1 / 39

Chemistry Packages at CHPC

Chemistry Packages at CHPC. Anita M. Orendt Center for High Performance Computing anita.orendt@utah.edu Fall 2012. Identify the computational chemistry software and related tools currently available at CHPC Present brief overview of these packages Present how to access packages on CHPC

yoko
Télécharger la présentation

Chemistry Packages at CHPC

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Chemistry Packages at CHPC Anita M. Orendt Center for High Performance Computing anita.orendt@utah.edu Fall 2012

  2. Identify the computational chemistry software and related tools currently available at CHPC Present brief overview of these packages Present how to access packages on CHPC Next presentation – Gaussian09 & GaussView 18 October 2012 Purpose of Presentation http://www.chpc.utah.edu

  3. Brief Overview CHPC Resources • Computational Clusters – sanddunearch, updraft and ember • Home directory – NFS mounted on all clusters • /uufs/chpc.utah.edu/common/home/<uNID> • generally not backed up (there are exceptions) • Scratch systems • /scratch/serial – all clusters – 15 TB NFS • /scratch/general – updraft only – 3.5TB NFS • /scratch/ibrix/chpc_gen – updraft and ember – 55TB • /scratch/local on compute nodes (60GB sda, 200GB updraft, 400GB ember) • Applications • /uufs/arches/sys/pkg • /uufs/chpc.utah.edu/sys/pkg • /uufs/cluster.arches/sys/pkg where cluster = sanddunearch, updraft or ember http://www.chpc.utah.edu

  4. Sanddunearch 156 nodes/624 cores Infiniband and GigE Updraft 256 nodes/2048 cores Infiniband and GigE 85 nodes general usage Owner nodes Switch Ember about 382 nodes/4584 cores Infiniband and GigE 67 nodes general usage Turret Arch Telluride 12 GPU nodes (6 CHPC) Meteorology /scratch/ibrix/chpc_gen ember, updraft IBRIX Administrative Nodes scratch systems serial – all clusters general – updraft NFS NFS Home Directories http://www.chpc.utah.edu

  5. Getting Started at CHPC • Account application – an online process • https://www.chpc.utah.edu/apps/profile/account_request.php • Username is your unid with password administrated by campus • Interactive nodes • two CHPC owned nodes per cluster (cluster.chpc.utah.edu) with round-robin access to divide load • CHPC environment scripts – in account when created • www.chpc.utah.edu/docs/manuals/getting_started/codes/chpc.tcshrc • www.chpc.utah.edu/docs/manuals/getting_started/codes/chpc.bashrc • Getting started guide • www.chpc.utah.edu/docs/manuals/getting_started • Problem reporting system • http://jira.chpc.utah.edu or email to issues@chpc.utah.edu http://www.chpc.utah.edu

  6. Interactive Node Usage • Interactive nodes for prepping/testing of input files, analyzing results, compilations, debugging, data transfer, etc • no running of jobs • 15 min MAX cpu • no jobs of any time length that negatively impact ability of other users to get work done (e.g., heavy cpu, memory usage and/or i/o) • https://wiki.chpc.utah.edu/display/policy/2.1.1+Cluster+Interactive+Node+Policy http://www.chpc.utah.edu

  7. Batch System • All use of compute nodes go through a batch system using Torque (PBS) and Maui (Moab) for scheduling #PBS -S /bin/csh #PBS – A account #PBS –l walltime=24:00:00,nodes=2:ppn=8 • qsub –I to get interactive use of a compute node (-X if X11 forwarding needed) • Walltime limits • 72 hours on sanddunearch • 24 hours on updraft • 72 hours on ember (long qos by request) http://www.chpc.utah.edu

  8. Allocation Procedure • Allocation process now within jira https://jira.chpc.utah.edu/secure/CreateIssue.jspa?pid=10130&issuetype=12 • Allocations on a calendar quarter basis • Next requests due about Dec 1 for Jan-Mar 2013 • Can request for up to 4 quarters at a time • Allocations for different clusters are kept separate • Sanddunearch is no longer being allocated – all freecycle • One allocation per research group; accessible by all members of group http://www.chpc.utah.edu

  9. Out of Allocation Options • If your group did not request any allocation – can get a quick allocation (limited to 5000 units) on one of the clusters • https://jira.chpc.utah.edu/secure/CreateIssue.jspa?pid=10130&issuetype=13 • Can run in freecycle mode on sanddunearch; once job starts it will run until done or walltime requested is reached • Can run on smithp-guest on smithp nodes ember or freecycle on CHPC nodes on either ember or updraft (jobs are preemptable) http://www.chpc.utah.edu

  10. Security Policies (1) • 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 account • Do not introduce classified or sensitive work onto CHPC systems • Use a good password and protect it – see gate.acs.utah.edu for tips on good passwords http://www.chpc.utah.edu

  11. Security Policies (2) • 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 • Do not distribute or copy privileged data or software • Report suspicions to CHPC (security@chpc.utah.edu) • Please see http://www.chpc.utah.edu/docs/policies/security.html for more details http://www.chpc.utah.edu

  12. Access to Interactive Nodes • From Windows machine: • Need ssh client • PuTTY: http://www.chiark.greenend.org.uk/~sgtatham/putty/ • Xshell 4: http://www.netsarang.com/products/xsh_overview.html • For Xwindowing – need tool to display graphical interfaces such as Gaussview, ECCE, AutoDockTools • Xming (use Mesa version) - http://www.straightrunning.com/XmingNotes http://www.chpc.utah.edu

  13. Default login scripts • CHPC maintains default login scripts that will set up necessary 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 • Located in your home directory as .tcshrcor .bashrc • Can comment out setups for packages not used • Default ones provided have chemistry package setups commented out – need to remove # at start of line • Can customize by creating .aliases file that is sourced at end of the CHPC script – do not customize .tcshrc/.bashrc file as you will need to occasionally get a new version http://www.chpc.utah.edu

  14. Location of Installations • Have a three layer system for installations: • /uufs/chpc.utah.edu/sys/pkg • Accessible on all clusters and CHPC supported linux desktops • /uufs/arches/sys/pkg • Accessible on all clusters, but not desktops • /uufs/cluster.arches/sys/pkg • Single cluster access • For builds of packages customized to some feature (usually for the MPI) of the given cluster 10/21/2010 http://www.chpc.utah.edu Slide 13

  15. Software - General Information • Available on CHPC web pages/wiki • Can get to from www.chpc.utah.edu → Software documentation → More (for complete list) http://www.chpc.utah.edu/docs/manuals/software • Available for most packages • Has information on licensing restrictions, example batch scripts, where to get more information on a specific package • Also has useful information on running of jobs (scaling, issues, etc) for some applications http://www.chpc.utah.edu

  16. Types of Chemistry Packages • Molecular Mechanics/Dynamics • Electronic Structure Calculations • Plane Wave Pseudopotential based packages – allows for periodic boundary conditions • Support Packages • Integrated Modeling Platforms http://www.chpc.utah.edu

  17. Molecular Mechanics/Dynamics • Amber • Gromacs • NAMD • LAMMPS • Charmm(licensed by research group) Note – Gaussian and NWChem also have MM capabilities http://www.chpc.utah.edu

  18. Quantum (Mainly) Packages • Gaussian03/09 • NWChem • GAMESS • Molpro – serial only • Dalton – serial only • Orca • Psi • SIESTA – licensed by individual research group but can add others to license at no charge • CFOUR http://www.chpc.utah.edu

  19. Plane Wave Pseudopotential(good for periodic systems) • Quantum Espresso • CPMD • VASP – licensed by group • BigDFT (wavelet basis set) http://www.chpc.utah.edu

  20. Integrated Molecular Platforms • Schrodinger – owned by individual groups http://www.chpc.utah.edu

  21. SupportPackages • Gaussview • Molden • VMD • NBOView • Babel (Openbabel) • Dock • AutoDock (and AutodockVina) • Cambridge Structural Database • ECCE • Special case – installed on carbon.chpc.utah.edu • Talk to me first if you want to use http://www.chpc.utah.edu

  22. GaussView • Molecular builder and viewer for Gaussian input/output files • CHPC provides campus license for linux version • For Gaussian03 – standard is version 4 • For Gaussian09 – standard is version 5 • Chemistry Department has campus license for GV5 for windows; can buy into license • Access with gv & – 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 system http://www.chpc.utah.edu

  23. NBOView • Package to view NBO orbitals • Works only with G03 (not G09) • For information see http://www.chem.wisc.edu/~nbo5/v_manual.htm • How to use at CHPC: • Add to your path: /uufs/chpc.utah.edu/sys/pkg/nboview/nboview1.1 • nboview http://www.chpc.utah.edu

  24. Molden • Another program for viewing molecular/electronic structures; version 4.7 • Works with Gamess, Gaussian, Molpro • Supports plots of electronic density, MOs, etc • More information at http://www.cmbi.ru.nl/molden/molden.html • How to use at CHPC: • Make sure your path includes /uufs/chpc.utah.edu/sys/pkg/molden/std • molden & http://www.chpc.utah.edu

  25. VMD • Visualization, mainly for MM/MD • latest version (1.9.1) installed • Reads a number of different file formats • Information at http://www.ks.uiuc.edu/Research/vmd • Can install on own desktop (windows/mac/linux versions available) • /uufs/chpc.utah.edu/sys/pkg/vmd/vmd-std/bin/vmd (can uncomment setup in .tcshrc then vmd) • Can use for 3D viewing on CHPC’s vis wall http://www.chpc.utah.edu

  26. ECCE • Extensible Computational Chemistry Environment • Package developed at EMSL at PNNL • See ecce.pnl.gov for info • Set of modules to manage computational chemistry computer jobs (Gaussian, NWChem) from start (including building system) to finish (analyzing output) all from your desktop system • Installed on carbon.chpc.utah.edu • User accounts need setup – see me if interested as carbon is not always kept running http://www.chpc.utah.edu

  27. OpenBabel • Tool to interconvert structure files between a number of formats used in molecular modeling • See openbabel.org for more information • To run: • source /uufs/chpc.utah.edu/sys/openbabel/etc/babel.csh (or uncomment in your .tcshrc) • babel -i < input-type > < infile > -o < output-type > < outfile > • babel –H to see format for usage, options, and input/output file-types http://www.chpc.utah.edu

  28. Dock/AutoDock • Programs to look at binding of a small molecule within the active site of a receptor, usually a macromolecule • Dock • version 6.5 installed • get info at: http://dock.compbio.ucsf.edu • source /uufs/chpc.utah.edu/sys/pkg/dock/etc/dock.csh • dock6.mpi to start (needs arguments) • Autodock • version 4.2 • info available at http://autodock.scripps.edu • source /uufs/chpc.utah.edu/sys/pkg/autodock/etc/autodock.csh • autodock4 (with proper arguments) or autogrid4 • autodocktools, a GUI interface, installed – start with adt & • AutodockVina – multicore performance and enhanced accuracy – start with vina & http://www.chpc.utah.edu

  29. Cambridge Structural Database • Moved from library to CHPC summer 2006 – additions to the database are made every 3-4 months; package updated annually • www.ccdc.cam.ac.uk for information • Need CHPC account to use • From PC need Xterm/Xwindowing software (Putty/XMing work well) to start session on any of the interactive nodes • source (or uncomment line in .tchsrc) /uufs/chpc.utah.edu/sys/pkg/CSD/std/cambridge/etc/csd.csh • cq & <- to start conquest (search engine) • mercury & <- to start crystal structure viewer • The first time you use it on a given computer you will be asked to confirm licensing • need to provide site/license codes (840/7E92A7) http://www.chpc.utah.edu

  30. Amber • Molecular mechanics/dynamics package Current version is Amber 12 (Amber 11 still active) • Basic information on getting started: http://www.chpc.utah.edu/docs/manuals/software/amber.html • For more information see http://ambermd.org • The Amber Mail Reflector Archive and mailing list is very useful! • Different parallel builds available for each cluster to make use of the different interconnects • Have GPU version – initial tests show impressive performance gains http://www.chpc.utah.edu

  31. Other MM/MD packages -- All have builds optimized for individual clusters -- • Gromacs - http://www.gromacs.org/ • version 4.5.4 installed with builds of both single and double precision • LAMMPS - http://lammps.sandia.gov/ • NAMD: http://www.ks.uiuc.edu/Research/namd/ • version 2.6 on sanddunearch (2.7 current) • NWChem also has MM/MD capabilities and Gaussian09 also has limited MM capabilities http://www.chpc.utah.edu

  32. CHARMM • Package is licensed per research group and for a specific version • If interested – get license and we can do installation such that only your group has access • See www.charmm.org for details http://www.chpc.utah.edu

  33. Gaussian03/09 • Commercial electronic structure package • http://www.gaussian.com for information and User’s Guide • Last installed revision of G03 is E.01 • /uufs/chpc.utah.edu/sys/pkg/gaussian03/std • Has been updated to include latest NBO5 • Version C.01 of G09 installed • /uufs/chpc.utah.edu/sys/pkg/gaussian09/AMD64 • /uufs/chpc.utah.edu/sys/pkg/gaussian09/EM64T • For information on accessing the CHPC installation • http://www.chpc.utah.edu/docs/manuals/software/g03.html http://www.chpc.utah.edu

  34. NWChem • Package developed at PNNL to work on massively parallel systems • http://www.nwchem-sw.org • Goal: Computational chemistry solutions that are scalable with respect to both chemical system size and MPP hardware size • Has quantum mechanics, molecular mechanics/dynamics, and quantum molecular dynamics, plane waves for periodic systems • Version 6.1 (with Python) – 5.1.1 still available in chpc.utah.edu • /uufs/chpc.utah.edu/sys/pkg/nwchem/nwchem-6.1/bin/LINUX64 • /uufs/ember.arches/sys/pkg/nwchem/nwchem-6.1/bin/LINUX64 (not tested) • /uufs/updraft.arches/sys/pkg/nwchem/nwchem-6.1/bin/LINUX64 (not tested) • To run: • source appropriate etc/nwchem.csh • must have $HOME/pdir directory if running parallel • More information and example batch script at • http://www.chpc.utah.edu/docs/manuals/software/nwchem.html http://www.chpc.utah.edu

  35. GAMESS • General Atomic and Molecular Electronic Structure System • Another option for most ab initio quantum calculations • On 22 February 2006 version – can be updated if needed • /uufs/chpc.utah.edu/sys/pkg/GAMESS/gamess • 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 http://www.chpc.utah.edu

  36. Other Quantum Codes -- Mainly codes that are specialized in terms of functionality -- • Dalton – only serial build • Focus on property calculations at HF, DFT, MCSCF and CC levels of theory • version 2.0 installed; Dalton2011 recently released • http://dirac.chem.sdu.dk/daltonprogram.org/ • Molpro– only serial build • Emphasis on highly accurate calculation methods • Version 2006.1 installed; new 2012.1 available • http://www.molpro.net/ • Psi - http://www.psicode.org/ • Orca - http://www.thch.uni-bonn.de/tc/orca/ • CFOUR - http://www.cfour.de/ http://www.chpc.utah.edu

  37. Plane Wave Codes Plane wave codes for the study of systems under periodic boundary conditions (PBC) • NWChem has some functionality • VASP – http://cms.mpi.univie.ac.at/vasp/ • Ab initio QM/MD • Licensed per research group (have 1 group with an old version) • Quantum Espresso - http://www.quantum-espresso.org/ • Understands crystal space groups • Has GIPAW module to do NMR calculations • J-ICE and XCrysDen to view • CPMD - http://www.cpmd.org/ • BigDFT - http://inac.cea.fr/L_Sim/BigDFT/ http://www.chpc.utah.edu

  38. Schrodinger Suite • Commercial package geared for chemical modeling and simulation in the pharmaceutical field, specifically drug discovery • http://www.schrodinger.com/ • Interface – Maestro (free for academia) • Calculation code includes Jaguar (Quantum), Macromodel (MM), Qsite (QM/MM) • Interfaces with Desmond for MD (installed) • Tools for structure based drug design • Docking, ligand design, binding affinities, screening libraries • Year to Year licensing • Token based, so limited in number of concurrent uses • Purchased by two groups in Medicinal Chemistry • If interested in using – come talk to me http://www.chpc.utah.edu

  39. Finally….. • 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, usage needs • Any questions – contact me • anita.orendt@utah.edu • Phone: 801-231-2762 • Office: 422 INSCC http://www.chpc.utah.edu

More Related