Quantum Chemistry at MCSR
Brian W. Hopkins
Mississippi 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
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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
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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 surfacescanning 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.