Presentation - Center for High Performance Computing
Contents
1. Platforms Download 4 29 08 http www chpc utah edu Slide 30 Aliso need to have e To run source uufs arches sys nwchem etc nwchem csh e More inforation and example batch script at http www chpc utah edu docs manuals software nwchem htnil 4 29 08 http www chpc utah edu Slide 31 Center for GAMESS Computing General Atomic and Molecular Electronic Structure System Another option for most ab initio quantum calculations On 22 February 2006 version http www msg ameslab gov GAMESS for information on usage and capabilities Can run both parallel or serial For information on accessing the CHPC installation see http www chpc utah edu docs manuals software gamess html 4 29 08 http www chpc utah edu Slide 32 Center for Finally Computing e Let us know if there is some other package that does something that our current packages do not we can look into the possibility of getting it Factors cost hardware OS requirements licensing issues e Any questions contact me anita orendt utah edu Phone 231 2762 Office 422 INSCC 4 29 08 http www chpc utah edu Slide 332. net e Current version 2006 1 only serial operation available e Installed on arches uufs arches sys pkg molpro std serial bin e Sample script available on molpro on chpc software pages http www chpc utah edu docs manuals software molpro html 4 29 08 http www chpc utah edu Slide 24 Center for Dalton Computing e Focus on property calculations at HF DFT MCSCF and CC levels of theory e have sample input files for NMR shielding calculations e Version 2 0 installed e For more information http www kjemi uio no software dalton dalton html e Only serial build available currently e Location uufs arches sys dalton serial bin e For information on accessing CHPC installation http www chpc utah edu docs manuals software dalton html 4 29 08 http www chpc utah edu Slide 25 Center for Computing Gaussian0O3 e Commercial electronic structure package http www gaussian com for information and User s Guide e Current installed revision of GO3 is E 01 on arches uufs arches sys g03 Has been updated to include latest NBO5 e For information on accessing the CHPC installation http www chpc utah edu docs manuals software g03 html http www chpc utah edu Slide 26 4 29 08 Center General Info on Arches Computing e To run G03 on arches you will need to have the tcshrc file that CHPC provides in your home directory even if you
3. normally run a bash shell as gaussian jobs run under a csh environment Users need to request to be put in the gaussian users group so that they have permission to access installation e Exampe test files can be found in uufs arches sys g03 g03 tests com input files uufs arches sys g03 g03 tests ia64 output files Great resource for examples of different functionalities 4 29 08 http www chpc utah edu Slide 27 Batch Execution e Sample PBS scripts for Gaussian03 on all platforms are availaible on the Gaussian03 CHPC web pages http www chpc utah edu docs manuals software g03 html More detailed info on use next week s talk 4 29 08 http www chpc utah edu Slide 28 Center for NWChem Computing Package developed at PNNL to work on massively parallel systems Goal Computational chemistry solutions that are scaleable with respect to both chemical system size and MPP hardware size Has quantum mechanics molecular mechanics dynamics and quantum molecular dynamics version 5 0 installed on arches with Python uufs arches sys nwchem bin LINUX64 ttp www chpc utah edu Slide 29 Center for NWChem Web Pages Computing http www emsl pni gov docs nwchem nwchem html The site is searchable and covers Capabilities User s Manual and Programmer s Manual searchable Support Tutorial Benchmarks Applications FAQ s Known Bugs
4. to finish all from your desktop system Installed on carbon chpc utah edu User accounts need setup see me if interested carbon is not always kept running 4 29 08 http www chpc utah edu Slide 16 Center for Within ECCE you can Computing e Build molecules import structures e Create input files for jobs using pull down menus of possible options e Look at what resources available on different computer systems e Launch jobs on any of these resources and then monitor job progress view output e Store organize results in personal database e Needs Xwindowing software if using from a PC e If there is interest can schedule a separate demonstration on ECCE amp its capabilities or user can schedule an appointment for a demo 4 29 08 http www chpc utah edu Slide 17 Center for Molden Computing e Another program for viewing molecular electronic structures e Works with Gamess Gaussian Molpro e Supports plots of Electronic density MOs etc More information at http www cmbti ru nl moliden molden html e How to use at CHPC Make sure your path includes uufs arches sys pkg molden Molden4 6 amp 4 29 08 http www chpc utah edu Slide 18 Center for Dock Computing Programs to look at binding of a small molecule within the active site of a receptor usually a macromolecule Version 6 1installed 6 2 available Get info at http dock compbio ucsf edu Avai
5. Center for Hi h i Performance Computing the Computational Chemistry Packages at CHPC Anita Orendt Center for High Performance Computing University of Utah anita orendt utah edu April 17 2008 http www chpc utah edu Center for Purpose of Presentation Computing e Identify the computational chemistry software and related tools currently available at CHPC e General overview of package capabilities e Next talk April 24 2008 Focus on use of GaussianO3 and Gaussview at CHPC 4 29 08 http www chpc utah edu Slide 2 Arches Metacluster Computing marchingmen chpc utah edu MM e 179 dual processor nodes e 2GB memory node e scratch serial scratch mm scratch serial old local scratch tmp 72 hr walitime maximum tunnelarch chpc utah edu TA 63 dual processor nodes 4GB memory node scratch serial scratch serial old local scratch tmp 120 hr walitime maximum Can get increase of max walltime if needed delicatearch chpc utah edu DA e 256 dual processor nodes e 2GB memory node e scratch serial scratch da scratch serial old local scratch tmp e 72 hr walitime maximum NEW sanddunearch chpc utah edu SDA e 156 quad processor nodes 8GB memory node e scratch serial scratch serial old local scratch tmp 72 hr walitime maximum landscapearch chpc utah edu LA Pl Owned nodes of differing types dual and quad and amounts of memory e Must belong
6. ary environment for batch commands and many of the programs to work http www chpc utah edu docs manuals getting started code chpc tcshrc http www chpc utah edu docs manuals getting started code chpc bashrc e Copy and put in your home directory as tcshrc or bashrc This ts being done on new accounts e Can comment out setups for packages not used e Default ones provided have chemistry package setups commented out need to remove at start of line e Can customize by creating aliases file that is sourced at end of the CHPC script 4 29 08 http www chpc utah edu Slide 10 Current Computational ZH Chemistry Packages Computing e Gaussian03 e NWChem e GAMESS Amber e Molpro serial only e Dalton serial only e There are several other packages that CHPC has experience installing but that have to be licensed on a research group basis Charmm VASP Crystal 98 version e Most installations are in uufs arches sys pkg 4 29 08 http www chpc utah edu Slide 11 Center r my Nilo Other Useful Tools Computing On arches Gaussview Molden Babel Openbabel Dock and AutoDock relatively untested Cambridge Structural Database e Others ECCE e access from carbon chpc utah edu 4 29 08 http www chpc utah edu Slide 12 Center for General Information Perfor e Available on CHPC web pages e Can get to from www chpc utah edu gt Docs gt So
7. d e Basic information on getting started on arches http www chpc utah edu docs manuals software amber html e For further assistance the Amber email reflector is very useful Can also contact Tom Cheatham Amber developer at cheatham chpc utah edu e For more information see http amber scripps edu 4 29 08 http www chpc utah edu Slide 22 Center r Amber getting started Computing e setenv AMBERHOME appropriately SERIAL uufs arches sys pkg amber amber9 opteron pathscale serial static exe PARALLEL DA with myrinet uufs arches sys pkg amber amber9 opteron pathscale mpich mx exe PARALLEL SDA with infiniband uufs arches sys pkg amber amber9 opteron pathscale mpich mvapich exe PARALLEL TA and MM uufs arches sys pkg amber amber9 opteron pathscale mpich exe e set path path AMBERHOME exe e sander Program in amber that does actual energy minimization parallel version mpi exists Example scripts on chpc web page e antechamber and xleap Interactive programs in amber to help create input files find with serial build e New ambertools package now available 4 29 08 http www chpc utah edu Slide 23 Center for Molpro Computing e Program emphasis is on highly accurate computations with extensive treatment of the electron correlation through multi configuration reference Cl coupled cluster and associated methods e For more information http www molpro
8. ftware http www chpc utah edu docs manuals software Available for most packages e Has information on licensing restrictions example batch scripts where to get more information on a specific package e Also has useful information on running of jobs scaling issues etc 4 29 08 http www chpc utah edu Slide 13 OpenBabel e Tool to interconvert structure files between a number of formats used in molecular modeling e To run source uufs arches sys openbabel etc babel csh or uncomment in your tcsh babel i lt input type gt lt infile gt o lt output type gt lt outfile gt babel H to see format for usage options and input output file types 4 29 08 http www chpc utah edu Slide 14 GaussView Molecular builder and viewer for Gaussian input output files Have version 4 std on arches Have campus licenses for linux version Still have old GaussView 3 09 for windows Access with gv amp provided you have uncommented the Gaussian setup from the standard tcshrc DO NOT submit jobs from within GaussView instead create and save input file and use batch 4 29 08 http www chpc utah edu Slide 15 Center for ECCE Computing Extensible Computational Chemistry Environment current version 4 5 1 CHPC has 4 0 1 installed Package developed at EMSL at PNNL Set of modules to manage computational chemistry computer jobs Gaussian03 NWChem from start
9. lable on all of arches at uufs arches sys pkg dock std bin To run source uufs arches sys pkg dock etc dock csh dock6 mpi to start needs arguments 4 29 08 http www chpc utah edu Slide 19 Center for Autodock Computing Also docks ligands flexible to macromolecular receptors http autodock scripps edu We have version 3 Will update to version 4 in near future Will look at possibility of installing the AutoDockTools for graphical interface Available on all of arches at uufs arches sys pkg autodock std To run source uufs arches sys pkg autodock etc autodock csh autodock3 4 29 08 http www chpc utah edu Slide 20 Center for Cambridge Structural Database Computing e Moved from library to CHPC summer 2006 e www ccdc cam ac uk for information e Need CHPC account to use e Need to have PC with Xterm Xwindowing software Putty XLiveCD work well to start session on any of arches interactive nodes source uufs arches sys pkg CSD std cambridge etc csd csh cq amp lt to start conquest search engine mercury amp lt to start crystal structure viewer The first time you use it will ask you to confirm licensing tie to provide site license codes 840 097537 first 4 29 08 http www chpc utah edu Slide 21 Center for Amber Perfort e Molecular mechanics dynamics package with associated force field e Current version is Amber9 Amber10 just ordere
10. nt e Do not introduce classified or sensitive work onto CHPC systems e Use a good password and protect it 4 29 08 http www chpc utah edu Slide 6 Security Policies e Do not try to break passwords tamper with files look into anyone else s directory etc your privileges do not extend beyond your own directory e Do not distribute or copy privileged data or software e Report suspicions to CHPC security chpc utah edu Please see http www chpc utah edu docs policies security html for more details 4 29 08 http www chpc utah edu Slide 7 Center for Username Password Computing e CHPC has moved to the use of unids UU ID number with first 0 replaced by u and associated password e Authentication password maintenance done on campus level e See nid utah edu for more information on setting changing passwords 4 29 08 http www chpc utah edu Slide 8 Center for Access to CHPC Systems Computing e From Windows machine Need ssh client recommend PuTTY http www chiark greenend org uk sgtatham putty For Xwindowing need tool to display for Gaussview and ECCE e XLiveCD http xlivecd indiana edu e Exceed need 3D available through OSL www osl utah edu for about 100 e XWin32 free through OSL 4 29 08 http www chpc utah edu Slide 9 Center for Default login script Computing e CHPC maintains default login scripts that will set up necess
11. to owner group to use 4 29 ne CHPC owned node quadpyithv 2GR memonyedrequest access if needed Slide 3 Center for Computing All use of compute nodes go through a batch system using Torque PBS and Maui Moab for scheduling PBS S bin csh PBS I walltime 24 00 00 nodes 1 ppn 2 PBS N test e Login nodes only for prepping input files analyzing results compilations etc no running of jobs 4 29 08 http www chpc utah edu Slide 4 Center for Arches scratch Computing e Details on scratch systems available Local tmp is about 30gb on most of arches higher on SDA 60gb and varies among LA nodes scratch serial old scratch mm scratch da nfs e Each about 1 1 TB scratch serial nfs NEW 16 5 TB scratch parallel will be gone in the next month or two e Scratch space should not be used for storage of important files the space is not backed up e CHPC reserves the right to scrub files older than 14 days as needed e CHPC currently scrubbing files untouched for 60 days on a weekly basis e Users need to be diligent about cleaning up after jobs especially jobs that run out of time or do not finish properly 4 29 08 http www chpc utah edu Slide 5 Center for Security Policies Computing e You may No clear text passwords use ssh and scp Do not share your account under any circumstances Don t leave your terminal unattended while logged into your accou
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