Quantum Chemistry at MCSR

1
Quantum Chemistry at MCSR

• Brian W. Hopkins
• Mississippi Center for Supercomputing Research
• 12 February 2009

2
What Were Doing Here

• Talk about quantum chemistry procedures.
• Talk about available quantum programs.
• Discuss user needs and program options.
• Emphasis will be on modernization.

3
QChem Anatomy of A Project

• Choose a chemical problem youre interested in.
• Construct a methodology for examining this
  problem.
• Build a (crude) model system.
• Choose theoretical methods that provide a good
  balance of accuracy and efficiency.
• Select a program suite that can perform the
  necessary calculations.
• Build the program on an appropriate computer.
• Organize and run the jobs efficiently.
• Manage data.
• Analyze results.
• Write papers.

4
Program Selection Basis

• Most every program has two methods for using GTO
  basis sets
• A standard library. ? be careful!
• A parser. ? https//bse.pnl.gov/bse/portal
• Sticking points
• Plane waves.
• STOs.
• Pseudopotentials.

5
Program Selection Electronic Structure Methods

• Most QC programs have base functionality
• Single-reference HF, DFT, MP, CC and CI
• Multi-reference HF (eg. MCSCF or CASSCF)
• Exotic or cutting edge methods tend to be much
  more limited
• Multi-reference, post-HF
• Excited-state theories (EOM, TD)

6
Program Selection Other Methodological Concerns

• 1st and 2nd Derivatives
• Periodic boundary conditions
• Scanning or sampling techniques
• c.

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Program Selection Performance

• Generality
• Some codes have had most development attention
  focused on adding features
• Performance
• Some codes have had most development attention
  focused on improving performance

8
Program Selection Ease of Use

• Ease of use is important!
• Being concerned about this doesnt make you lazy.
• We must make rational decisions about the amount
  of time that ought to be invested in learning to
  work a program.
• This time investment needs to be balanced against
  the expected benefit of using the new program.

9
Program Selection License

• QC programs are big producing them is very labor
  intensive.
• The authors of these programs have rights that
  must be respected.
• Authors have the right to distribute programs as
  they see fit.
• DO NOT install any program on a UM or MCSR
  computer in violation of its license!

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Thats A Lot! Where Do I Start?

• Ask your coworkers.
• Consult online program manuals.
• Read papers, and pay attention to the
  Computational Details or similar sections.

http//en.wikipedia.org/wiki/Quantum_chemistry_com
puter_programs
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A Note On Program Promiscuity

• Can you mix results from different programs?
• Generally yes.
• Sometimes no.
• Things to watch out for
• DFT flavors integration grids
• Basis set details
• Various program defaults (FC, c.)
• Symmetry tolerances

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So What Have We Got? 1.

• Gaussian 03
• Lots of different capabilities
• Very easy to use
• Limited scalability
• Excels with optimization and surface-scanning
  techniques
• Complete site license for Ole Miss
• Fully functional on all MCSR systems
• Automated PBS interface g03sub

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So What Have We Got? 2.

• NWChem
• Lots of different capabilities
• Very easy to use
• Good scalability
• Poor serial efficiency for some methods
• Free academic license
• Fully functional on sweetgum, redwood, and
  mimosa.
• Automated PBS interface nwchemsub.

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So What Have We Got? 3.

• GAMESS
• Lots of different capabilities
• Fairly easy to use
• Some scalability
• Free academic license
• Functioning on sequoia (single-node only)
• No automated PBS interface

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So What Have We Got? 4.

• MOLPRO
• Excels for MR and correlated treatments.
• Screaming fast serial code for many methods.
• Difficult to use
• Some scalability
• Commercial license for MCSR machines
• Functioning on sequoia (single-node only)
• No automated PBS interface

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So What Have We Got? 5.

• MPQC
• Does only a few things.
• Difficult to use
• Screaming fast.
• Extreme scalability
• Free academic license
• Functioning on sequoia (single-node only)
• No automated PBS interface

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So What Have We Got? 6.

• We will support most any application you can put
  in our hands.
• Stuff thats free
• PSI, ACES, CPMD, CP2K, c.
• Stuff that you buy a license for
• Jaguar, TURBOMOL, Qchem, c.
• We will probably not buy licenses.
• We will not violate any software license.

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So Ive Chosen a Program. What Now?

• Choose a system
• Build it!
• Most scientific codes are distributed as source
  and have to be compiled.
• We are almost always willing to build stuff for
  you.
• Theres a separate seminar on building comp.
  chemistry apps scheduled for March 4th.
• We have special queue facilities for building and
  testing new apps.

http//www.mcsr.olemiss.edu/educationsubpage.php?p
agenamemarcamp09.inc
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After The Build

• Develop PBS scripts for running jobs.
• Please dont run I/O intensive QC jobs in /ptmp!
• We have examples and can help!
• Run jobs
• If queues bog down, dont be afraid to ask for
  special help!

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Data Management

• Not usually an issue with QC work.
• Exceptions
• During-job scratch
• Relocate to scratch filesystem
• Checkpoint files
• Keep these zipped when not in use, delete them
  ASAP
• Core files
• limit coredumpsize 1k

21
Data Analysis

• Automated analysis is best!
• All of our systems have tools to facilitate
  automated data analysis
• C and Fortran compilers
• Ask us about MPI!
• Perl and Python interpreters
• Linux utilities (eg, awk)
• We can help build, debug, and run your analysis
  code as needed.