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Updated readme and license, cleaning up unneeded files.

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Niels Müller
2017-11-14 12:39:29 +01:00
parent d178df5c7f
commit 5030322f87
8 changed files with 34 additions and 85 deletions
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3
.gitmodules vendored
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[submodule "gromacs"]
path = gromacs
url = git://git.gromacs.org/gromacs.git

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LICENSE
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MIT License Copyright (c) 2017, Niels Müller.
All rights reserved.
Copyright (c) 2016 Niels A. Müller Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
Permission is hereby granted, free of charge, to any person obtaining a copy * Redistributions of source code must retain the above copyright
of this software and associated documentation files (the "Software"), to deal notice, this list of conditions and the following disclaimer.
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all * Redistributions in binary form must reproduce the above
copies or substantial portions of the Software. copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * Neither the name of the copyright holder nor the names of any
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, contributors may be used to endorse or promote products derived
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE from this software without specific prior written permission.
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
SOFTWARE. LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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README.md
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# Pygmx # Pygmx
A Cython wrapper for the shared library of GROMACS 5.1. A Cython wrapper for the shared library of GROMACS 2016
## Installation ## Installation
Pygmx requires some python packages and an installation of GROMACS 5.1. Pygmx requires some python packages and an installation of GROMACS 2016.
### Python requirements ### Python requirements
@ -15,48 +15,30 @@ Pygmx needs mainly two python packages to be installed, which are available in a
### Gromacs installation ### Gromacs installation
Pygmx requires the shared library and header files of Gromacs 5.1 or higher to be installed. Pygmx requires the shared library and header files of Gromacs 2016 to be installed.
Note that pygmx also supports the Gromacs-2016 version.
Checkout the followng git branch if this version of Gromacs is desired:
git checkout gromacs-2016
Note that Gromacs is backwards compatible, i. e. files produced by the 5.1 version will also work in the 2016 version.
But Gromacs-2016 is required to load files of the 2016 version.
#### Using a module
If gromacs is installed as a module in your system, run
module load gromacs/5.1
and skip to the section *Installing pygmx*.
Note that on the AG Vogel intranet pygmx is available through the module `mdevaluate`.
#### Through package manager #### Through package manager
On many Unix distributions Gromacs may be installed through the package manager. On many Unix distributions, Gromacs may be installed through the package manager.
The required packages, which provide the headers, are usually named `gromacs-devel` or `gromcas-dev`. The required packages, which provide the headers, are usually named `gromacs-devel` or `gromcas-dev`.
#### Manual build #### Manual build
To build the shared library manually, follow the [official installation instructions](http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html). To build the shared library manually, follow the [official installation instructions](http://manual.gromacs.org/documentation/2016.4/install-guide/index.html).
Make sure to source the `GMXRC` script, which sets the environment variable `LD_LIBRARY_PATH` to the correct location or set this variable manually. Make sure to source the `GMXRC` script, which sets the environment variable `LD_LIBRARY_PATH` to the correct location or set this variable manually.
Don't bother with advanced features like GPU support if the Gromacs installation will only be used for pygmx, Don't bother with advanced features like GPU support if the Gromacs installation will only be used for pygmx,
since the file io functions do not use these features. since the file io functions do not use these features.
### Installing pygmx ### Installing pygmx
When the requirements are met, the installation should be easy. When the requirements are met, installing pygmx into the local Python installation can be achieved by navigating to the top folder of the repository and running the command
Navigate to the top folder of the repository and run the command
python setup.py install python setup.py install
This builds the cython modules and installs them into the local python distribution. This builds the cython modules and installs them into the local python distribution.
To check if everyting works run To check if everyting works, run the following command from a directory out of the repository
python -c 'import pygmx' python -c 'import pygmx'
If this raises an error that refers to `libgromacs.so`, this means the Gromacs library could not be found. If this raises an error that refers to `libgromacs.so`, the Gromacs library could not be found.
Make sure it is either in a standard location or `LD_LIBRARY_PATH` is set correctly. Make sure it is either in a standard location or `LD_LIBRARY_PATH` is set correctly.

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bld.bat
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"%PYTHON%" setup.py install
if errorlevel 1 exit 1

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build.sh
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#!/bin/bash
${PYTHON} setup.py install || exit 1;

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deploy.sh
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#!/bin/bash -l
module purge
module load mdevaluate/dev
python --version
TMPDIR="./tmp"
PYVERSION="$(python -c 'import sys; print("python{}.{}".format(sys.version_info.major, sys.version_info.minor))')"
PYLIBDIR="$TMPDIR/lib/$PYVERSION/site-packages"
rm -rf $TMPDIR
mkdir -p $PYLIBDIR
PYTHONPATH="$PYLIBDIR:$PYTHONPATH"
if PYTHONPATH="$PYLIBDIR:$PYTHONPATH" python setup.py install --prefix=$TMPDIR
then
scp -r $PYLIBDIR/*.egg niels@nas2:/nfsopt/mdevaluate/mdevaluate-dev/lib/$PYVERSION/site-packages
fi

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gromacs

Submodule gromacs deleted from d1a07e21a9

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meta.yaml
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package:
name: "pygmx"
version: "0.2"
source:
path: .
requirements:
build:
- cython
- numpy
run:
- numpy