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cluster:180 [2019/07/18 12:03]
hmeij07 		cluster:180 [2019/07/31 18:56] (current)
hmeij07
Line 32: Line 32:
 -- Found FFTW: /share/apps/CENTOS6/fftw/3.3.8-enable-single/lib/libfftw3f.so -- 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") -- 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]
 +
 +
 +</code>
  
  
 ====== Compilations ====== ====== Compilations ======
  
-Use ''gcc'' => 4.5+Use ''gcc'' greater than or equal to 4.5
  
 <code> <code>
Line 45: Line 62:
 export PATH=/share/apps/CENTOS6/cmake/3.12.1/bin:$PATH export PATH=/share/apps/CENTOS6/cmake/3.12.1/bin:$PATH
  
-tar zxvf ../Python-2.7.15.tgz                                                                                                       +tar zxvf ../Python-2.7.15.tgz
 cd Python-2.7.15/  cd Python-2.7.15/ 
-./configure --prefix=/share/apps/CENTOS6/python/2.7.15 --enable-shared                                                              +./configure --prefix=/share/apps/CENTOS6/python/2.7.15 --enable-shared
 export PATH=/share/apps/CENTOS6/python/2.7.15/bin:$PATH export PATH=/share/apps/CENTOS6/python/2.7.15/bin:$PATH
 export LD_LIBRARY_PATH=/share/apps/CENTOS6/python/2.7.15/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/python/2.7.15/lib:$LD_LIBRARY_PATH
-python ../get-pip.py                                                                                                                +python ../get-pip.py
 pip install numpy scipy  pip install numpy scipy 
  
-wget https://dl.bintray.com/boostorg/release/1.68.0/source/boost_1_68_0.tar.gz`+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 \ ./bootstrap.sh --prefix=/share/apps/CENTOS6/boost/1.68.0 \
 --with-python=/share/apps/CENTOS6/python/2.7.15/bin/python \ --with-python=/share/apps/CENTOS6/python/2.7.15/bin/python \
Line 59: Line 78:
 ./b2 install ./b2 install
 export LD_LIBRARY_PATH=/share/apps/CENTOS6/boost/1.68.0/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/boost/1.68.0/lib:$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 wget http://bitbucket.org/eigen/eigen/get/3.2.10.tar.gz
Line 75: Line 98:
 cd fftw-3.3.8/ cd fftw-3.3.8/
 mkdir -p /share/apps/CENTOS6/fftw/3.3.8-enable-single mkdir -p /share/apps/CENTOS6/fftw/3.3.8-enable-single
-./configure --enable-shared --enable-single --prefix=/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
 make install make install
Line 88: Line 112:
 export LD_LIBRARY_PATH=/share/apps/CENTOS6/zlib/1.2.11/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/zlib/1.2.11/lib:$LD_LIBRARY_PATH
  
-tar -zxvf ../libpng-1.6.37.tar.gz+tar zxvf ../libpng-1.6.37.tar.gz
 cd libpng-1.6.37/ cd libpng-1.6.37/
 ./configure --prefix=/share/apps/CENTOS6/lpng/1.6.37 ./configure --prefix=/share/apps/CENTOS6/lpng/1.6.37
Line 104: Line 128:
 export LD_LIBRARY_PATH=/share/apps/CENTOS6/tiff/4.0.9/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/tiff/4.0.9/lib:$LD_LIBRARY_PATH
  
 +# openstructure
  
 git clone https://git.scicore.unibas.ch/schwede/openstructure.git openstructure-1.9 git clone https://git.scicore.unibas.ch/schwede/openstructure.git openstructure-1.9
 cd openstructure-1.9/ cd openstructure-1.9/
-cd /share/apps/CENTOS6/boost/1.68.0//lib +cd /share/apps/CENTOS6/boost/1.68.0/lib
-# 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+
  
 rm -f cmakelog; cmake \ rm -f cmakelog; cmake \
Line 129: Line 150:
 -DUSE_NUMPY=ON -DENABLE_MM=OFF \ -DUSE_NUMPY=ON -DENABLE_MM=OFF \
 -DENABLE_STATIC=OFF | tee cmake.log -DENABLE_STATIC=OFF | tee cmake.log
- 
 make make
 make install make install
 +
 # [100%] Built target actions # [100%] Built target actions
 +
 export PATH=/share/apps/CENTOS6/openstructure/1.9/bin:$PATH export PATH=/share/apps/CENTOS6/openstructure/1.9/bin:$PATH
 export LD_LIBRARY_PATH=/share/apps/CENTOS6/openstructure/1.9/lib64:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/openstructure/1.9/lib64:$LD_LIBRARY_PATH
 +
 </code> </code>
  
 +Remarkably complex compilations.
  
 +Notes (from developers):
  
-# setup the environment +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 \\ 
-egrep ^export /share/apps/CENTOS6/openstructure/1.9-install.txt+where "1.9.0" can be replaced with any git-tag).
  
-ost --help +====== cmake.log ======
-Usage:+
  
-    ost [ost options] [script to execute] [script parameters] +<code>
- +
-or +
-    ost [action name] [action options]+
  
 +-- 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> </code>
  
-Remarkably complex compilations.+\\ 
 +**[[cluster:0|Back]]**
  
  
cluster/180.1563451419.txt.gz · Last modified: 2019/07/18 12:03 by hmeij07

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