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The following packages are required for basiv ASE functionality: 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`_.

   **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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   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.

.. _version 24.2: http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=1351
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   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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   A `rasmol src`_ and `binary rpm`_ can be use for installing Rasmol on linux.
You can run ASE without RasMol, you just won't be able to plot atoms with the RasMol plotter.
   You can run ASE without RasMol, you just won't be able to plot atoms with the *RasMol* plotter.
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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
.. _version 24.2: http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=1351
   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*.

   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.
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   At CAMP/Niflheim we call this RPM *python-gnuplot*.    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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   The current version of Pexpect is 2.1, but at Niflheim we use an old version 0.999.    The current version of *Pexpect* is 2.1, but at Niflheim we use an old version 0.999.
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7) **Matplotlib** (Jens Jørgen ?).    RPM packages for *Pexpect* can be found on
   `rpmfind <http://www.rpmfind.net/linux/rpm2html/search.php?query=pexpect&submit=Search+...&system=&arch=>`_.

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>`_.

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.
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or from a CVS repository. or from a svn repository.
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The latest version of Campos ASE is version 2.3. Get the tar-ball here: campos-ase-2.3.4.tar.gz_.
For CVS access to the Campos ASE code see the `Campos CVS`_ page (simply ``cvs checkout CamposASE2``).
Get the source of the latest Campos ASE from svn::
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.. _campos-ase-2.3.4.tar.gz: attachment:campos-ase-2.3.4.tar.gz     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]]
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CentOS Linux
------------

Installation on CentOS Linux is described in the document `Cluster software RPMS <https://wiki.fysik.dtu.dk/niflheim/Cluster_software_-_RPMS>`_.

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)