Re: [Rdkit-discuss] Building on CentOS 5.8: Python-related tests fail
On Sat, Jun 23, 2012 at 5:39 AM, Greg Landrum greg.land...@gmail.com wrote: Based on what I've been able to find on the 'net, the error is typical for a version mismatch between the python you're using and the one that boost was linked against. You can check this with ldd; % ldd /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/boost/lib/libboost_python.so.1.49.0 $ ldd /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/boost/lib/libboost_py thon.so.1.49.0 linux-vdso.so.1 = (0x7fff4d9fd000) libutil.so.1 = /lib64/libutil.so.1 (0x2b8a43957000) libpthread.so.0 = /lib64/libpthread.so.0 (0x2b8a43b5b000) libdl.so.2 = /lib64/libdl.so.2 (0x2b8a43d76000) librt.so.1 = /lib64/librt.so.1 (0x2b8a43f7a000) libstdc++.so.6 = /usr/lib64/libstdc++.so.6 (0x2b8a44184000) libm.so.6 = /lib64/libm.so.6 (0x2b8a44484000) libgcc_s.so.1 = /lib64/libgcc_s.so.1 (0x2b8a44707000) libc.so.6 = /lib64/libc.so.6 (0x2b8a44916000) /lib64/ld-linux-x86-64.so.2 (0x003b6960) I doesn't seem to show a linked python library... If it is using the wrong version of python, I'm afraid you'll have to re-build boost. There's documentation here that describes how to ensure the correct python version is being used: http://www.boost.org/doc/libs/1_49_0/libs/python/doc/building.html#python-configuration-parameters I realized that I built boost with the default python version in the system (2.4), so I followed the instructions from the link you sent above and re-built boost with python 2.6. But after re-building RDKit I get the same errors as before, and there are not changes to the output of ldd above. An aside: my successful (and easy) build of the RDKit on CenOS 5.7 used a self-installed version of python 2.7. It's documented here: http://code.google.com/p/rdkit/wiki/BuildingOnCentOS57 Finally, I gave up on trying to get it to work with python 2.6 and followed your instructions for building it with 2.7. All tests pass now. Having RDKit with python 2.7 is even better for me, since I'll be able to run my code with the same python version across different platforms. Thank you very much for the help! Best, Leo -- Leonardo Trabuco, Postdoctoral fellow (Russell group) CellNetworks, University of Heidelberg, Germany http://www.russelllab.org/people/leo/ -- 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/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building on CentOS 5.8: Python-related tests fail
Thanks for letting us know how things turned out; it is interesting, though I guess not 100% surprising that the system python doesn't work. In any case: it's good to know for the next time the question comes up. Glad you have a working rdkit build now, -greg On Sunday, June 24, 2012, Leonardo Trabuco wrote: On Sat, Jun 23, 2012 at 5:39 AM, Greg Landrum greg.land...@gmail.comjavascript:; wrote: Based on what I've been able to find on the 'net, the error is typical for a version mismatch between the python you're using and the one that boost was linked against. You can check this with ldd; % ldd /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/boost/lib/libboost_python.so.1.49.0 $ ldd /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/boost/lib/libboost_py thon.so.1.49.0 linux-vdso.so.1 = (0x7fff4d9fd000) libutil.so.1 = /lib64/libutil.so.1 (0x2b8a43957000) libpthread.so.0 = /lib64/libpthread.so.0 (0x2b8a43b5b000) libdl.so.2 = /lib64/libdl.so.2 (0x2b8a43d76000) librt.so.1 = /lib64/librt.so.1 (0x2b8a43f7a000) libstdc++.so.6 = /usr/lib64/libstdc++.so.6 (0x2b8a44184000) libm.so.6 = /lib64/libm.so.6 (0x2b8a44484000) libgcc_s.so.1 = /lib64/libgcc_s.so.1 (0x2b8a44707000) libc.so.6 = /lib64/libc.so.6 (0x2b8a44916000) /lib64/ld-linux-x86-64.so.2 (0x003b6960) I doesn't seem to show a linked python library... If it is using the wrong version of python, I'm afraid you'll have to re-build boost. There's documentation here that describes how to ensure the correct python version is being used: http://www.boost.org/doc/libs/1_49_0/libs/python/doc/building.html#python-configuration-parameters I realized that I built boost with the default python version in the system (2.4), so I followed the instructions from the link you sent above and re-built boost with python 2.6. But after re-building RDKit I get the same errors as before, and there are not changes to the output of ldd above. An aside: my successful (and easy) build of the RDKit on CenOS 5.7 used a self-installed version of python 2.7. It's documented here: http://code.google.com/p/rdkit/wiki/BuildingOnCentOS57 Finally, I gave up on trying to get it to work with python 2.6 and followed your instructions for building it with 2.7. All tests pass now. Having RDKit with python 2.7 is even better for me, since I'll be able to run my code with the same python version across different platforms. Thank you very much for the help! Best, Leo -- Leonardo Trabuco, Postdoctoral fellow (Russell group) CellNetworks, University of Heidelberg, Germany http://www.russelllab.org/people/leo/ -- 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/___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building on CentOS 5.8: Python-related tests fail
On 23/06/12 14:05, Paul Emsley wrote: if you do encounter such, your solution may be somewhat simpler. Ooops, I meant: if you do *not* encounter such ... -- 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/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building on CentOS 5.8: Python-related tests fail
On Fri, Jun 22, 2012 at 5:46 PM, Leonardo Trabuco ltrab...@gmail.com wrote: Thanks for following up. Below is the output you asked for. Looks like an import error in the boost library. Any ideas? Based on what I've been able to find on the 'net, the error is typical for a version mismatch between the python you're using and the one that boost was linked against. You can check this with ldd; % ldd /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/boost/lib/libboost_python.so.1.49.0 If it is using the wrong version of python, I'm afraid you'll have to re-build boost. There's documentation here that describes how to ensure the correct python version is being used: http://www.boost.org/doc/libs/1_49_0/libs/python/doc/building.html#python-configuration-parameters An aside: my successful (and easy) build of the RDKit on CenOS 5.7 used a self-installed version of python 2.7. It's documented here: http://code.google.com/p/rdkit/wiki/BuildingOnCentOS57 -greg UpdateCTestConfiguration from :/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/DartConfiguration.tcl Start processing tests UpdateCTestConfiguration from :/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/DartConfiguration.tcl Test project /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build Constructing a list of tests Done constructing a list of tests Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/RDGeneral Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DataStructs Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DataStructs/Wrap 3/ 76 Testing pyBV Test command: /usr/bin/python2.6 /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/Code/DataStructs/Wrap/testBV.py Test timeout computed to be: 9.99988e+06 Traceback (most recent call last): File /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/Code/DataStructs/Wrap/testBV.py, line 1, in module from rdkit import DataStructs File /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/rdkit/DataStructs/__init__.py, line 11, in module from rdkit import rdBase ImportError: /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/boost/lib/libboost_python.so.1.49.0: undefined symbol: Py_InitModule4 -- Process completed ***Failed Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Geometry Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Geometry/Wrap Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Numerics Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Numerics/Alignment Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Numerics/Alignment/Wrap Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Numerics/Optimizer Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/ForceField Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DistGeom Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DistGeom/Wrap Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Depictor Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Depictor/Wrap Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/SmilesParse Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/FileParsers Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Substruct Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/ChemReactions Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/ChemReactions/Wrap Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/ChemTransforms Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Subgraphs Changing directory into /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/FragCatalog Changing directory into
