\\
**[[cluster:28|Back]]**

<hi #ffff00>THIS IS THE LIST OF SOFTWARE FOR THE HOST SWALLOWTAIL UNDER OCS 4.4.1, RHEL 4, GlibC 2.3.5-2.19</hi>

The listings below will be updated as software is installed.

In no particular order ...

===== PyPat =====

  * program: python egg, version 1.0)
  * install dir: /share/apps/python-2.6.1/lib/python2.6/site-packages/
  * docs: /share/apps/docs/pypat-1.0
  * www: http://sitemaker.umich.edu/carlsonlab/home.html

The dependencies for PyPal ... drummroll ... incredible!

In order to run some PyPal programs or invoke some of the underlying programs you may have to set some of the publiched environment variables listed below.


**Python**

  * Installed 2.6.1 (see notes below)
  * Must be compiled with zlib module (unsure)
  * Must have Python-PMW (PyMol requirement, unsure)

<code>
export PYTHONHOME=/share/apps/python-2.6.1
</code>

**ImageMagick**

  * Installed 6.4.8-5 (see notes below)

** NumPy**

  * program: (python egg, version 1.2.1)
  * install dir: /share/apps/python-2.6.1/lib/python-2.6.1/site-packages
  * docs: guide posted on web site
  * www: http://numpy.scipy.org

NumPy was configured against the CMKL BLAS and LAPACK by uncommenting the lines for [cmkl] in site.cfg

<code>
export LD_LIBRARY_PATH=/share/apps/intel/cmkl/10.0.011/lib/em64t:$LD_LIBRARY_PATH
export PYTHONHOME=/share/apps/python-2.6.1
</code>

NumPy require the installation of Nose.

**Nose**

  * program: (python egg, version 0.10.4)
  * install dir: /share/apps/python-2.6.1/lib/python-2.6.1/site-packages
  * docs: guide posted on web site
  * www: http://somethingaboutorange.com/mrl/projects/nose

**MatPlotLib**

  * program: (python egg, version 0.98.5.2)
  * install dir: /share/apps/python-2.6.1/lib/python-2.6.1/site-packages
  * docs: 
  * www: http://sourceforge.net/projects/matplotlib

Note: needed to add the location of the numpy python egg to the ''basedir'' array so that setup.py could find the egg.

<code>
export LD_LIBRARY_PATH=/share/apps/intel/cmkl/10.0.011/lib/em64t:$LD_LIBRARY_PATH
export PYTHONHOME=/share/apps/python-2.6.1
</code>

**PyMOL**

  * program: (python egg, versionless)
  * install dir: /share/apps/python-2.6.1/lib/python-2.6.1/site-packages
  * docs: 
  * www: http://sourceforge.net/projects/pymol

  * Note1: Also installed in /share/apps/python/2.5.4: Numpy (against default BLAS and LAPACK libs), MatPlotLib, and PIL in order to install PyMol in this python version (for RIP-scripts to work; did not work because tk-devel include files missing).
  * Note2: Installed /share/apps/python/2.5.4.tk and retraced Note1. Did set for compiling python: ''export LD_RUN_PATH=/usr/lib64''
  * Note3: Also installed package Pmw for 2.5.4.tk.
  * Note4: /share/apps/bin/mypol is the viewer for this python 2.5.4.tk version.

<code>
export LD_LIBRARY_PATH=/share/apps/intel/cmkl/10.0.011/lib/em64t:$LD_LIBRARY_PATH
export PYTHONHOME=/share/apps/python-2.6.1
export PYMOL_PATH=/share/apps/python-2.6.1/lib/python-2.6.1/site-packages/pymol
</code>

PyMOL required the presence of ''libglut'', part of the ''Mesa 3D Graphics Library''.  Had to make apprpriate links in /lib and /lib64.  Then, the Glut.h could nto be found in /usr/include/GL so needed to download and install ''rpm -ivh freeglut-devel-2.2.0-14.x86_64.rpm'' package, on swallowtail only for now.

PyMOL libraries have also been installed in the following location:

<code>
export LD_LIBRARY_PATH=/share/apps/pymol/1.1:$LD_LIBRARY_PATH
</code>





===== NAMD =====

  * program: ''namd2'' (as well as some others) located in **/share/apps/NAMD/NAMD_2.6_Source/Linux-amd64-MPI/**
  * install dir: /share/apps/NAMD
  * docs: on web site
  * www: http://www.ks.uiuc.edu/Research/namd/

there is a sample page here: [[cluster:69|LINK]]

===== NAB =====

  * program: several programs in bin/ directories; main compiler ''nab''
  * install dir: /share/apps/nab-5.1.2
  * docs:doc and examples directories in install dir
  * www: http://www.scripps.edu/mb/case/

Users should set the NABHOME environment variable.  Programs were compiled with ''icc'' with the ''-mpi'' flag.

If using csh/tcsh add to ~/.cshrc

  * source /share/apps/nab-5.1.2/env.csh

or if using sh/bash add to ~/.bashrc

  * . /share/apps/nab-5.1.2/env.sh

===== Dowser =====

  * program: several programs in bin/ and bin/linux/ directories 
  * install dir: /share/apps/dowser
  * docs: DOCS/ directory in install dir
  * www: http://hekto.med.unc.edu:8080/HERMANS/software/DOWSER/index.html

Note: users of dowser should add one of the following lines ...

if using csh/tcsh add to ~/.cshrc


  * source /share/apps/dowser/dowserinit.csh

or if using sh/bash add to ~/.bashrc


  * . /share/apps/dowser/dowserinit.sh




===== Python =====

  * program: python 
  * install dir: /share/apps/python-2.6.1
  * docs: http://www.python.org/doc/
  * www: http://www.python.org/

This newer version of python is in /share/apps/python-2.6.1.  You need to reset your PYTHONPATH and PYTHONHOME env variables to use this version.  For syntax, see the Autodock section below.

  * program: python 
  * install dir: /share/apps/python-2.5.1
  * docs: http://www.python.org/doc/
  * www: http://www.python.org/

The default python is v 2.3.4 installed in /usr/sbin.  The newer version of python is in /share/apps/python-2.5.1.  You need to reset your PYTHONPATH and PYTHONHOME env variables to use this version.  For syntax, see the Autodock section below.

Note:  there is another version of Python (2.4.2) hiding inside MGLtools at  ''/share/apps/mgltools-1.4.6/i86Linux2bin/python''.  Read the section on MGLtools for more information.


===== AutoDock =====

  * program: AutoDock 4.0.1 and AutoGrid 4.0.0 (''autodock4, autogrid4'')
  * install dir: /share/apps/autodock
  * docs: unknown, check web site
  * www: http://autodock.scripps.edu/

  * program Openbabel (v 2.1.1)
  * install dir: /share/apps/openbabel-2.1.1
  * docs: check web site

Note. You need to add the following lines to your ~/.bashrc file or program.

<code>
export PATH=/share/apps/autodock:/share/apps/openbabel-2.1.1/bin:$PATH
export PYTHONPATH=/share/apps/openbabel-2.1.1/site-packages:$PYTHONPATH
export PERL5LIB=/share/apps/openbabel-2.1.1/lib/perl:$PERL5LIB
export LD_LIBRARY_PATH=/share/apps/openbabel-2.1.1/lib:$LD_LIBRARY_PATH
</code>

Note. The perl plugin will not compile. Have a message to the list.\\
 --- //[[hmeij@wesleyan.edu|Meij, Henk]] 2008/01/25 15:39//


===== MGLTools =====

Upgraded to 1.5.2\\
/share/apps/MGLTools/MGLTools-1.5.2/bin\\
 --- //[[hmeij@wesleyan.edu|Meij, Henk]] 2008/08/07 15:37//

  * program: MGLTools v 1.4.6 (''pmv'',''adt'',''vision'',''pythonsh'')
  * install dir: /share/apps/mgltools-1.4.6.
  * docs: http://mgltools.scripps.edu/documentation
  * www: http://mgltools.scripps.edu/

This package works with Autodock.  The 32-bit version of the tools were installed because of the lack of GLIBC-2.4.  You will need to adjust your PYTHONHOME and PYTHONPATH variables. Or you could simply pick one method from these options:

<code>
#1 add the /share/apps/mgltools-1.4.6/share/bin to the path environment variable in .cshrc or .bashrc:
.cshrc:

set path = (/share/apps/mgltools-1.4.6/share/bin /share/apps/mgltools-1.4.6/x86_64Linux2/bin $path)

.bashrc
export PATH=/share/apps/mgltools-1.4.6/share/bin:/share/apps/mgltools-1.4.6/x86_64Linux2/bin:$PATH

#2 create aliases in your .cshrc or .bashrc 

.cshrc:
alias pmv /share/apps/mgltools-1.4.6/share/bin/pmv
alias adt /share/apps/mgltools-1.4.6/share/bin/adt
alias vision /share/apps/mgltools-1.4.6/share/bin/vision
alias pythonsh /share/apps/mgltools-1.4.6/share/bin/pythonsh

.bashrc
alias pmv='/share/apps/mgltools-1.4.6/share/bin/pmv'
alias adt='/share/apps/mgltools-1.4.6/share/bin/adt'
alias vision='/share/apps/mgltools-1.4.6/share/bin/vision'
alias pythonsh='/share/apps/mgltools-1.4.6/share/bin/pythonsh'

#3 source initMGLtools.sh (bash) or initMGLtools.csh (c-shell) found in /share/apps/mgltools-1.4.6
</code>

===== Gaussian =====

  * program: Gaussian 03 Revision D.01/D.02 (''g03'')
  * install dir: /share/apps/gaussian
  * docs: unknown (perhaps ask gpetersson@wes)
  * www: http://gaussian.com/

Note:  in order to use this product you must be a member of group ''gaussian''.  Please send request to the administrator.  You must agree to the terms of our license, and a PDF file will be send to uyou when you request membership.

Details about the Gaussian installation and __how to run Gaussian jobs__ on the cluster can be found at this **[[cluster:47|Link]]**. Please read that page.


===== Java =====

  * program: java, javac etc
  * install dir: /share/apps/java/<version>
  * docs: install install_dir
  * www: http://java.sun.com/

Versions are installed with the most recent linked into users' environments via /usr/local/bin.  To set another flavor as your default java, add the appropriate version to the front of your $PATH variable.

<code>
drwxrwxr-x   9 root root 4096 Aug 20  2007 j2sdk1.4.2_07
drwxr-xr-x   9 root root 4096 Oct  5 06:05 jdk1.5.0_14
drwxr-xr-x   9 root root 4096 Jun 14  2007 jdk1.6.0_02
drwxr-xr-x   7 root root 4096 Nov 10  2005 jre1.5.0_06
drwxr-xr-x  20 root root 4096 Feb 20 11:20 netbeans-6.0.1
</code>

  * program: NetBeans IDE 6.0 (netbeans)
  * install dir: /share/apps/java/
  * docs: 
  * www: http://www.netbeans.org/



===== Matlab =====

  * program: Matlab R2007a with Distributed Computing Engine
  * install dir: /share/apps/matlab/2007a
  * docs: can be loaded via GUI
  * www: [[http://www.mathworks.com/products/distribtb/index.html?s_cid=HP_FP_ML_DistributedComputingToolbox|Distributed Computing Toolbox Link]]

Details about the Matlab configuration/installation and __how to run Matlab jobs__ on the cluster can be found at this **[[cluster:39|Link]]**. Please read that page, the distributed and parallel job submissions are quite different from we were used to on our  matlab host "rintintin".

To install a "client", please obtain the cdroms from Jolee West.  Do not install the license manager.  When prompted for a license file, point the installer to a local file with the relevant license information found in /share/apps/matlab/2007a/LICENSE_FILE.TXT ... you will need to buy the Distributed Computing Toolbox for the "client" install.  Here are some documents with install information and client configurations.

  * Windows {{:cluster:windctcluster.pdf|PDF Link}}
  * Linux {{:cluster:linuxdctcluster.pdf|PDF Link}}

===== R & libRmath =====

  * program: R v2.5.1
  * install dir: (RPM based)
  * docs: rpm -ql R and rpm -ql libRmath
  * www: http://www.r-project.org/


===== Delphi =====

  * program: delphi v4 (precompiled binaries by [[http://luna.bioc.columbia.edu/honiglab/software/DelPhi/readme.html|Honig Labs]])
  * install dir: /share/apps/DELPHI_2004_LINUX
  * docs: examples and data dirs inside install_dir
  * www: http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Main_Page

===== Amber 9 =====

  * program: sander.MPI, pmemd (compiled with intel v10 ifort against TopSpin MPICH libraries)
  * install dir: /share/apps/amber/9
  * docs: doc dir inside install_dir
  * www: http://amber.scripps.edu

For a sample invocation using the TopSpin mpirun view install_dir program 'RUN.SAMPLE'

Some related details about the Amber installation(s) and __how to run Amber jobs__ on the cluster can be found at this **[[cluster:42|Link]]**. Please read that page.

For ''pmemd'' please add the following line to your ~/.bashrc file
<code>
export LD_LIBRARY_PATH=/share/apps/intel/cmkl/9.1.021/lib/em64t:$LD_LIBRARY_PATH
</code>

RIPscripts from http://boscoh/rip was added to the main amber directory.  Required python's imaging library PIL.

===== Amber 10 =====

  * program: sander.MPI, sander.LES.MPI, pmemd (compiled with intel v10 ifort against TopSpin MPICH libraries)
  * install dir: /share/apps/amber/10
  * docs: doc dir inside install_dir, please read Amber10.pdf
  * www: http://amber.scripps.edu

For a sample invocation using the TopSpin mpirun view install_dir program 'RUN.SAMPLE'

Some related details about the Amber installation(s) and __how to run Amber jobs__ on the cluster can be found at this **[[cluster:42|Link]]**. Please read that page.

For ''pmemd'' please add the following line to your ~/.bashrc file
<code>
export LD_LIBRARY_PATH=/share/apps/intel/cmkl/10.0.011/lib/em64t:$LD_LIBRARY_PATH
</code>

AmberTools 1.2 has been installed
 --- //[[hmeij@wesleyan.edu|Meij, Henk]] 2008/07/31 15:26//

===== Compilers =====

==== GNU BinUtils  ====

  * program: several v 2.1.17
  * install dir: /usr/local/[bin|sbin|libexec|man|share|etc...]
  * docs: man program_name
  * www: http://www.gnu.org/software/binutils/

Note:  these binary are located in /usr/local/bin and thus found **before** the Redhat AS4 installed version.  Manipulate your PATH to change that ... for example, set /usr/local at the end of your PATH.

==== G95 Compiler  ====

  * program: G95 v 0.9.1 compiler (g95) compiled with GCC v 4.0.3 (core)
  * install dir: /share/apps/g95-0.9.1
  * docs: G95Manual.pdf inside install_dir
  * www: http://www.g95.org

==== GNU Compilers  ====

  * program: GCC v 4.2.0 compilers (gcc, g++, c++, gcj, gij ... no fortran)
  * install dir: /share/apps/gcc-4.2.0
  * docs: man inside install_dir
  * www: http://gcc.gnu.org

  * program: GCC v 3.4.5
  * install dir: (RPM based)
  * docs: rpm -ql gcc
  * www: http://gcc.gnu.org



==== Intel Compilers (2-user float license) ====

  * can be used on all login nodes as well ...
  * program: Intel compilers (icc, ifort, idbe ... by default in users' $PATH)
  * install dir: /share/apps/intel/[cce|fce|idbe]/10.0.025/
  * (v9.1.043 was our evaluation copy and will remain for some time for compiled programs)

  * docs: man 'compiler_name' and 'compiler_name -help' ... also install_dir/compiler_name/version/doc

  * cluster math library in /share/apps/intel/cmkl/10.0.011 ... by default as MKL_HOME in user ENV
  * cluster math library in /share/apps/intel/cmkl/9.1.023 ... [old]

  * www: http://www.intel.com/cd/software/products/asmo-na/eng/download/eval/219690.htm


==== Intel Threading Building Blocks ====

  * tied to our Intel C compiler license ... v 2.0
  * relevant files sourced at login (setting up LIBRARY_PATH and DYLD_LIBRARY_PATH)
  * install_dir: /share/apps/intel/tbb/2.0
  * docs: docs/ directory inside install_dir
  * web: [[http://www.intel.com/cd/software/products/asmo-na/eng/threading/threadbuildblocks/294797.htm|TBB]]
  

===== Tools =====


==== ImageMagick ====

  * program: ImageMagick-6.4.8-5 
  * install dir: /share/apps/ImageMagick/6.4.8-5
  * docs: inside install_dir/share
  * www: https://www.imagemagick.org/

In order to make this the default in your PATH please issue the command

export PATH=/share/apps/ImageMagick/6.4.8-5/bin:${PATH}

in your shell or add it to ~/.bashrc

==== Rosetta++ ====

  * program: Rosetta++ 2.2.0 (linked in via /usr/local/bin on head node as ''rosetta'') 
  * install dir: /share/apps/rosetta/2.2.0
  * scripts, database & docs: inside install_dir
  * www: https://www.rosettacommons.org/

Please read the license at **''/share/apps/rosetta/LICENSE''**

Note:  this is a 32-bit compilation using target ''gcc64'' and therefore is an "unsupported" configuration.

==== Mopac ====

  * program: mopac.exe (run via command ./runmopac "jobname", expects a "jobname.dat" file) 
  * install dir: /share/apps/Mopac/mopac7
  * example, docs: inside install_dir
  * www: http://www.webmo.net/support/binaries_linux.html#mopac7

==== Misc ====

  * programs: gcmc.exe, mmc.exe , micm, 
  * install dir: /share/apps/bin
  * no documentation, contact the beveridge research group

==== VMD ====

  * program: Visual Molecular Dynamics v1.8.6
  * install dir: /usr/local/bin (with libraries in /usr/local/lib/vmd)
  * docs: http://www.ks.uiuc.edu/Research/vmd/current/docs.html
  * www: http://www.ks.uiuc.edu/Research/vmd/

  * tutorial tools installed ...
  * located at: [[http://www.ks.uiuc.edu/Training/Tutorials/vmd-ref/imgmv/tutorial-html/node1.html#SECTION0001100000000000000|External Link]]

  * POV-Ray v3.6 (program ''povray'')
  * install dir: /usr/local/bin)
  * docs: /usr/local/share/doc/povray-3.6/html/
  * www: http://www.povray.org

Note:  if users wish to further customize their home dir installation, enter these commands


| cd /share/apps/src/vmd/povray-3.6 |
| ./install -no-arch-check user |
| ./install -no-arch-check kde |
| ./install -no-arch-check test |

  * MSMS (not installed)
  * (url not found)

  * ImageMagick v6.0.7.1-14
  * install dir: (RPM based)
  * docs: rpm -ql ImageMagick

  * NetPBM v10.25-2
  * install dir: (RPM based)
  * docs: rpm -ql netpbm


==== Qt ====

  * program: Qt v 4.3.0 
  * install dir: /share/apps/qt-4.3.0
  * docs: doc/html inside install_dir
  * www: http://trolltech.com

==== xmgrace ====

  * program: Grace v 5.1.20 (with X11, EPS, MIF, JPEG, PNG support)
  * install dir: /share/apps/grace
  * docs: user guide is located in doc/ inside install dir
  * www: http://plasma-gate.weizmann.ac.il/Grace/


==== ddd ====

  * program: Data Display Debugger v 3.3.9
  * install dir: (RPM based)
  * docs: rpm -ql ddd
  * www: http://www.gnu.org/software/ddd/


==== MPlayer ====
  * program: MPlayer Media Player v 1.0rc2
  * executable location: /share/apps/bin/mplayer
  * docs: http://linuxhelp.150m.com/installs/mplayer.htm
  * www: http://www.mplayerhq.hu

==== PCASuite ====
  * program: PCAsuite - Molecular Modelling and Bioinformatics Group
  * executable location: /usr/local/bin on swallowtail: pcazip, pcaunzip, pczdump
  * docs: http://mmb.pcb.ub.es/software/pcasuite.html
  * www: http://mmb.pcb.ub.es

===== MPI =====

==== MVAMPICH 0.9.9 ====

  * program: Message Passing Interface v 0.9.9
  * install dir: /share/apps/mvampich
  * docs: inside install dir in dirs man & doc
  * www: http://mvapich.cse.ohio-state.edu/index.shtml


==== OpenMPI 1.2 ====

  * program: Message Passing Interface v 1.2.2
  * install dir: /share/apps/openmpi-1.2/bin/  (compiled with gcc/g95, no infiniband libs)
  * install dir: /share/apps/openmpi-1.2_intel/bin/  (compiled with icc/ifort, with infiniband libs)
  * docs: inside install dir in dirs man & share
  * www: http://www.open-mpi.org/

==== TopSpin 0.9.5 ====

install dir: /usr/local/topsin/mpi/mpich/bin/

==== Gnu MPICH 1.2.7 ====

install dir: /opt/mpich/gnu/bin/

\\
**[[cluster:28|Back]]**