Differences

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--- cluster:180 [2019/07/18 12:04] – 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 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 ======
-Use ''gcc'' => 4.5
+Use ''gcc'' greater than or equal to 4.5
 <code>
@@ Line 46: / Line 62: @@
 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:$LD_LIBRARY_PATH
 python ../get-pip.py
 pip install numpy scipy
-wget https://dl.bintray.com/boostorg/release/1.68.0/source/boost_1_68_0.tar.gz`
+wget https://dl.bintray.com/boostorg/release/1.68.0/source/boost_1_68_0.tar.gz
+tar zxvf boost_1_68_0.tar
+cd boost_1_68_0.tar
 ./bootstrap.sh --prefix=/share/apps/CENTOS6/boost/1.68.0 \
 --with-python=/share/apps/CENTOS6/python/2.7.15/bin/python \
@@ Line 60: / Line 78: @@
 ./b2 install
 export LD_LIBRARY_PATH=/share/apps/CENTOS6/boost/1.68.0/lib:$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
@@ Line 76: / Line 98: @@
 cd fftw-3.3.8/
 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 install
@@ Line 89: / Line 112: @@
 export LD_LIBRARY_PATH=/share/apps/CENTOS6/zlib/1.2.11/lib:$LD_LIBRARY_PATH
-tar -zxvf ../libpng-1.6.37.tar.gz
+tar zxvf ../libpng-1.6.37.tar.gz
 cd libpng-1.6.37/
 ./configure --prefix=/share/apps/CENTOS6/lpng/1.6.37
@@ Line 105: / Line 128: @@
 export LD_LIBRARY_PATH=/share/apps/CENTOS6/tiff/4.0.9/lib:$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
+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 \
@@ Line 130: / Line 150: @@
 -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):
-# 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>
-Remarkably complex compilations.
+\\
+**[[cluster:0|Back]]**