lab periods calculating various optimization energies and visualizing molecular orbitals for simple molecules (H2, H2O, and benzene). While working individually, students were more engaged with the experiment than past lab classes that were forced to work in groups. One student went on to use the Web site to run calculations on a compound for her research, and another student expressed a desire to augment other wet-chemistry experiments with theory.
Input File Submission and Hardware Description
The student then uploads the input file to the Web server which forwards the job to the master computational node. The master node runs the freely available Sun Grid Engine22 (SGE) batch queuing system which distributes jobs in parallel among any number of compute nodes. The user can specify how many processor cores they need for their job to run in a reasonable amount of time. The compute nodes can be any computer running Linux, from very powerful commercial rack servers to ordinary desktop computers. The compute nodes used are four inexpensive tower computers, each with one quad-core Xeon processor ($500 each). With this system, a typical student calculation takes less than 1 min using one node (e.g., geometry optimization of benzene using RHF 6-31G(d,p) requires a total of 38 s wall time on one node). Four such computers can easily handle an 18 student lab section, as each student tends to work at a different pace. One of the advantages of this system is that longer (hours-long) calculations can be set up at the end of a lab section or set up by students as a prelab exercise and the queuing software will handle all jobs submitted; the results will be available at the start of the next lab session, so that the students can spend the lab time visualizing the results and discussing them with the lab instructor. The system logs all jobs submitted, and the instructor can view these through the administrator access on the Web site if they desire to view what and when a job was run. The input files can be downloaded by the student after submission, so that they can easily rerun a job from any computer. Research students can submit jobs using the full power of the computing cluster when this particular lab is not being run. Many students prefer to work at night, and this system provides 24 h access to their jobs from home. The queuing software can be programmed to use all or part of each compute node’s computing power. If only part is used, the nodes can double as a department’s student computer lab, allowing students to perform word processing, spreadsheet, and Web browsing while jobs are running in the background. Finally, the system can be adapted to other Linux-based computationally intensive programs.
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ASSOCIATED CONTENT
S Supporting Information *
All HTML files and python scripts are attached as a tar file. This material is available via the Internet at http://pubs.acs.org.
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AUTHOR INFORMATION
Corresponding Author
*E-mail:
[email protected]. Notes
The authors declare no competing financial interest.
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ACKNOWLEDGMENTS This work was funded by Sonoma State University’s Research Scholarship and Creative Activities Program. REFERENCES
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Downloading Results and Visualization
When a job has completed, the student simply clicks a button on the Web page to download the output file. The Web site uses cookies to keep track of the last job submitted by the student. If a student will submit multiple jobs, they can write down their 6 digit job number to access their job status and output at any time. The job number is random to discourage B
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(7) Parnis, J. M.; Thompson, M. G. K. Modeling Stretching Modes of Common Organic Molecules with the Quantum Mechanical Harmonic OscillatorAn Undergraduate Vibrational Spectroscopy Laboratory Exercise. J. Chem. Educ. 2004, 81 (8), 1196−1198. (8) Ruddick, K. R.; Parrill, A. L.; Petersen, R. L. Introductory Molecular Orbital Theory: An Honors General Chemistry Computational Lab As Implemented Using Three-Dimensional Modeling Software. J. Chem. Educ. 2012, 89 (11), 1358−1363. (9) M.S.Gordon, M. W. S. Advances in Electronic Structure Theory: GAMESS a Decade Later. In Theory and Applications of Computational Chemistry: The First Forty Years; Dykstra, C. E., frenking, G., Kim, K. S., Scuseria, G. E., Eds.; Elsevier: Amsterdam, 2005; pp 1167−1189. (10) Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. General Atomic and Molecular Electronic Structure System. J. Comput. Chem. 1993, 14 (11), 1347−1363. (11) SuenagaM.Facio; Department of Chemistry, Graduate School of Sciences: Kyushu University, Japan, 2014. (12) Allouche, A.-R. GabeditA Graphical User Interface for Computational Chemistry Softwares. J. Comput. Chem. 2011, 32 (1), 174−182. (13) Schaftenaar, G.; Noordik, J. H. Molden: A Pre- And PostProcessing Program for Molecular and Electronic Structures. J. Comput.−Aided Mol. Des. 2000, 14 (2), 123−134. (14) Schmidt, J. R.; Polik, W. F. WebMO; WebMO LLC: Holland, MI, 2013. (15) Jensen, J. H.; Kromann, J. C. The Molecule Calculator: A Web Application for Fast Quantum Mechanics-Based Estimation of Molecular Properties. J. Chem. Educ. 2013, 90 (8), 1093−1095. (16) Kavathekar, R.; Khire, S.; Ganesh, V.; Rahalkar, A. P.; Gadre, S. R. WebMTA: A Web-Interface for ab Initio Geometry Optimization of Large Molecules Using Molecular Tailoring Approach. J. Comput. Chem. 2009, 30 (7), 1167−1173. (17) Apache Software Foundation. Apache HTTP Server; Apache Software Foundation: Forest Hill, MI, 2013. (18) Hellkamp, M. Bottle: Python Web Framework, 0.13-dev, 2013. (19) Avogadro: An Open-Source Molecular Builder and Visualization tool. Version 1.1.1. http://avogadro.openmolecules.net/. (20) Hanwell, M.; Curtis, D.; Lonie, D.; Vandermeersch, T.; Zurek, E.; Hutchison, G. Avogadro: An Advanced Semantic Chemical Editor, Visualization, And Analysis Platform. J. Cheminf. 2012, 4 (1), 17. (21) Bode, B. M.; Gordon, M. S. Macmolplt: A Graphical User Interface for GAMESS. J. Mol. Graphics Modell. 1998, 16 (3), 133− 138. (22) Oracle Corporation; Sun Grid Engine, 6.2u4.
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