Quantum Chemistry at MCSR

Quantum Chemistry at MCSR

Brian W. HopkinsMississippi Center for Supercomputing Research

12 February 2009

What We’re Doing Here

• Talk about quantum chemistry procedures.

• Talk about available quantum programs.• Discuss user needs and program

options.• Emphasis will be on modernization.

QChem: Anatomy of A Project• Choose a chemical problem you’re 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.

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.

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)

Program Selection: Other Methodological Concerns

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

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

Program Selection: Ease of Use

• Ease of use is important!• Being concerned about this doesn’t 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.

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!

That’s 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_computer_programs

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

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

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.

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

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

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

So What Have We Got? 6.

• We will support most any application you can put in our hands.– Stuff that’s 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.

So I’ve 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.– There’s 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?pagename=marcamp09.inc

After The Build

• Develop PBS scripts for running jobs.– Please don’t run I/O intensive QC jobs in

/ptmp!– We have examples and can help!

• Run jobs– If queues bog down, don’t be afraid to ask

for special help!

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

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.