Quantum Chemistry at MCSR

1. Quantum Chemistry at MCSR Brian W. Hopkins Mississippi Center for Supercomputing Research 12 February 2009

2. 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.

3. 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.

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.

7. 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 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.

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!

10. 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

11. 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

12. 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

13. 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.

14. 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

15. 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

16. 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

17. 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.

18. 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

19. 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!

20. 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.