Keck Center Wiki

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====== Available Software ======

These are some of the scientific packages installed on Keck Center workstations:

^ Installed software                             ^ Version       ^ Executable ^
|[[http://ambermd.org|Amber]]                   | 20            |sander, pmemd, pmemd.cuda |
|[[http://avogadro.sourceforge.net/|Avogadro]]  | 1.0.3         |avogadro |
|[[http://www.poissonboltzmann.org/apbs|APBS]]  | 3.0.0         |apbs |
|[[http://browndye.ucsd.edu/|BrownDye]]         | 2.0           |bd_top |
|[[http://www.charmm.org|charmm]]               | c41b2         |charmm | 
|[[http://daltonprogram.org/|Dalton]]           | 2016.2        |dalton.x  |
|[[http://diracprogram.org/|Dirac]]             | 16.0          |dirac.x  |
|[[http://www.gaussian.com/|Gaussian]]          | g16.B01       |g16 |
|[[http://www.gaussian.com/|Gaussview]]         | 5.0.9         |gview.exe |
|[[http://www.gromacs.org/|Gromacs]]            | 5.1.2         |gmx  |
|[[http://www.mathworks.com/products/matlab/|Matlab]] | 2018a   |matlab |
|[[http://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm|moe]]| 2020   |moe |
|[[http://simtk.org/home/msmbuilder|MSMBuilder]]| 2.5           |misc.  |
|[[http://www.ks.uiuc.edu/Research/namd/|NAMD]] | 3.0           |namd3 |
|[[http://orcaforum.cec.mpg.de/|ORCA]]          | 5.0.1         |orca |
|[[http://www.pymol.org|Pymol]]                 | 2.4.0         |pymol |
|[[https://www.rosettacommons.org/|Rosetta]]    | 3.9           |   |
|[[http://www.schrodinger.com|Schrodinger]]     | 2021          |maestro |
|[[http://www.ks.uiuc.edu/Research/vmd|VMD]]    | 1.9.4         |vmd |

====== How to use it ======


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:

<code>
# module avail
-------------------------------------- /software/modules/compilers --------------------------------------
gcc/4.8        gcc/4.9        gcc/5.5        gcc/7.3        gcc/8.1        icc/2018.3.222

--------------------------------------- /software/modules/python ----------------------------------------
anaconda2 anaconda3

--------------------------------------- /software/modules/nonfree ---------------------------------------
intel/common/2018u2    intel/mkl/2018u2       intel/tbb/2018u2       matlab/2015b
intel/compilers/2018u2 intel/mpi/2018u2       intel/vtune/2018u2     matlab/2018a

----------------------------------------- /software/modules/mpi -----------------------------------------
openmpi/1.10      openmpi/2.0.2     openmpi/3.0.0     openmpi/3.1/3.1.3
openmpi/1.10.6    openmpi/2.1       openmpi/3.1/3.1.0 openmpi/3.1/3.1.4
openmpi/2.0       openmpi/3.0       openmpi/3.1/3.1.2

---------------------------------------- /software/modules/cuda -----------------------------------------
cuda-10.1 cuda-7.5  cuda-8.0  cuda-9.0  cuda-9.1  cuda-9.2

---------------------------------- /software/modules/moleculardynamics ----------------------------------
amber/16                    moe/2016                    pymol/1.8.6.0
amber/18                    moe/2018                    pymol/2.1.1
apbs/2018.2.1               moe/2019                    pymol/2.3.0
autodock/4.2.6              namd/2.12-multicore         rosetta/3.5
blender/2.79-git            namd/2.12-multicore-CUDA    rosetta/3.9
browndye/2018.5.1           namd/2.13-multicore         schrodinger/2018u4
browndye/2.0-2018.6.12      namd/2.13-multicore-CUDA    schrodinger/2019u1
charmm/41b2                 openeye/2018                schrodinger/2019u2(default)
do_x3dna/2016.4             openeye/2019(default)       situs/2.8
gromacs/2018.3-ubuntu       pdb2pqr/2018.2.1            vmd/1.9.3
gromacs/5.1.2               povme/2.0                   vmd/1.9.4a35
mgltools/1.5.7rc1           povme/2018.6.21-git         x3dna/2.3
modeller/9.19               povray/3.7                  xmgrace/5.1.25

----------------------------------------- /software/modules/qm ------------------------------------------
dftbplus/18.1(default)     gaussian/09.d01            orca/4.0.1
dftbplus/openmpi/1.10/18.1 gaussian/09-D01            orca/4.0.1.2
dftbplus/openmpi/2.0/18.1  gaussian/16.B01-avx2       orca/4.1.1
dftbplus/openmpi/2.1/18.1  gaussian/16.B01-sse4       orca/4.2.0
dftbplus/openmpi/3.0/18.1  gaussview/5.0.9            postg/2018-06-12
dftbplus/openmpi/3.1/18.1  nbo/6.0
gaussian/09.c01            orca/4.0.0

------------------------------------ /usr/share/Modules/modulefiles -------------------------------------
dot         module-git  module-info modules     null        use.own

------------------------------------------- /etc/modulefiles --------------------------------------------
mpi/openmpi-x86_64
</code>

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:

<code>
module load pymol/2.3.0
pymol
</code>

To get help about the package:

<code>
module help namd/2.13-multicore
</code>

You can find more information about the modules management [[http://modules.sourceforge.net|package]] on this help [[https://www.nersc.gov/users/software/nersc-user-environment/modules/|page]]. Also here is the module [[http://modules.sourceforge.net/man/module.html|man page]].
====== Application specific notes ======


===== Gaussian/Gaussview =====

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.

====== Running non-interactive long jobs ======

The Keck workstations can be used to run non-interactive, long, computationally intensive jobs. All these jobs must be submitted through the SLURM queue manger. More information can be found [[wiki:slurm|here]].