Various scientific applications are used on CCB clusters. In general, Research Groups are responsible for knowing their software. In many cases, ChemIT staff can assist researchers, but cannot take responsibility or expend unlimited effort.
This page refers only to Applications, in the "stack" of all software needed to run a cluster. See relevant "Roles and responsibilities" page for stack and all the other software ChemIT is responsible for installing, configuring, debugging, and otherwise maintaining.

Cluster software supported by ChemIT

ChemIT primarily responsible for installation and  configuration of these software applications.

  • Researches, who know the associated science, must confirm software is properly installed and configured using known-good sample test-run files.
  • This software is often stored in a software directory managed exclusively by ChemIT. For example, for Hoffmann's cluster, it's /software.

Research group members are still responsible for learning how to use the software, ensuring their own run files are correct, and any associated de-bugging of their files.

Software

Used by which Research groups

Comments

Gaussian

Collum, Hoffmann, Scheraga

Linux and Mac (64-bit).versions are source code which ChemIT must compile using expensive PGI compiler (below).
(N.B. Executable provided to CCB of Windows versions 32- and 64-bit.)

Orca

 Lancaster (not used by Crane group)

May have been used, but no longer actively maintained, if have it at all: Collum, Hoffmann

SBGrid setup

Crane

 

gromacs

Crane (Lancaster), Lancaster, Scheraga, Widom

 

Compiler: Intel

Scheraga
Hoffmann borrowing it, a bit.

Also, Ananth (at CAC cluster)

Compiler: GCC

 

 

Compiler: PGI

(Q: Installed on any cluster, or is compilation work done on a dedicated Linux workstation instead?)

Used by ChemIT since required to compile Gaussian.

YUM

 

(Yellow Dog) Update manager

Driver: CUDA

Scheraga

 

Cluster software

Researchers are primarily responsible for installation and configuration of these software applications.

  • This software, sometimes used by more than one member (or future member), normally should be stored in the shared software directory dedicated for this purpose. And not in individual's home directory. For example, for Hoffmann's cluster, the shared software directory is /home/hoffmann/bin.

Research group members are still responsible for learning how to use the software, ensuring their own run files are correct, and any associated de-bugging of their files.

Software

Research Group

Group lead for this software

Comments

gamess

Hoffmann
Scheraga?

 

Also, Ananth (at CAC cluster)?
4/2014, on Hoffmann's: As a favor, ChemIT helped researcher finish installation.

VASP

Hoffmann

 

Unusual licensing, via Hoffmann
2011 license (v5.2, as of 4/14). Arrives in source, so must compile (Fotran).
Q: Andreas: Used non-licensed Intel compiler for OpenMPI. But compilers must match?
4/2014: As a favor, ChemIT installed v5.3.5, compiled with GCC compiler.

OpenMPI

Hoffmann

 

See VASP, above. Compilers must match versions? Needs both Fortran and C compilers?

ADF

Hoffmann

 

 

Materials Studio

Hoffmann

 

 

yaehmop

Hoffmann

 

 

molden

Hoffmann

 

 

Quantum Expresso

Hoffmann

 

Also, Ananth (at CAC cluster)?

CUDA coding

Scheraga

Yi He

 

pppp

  • No labels