Hoffman2:Software Tools: Difference between revisions

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: '''NOTE: If you've never used a *NIX text editor, please read a bit about some of them [[Text Editors|here]] before proceeding.'''
[[Hoffman2|Back to all things Hoffman2]]
[[Hoffman2|Back to all things Hoffman2]]


==Setting Up Your Account to Access the Tools==
: '''NOTE: If you've never used a *NIX text editor, please read a bit about some of them [[Text Editors|here]] before proceeding.'''
In order to access all the great software packages that have been installed on Hoffman2 for the FMRI usergroup (list below), you need to edit your Bash Profile on the cluster.  Follow these easy steps:
In order to access all the great software packages that have been installed on Hoffman2 for the FMRI usergroup (list below), you need to edit your Bash Profile on the cluster.  Follow these easy steps:
# [[Hoffman2:Accessing the Cluster#SSH - Command Line|SSH into Hoffman2]] and make sure you are in your home directory (type the command <code>cd</code> and press enter).
# [[Hoffman2:Accessing the Cluster#SSH - Command Line|SSH into Hoffman2]] and make sure you are in your home directory (type the command <code>cd</code> and press enter).
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#:: CTRL+c</code>
#:: CTRL+c</code>
# Logout of Hoffman2.  The next time you log in, extra login messages will appear and you will have access to the FMRI usergroup software packages.
# Logout of Hoffman2.  The next time you log in, extra login messages will appear and you will have access to the FMRI usergroup software packages.
==List of Tools==
Under Construction...
===GCC===
===LAPACK===
===BLAS===
===GLIB===
===C++===
===CMake===
===CPACK===
===
===Python2.7===
====Packages====
=====CVXOPT=====
=====Cython=====
=====Gnuplot=====
=====IPython=====
=====matplotlib=====
=====nibabel=====
=====nifti=====
=====nipype=====
=====nose=====
=====numpy=====
=====pydicom=====
=====pygments=====
=====pypr=====
=====PyQt4=====
=====pytz=====
=====pywt=====
=====pyximport=====
=====scikits=====
=====scipy=====
=====sklearn=====
=====sphinx=====
=====sympy=====
=====traits=====
=====virtualenv=====
=====xcbgen=====

Revision as of 00:06, 14 March 2012

Back to all things Hoffman2

Setting Up Your Account to Access the Tools

NOTE: If you've never used a *NIX text editor, please read a bit about some of them here before proceeding.

In order to access all the great software packages that have been installed on Hoffman2 for the FMRI usergroup (list below), you need to edit your Bash Profile on the cluster. Follow these easy steps:

  1. SSH into Hoffman2 and make sure you are in your home directory (type the command cd and press enter).
  2. Open the file .bash_profile for editing. With VIM you would type
    With VIM you would type
    vim .bash_profile
    With Emacs you would type
    emacs .bash_profile
  3. Paste in the lines
    source /u/home/FMRI/apps/etc/profile
    umask 007
  4. Save and close out the file
    With VIM you would type
    ESC
    :wq
    ENTER
    With Emacs you would type
    CTRL+x
    CTRL+c
  5. Logout of Hoffman2. The next time you log in, extra login messages will appear and you will have access to the FMRI usergroup software packages.


List of Tools

Under Construction...

GCC

LAPACK

BLAS

GLIB

C++

CMake

CPACK

=

Python2.7

Packages

CVXOPT
Cython
Gnuplot
IPython
matplotlib
nibabel
nifti
nipype
nose
numpy
pydicom
pygments
pypr
PyQt4
pytz
pywt
pyximport
scikits
scipy
sklearn
sphinx
sympy
traits
virtualenv
xcbgen