O , 2012-05-29 13:48 -0700, Craig James rakstīja: > On Tue, May 29, 2012 at 11:42 AM, My Th <rei4...@gmail.com> wrote: > > I don't know why my results are different than the build > platform, but > > I'm virtually certain that the test failures are not due to > an error > > or misconfiguration on my part. > > I made a fresh checkout just now and it works for me on > Gentoo. This is > what I did: > $ svn co > https://openbabel.svn.sourceforge.net/svnroot/openbabel > test-svn > $ cd test-svn > $ svn co -r4758 > $ cd .. > $ mkdir build_test-svn > $ cd build_test-svn > $ ccmake ../test-svn/openbabel/trunk/ > $ make -j4 > $ LD_LIBRARY_PATH=./lib/ BABEL_LIBDIR=./lib/ > BABEL_DATADIR=../test-svn/openbabel/trunk/data/ make test > > Note, that I have to set paths (and they have to be absolute, > here > listed relative for briefness) for running tests otherwise it > picks up > my system installation and tautomer test segfaults because of > ABI break. > > Stranger and stranger .... It works when I run it from the build > directory (as you suggest). But, now things get weird: > > - clean out the install directory ("rm -rf > $HOME/openbabel-2.3.x/*") > - verify that it's empty > - "make install" > - verify that it's installed in $HOME/openbabel-2.3.x > - export LD_LIBRARY_PATH=$HOME/openbabel-2.3.x/lib > > Then it segfaults: > > $ bin/test_automorphism > testAutomorphisms > 8 > Hao, Xu paper, fig. 2: structure 1 > Hao, Xu paper, fig. 2: structure 2 > Hao, Xu paper, fig. 2: structure 3 > Hao, Xu paper, fig. 2: structure 4 > Hao, Xu paper, fig. 2: structure 5 > Hao, Xu paper, fig. 2: structure 6 > Hao, Xu paper, fig. 2: structure 7 > Hao, Xu paper, fig. 2: structure 8 > Hao, Xu paper, fig. 2: structure 9 > Segmentation fault
Try to look at the output of ldd bin/test_automorphism and see to which libraries it links (both versions - installed and the one in build dir). > The odd thing is that if I try to checksum the installed libraries, > the checksums on the libraries it installs don't match the ones in the > build directory. Does the cmake(1) system alter the shared objects as > it installs them? My guess is that on installation cmake rewrites rpath (with CMAKE_SKIP_INSTALL_RPATH=OFF), so you should run test from $HOME/openbabel-2.3.x/bin if you are setting library path to $HOME/openbabel-2.3.x/lib, or run the one from build dir if you are setting path to lib in your build directory. There are some rpath related options in ccmake configuration menu under advanced (t). I think the easiest is just to run tests from build directory without installation. > I'd sure appreciate any ideas anyone has on this -- I've spent days > tracking this down, and it has nothing to do with what I'm trying to > get done. I hope this helps to get forward. Reinis ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
