Title: Personal Perspectives on Virtual Laboratory of Computational Chemistry
1Personal Perspectives on Virtual Laboratory of
Computational Chemistry
- Shubin Liu, Ph.D.
- Academic Technology Networks
- University of North Carolina
- Chapel Hill, North Carolina, USA
2Agenda
- Self-Introduction
- Research Interests
- Hardware and Software in Use
- Personal Suggestions
- What Can I Contribute?
- Technical Issues and Concerns
3Brief Self-Introduction
- Education
- Ph.D. University of North Carolina, 1996, Advisor
Robert G. Parr - M.Sc. Lanzhou University, 1988, Advisor Zhouren
Peng - B.Sc. Hunan Normal University, 1985, Major
Chemistry - Professional Experience
- Postdoc. Duke Universtiy, 1998-2000, Advisor
Weitao Yang - Postdoc. University of North Carolina, 1996-1998,
Advisor R.G. Parr - Present Position
- Title Senior Computational Scientist
- High Performance Computing Group, ITS, UNC, since
September 2000 - Permanent staff position
- Duties
- Computational Chemistry software installation,
test, and support for entire campus - Computational Chemistry research and
collaboration with world-wide researchers
4Research Interests
- Density Functional Theory
- Theoretical, conceptual and methodological
development - Applications to biological and material systems
- Structure Theory of Macromolecules
- New theory of molecular structure and change
- Structural bioinformatics
5Ongoing CPU/IO-Demanding Projects
- Cytochrome human P450 protein mechanism
- System 100 atoms of QM core, 3500 atoms of MM
environment - Methods DFT, QM/MM
- Software Gaussian, GAMESS
- Quantum Molecular Dynamics
- System 100 atoms, 20-100 ps of dynamics
- Software NWChem/ECCE
- Structure Bioinformatics
- Self-developed algorithm/codes
- Huge database (gt10GB raw data from one cycle)
- Both CPU and I/O intensive
6Active Site of P450cam Protein
7Ongoing CPU/IO-Demanding Projects
- Cytochrome human P450 protein mechanism
- System 100 atoms of QM core, 3500 atoms of MM
environment - Methods DFT, QM/MM
- Software Gaussian, GAMESS
- Quantum Molecular Dynamics
- System 100 atoms, 20-100 ps of dynamics
- Software NWChem/ECCE
- Structure Bioinformatics
- Self-developed algorithm/codes
- Huge database (gt10GB raw data from one cycle)
- Both CPU and I/O intensive
8QMD Chloride in Water Cluster
9Ongoing CPU/IO-Demanding Projects
- Cytochrome human P450 protein mechanism
- System 100 atoms of QM core, 3500 atoms of MM
environment - Methods DFT, QM/MM
- Software Gaussian, GAMESS
- Quantum Molecular Dynamics
- System 100 atoms, 20-100 ps of dynamics
- Software NWChem/ECCE
- Structure Bioinformatics
- Self-developed algorithms/codes
- Huge database (gt10GB raw data from one cycle)
- Both CPU and I/O intensive
10Structure Bioinformatics Helix Propensity
Huge database, self-developed algorithm, both CPU
I/O intensive. Unpublished results.
11Hardware in Use
- SGI Origin 3800, 500MHz, 64 CPU, 128 GB memory
- IBM P690 (Regatta), 1.7GHz, 32 CPU, 128 GB memory
- LINUX cluster, 1.4-2.8GHz, 352 CPU, 1.5GB
memory/CPU AMD Athlon and IBM BladeCenter - Shared scratch disk space over 10 TB
- All machines for scientific/research computing
- Shared by all users on campus
12Software in Use
- Quantum Chemistry
- Gaussian
- NWChem
- GAMESS
- ADF/Band
- Cerius2
- SPARTAN
- Molpro
- CPMD
- ABINIT
- Molecular Dynamics
- AMBER
- CHARMM
- Gromacs
- Tinker
- Sybyl
- InsightII
- MacroModel
- Quanta
- O
13Software in Use
- Visualization
- GaussView
- ECCE (with NWChem)
- Cerius2
- Sybyl
- InsightII
- Molscript
- Spartan
- Molden
- Miscellaneous
- Babel (OpenBabel)
- Cambridge database
- NBO/NBOView
- Blast/Pise
- BLAS/LAPACK
- IMSL
- Matlab, Mathematica
- etc.
14Suggestions Operational
- CPU-time allocation based on proposals
- A Scientific Steering Committee reviews proposals
- Renewal yearly on the basis of progress report
- Different kinds of account
- Training account
- Student account
- Research/member account
- Mandatory prior training (system, etc) for any
new user
15Suggestions Scientific
- Install a selective list of computational
chemistry software at system level and shared by
all CC users - Categories QM, MD, Visualization, utility
- Priority given to parallel codes/packages
- A few use-friendly GUIs for each category
- Symposiums
- have peers get together often and invite
experts to come and talk - User forums
- display what users achieve, harvest feedbacks
from users, and provide opportunity for users and
system people to have direct talks.
16Suggestions Training
- Training and short courses
- For new users, students, professionals, etc.
- Format Online and/or onsite
- Contents
- System usage, job submission, HPC technology
(MPI, OpenMP, etc.) - Programming languages (FORTRAN 77/90/95, C)
- Comp Chem general introduction, package
introduction, etc. - Summer schools with credit points
- Onsite, short-term, intensive, focused, hands-on,
project-oriented
17Suggestions Miscellaneous
- List server -- for Lab members
- Website to general public
- User group of all Comp Chem users
18My Purpose to be a Member
- To provide voluntary service, based on my years
of HPC experience, to make the Lab more effective
and efficient - To get to know peers within our country
- To make use of the great facility and resources
for own research
19What Can I Contribute?
- Software
- Selection of a list of CC software
- Free, commercial
- Serial, parallel
- QM, MD, visualization, utility, etc
- Installation, testing, documentation and
benchmarking - Consultation
- User (front-end) support
- Technical (back-end) support
- Scientific steering committee
- Training/Workshop/Summer School
- Symposium
20Technical Issues and Concerns
- How to share data within a group?
- How to guarantee data privacy if needed?
- How much is the disk space quota for a regular
user? - Whats the limit of CPU usage per user?
- Is there any permanent mass storage?
- How big is the scratch space, where there is no
limit to store raw data and to run jobs? How long
can raw data be kept on the scratch space? - Is there any backup plan? If yes, what parts of
disk spaces are to be backed up? - Any packages/compilers/libraries (BLAS/LAPACK/
IMSL/etc) installed by system people that are
available for all users?
21QUESTIONS???
Please contact me at shubin_at_unc.edu.
THANK YOU!