The following scientific packages are installed on Keck Center workstations:

The Intel compilers version 12.1.5 are installed in /soft/pkg/intel directory. Use the following command to initialize your environment before using the compilers:

 module load intel

Additionally, a recent version of OpenMPI (v. 1.6.5) is installed in /soft/pkg/openmpi-1.6.5-intel.

The modules package is used to manage, enable and configure scientific applications on the Keck Center workstations. To see what software is available run the following command:

 module avail

you should see something similar to this:

# module avail
------------------------------------------- /soft/etc/modules -------------------------------------------
amber/14(default)             gromacs-cuda/5.0-gcc(default) openmpi/1.6.2
apbs/1.4                      gromacs-cuda/5.0.4-gcc        openmpi/1.6.5(default)
autodock/4.2.6                intel/12.1.5                  openmpi-gcc/1.6.2
browndye/2016.2.5(default)    kepler/2.4                    orca/2.9.1
calvr/2013.12.2               matlab/2013b(default)         orca/3.0.0
chem185/1.0                   mgltools/1.5.7r1(default)     orca/3.0.1
csds/2014                     mmv/2.5.0                     orca/3.0.2
cuda/5.0.35(default)          moe/2013                      orca/3.0.3(default)
cuda/5.5.22                   moe/2014(default)             pymol/1.5
gaussian/g09.a02              msmbuilder/2.5                pyrx/0.9
gaussian/g09.c01              msms/2.6.1                    rosetta/3.5
gaussian/g09.d01(default)     namd/2.10                     schrodinger/2015u4
gaussview/5.0.9               namd/2.11(default)            schrodinger/2016u1
gcc/4.9.3                     namd-cuda/2.10                schrodinger/2016u2
glove/2015                    namd-cuda/2.11(default)       schrodinger/2016u3(default)
gromacs/4.6b2-gcc             namd-cuda/2.9                 vina/1.1.2
gromacs/4.6b2-icc             nbo/6.0                       vmd/1.9.1
gromacs/5.0-gcc(default)      nvidia/4.2.9                  vmd/1.9.2(default)
gromacs/5.0-intel             nvidia/5.0.35(default)
gromacs-cuda/4.6.1-gcc        nvidia/5.5.22

To actually use one of the installed application you need to load the application's environment first and then start the application. For example, to run pymol you need to execute these two steps:

module load pymol
pymol

To get help about the package:

module help namd

You can find more information about the modules management package on this help page. Also here is the module man page.

Before running the CUDA enabled version of pmemd you need to initialize your environment with these two commands:

module load amber/16
module load cuda/7.5.18

To use CSDS execute the following:

module load csds
cq

If you want to run Gaussian or Gaussview you have to be added to the Gaussian unix group - please contact keck-help@keck2.ucsd.edu for assistance.

The Keck II workstations can be used to run non-interactive, long, computationally intensive jobs. All these jobs must be submitted through the SGE queue manger. More information can be found here.