--- title: Gaussian16 published: true taxonomy: category: - docs external_links: process: true no_follow: true target: _blank mode: active --- [toc] ## Environment Settings{#enviroment} ### Software Version and System Requirements{#version} #### Gaussian Supports parallel execution on one node. Version | System A | System B | System C ------------------------ | -------- | -------- | -------- Gaussian16 Revision C.01 (default) | + | + | + Gaussian16 Revision B.01 | + | + | + Gaussian16 Revision A.03 | + | + | + #### Gaussian (with LINDA) Supports parallel execution on multiple nodes. Version | System A | System B | System C ------------------------- | -------- | -------- | -------- Gaussian16 Revision C.01 LINDA | ― | + | + Gaussian16 Revision B.01 LINDA | ― | + | + Gaussian16 Revision A.03 LINDA | ― | + | + #### GaussView Version | System A | System B | System C ------------------------- | -------- | -------- | -------- Revision 6.1.1 (default) | ― | + | + Revision 6.0.16 | ― | + | + Key: AU = Available for academic users only, ― = Not available for use. ### Registration for Use{#regist} You must register for use of Gaussian via the [User Portal](http://www.iimc.kyoto-u.ac.jp/en/services/comp/other/portal.html). ### Modules{#modules} Modules software package dynamically adjusts the environment settings for using applications, by using the module command. It also makes changing the environment settings easy when switching between different versions of applications. For details, see [Modules](/config/modules). #### Gaussian Version | Module File | Note ------------------------ | ---------------------- | ----- Gaussian16 Revision C.01 | gaussian16/c01 | Gaussview 6.1.1 is available Gaussian16 Revision B.01 | gaussian16/b01 | Gaussview 6.0.16 is available Gaussian16 Revision A.03 | gaussian16/a03 | Gaussview 6.0.16 is available #### Gaussian (with LINDA) The module file is the same as one w/o LINDA. Version | Module File | Note ------------------------ | ---------------------- | ----- Gaussian16 Revision C.01 LINDA | gaussian16/c01 | Gaussview 6.1.1 is available Gaussian16 Revision B.01 LINDA | gaussian16/b01 | Gaussview 6.0.16 is available Gaussian16 Revision A.03 LINDA | gaussian16/a03 | Gaussview 6.0.16 is available You can see the list of module files available by using the module avail command. ## Software Overview{#overview} Gaussian is an electronic structure modeling program. It allows users to investigate and estimate characteristics of molecules and reactions in various conditions from the basic formula of quantum mechanics. Gaussian can be used for investigating characteristics which are impossible or difficult to make observations by the experimentation. ### Software Features{#functions} On every updates, Gaussian is reinforced by functional expansion of the ONIOM method and the solvation model, addition of new functions, and many other new features. It is also consolidated in its parallel computation capability. For more details, see the information at [Official Gaussian Website](http://www.gaussian.com/). * Single point energy calculation * Energy calculation of molecular systems, Molecular Orbital Method Calculation, and prediction of multiple moments and atomic charges * Structure optimization * Potential energy, optimization and convergence criteria, minimization, and transition structure search * Calculation of vibration frequency * Calculation of vibration frequency, interpretation of normal vibration, and characterization of stationary point * ONIOM functions * Modeling process on a high accuracy layer * Customization and efficient ONIOM calculation of molecular mechanics * ONIOM calculation of electric and electromagnetic properties ### Areas of Application{#app_area} * Chemistry * Chemical engineering * Biochemistry * Physics, etc. ## How to Use Gaussian{#usage_gaussian} ### Setting Up Environment (Executing the module Command){#env_set} Set up the environment by using the module command.(The module file you want is loaded.) #### Example ```nohighlight $ module load gaussian16 ``` ### Executing utility{#utility} #### Using tssrun * Format ```nohighlight tssrun g16 input_file ``` * Example (4 threads on one node) ```nohighlight $ tssrun -A t=4:c=4 g16 water.com ``` Parallel execution is available via -A option. Note that the progress is not shown on the terminal as the progress and results are written in .log file. For details of **tssrun** , see [Interactive Processing](/run/interactive). #### Using batchjob #### Using batchjob An Example of jobscript is shown below. * System A ```nohighlight #!/bin/bash #QSUB -q gr19999a #QSUB -ug gr19999 #QSUB -A p=1:t=4:c=4:m=90G aprun -n $QSUB_PROCS -d $QSUB_THREADS -N $QSUB_PPN g16 test0000.com ``` * System B ```nohighlight #!/bin/bash #QSUB -q gr19999b #QSUB -ug gr19999 #QSUB -A p=1:t=4:c=4:m=120G g16 test0000.com ``` ### Submitting Batch Job by the subg Command{#batchjob} The subg command is used for submitting batch jobs specifying a queue name, an input file, and other parameters. The qsub command options and parallel execution on multiple nodes are available via the subg command. #### Format * Gaussian16 ```nohighlight subg16 queue_name input_file [-scrdir dir] [qsub_command_option ...] ``` #### Example: Executing on a queue of entry course ```nohighlight $ subg16 eb water.com ``` #### Example: Specifying 4-fold parallelization on one node and total 30 GB of memory size in gr19999b. ```nohighlight $ subg16 gr19999b water.com -A p=1:t=4:c=4:m=30G ``` ### Executing Gaussian With Linda{#linda} This feature is supported only on the system B/C. #### Setting Up Environment (Executing the module Command) Execute the module command to make a environment settings. ```nohighlight $ module load gaussian16/a03 ``` #### Input File Include "%LindaWorkers=LINDA" at the beginning of the input file to specify inter-node parallelization. The number of nodes should be specified by "-A p" option for subg command (mentioned later). Also, use the %NProcShared to specify the number of processors, when executing a shared memory parallel execution per node together. e.g.) ```nohighlight %LindaWorkers=LINDA %NprocShared=16 ``` #### Executing (Submitting a Job) When executing Gaussian with Linda, use the subg command to submit a job. #### Format ```nohighlight subg16 queue_name input_file [-scrdir dir] [qsub_command_option ...] ``` #### Example: Specifying two nodes and 16-fold parallelization per node (total 32 cores) in gr19999b. input file ```nohighlight %LindaWorkers=LINDA %NprocShared=16 ``` submission command (note: the values of t and c must be same as %NprocShared) ```nohighlight $ subg16 gr19999b water.com -A p=2:t=16:c=16:m=120G ``` ### Gaussian execution using burst buffer (only System B/C){#burstbuffer} [Burst Buffer (IME)](/filesystem/ime) is the name of a high-speed temporary storage system which is different from the normal file system, and enables high-speed reading and writing of files. Gaussian generates RWF files, scratch files, and so on during job execution, and reads and writes files regularly and frequently. Therefore it is expected to improve the computing speed and reduce the load on the file system by using the burst buffer. [Application Request](/filesystem/ime#application) is required to use the burst buffer. System A does not support the job execution using this method. #### Format ```nohighlight subg16 queue_name input_file [-scrdir dir] [-bb capacity={IMESize}] [qsub_command_option ...] ``` #### Example: Specifying 4-fold parallelization on one node, total 30 GB of memory size and using burst buffer (200GB) in gr19999b ```nohighlight $ subg16 gr19999b water.com -A p=1:t=4:c=4:m=30G -bb capacity=200G ``` When you specify to use the burst buffer(-bb option), please execute the job after placing the file on the large volume disk (/LARGE0). When the job which uses the burst buffer is executed, "{input file name}.SCRDIR" directory is newly created under the current directory. Although RWF files and scratch files generated during the job execution are output to the directory, the file size will be "0 byte" until the job is finished since reading and writing is performed on the IME during the job execution. When the calculation process of Gaussian is finished, the data synchronization from IME to LARGE will be started automatically. Therefore, please wait to access and read/write files to "{input file name}.SCRDIR" directory until the job is finished. When an input file with the same name is executed by multiple jobs at the same time, you may get unintended calculation results or the calculation process may be terminated in the middle. When you run multiple jobs at the same time, please be careful not to share the input file with the same name. ### How to resume an interrupted job{#resume} Please see the below. [How can I restart a job that was interrupted?](http://gaussian.com/faq2/) ## How to Use GaussView{#usage_gaussview} ### Starting GaussView{#gaussview} ```nohighlight $ xrun gview ``` GaussView is a GUI application, so you need to log in to the supercomputer system using the Exceed onDemand. For how to install and how to use, see [Logging In With Exceed onDemand](/login/eod). #### If GaussView Does Not Work Normally GaussView sometimes works normally by using -soft option on startup. ```nohighlight $ xrun gview -soft ``` ## Reference Documents{#references} ### In Japanese{#ref_ja} No documents ### In English{#ref_en} * [Technical Support Information (Gaussian, Inc.)](http://www.gaussian.com/g_tech/1.htm) * [Gaussian 16 User Reference (Gaussian, Inc.)](http://gaussian.com/man/) ## Links{#link} ### External Links{#ex_link} * [Official Gaussian Website (Gaussian, Inc)](http://www.gaussian.com/) ## Programming Seminars{#seminar} We periodically offer [programming seminars](http://www.iimc.kyoto-u.ac.jp/en/services/comp/support/course/), and distribute the handouts. (Japanese version only)