cluster:180
Table of Contents
OpenStructure
Open-Source Computational Structural Biology Framework. “This project aims to provide an open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested method developers in the field of structural bioinformatics.” Please visit their web site for more details.
- v 1.9 installed
- recipe at /share/apps/CENTOS6/openstructure/1.9-install.txt
OpenStructure relies on these applications and Python 2.7.15. All applications including Python need to compiled with –enable-share in the configuration step, if possible. A step by step process is listed below.
-- Boost version: 1.68.0
-- Found the following Boost libraries:
-- python
-- unit_test_framework
-- filesystem
-- system
-- iostreams
-- program_options
-- regex
-- thread
-- Found ZLIB: /share/apps/CENTOS6/zlib/1.2.11/lib/libz.so (found version "1.2.11")
-- Found PNG: /share/apps/CENTOS6/lpng/1.6.37/lib/libpng.so (found version "1.2.49")
-- Found EIGEN: /share/apps/CENTOS6/eigen/3.2.10
-- Numpy headers found
-- Found FFTW: /share/apps/CENTOS6/fftw/3.3.8-enable-single/lib/libfftw3f.so
-- Found TIFF: /share/apps/CENTOS6/tiff/4.0.9/lib/libtiff.so (found version "4.0.9")
# setup the environment
egrep ^export /share/apps/CENTOS6/openstructure/1.9-install.txt
# invoke CLI
ost --help
Usage:
ost [ost options] [script to execute] [script parameters]
or
ost [action name] [action options]
Compilations
Use gcc greater than or equal to 4.5
export PATH=/share/apps/CENTOS6/gcc/4.8.4/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/CENTOS6/gcc/4.8.4/lib:$LD_LIBRARY_PATH
export PATH=/share/apps/CENTOS6/cmake/3.12.1/bin:$PATH
tar zxvf ../Python-2.7.15.tgz
cd Python-2.7.15/
./configure --prefix=/share/apps/CENTOS6/python/2.7.15 --enable-shared
export PATH=/share/apps/CENTOS6/python/2.7.15/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/CENTOS6/python/2.7.15/lib:$LD_LIBRARY_PATH
python ../get-pip.py
pip install numpy scipy
wget https://dl.bintray.com/boostorg/release/1.68.0/source/boost_1_68_0.tar.gz
tar zxvf boost_1_68_0.tar
cd boost_1_68_0.tar
./bootstrap.sh --prefix=/share/apps/CENTOS6/boost/1.68.0 \
--with-python=/share/apps/CENTOS6/python/2.7.15/bin/python \
--with-python-root=/share/apps/CENTOS6/python/2.7.15
./b2 install
export LD_LIBRARY_PATH=/share/apps/CENTOS6/boost/1.68.0/lib:$LD_LIBRARY_PATH
# brute fix for boost to find libs
cp -p libboost_python27.a libboost_python.a
cp -p libboost_python27.so.1.68.0 libboost_python.so
wget http://bitbucket.org/eigen/eigen/get/3.2.10.tar.gz
mv ../3.2.10.tar.gz ../eigen-3.2.10.tar.gz
tar zxvf ../eigen-3.2.10.tar.gz
cd eigen-eigen-b9cd8366d4e8/
mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=/share/apps/CENTOS6/eigen/3.2.10
make blas
make install
scp -rp ./* /share/apps/CENTOS6/eigen/3.2.10/
wget http://fftw.org/fftw-3.3.8.tar.gz
tar zxvf ../fftw-3.3.8.tar.gz
cd fftw-3.3.8/
mkdir -p /share/apps/CENTOS6/fftw/3.3.8-enable-single
./configure --enable-share --enable-single \
--prefix=/share/apps/CENTOS6/fftw/3.3.8-enable-single
make
make install
export PATH=/share/apps/CENTOS6/fftw/3.3.8-enable-single/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/CENTOS6/fftw/3.3.8-enable-single/lib:$LD_LIBRARY_PATH
tar zxvf ../zlib-1.2.11.tar.gz
cd zlib-1.2.11/
./configure --prefix=/share/apps/CENTOS6/zlib/1.2.11
make
make install
export LD_LIBRARY_PATH=/share/apps/CENTOS6/zlib/1.2.11/lib:$LD_LIBRARY_PATH
tar zxvf ../libpng-1.6.37.tar.gz
cd libpng-1.6.37/
./configure --prefix=/share/apps/CENTOS6/lpng/1.6.37
make
make install
export PATH=/share/apps/CENTOS6/lpng/1.6.37/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/CENTOS6/lpng/1.6.37/lib:$LD_LIBRARY_PATH
tar xvfz ../tiff-4.0.9.tar.gz
cd tiff-4.0.9/
./configure --prefix=/share/apps/CENTOS6/tiff/4.0.9
make
make install
export PATH=/share/apps/CENTOS6/tiff/4.0.9/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/CENTOS6/tiff/4.0.9/lib:$LD_LIBRARY_PATH
# openstructure
git clone https://git.scicore.unibas.ch/schwede/openstructure.git openstructure-1.9
cd openstructure-1.9/
cd /share/apps/CENTOS6/boost/1.68.0/lib
rm -f cmakelog; cmake \
-DCMAKE_INSTALL_PREFIX=/share/apps/CENTOS6/openstructure/1.9 \
-DBOOST_ROOT=/share/apps/CENTOS6/boost/1.68.0 \
-DPYTHON_ROOT=/share/apps/CENTOS6/python/2.7.15 \
-DEIGEN3_INCLUDE_DIR=/share/apps/CENTOS6/eigen/3.2.10 \
-DFFTW_LIBRARY=/share/apps/CENTOS6/fftw/3.3.8-enable-single/lib/libfftw3f.so \
-DFFTW_INCLUDE_DIR=/share/apps/CENTOS6/fftw/3.3.8-enable-single/include \
-DZLIB_LIBRARY=/share/apps/CENTOS6/zlib/1.2.11/lib/libz.so \
-DZLIB_INCLUDE_DIR=/share/apps/CENTOS6/zlib/1.2.11/include \
-DPNG_LIBRARY=/share/apps/CENTOS6/lpng/1.6.37/lib/libpng.so \
-DPNG_INCLUDE_DIR=/share/apps/CENTOS6/lpng/1.6.37/include \
-DTIFF_LIBRARY=/share/apps/CENTOS6/tiff/4.0.9/lib/libtiff.so \
-DTIFF_INCLUDE_DIR=/share/apps/CENTOS6/tiff/4.0.9/include \
-DENABLE_GUI=OFF -DENABLE_GFX=OFF -DENABLE_INFO=OFF \
-DUSE_NUMPY=ON -DENABLE_MM=OFF \
-DENABLE_STATIC=OFF | tee cmake.log
make
make install
# [100%] Built target actions
export PATH=/share/apps/CENTOS6/openstructure/1.9/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/CENTOS6/openstructure/1.9/lib64:$LD_LIBRARY_PATH
Remarkably complex compilations.
Notes (from developers):
With the 1.10 release, you won't need the “brute fix for boost to find libs anymore. This page instructions to be for 1.9 by either doing a “git checkout 1.9.0” after “cd openstructure-1.9” or by fetching a tagged tar ball directly (in gitlab, the URL for that would be
https://git.scicore.unibas.ch/schwede/openstructure/repository/1.9.0/archive.tar.gz
where “1.9.0” can be replaced with any git-tag).
cmake.log
-- The CXX compiler identification is GNU 4.8.4
-- The C compiler identification is GNU 4.8.4
-- Check for working CXX compiler: /share/apps/CENTOS6/gcc/4.8.4/bin/c++
-- Check for working CXX compiler: /share/apps/CENTOS6/gcc/4.8.4/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /share/apps/CENTOS6/gcc/4.8.4/bin/gcc
-- Check for working C compiler: /share/apps/CENTOS6/gcc/4.8.4/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of void*
-- Check size of void* - done
-- Boost version: 1.68.0
-- Found the following Boost libraries:
-- python
-- Boost version: 1.68.0
-- Found the following Boost libraries:
-- unit_test_framework
-- Boost version: 1.68.0
-- Found the following Boost libraries:
-- filesystem
-- system
-- Boost version: 1.68.0
-- Found the following Boost libraries:
-- iostreams
-- Boost version: 1.68.0
-- Found the following Boost libraries:
-- program_options
-- Boost version: 1.68.0
-- Found the following Boost libraries:
-- regex
-- Boost version: 1.68.0
-- Found the following Boost libraries:
-- thread
-- Found ZLIB: /share/apps/CENTOS6/zlib/1.2.11/lib/libz.so (found version "1.2.11")
-- Found PNG: /share/apps/CENTOS6/lpng/1.6.37/lib/libpng.so (found version "1.2.49")
-- Found EIGEN: /share/apps/CENTOS6/eigen/3.2.10
-- Numpy headers found
-- Found FFTW: /share/apps/CENTOS6/fftw/3.3.8-enable-single/lib/libfftw3f.so
-- Found TIFF: /share/apps/CENTOS6/tiff/4.0.9/lib/libtiff.so (found version "4.0.9")
-- LSB-Release system information::
LSB Distributor-ID: centos
LSB Release: 6.10
LSB Codename: final
System bit type: 64 bit
-- OpenStructure will be built with the following options:
Install Prefix (-DPREFIX) : /share/apps/CENTOS6/openstructure/1.9
RPath in install (-DUSE_RPATH) : OFF
Info support (-DENABLE_INFO) : OFF
Graphical interface (-DENABLE_GUI) : OFF
OpenGL support (-DENABLE_GFX) : OFF
OpenGL via Mesa (-DUSE_MESA) :
Image Processing support (-DENABLE_IMG) : ON
Shader support (-DUSE_SHADER) : OFF
Numpy support (-DUSE_NUMPY) : ON
SpaceNav Device support (-DENABLE_SPNAV) : OFF
OpenMM support (-DENABLE_MM) : OFF
OpenMM plugins (-DOPEN_MM_PLUGIN_DIR) : NONE
Optimize (-DOPTIMIZE) : OFF
Profiling support (-DPROFILE) : OFF
Double Precision (-DUSE_DOUBLE_PRECISION) : OFF
Compound Lib (-DCOMPOUND_LIB) : NONE
TMAlign and TMScore (-DCOMPILE_TMTOOLS) : OFF
Static Libraries (-DENABLE_STATIC) : OFF
Debian/Ubuntu directory layout (-DUBUNTU_LAYOUT) : OFF
Hidden object visibility (-DHIDDEN_VISIBILITY) : OFF
-- Configuring done
-- Generating done
-- Build files have been written to: /usr/local/src/tmp/openstructure-1.9
cluster/180.txt · Last modified: 2019/07/31 18:56 by hmeij07
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