Differences

This shows you the differences between two versions of the page.

--- wiki:software [2016/08/03 12:03] – admin
+++ wiki:software [2021/07/29 15:48] (current) – [Available Software] admin
@@ Line 1: / Line 1: @@
 ====== Available Software ======
-The following scientific packages are installed on KeckII workstations:
+These are some of the scientific packages installed on Keck Center workstations:
-^ Installed software                             ^ Version    ^ Location                    ^ Executable ^
+^ Installed software                             ^ Version       ^ Executable ^
-|[[http://amber|Amber]]                         |  14         |/soft/pkg/ambe         |sander, pmemd, pmemd.cuda |
+|[[http://ambermd.org|Amber]]                   | 20            |sander, pmemd, pmemd.cuda |
-|[[http://avogadro.sourceforge.net/|Avogadro]]  |  1.0.3      |                              |avogadro  |
+|[[http://avogadro.sourceforge.net/|Avogadro]]  | 1.0.3         |avogadro |
-|[[http://www.poissonboltzmann.org/apbs|APBS]]  |  1.4        |/soft/pkg/APBS            |apbs |
+|[[http://www.poissonboltzmann.org/apbs|APBS]]  | 3.0.0         |apbs |
-|[[http://browndye.ucsd.edu/|BrownDye]]         |  2012.9.25  |/soft/pkg/browndye  |bd_top |
+|[[http://browndye.ucsd.edu/|BrownDye]]         | 2.0           |bd_top |
-|[[http://ivl.calit2.net/wiki/index.php/CalVR|CalVR]]|  2013.12.2  |/soft/pkg/calvr  |CalVR |
+|[[http://www.charmm.org|charmm]]               | c41b2         |charmm |
-|[[http://www.ccdc.cam.ac.uk| Cambridge Structural Database]] |  2014  | /soft/pkg/csds  | cq  |
+|[[http://daltonprogram.org/|Dalton]]           | 2016.2        |dalton.x  |
-|[[http://www.gaussian.com/|Gaussian]]          |  g09.d01    |/soft/pkg/g09.d01             |g09 |
+|[[http://diracprogram.org/|Dirac]]             | 16.0          |dirac.x  |
-|[[http://www.gaussian.com/|Gaussview]]         |  5.0.9      |/soft/pkg/gv            |gview.exe |
+|[[http://www.gaussian.com/|Gaussian]]          | g16.B01       |g16 |
-|[[http://www.gromacs.org/|Gromacs]]             |  5.0        |/soft/pkg/gromacs         |gmx  |
+|[[http://www.gaussian.com/|Gaussview]]         | 5.0.9         |gview.exe |
-|[[http://kepler-project.org|Kepler]]           |  2.4        |/soft/pkg/kepler          |kepler.sh |
+|[[http://www.gromacs.org/|Gromacs]]            | 5.1.2         |gmx  |
-|[[http://www.mathworks.com/products/matlab/|Matlab]] |  2013b  |/soft/pkg/matlab     |matlab |
+|[[http://www.mathworks.com/products/matlab/|Matlab]] | 2018a   |matlab |
-|[[http://mgltools.scripps.edu/|mgltools]]      |  1.5.6r3    |/soft/pkg/mgltools   |pmv |
+|[[http://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm|moe]]| 2020   |moe |
-|[[http://www.clcbio.com/products/molegro/|MMV]] |  2.5.0     |/soft/pkg/Molegro/MMV         |mmv |
+|[[http://simtk.org/home/msmbuilder|MSMBuilder]]| 2.5           |misc.  |
-|[[http://simtk.org/home/msmbuilder|MSMBuilder]] |  2.5       |/soft/pkg/msmbuilder      |misc.  |
+|[[http://www.ks.uiuc.edu/Research/namd/|NAMD]] | 3.0           |namd3 |
-|[[http://www.ks.uiuc.edu/Research/namd/|NAMD]] |  2.9        |/soft/pkg/NAMD          |namd2 |
+|[[http://orcaforum.cec.mpg.de/|ORCA]]          | 5.0.1         |orca |
-|[[http://cec.mpg.de/forum/|ORCA]]              |  3.0.2      |/soft/pkg/orca          |orca |
+|[[http://www.pymol.org|Pymol]]                 | 2.4.0         |pymol |
-|[[http://www.pymol.org|Pymol]]                 |  1.5        |/soft/pkg/pymol |pymol |
+|[[https://www.rosettacommons.org/|Rosetta]]    | 3.9           |   |
-|[[http://pyrx.sourceforge.net|PyRx]]           |  0.9        |/soft/pkg/PyRx            |run.sh |
+|[[http://www.schrodinger.com|Schrodinger]]     | 2021          |maestro |
-|[[https://www.rosettacommons.org/|Rosetta]]    |  3.0        |/soft/pkg/Rosetta             |       |
+|[[http://www.ks.uiuc.edu/Research/vmd|VMD]]    | 1.9.4         |vmd |
-|[[http://www.schrodinger.com|Schrodinger]]     |  2016       |/soft/pkg/schrodinger  |maestro |
-|[[http://vina.scripps.edu/|vina]]              |  1.1.2      |/soft/pkg/autodock_vina |vina |
-|[[http://www.ks.uiuc.edu/Research/vmd|VMD]]    |  1.9.1      |/soft/pkg/vmd           |vmd |
-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. 1.6.2) is installed in ''/soft/pkg/openmpi-1.6.2-intel''.
 ====== How to use it ======
-The ''modules'' package is used to manage, enable and configure scientific applications on the KeckII workstations. To see what software is available run the following command:
+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
@@ Line 45: / Line 35: @@
 <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
--------------------------------- /soft/etc/modules --------------------------------
+--------------------------------------- /software/modules/python ----------------------------------------
-amber/12                  gaussview/5.0.9           namd-cuda/2.9
+anaconda2 anaconda3
-apbs/1.4                  intel/12.1.5              nvidia/cuda/4.2.9
-browndye/2012.9.25        matlab/2012a              pymol/1.5
+--------------------------------------- /software/modules/nonfree ---------------------------------------
-gaussian/g09.a02          mgltools/1.5.6r3          schrodinger/2012
+intel/common/2018u2    intel/mkl/2018u2       intel/tbb/2018u2       matlab/2015b
-gaussian/g09.c01(default) namd/2.9                  vina/1.1.2
+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>
@@ Line 57: / Line 87: @@
 <code>
-module load pymol
+module load pymol/2.3.0
 pymol
 </code>
@@ Line 64: / Line 94: @@
 <code>
-module help namd
+module help namd/2.13-multicore
 </code>
@@ Line 70: / Line 100: @@
 ====== Application specific notes ======
-===== Amber =====
-Before running the CUDA enabled version of pmemd you need to initialize your environment with these two commands:
-<code>
-module load amber
-module load nvidia
-</code>
-===== Cambridge Structural Database =====
-To use CSDS execute the following:
-<code>
-module load csds
-cq
-</code>
 ===== Gaussian/Gaussview =====
@@ Line 93: / Line 107: @@
 ====== Running non-interactive long jobs ======
-The KeckII 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 [[wiki:sge|here]].
+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]].