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--- cluster:180 [2019/07/18 07:54]
hmeij07 created
+++ cluster:180 [2019/07/31 14:56] (current)
hmeij07
@@ Line 1: / Line 1: @@
+\\
+**[[cluster:0|Back]]**
 ====== OpenStructure ======
-Open-Source Computational Structural Biology Framework
+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
+  * v 1.9 installed
   * https://openstructure.org/
   * recipe at /share/apps/CENTOS6/openstructure/1.9-install.txt
-OpenStructure relies on these applications and Python 2.7.15 (see python2 section).
+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.
 <code>
@@ Line 27: / Line 32: @@
 -- 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`
+egrep ^export /share/apps/CENTOS6/openstructure/1.9-install.txt
+# invoke CLI
 ost --help
 Usage:
@@ Line 40: / Line 47: @@
     ost [action name] [action options]
+</code>
+====== Compilations ======
+Use ''gcc'' greater than or equal to 4.5
+<code>
+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
 </code>
 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 ======
+<code>
+-- 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
+</code>
+\\
+**[[cluster:0|Back]]**

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