I downloaded boost_1_56_0.tar.gz, built and installed it successfully, then tried this configure statement, which failed. What is the recommended configure/make options to use a downloaded boost and installed in a nonstandard location? Here are the steps and result: # download and build boost using bootstrap.sh $ sudo mv boost_1_56_0 /usr/local $ sudo ln -s /usr/local/boost_1_56_0 /usr/local/boost $ ./configure --with-sparsehash-prefix=google --with-boost=/usr/local/boost --with-boost-libdir=/usr/local/boost/stage/lib $ make … CXX graph_subgraph_isomorphism.lo … boost::mpl::vector<boost::unchecked_vector_property_map<int, boost::adj_edge_index_property_map<long unsigned int> >, graph_tool::ConstantPropertyMap<bool, boost::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>}]' graph_subgraph_isomorphism.cc:178:56: required from here graph_subgraph_isomorphism.cc:108:114: error: 'vf2_subgraph_mono' was not declared in this scope make[4]: *** [graph_subgraph_isomorphism.lo] Error 1 make[4]: Leaving directory `/home/user/Downloads/graph-tool-2.2.35/src/graph/topology' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/user/Downloads/graph-tool-2.2.35/src/graph' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/user/Downloads/graph-tool-2.2.35/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/user/Downloads/graph-tool-2.2.35' make: *** [all] Error 2 On Oct 2, 2014, at 4:53 PM, Smith, Steven - 1004 - MITLL <stsmith@ll.mit.edu> wrote:

Thank you, Tiago.

Indeed, CentOS 7 server is bundled with boost 1.53. Untangling this on CentOS looks complicated:

$ rpm -e boost-1.53.0-18.el7.x86_64 error: Failed dependencies: boost = 1.53.0-18.el7 is needed by (installed) boost-devel-1.53.0-18.el7.x86_64 $ rpm -e boost-devel-1.53.0-18.el7.x86_64 error: Failed dependencies: boost-devel is needed by (installed) kdepimlibs-devel-4.10.5-3.el7.x86_64

I suppose I could build the latest 1.56 from source and set some flag to point to that, while keeping the rpm package 1.53 installed.

Any pointers on how to accomplish this while dealing with rpm dependency hell?

Steve

On Oct 2, 2014, at 3:18 PM, Tiago de Paula Peixoto <tiago@skewed.de> wrote:

...

You need boost version 1.54 or above. Which one do you have installed?

Best, Tiago

_______________________________________________ graph-tool mailing list graph-tool@skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool

Thanks again Tiago. No luck so far. I tried both these configuration commands: ./configure --with-sparsehash-prefix=google --with-boost=/usr/local/boost --with-boost-libdir=/usr/local/boost/stage/lib CPPFLAGS="-I/usr/local/include -I/usr/local/boost/libs" LDFLAGS="-L/usr/local/lib -L/usr/local/boost/stage/lib” and ./configure --with-sparsehash-prefix=google --with-boost=/usr/local/boost --with-boost-libdir=/usr/local/boost/stage/lib CPPFLAGS="-I/usr/local/boost/libs" LDFLAGS=“-L/usr/local/boost/stage/lib" A dry run of make (make -n) shows the failed compile command: cd src/graph/topology echo " CXX " graph_subgraph_isomorphism.lo;/bin/sh ../../../libtool --silent --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../.. -I. -I./.. -I./../../boost-workaround -DHAVE_CONFIG_H -I/usr/local/boost/libs -I/usr/include/python2.7 -I/usr/local/boost/include -I/usr/lib64/python2.7/site-packages/numpy/core/include/numpy -I/usr/lib64/python2.7/site-packages/scipy -DSPARSEHASH_PREFIX=google -Wall -Wextra -Wno-unused-local-typedefs -Wno-unused-parameter -std=gnu++11 -ftemplate-depth-250 -Wno-deprecated -Wno-unknown-pragmas -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-unknown-pragmas -DSPARSEHASH_PREFIX=google -MT graph_subgraph_isomorphism.lo -MD -MP -MF .deps/graph_subgraph_isomorphism.Tpo -c -o graph_subgraph_isomorphism.lo graph_subgraph_isomorphism.cc Error: … st::adj_list<long unsigned int>::edge_descriptor>, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na, mpl_::na>}]' graph_subgraph_isomorphism.cc:178:56: required from here graph_subgraph_isomorphism.cc:108:114: error: 'vf2_subgraph_mono' was not declared in this scope On Oct 3, 2014, at 4:02 AM, Tiago de Paula Peixoto <tiago@skewed.de> wrote:

On 03.10.2014 02:34, Smith, Steven - 1004 - MITLL wrote:

...

I downloaded boost_1_56_0.tar.gz, built and installed it successfully, then tried this configure statement, which failed.

What is the recommended configure/make options to use a downloaded boost and installed in a nonstandard location?

Here are the steps and result:

# download and build boost using bootstrap.sh $ sudo mv boost_1_56_0 /usr/local $ sudo ln -s /usr/local/boost_1_56_0 /usr/local/boost $ ./configure --with-sparsehash-prefix=google --with-boost=/usr/local/boost --with-boost-libdir=/usr/local/boost/stage/lib

You still need to inform the compiler and linker where they should search for libraries, which is done via CPPFLAGS and LDFLAGS:

./configure --with-sparsehash-prefix=google CPPFLAGS="-I/usr/local/include" LDFLAGS="-L/usr/local/lib"

Assuming that you have installed boost with prefix "/usr/local".

Thanks Tiago — got it on CentOS 7 now. Until the standard repos update the boost library up to v. 1.54, you build boost yourself from download, stick it in /usr/local with a symbolic link /usr/local/boost that points to it, then run the following configure command for graph-tool. My last mistake was the setting for --with-boost, which wants to point to the top directory. ./configure --with-sparsehash-prefix=google --with-boost=/usr/local/boost --with-boost-libdir=/usr/local/boost/stage/lib CPPFLAGS="-I/usr/local/boost" LDFLAGS="-L/usr/local/boost/stage/lib” make This compiles and runs under CentOS 7 now. Best, Steve

On 06.10.2014 18:45, Smith, Steven - 1004 - MITLL wrote:

One more mishap — how to I tell the graph_tool python package where the boost libraries reside? Here’s what happens on import:

You should not tell graph-tool itself, but rather the linker library. This is done via the LD_LIBRARY_PATH environment variable, which must include the directories to be search. In your case, before you start the python interpreter, you should do export LD_LIBRARY_PATH="/usr/local/boost_1_56_0/stage/lib/" Best Tiago -- Tiago de Paula Peixoto <tiago@skewed.de>

I’m having trouble updating load libraries when to the latest version of boost: $ export LD_LIBRARY_PATH="/usr/local/lib:/usr/local/boost/stage/lib” $ ipython In [1]: import graph_tool.all … ImportError: libboost_thread.so.1.57.0: cannot open shared object file: No such file or directory Why is graph-tool still pointing at the old, nonexistent boost library?? I’m certain I’ve removed the old boost libraries, and sanity checked with the command $ ( cd / ; sudo updatedb ) $ locate boost | fgrep 1.57 # Empty result # Remove old graph-tool libraries by hand $ sudo rm -fr /usr/lib/python2.7/site-packages/graph_tool /usr/lib64/python2.7/site-packages/graph_tool This really leaves me scratching my head because I’ve expunged boost version 1.57 from everywhere, downloaded/compiled/installed boost version 1.58 from scratch, and configured graph-tool to use all the boost 1.58 directories. Here’s the setup: # boost build and install $ cd /usr/local/boost_1_58_0/ $ sudo ln -s /usr/local/boost_1_58_0 /usr/local/boost $ ./bootstrap.sh $ ./b2 $ sudo ./b2 install # graph-tool build and install $ cd ~/Downloads/graph-tool-2.2.43/ $ export LD_LIBRARY_PATH="/usr/local/lib:/usr/local/boost/stage/lib” $ ls -l /usr/local/boost lrwxrwxr-x. 1 root root 24 Jun 25 12:20 /usr/local/boost -> /usr/local/boost_1_58_0/ $ ./configure --with-sparsehash-prefix=google --with-boost=/usr/local/boost --with-boost-libdir=/usr/local/boost/stage/lib CPPFLAGS="-I/usr/local/boost" LDFLAGS="-L/usr/local/boost/stage/lib" $ make $ sudo make install

On Oct 6, 2014, at 2:18 PM, Steven Thomas Smith <stsmith@ll.mit.edu> wrote:

Thanks — that’s it. I had to set it to this to handle a local install of CGAL in /usr/local/lib/libCGAL.so.10.0.3:

export LD_LIBRARY_PATH="/usr/local/lib:/usr/local/boost/stage/lib/"

All is working now.

Steve

...

You should not tell graph-tool itself, but rather the linker library. This is done via the LD_LIBRARY_PATH environment variable, which must include the directories to be search. In your case, before you start the python interpreter, you should do

export LD_LIBRARY_PATH="/usr/local/boost_1_56_0/stage/lib/"

I hit this issue again and found the fix. I'm posting the steps in case it's useful to others in the future. When upgrading (or downgrading) to a new version of Boost, it's necessary to rebuild the entire stack in order (gcc, Boost, CGAL, graph-tool) by hand on CentOS. It's also necessary to start with fresh cmake or autoconf configurations, otherwise, there will be pointers somewhere in the stack to old Boost versions. Here's what I did on a fresh CentOS image: *Necessary Packages and Environment* sudo -E yum -y groupinstall 'Development Tools' sudo -E yum -y install python-pip cairomm-devel pycairo-devel bzip2-devel # dependency troubleshooting sudo -E yum whatprovides */bzlib.h export PATH="/usr/local/bin:$PATH" export LD_LIBRARY_PATH="/usr/local/lib64/:/usr/local/boost/stage/lib/" *gcc* https://stackoverflow.com/questions/36327805/how-to-install-gcc-5-3-with-yum... cd ~/Downloads curl ftp://ftp.gnu.org/pub/gnu/gcc/gcc-5.4.0/gcc-5.4.0.tar.bz2 -O curl ftp://ftp.gnu.org/pub/gnu/gcc/gcc-5.4.0/gcc-5.4.0.tar.bz2.sig -O gpg --verify gcc-5.4.0.tar.bz2.sig gcc-5.4.0.tar.bz2 tar xjfp gcc-5.4.0.tar.bz2 cd gcc-5.4.0 ./configure --with-system-zlib --disable-multilib --enable-languages=c,c++ make -j 4 sudo make install cd rm -fr ~/Downloads/gcc-5.4.0/ gcc --version g++ --version *Boost* http://www.boost.org/users/download/ cd ~/Downloads tar xfjp boost_1_61_0.tar.bz2 cd boost_1_61_0 ./bootstrap.sh ./b2 # make sure latest gcc is in root's PATH sudo bash -c 'export PATH=/usr/local/bin:$PATH; ./b2 install' cd ~/Downloads sudo mv ./boost_1_61_0 /usr/local sudo ln -s /usr/local/boost_1_61_0 /usr/local/boost ls -ld /usr/local/boost # locate old Boost dynamic libraries and rm sudo bash -c 'cd / ; updatedb' locate 1.60 | grep boost *CGAL* https://github.com/CGAL/cgal/releases tar xfJp CGAL-4.9.tar.xz cd CGAL-4.9 cmake . make sudo bash -c 'export PATH=/usr/local/bin:$PATH; make install' *graph-tool* https://graph-tool.skewed.de/ cd ~/Downloads tar xfjp graph-tool-2.18.tar.bz2 cd graph-tool-2.18 ./configure --with-sparsehash-prefix=google --with-boost=/usr/local/boost --with-boost-libdir=/usr/local/boost/stage/lib CPPFLAGS="-I/usr/local/boost" LDFLAGS="-L/usr/local/boost/stage/lib" less config.log # Make sure graph-tool points at the correct boost directories make sudo make install cd # CentOS issues with matplotlib versions, https://stackoverflow.com/questions/33720656/python-2-import-error-cannot-im... sudo -E pip uninstall matplotlib sudo -E pip uninstall matplotlib sudo -E pip install --upgrade matplotlib sudo -E yum -y install python ipython import graph_tool.all as gt g = gt.Graph() v = g.add_vertex() u = g.add_vertex() e = g.add_edge(v,u) gt.graph_draw(g) -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.