Chemistry Packages at CHPC. Anita M. Orendt Center for High Performance Computing Fall 2011

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1 Chemistry Packages at CHPC Anita M. Orendt Center for High Performance Computing Fall 2011

2 Purpose of Presentation 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 17 November 2011

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 16 TB NFS /scratch/general updraft only 3.5TB NFS /scratch/ibrix/chpc_gen updraft and ember - 60 TB /scratch/local on compute nodes (60 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

4 Sand Dune Arch 156 nodes/624 cores Infiniband and GigE Owner nodes Turret Arch Telluride Meteorology Switch Updraft 256 nodes/2048 cores Infiniband and GigE 85 nodes general usage Ember about 334 nodes/4008 cores Infiniband and GigE 53 nodes general usage GPU nodes (6 CHPC) Administrative Nodes NFS Home Directories NFS scratch systems serial all clusters general updraft IBRIX /scratch/ibrix/chpc_gen ember, updraft

5 Getting Started at CHPC Account application an online process Username is your unid with password administrated by campus Interactive nodes two CHPC owned nodes per cluster (cluster.chpc.utah.edu) with roundrobin access to divide load CHPC environment scripts in account when created Getting started guide Problem reporting system or to

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 and/or memory usage, heavy i/o)

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)

8 Allocation Procedure Allocation process now within jira pid=10130&issuetype=12 Allocations on a calendar quarter basis Next requests due about Dec 1 for Jan-Mar 2012 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

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 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)

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

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 /docs/policies/security.html for more details

12 Access to Interactive Nodes From Windows machine: Need ssh client PuTTY: Xshell 4: For Xwindowing need tool to display graphical interfaces such as Gaussview, ECCE, AutoDockTools Xming (Mesa version) - XLiveCD - XWin32 free through OSL

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 /docs/manuals/getting_started/code/ chpc.tcshrc /docs/manuals/getting_started/code/ chpc.bashrc Located in your home directory as.tcshrc or.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

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 Slide 13

15 Software - General Information Available on CHPC web pages Can get to from -> Software documentation -> More (for complete list) /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

16 Chemistry Packages Quantum/Ab Initio Codes for Molecules Molecular Mechanics/Dynamics Plane Wave for Solids Support Packages visualization docking conversion of file formats structure database

17 Electronic Structure 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

18 Molecular Mechanics/Dynamics Amber Gromacs NAMD LAMMPS Charmm (licensed by research group)

Structural Database ECCE Special case installed

19 Support Packages Gaussview Molden VMD NBOView Babel (Openbabel) Dock and AutoDock Cambridge Structural Database ECCE Special case installed oncarbon.chpc.utah.edu Talk to me first if you want to use

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

20 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

NBOView Package to view NBO orbitals Works only with G03 (not G09) For information see http://www.chem.wisc.

21 NBOView Package to view NBO orbitals Works only with G03 (not G09) For information see How to use at CHPC: Add to your path: /uufs/chpc.utah.edu/sys/pkg/ nboview/nboview1.1 nboview

22 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 How to use at CHPC: Make sure your path includes /uufs/chpc.utah.edu/sys/pkg/ molden/std molden &

VMD Visualization, mainly for MM/MD Reads a number of different file formats Information at http://www.ks.uiuc.

23 VMD Visualization, mainly for MM/MD Reads a number of different file formats Information at Can either install on own desktop (windows/mac/linux versions available) or use CHPC installation /uufs/ chpc.utah.edu/sys/pkg/vmd/vmd-std/bin/vmd latest version (1.9) installed

ECCE Extensible Computational Chemistry Environment Package developed at EMSL at PNNL Set of modules to manage computational chemistry computer jobs (Gaussian, NWChem) from start (including

24 ECCE Extensible Computational Chemistry Environment Package developed at EMSL at PNNL 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

OpenBabel Tool to interconvert structure files between a number of formats used in molecular modeling To run: source /uufs/chpc.utah.edu/sys/openbabel/etc/ babel.

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

Dock/AutoDock Programs to look at binding of a small molecule within the active site of a receptor, usually a macromolecule Dock version 6.4 installed (6.5 is current) get info at: http://dock.

26 Dock/AutoDock Programs to look at binding of a small molecule within the active site of a receptor, usually a macromolecule Dock version 6.4 installed (6.5 is current) get info at: source /uufs/chpc.utah.edu/sys/pkg/dock/etc/dock.csh dock6.mpi to start (needs arguments) Autodock version 4.2 info available at source /uufs/chpc.utah.edu/sys/pkg/autodock/etc/autodock.csh autodock4 (with proper arguments) or autogrid4 Also have autodocktools, a GUI interface, installed start with adt &

27 Cambridge Structural Database Moved from library to CHPC summer 2006 additions to the database are made every 3-4 months; package updated annually 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 /uufs/chpc.utah.edu/sys/pkg/csd/std/cambridge/etc/ csd.csh Can uncomment line in.tcshrc to do this upon login 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)

Amber Molecular mechanics/dynamics package Current version is Amber 11 Basic information on getting started: /docs/manuals/software/amber.html For more information see http://ambermd.

28 Amber Molecular mechanics/dynamics package Current version is Amber 11 Basic information on getting started: /docs/manuals/software/amber.html For more information see 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

29 Other MM/MD packages All built for individual clusters--- Gromacs - Recently updated; version installed with cluster optimized builds of both single and double precision LAMMPS - Installations need updating if there is interest NAMD: Version 2.6 on sanddunearch (2.7 current) NWChem also has MM/MD capabilities

30 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 for details

31 Gaussian03/09 Commercial electronic structure package 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 B.01 of G09 installed; C.01 just announced /uufs/chpc.utah.edu/sys/pkg/gaussian09/amd64 /uufs/chpc.utah.edu/sys/pkg/gaussian09/em64t For information on accessing the CHPC installation /docs/manuals/software/g03.html

NWChem Package developed at PNNL to work on massively parallel systems http://www.nwchem-sw.

32 NWChem Package developed at PNNL to work on massively parallel systems 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 (with Python) /uufs/chpc.utah.edu/sys/pkg/nwchem/nwchem-5.1.1/bin/linux64 To run: source appropriate etc/nwchem.csh must have $HOME/pdir directory if running parallel More information and example batch script at /docs/manuals/software/nwchem.html

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.

33 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 for information on usage and capabilities Can run both parallel or serial For information on accessing the CHPC installation see /docs/manuals/software/gamess.html

34 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 Molpro only serial build Emphasis on highly accurate calculation methods Psi - Orca - CFOUR -

35 Plane Wave Codes Plane wave codes for the study of systems under periodic boundary conditions (PBC) NWChem VASP Ab initio QM/MD Licensed per research group Quantum Espresso - Understands crystal space groups Has GIPAW module to do NMR calculations J-ICE and XCrysDen to view CPMD - BigDFT -

36 Schrodinger Suite Commercial package geared for chemical modeling and simulation in the pharmaceutical field, specifically drug discovery Interface Maestro (free for academia) Calculation code includes Jaguar (Quantum), Macromodel (MM), Qsite (QM/MM) Interfaces with Desmond for MD Tools for structure based drug design Docking, ligand design, binding affinities, screening libraries Have a year license (Oct 2011) Token based, so limited in number of concurrent uses Purchased by two groups in Medicinal Chemistry If interested in using come talk to me

37 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 Any questions contact me Phone: Office: 422 INSCC

CENTER FOR HIGH PERFORMANCE COMPUTING. Overview of CHPC. Martin Čuma, PhD. Center for High Performance Computing

Overview of CHPC Martin Čuma, PhD Center for High Performance Computing m.cuma@utah.edu Spring 2014 Overview CHPC Services HPC Clusters Specialized computing resources Access and Security Batch (PBS and