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wiki:software [2017/05/09 10:54] – adminwiki:software [2021/07/29 15:48] (current) – [Available Software] admin
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 ====== Available Software ====== ====== Available Software ======
  
-The following scientific packages are installed on Keck Center 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]]                         |  16         |/soft/pkg/amber     |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]]         |  2016.2.5  |/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://daltonprogram.org/|Dalton]]           |  2016.2   | /soft/pkg/dalton     | dalton.x  | +|[[http://diracprogram.org/|Dirac]]             | 16.0          |dirac.x  | 
-|[[http://diracprogram.org/|Dirac]]             |  16.0     | /soft/pkg/dirac      | dirac.x  | +|[[http://www.gaussian.com/|Gaussian]]          | g16.B01       |g16 | 
-|[[http://www.gaussian.com/|Gaussian]]          |  g09.d01  |/soft/pkg/g09.d01     |g09 | +|[[http://www.gaussian.com/|Gaussview]]         | 5.0.9         |gview.exe | 
-|[[http://www.gaussian.com/|Gaussview]]         |  5.0.9    |/soft/pkg/gv          |gview.exe | +|[[http://www.gromacs.org/|Gromacs]]            | 5.1.2         |gmx  | 
-|[[http://www.gromacs.org/|Gromacs]]            |  5.0.4   |/soft/pkg/gromacs      |gmx  | +|[[http://www.mathworks.com/products/matlab/|Matlab]] | 2018a   |matlab | 
-|[[http://kepler-project.org|Kepler]]           |  2.4      |/soft/pkg/kepler      |kepler.sh | +|[[http://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm|moe]]| 2020   |moe | 
-|[[http://www.mathworks.com/products/matlab/|Matlab]] |  2013b  |/soft/pkg/matlab  |matlab | +|[[http://simtk.org/home/msmbuilder|MSMBuilder]]| 2.5           |misc.  | 
-|[[http://mgltools.scripps.edu/|mgltools]]      |  1.5.7r1  |/soft/pkg/mgltools    |pmv | +|[[http://www.ks.uiuc.edu/Research/namd/|NAMD]] | 3.0           |namd3 | 
-|[[http://www.clcbio.com/products/molegro/|MMV]] |  2.5.0   |/soft/pkg/Molegro     |mmv | +|[[http://orcaforum.cec.mpg.de/|ORCA]]          | 5.0.1         |orca | 
-|[[http://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm|moe]]|  2014  |/soft/pkg/moe |moe | +|[[http://www.pymol.org|Pymol]]                 | 2.4.0         |pymol | 
-|[[http://simtk.org/home/msmbuilder|MSMBuilder]] |  2.5     |/soft/pkg/msmbuilder  |misc.  | +|[[https://www.rosettacommons.org/|Rosetta]]    | 3.9           |   | 
-|[[http://www.ks.uiuc.edu/Research/namd/|NAMD]] |  2.12     |/soft/pkg/NAMD        |namd2 | +|[[http://www.schrodinger.com|Schrodinger]]     | 2021          |maestro | 
-|[[http://cec.mpg.de/forum/|ORCA]]              |  4.0.0    |/soft/pkg/orca        |orca | +|[[http://www.ks.uiuc.edu/Research/vmd|VMD]]    | 1.9.4         |vmd |
-|[[http://www.pymol.org|Pymol]]                 |  1.8.6.0  |/soft/pkg/pymol       |pymol | +
-|[[http://pyrx.sourceforge.net|PyRx]]           |  0.9      |/soft/pkg/PyRx        |run.sh | +
-|[[https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page|Relion]] |  2.0  | /soft/pkg/relion |relion | +
-|[[https://www.rosettacommons.org/|Rosetta]]    |  3.5      |/soft/pkg/rosetta     |       | +
-|[[http://www.schrodinger.com|Schrodinger]]     |  2017     |/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]]    |  1.9.2    |/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. 1.6.5) is installed in ''/soft/pkg/openmpi-1.6.5-intel''.+
  
 ====== How to use it ====== ====== How to use it ======
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 <code> <code>
 # module avail # module avail
-------------------------------------------- /soft/etc/modules ------------------------------------------- +-------------------------------------- /software/modules/compilers -------------------------------------- 
-amber/14(default)             gromacs-cuda/5.0-gcc(default) openmpi/1.6.2 +gcc/4.8        gcc/4.9        gcc/5.5        gcc/7.3        gcc/8.1        icc/2018.3.222 
-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 +--------------------------------------- /software/modules/python ---------------------------------------- 
-browndye/2016.2.5(default)    kepler/2.4                    orca/2.9.1 +anaconda2 anaconda3 
-calvr/2013.12.2               matlab/2013b(default)         orca/3.0.0 + 
-chem185/1.0                   mgltools/1.5.7r1(default)     orca/3.0.1 +--------------------------------------- /software/modules/nonfree --------------------------------------- 
-csds/2014                     mmv/2.5.0                     orca/3.0.2 +intel/common/2018u2    intel/mkl/2018u2       intel/tbb/2018u2       matlab/2015b 
-cuda/5.0.35(default)          moe/2013                      orca/3.0.3(default) +intel/compilers/2018u2 intel/mpi/2018u2       intel/vtune/2018u2     matlab/2018a 
-cuda/5.5.22                   moe/2014(default)             pymol/1.5 + 
-gaussian/g09.a02              msmbuilder/2.5                pyrx/0.9 +----------------------------------------- /software/modules/mpi ----------------------------------------- 
-gaussian/g09.c01              msms/2.6.1                    rosetta/3.5 +openmpi/1.10      openmpi/2.0.2     openmpi/3.0.0     openmpi/3.1/3.1.3 
-gaussian/g09.d01(default)     namd/2.10                     schrodinger/2015u4 +openmpi/1.10.6    openmpi/2.1       openmpi/3.1/3.1.0 openmpi/3.1/3.1.4 
-gaussview/5.0.9               namd/2.11(default)            schrodinger/2016u1 +openmpi/2.0       openmpi/3.0       openmpi/3.1/3.1.2 
-gcc/4.9.3                     namd-cuda/2.10                schrodinger/2016u2 + 
-glove/2015                    namd-cuda/2.11(default)       schrodinger/2016u3(default) +---------------------------------------- /software/modules/cuda ----------------------------------------- 
-gromacs/4.6b2-gcc             namd-cuda/2.9                 vina/1.1.2 +cuda-10.1 cuda-7.5  cuda-8.0  cuda-9.0  cuda-9.1  cuda-9.2 
-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) +---------------------------------- /software/modules/moleculardynamics ---------------------------------- 
-gromacs/5.0-intel             nvidia/5.0.35(default) +amber/16                    moe/2016                    pymol/1.8.6.0 
-gromacs-cuda/4.6.1-gcc        nvidia/5.5.22+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> </code>
  
Line 75: Line 87:
  
 <code> <code>
-module load pymol+module load pymol/2.3.0
 pymol pymol
 </code> </code>
Line 82: Line 94:
  
 <code> <code>
-module help namd+module help namd/2.13-multicore
 </code> </code>
  
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 ====== Application specific notes ====== ====== 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/16 
-module load cuda/7.5.18 
-</code> 
- 
-===== Cambridge Structural Database ===== 
- 
-To use CSDS execute the following: 
- 
-<code> 
-module load csds 
-cq 
-</code> 
 ===== Gaussian/Gaussview ===== ===== Gaussian/Gaussview =====
  
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 ====== Running non-interactive long jobs ====== ====== Running non-interactive long jobs ======
  
-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 [[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]].
wiki/software.1494352471.txt.gz · Last modified: 2017/05/09 10:54 by admin