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Requirements for ASE
====================
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------------
Requirements
------------
The following packages are required for basic ASE functionality:
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1) Python 2.2 or later is required. Python is available from
  http://www.python.org.
1) **2.2 <= Python <= 2.4** is required. Python is available from `http://www.python.org`_.
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2) Numeric Python (http://numpy.sf.net).
   
   The latest version 24.0 **does not work**. XXXX CHECK THIS!
   **Warning** due to the unmaintained `Numeric <http://sourceforge.net/projects/numpy/files/Old%20Numeric/>`_ package, ASE2 does not work on 64-bit systems with python version > 2.4.
   If this is you case consider using the new `ase <https://wiki.fysik.dtu.dk/ase>`_ package.
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3) Scientific Python
   (http://starship.python.net/~hinsen/ScientificPython).
2) **Numeric Python**. Use the latest `version 24.2`_.
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   If you are using a Numeric version > 23.1, make sure to
   use the latest version of Scientific Python 2.4.9.
   Build preferably from our SRPM (see `Cluster software RPMS <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS>`_)
   or edit **customize.py** file to configure **Numeric Python** to use the system lapack library.
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4) Rasmol
   (http://www.openrasmol.org/)
.. _version 24.2: http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=1351
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   A `rasmol src`_ and `binary rpm`_ can be use for installing Rasmol on linux. 3) **Scientific Python** from `http://dirac.cnrs-orleans.fr/ScientificPython/`_.
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   You can run ASE without RasMol, you just won't be able to plot atoms with the RasMol plotter.    Use the 2.4.11 version. Make sure to install the full netcdf the package (containing required netcdf.h file)
   before bulding **Scientific Python**.
   See `Cluster software RPMS <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS>`_.
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.. _rasmol src: ../download/rasmol-2.7.2.1.1-2.rhfc1.fys.src.rpm
.. _binary rpm: ../download/rasmol-2.7.2.1.1-2.rhfc1.fys.i586.rpm
The following packages are optional, since they enable the use of some specific external tools.
You only need to install these tools if you want to use the extra tools mentioned:
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5) Gnuplot ??? XXXXXX 4) **Rasmol** from `http://www.openrasmol.org/`_.
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   You can run ASE without RasMol, you just won't be able to plot atoms with the *RasMol* plotter.
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------------
Installation
------------
   Build *RasMol* from our SRPM (see `Cluster software RPMS <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS>`_).
   Our SRPM uses a python wrapper
   (see http://bioinformatics.org/pipermail/molvis-list/2005q2/000173.html), which allows
   to run *RasMol* on remote displays (see below). Alternatively the source code of *RasMol*
   could be patched (see `<http://lists.centos.org/pipermail/centos/2006-February/060793.html>`_).
   For those who prefer to patch the source, it is included in SRPM, but requires
   uncommenting the corresponding line in the spec *file*.
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   A trick for running *Rasmol* on remote displays.
   Check out your X-Windows DISPLAY variable::
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From tar file
-------------
     # echo $DISPLAY
     localhost:11.0
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1) The latest version of Campos ASE is version 2.3. Get it here: CamposASE-2.3.tar.gz_    then replace ``localhost`` with ``127.0.0.1``::
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.. _CamposASE-2.3.tar.gz: http://www.camp.dtu.dk/campos/download/CamposASE-2.3.tar.gz      # setenv DISPLAY 127.0.0.1:11.0
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.. _nightly release: http://dcwww.fysik.dtu.dk/campos/ASE/asetest.html    (Be sure that the number after the : is the same as before!). Then Rasmol works!
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   Why does this work? Rasmol recognize the ``localhost`` in the ``$DISPLAY`` variable and then it uses a faster way to update the display, but one that only works locally -
   it is fooled by *ssh forwarding* the apparently local display to the remote machine you are sitting at.
   ``127.0.0.1`` is the IP number of ``localhost``, but Rasmol does not recognize that.
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2) Unpack the tarball and go to the ``CamposASE-x.y`` directory:: 5) **Gnuplot**. ASE can use *Gnuplot* via the Gnuplot-Python interface from `http://sourceforge.net/projects/gnuplot-py/`_.
   At CAMP/Niflheim we call this RPM *python-gnuplot*. Use the 1.7 version.
   See `Cluster software RPMS <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS>`_.
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     [hugo@cpu1 hugo]$ cd CamposASE-x.y 6) **Python Pexpect** from `http://pexpect.sourceforge.net/`_.
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3) Install with the standard::    The current version of *Pexpect* is 2.1, but at Niflheim we use an old version 0.999.
   Both versions can be downloaded from the above site.
   At CAMP/Niflheim we install the *Pexpect* RPM under the name of *python-pexpect*.
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     [hugo@cpu1 CamposASE-x.y]$ python setup.py install    RPM packages for *Pexpect* can be found on
   `rpmfind <http://www.rpmfind.net/linux/rpm2html/search.php?query=pexpect&submit=Search+...&system=&arch=>`_.
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4) Make sure that everything works by running the test suite:: 7) **Matplotlib** `http://matplotlib.sourceforge.net/`_.
   Use the 0.90.0 version.
   See `Cluster software RPMS <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS>`_.
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     [hugo@cpu1 CamposASE-x.y]$ cd ASE/Tests
     [hugo@cpu1 CamposASE-x.y]$ python test.py
8) **vtk** `http://www.vtk.org/`_.
   After installation you may need (if **libvtkRenderingPythonTkWidgets.so** is missing) to make a link::

        ln -s /usr/lib/libvtkRenderingPythonTkWidgets.so.5.0 /usr/lib/libvtkRenderingPythonTkWidgets.so

   and set the path manually::

        export VTK_TK_WIDGET_PATH=/usr/lib

   Use the 5.0.3 version.

Installation of a Python-based package
======================================

A Python-based package such as ASE or any of the above mentioned extra packages are usually downloaded as a tar-ball
or from a svn repository.

In order to install the package you have two options (both require superuser priviledges):

1. Install as a Python package::

      python setup.py install

2. Build an RPM package and install it on one or many machines::

      python setup.py bdist_rpm

   You have to locate the finished RPM package after building, it may be in the ``dist/`` subdirectory if correctly implemented,
   or in another directory such as ``build/bdist.linux-x86_64/rpm/RPMS/`` (for the x86_64 architecture).

If you don't have root permissions, you will need to add the package directory to your ``PYTHONPATH``
environment variable and use your local copy of the code.

Installation of ASE
===================

Get the source of the latest Campos ASE from svn::

    cd
    svn checkout https://USER@svn.fysik.dtu.dk/projects/CamposASE2/trunk CamposASE2

where "USER@" part has to be skipped for anonymous access.

Alternatively, get the tar-ball (usually slightly outdated) here: campos-ase-2.3.13.tar.gz_.

.. _campos-ase-2.3.13.tar.gz: [[attachment:campos-ase-2.3.13.tar.gz]]

Make sure that everything works by running the test suite::

     cd ASE/Tests
     python test.py
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4) To get started, point your browser at the CamposASE homepage
   (http://wiki.fysik.dtu.dk/ase).


Step 3 requires root permissions - if you don't have that, you will
need to put the ``CamposASE-x.y`` directory in your ``PYTHONPATH``
environment variable, and use your local copy of the code.

From CVS
--------

For CVS access to the CamposASE code see the
`Campos CVS`_ page.
After you have obtained the code via CVS, go to step 3 in the
previus section to install the code.
To get started with Campos ASE, point your browser at the `CamposASE homepage <http://wiki.fysik.dtu.dk/ase>`_.
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CentOS Linux
------------
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------- Installation on CentOS Linux is described in the document `Cluster software RPMS <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS>`_.
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------- =======

Download and install ASE

Requirements for ASE

The following packages are required for basic ASE functionality:

  1. 2.2 <= Python <= 2.4 is required. Python is available from http://www.python.org.

    Warning due to the unmaintained Numeric package, ASE2 does not work on 64-bit systems with python version > 2.4. If this is you case consider using the new ase package.

  2. Numeric Python. Use the latest version 24.2.

    Build preferably from our SRPM (see Cluster software RPMS) or edit customize.py file to configure Numeric Python to use the system lapack library.

  1. Scientific Python from http://dirac.cnrs-orleans.fr/ScientificPython/.

    Use the 2.4.11 version. Make sure to install the full netcdf the package (containing required netcdf.h file) before bulding Scientific Python. See Cluster software RPMS.

The following packages are optional, since they enable the use of some specific external tools. You only need to install these tools if you want to use the extra tools mentioned:

  1. Rasmol from http://www.openrasmol.org/.

    You can run ASE without RasMol, you just won't be able to plot atoms with the RasMol plotter.

    Build RasMol from our SRPM (see Cluster software RPMS). Our SRPM uses a python wrapper (see http://bioinformatics.org/pipermail/molvis-list/2005q2/000173.html), which allows to run RasMol on remote displays (see below). Alternatively the source code of RasMol could be patched (see http://lists.centos.org/pipermail/centos/2006-February/060793.html). For those who prefer to patch the source, it is included in SRPM, but requires uncommenting the corresponding line in the spec file.

    A trick for running Rasmol on remote displays. Check out your X-Windows DISPLAY variable:

    # echo $DISPLAY
    localhost:11.0

    then replace localhost with 127.0.0.1:

    # setenv DISPLAY 127.0.0.1:11.0

    (Be sure that the number after the : is the same as before!). Then Rasmol works!

    Why does this work? Rasmol recognize the localhost in the $DISPLAY variable and then it uses a faster way to update the display, but one that only works locally - it is fooled by ssh forwarding the apparently local display to the remote machine you are sitting at. 127.0.0.1 is the IP number of localhost, but Rasmol does not recognize that.

  2. Gnuplot. ASE can use Gnuplot via the Gnuplot-Python interface from http://sourceforge.net/projects/gnuplot-py/. At CAMP/Niflheim we call this RPM python-gnuplot. Use the 1.7 version. See Cluster software RPMS.
  3. Python Pexpect from http://pexpect.sourceforge.net/.

    The current version of Pexpect is 2.1, but at Niflheim we use an old version 0.999. Both versions can be downloaded from the above site. At CAMP/Niflheim we install the Pexpect RPM under the name of python-pexpect.

    RPM packages for Pexpect can be found on rpmfind.

  4. Matplotlib http://matplotlib.sourceforge.net/. Use the 0.90.0 version. See Cluster software RPMS.
  5. vtk http://www.vtk.org/. After installation you may need (if libvtkRenderingPythonTkWidgets.so is missing) to make a link:

    ln -s /usr/lib/libvtkRenderingPythonTkWidgets.so.5.0 /usr/lib/libvtkRenderingPythonTkWidgets.so

    and set the path manually:

    export VTK_TK_WIDGET_PATH=/usr/lib

    Use the 5.0.3 version.

Installation of a Python-based package

A Python-based package such as ASE or any of the above mentioned extra packages are usually downloaded as a tar-ball or from a svn repository.

In order to install the package you have two options (both require superuser priviledges):

  1. Install as a Python package:

    python setup.py install
  2. Build an RPM package and install it on one or many machines:

    python setup.py bdist_rpm

    You have to locate the finished RPM package after building, it may be in the dist/ subdirectory if correctly implemented, or in another directory such as build/bdist.linux-x86_64/rpm/RPMS/ (for the x86_64 architecture).

If you don't have root permissions, you will need to add the package directory to your PYTHONPATH environment variable and use your local copy of the code.

Installation of ASE

Get the source of the latest Campos ASE from svn:

cd
svn checkout https://USER@svn.fysik.dtu.dk/projects/CamposASE2/trunk CamposASE2

where "USER@" part has to be skipped for anonymous access.

Alternatively, get the tar-ball (usually slightly outdated) here: campos-ase-2.3.13.tar.gz.

Make sure that everything works by running the test suite:

cd ASE/Tests
python test.py

To get started with Campos ASE, point your browser at the CamposASE homepage.

Gentoo Linux

Installation on Gentoo Linux is described in the document Installing CAMPOS software on Gentoo Linux.

CentOS Linux

Installation on CentOS Linux is described in the document Cluster software RPMS.

License

The CAMPOS Atomic Simulation Environment is released under the GNU Public License version 2. See the file LICENSE which accompanies the downloaded files, or see the license at GNU's web server at http://www.gnu.org/licenses/gpl.html.

ase2: Download (last edited 2010-10-20 09:11:16 by localhost)