- IMP-users - salilab.org

compilation bus error
by Robert Brynmor Fenwick 24 Jan '11

24 Jan '11

Hi, I've just checked out this: svn co http://svn.salilab.org/imp/branches/stable imp .... Checked out revision 8381. and tried to compile it, I am using the same compiler that compiles the imp 1.0 version so I don't think it is a compiler problem Install file: "modules/cgal/include/internal/knn.h" as "build/include/IMP/cgal/internal/knn.h" g++ -o modules/cgal/src/internal/knn.os -c -Os -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -Wall -Wno-deprecated -Woverloaded-virtual -O2 -fno-finite-math-only -ftrapping-math -fsignaling-nans -fno-float-store -frounding-math -fno-strict-aliasing -DCGAL_DISABLE_ROUNDING_MATH_CHECK -fvisibility=hidden -fPIC -DIMPCGAL_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/sw/include modules/cgal/src/internal/knn.cpp modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData2::fill_nearest_neighbors_v(const IMP::algebra::VectorD<2u>&, unsigned int, double, IMP::Ints&) const': modules/cgal/src/internal/knn.cpp:122: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 2u]' modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData2::fill_nearest_neighbors_v(const IMP::algebra::VectorD<2u>&, double, double, IMP::Ints&) const': modules/cgal/src/internal/knn.cpp:122: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 2u]' modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData3::fill_nearest_neighbors_v(const IMP::algebra::VectorD<3u>&, unsigned int, double, IMP::Ints&) const': modules/cgal/src/internal/knn.cpp:123: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 3u]' modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData3::fill_nearest_neighbors_v(const IMP::algebra::VectorD<3u>&, double, double, IMP::Ints&) const': modules/cgal/src/internal/knn.cpp:123: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 3u]' modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData4::fill_nearest_neighbors_v(const IMP::algebra::VectorD<4u>&, unsigned int, double, IMP::Ints&) const': modules/cgal/src/internal/knn.cpp:124: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 4u]' modules/cgal/src/internal/knn.cpp: In member function 'void IMP::cgal::internal::KNNData4::fill_nearest_neighbors_v(const IMP::algebra::VectorD<4u>&, double, double, IMP::Ints&) const': modules/cgal/src/internal/knn.cpp:124: warning: passing negative value '-0x00000000000000001' for argument 1 to 'IMP::cgal::internal::VectorWithIndex<D>::VectorWithIndex(unsigned int, const IMP::algebra::VectorD<D>&) [with unsigned int D = 4u]' Install file: "modules/cgal/include/internal/polygons.h" as "build/include/IMP/cgal/internal/polygons.h" g++ -o modules/cgal/src/internal/polygons.os -c -Os -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -Wall -Wno-deprecated -Woverloaded-virtual -O2 -fno-finite-math-only -ftrapping-math -fsignaling-nans -fno-float-store -frounding-math -fno-strict-aliasing -DCGAL_DISABLE_ROUNDING_MATH_CHECK -fvisibility=hidden -fPIC -DIMPCGAL_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/sw/include modules/cgal/src/internal/polygons.cpp Install file: "modules/cgal/include/internal/polyhedrons.h" as "build/include/IMP/cgal/internal/polyhedrons.h" Install file: "modules/algebra/include/Plane3D.h" as "build/include/IMP/algebra/Plane3D.h" g++ -o modules/cgal/src/internal/polyhedrons.os -c -Os -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -Wall -Wno-deprecated -Woverloaded-virtual -O2 -fno-finite-math-only -ftrapping-math -fsignaling-nans -fno-float-store -frounding-math -fno-strict-aliasing -DCGAL_DISABLE_ROUNDING_MATH_CHECK -fvisibility=hidden -fPIC -DIMPCGAL_EXPORTS -DGCC_VISIBILITY -Ibuild/include -I/sw/include modules/cgal/src/internal/polyhedrons.cpp modules/cgal/src/internal/polyhedrons.cpp: In function 'std::vector<std::vector<IMP::algebra::VectorD<3u>, std::allocator<IMP::algebra::VectorD<3u> > >, std::allocator<std::vector<IMP::algebra::VectorD<3u>, std::allocator<IMP::algebra::VectorD<3u> > > > > IMP::cgal::internal::<unnamed>::get_facets(CGAL::Nef_polyhedron_3<K, typename CGAL::Default_items<Kernel>::Items, bool>&)': modules/cgal/src/internal/polyhedrons.cpp:99: internal compiler error: Bus error Please submit a full bug report, with preprocessed source if appropriate. See <URL:http://developer.apple.com/bugreporter> for instructions. scons: *** [modules/cgal/src/internal/polyhedrons.os] Error 1 scons: building terminated because of errors. Enabled dependencies: python, NetCDF, FFTW3, CGAL, Boost.FileSystem, Boost.ProgramOptions Disabled/unfound optional dependencies: ANN, ExampleLib, GSL, OpenCV, Bullet, OpenMM Enabled modules: kernel, cgal, algebra, core, container, atom, display, domino, em, example, misc, saxs, helper, statistics, restrainer, domino2, multifit, benchmark Disabled modules: gsl, modeller, em2d, bullet, openmm Errors building: modules/cgal/src/internal/polyhedrons.os -- R. Bryn Fenwick robert.fenwick(a)irbbarcelona.org Post-doctoral fellow Chemistry and Molecular Pharmacology Programme Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona Baldiri Reixac 10, 08028 Barcelona, SPAIN Tel. (+34) 9340 20460

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stable nightly build
by Robert Brynmor Fenwick 21 Jan '11

21 Jan '11

Hi, I am a bit new to svn and am trying get the most up to date version of the code that is available on the nightly builds. Any advice would be appreciated. Bryn -- R. Bryn Fenwick robert.fenwick(a)irbbarcelona.org Post-doctoral fellow Chemistry and Molecular Pharmacology Programme Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona Baldiri Reixac 10, 08028 Barcelona, SPAIN Tel. (+34) 9340 20460

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add_partial_profiles
by Robert Fenwick 21 Jan '11

21 Jan '11

Hi, I am having a bit of a tough time with writing a script and wondered if someone could help. I have installed the latest nightly builds and am trying to write the following: I wish to loop over n structures, calculate the summed partial saxs profile. I hope to achieve this using the attached code and example structures. I think that I should use the add_partial_profiles function, however I can not get it to work the way that I would like. Is there a way to access the values in the predicted saxs profiles using the python interface? Here is my current code, but it does not work as I would expect. Bryn R. Bryn Fenwick robert.fenwick(a)irbbarcelona.org Post-doctoral fellow Chemistry and Molecular Pharmacology Programme Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona Baldiri Reixac 10, 08028 Barcelona, SPAIN Tel. (+34) 9340 20460

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running error
by Robert Fenwick 20 Jan '11

20 Jan '11

Hi, I have installed IMP with the minimal requirements that I think that it needs and everything seems to compile without problems. However when I try to import the python modules I get some nasty import errors. Any help greatly appreciated. >>> import IMP.core >>> import IMP.atom Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/fenwick/opt/lib64/python2.5/site-packages/IMP/atom/__init__.py", line 28, in <module> import _IMP_atom ImportError: /home/fenwick/opt/lib64/python2.5/site-packages/_IMP_atom.so: undefined symbol: _ZN3IMP4atom14CHARMMTopology32CHARMMSegmentTopologyDataWrapperD1Ev >>> import IMP.saxs Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/fenwick/opt/lib64/python2.5/site-packages/IMP/saxs/__init__.py", line 163, in <module> import IMP.atom File "/home/fenwick/opt/lib64/python2.5/site-packages/IMP/atom/__init__.py", line 28, in <module> import _IMP_atom ImportError: /home/fenwick/opt/lib64/python2.5/site-packages/_IMP_atom.so: undefined symbol: _ZN3IMP4atom14CHARMMTopology32CHARMMSegmentTopologyDataWrapperD1Ev Here is the end of teh build process that appears to have worked. scons: done building targets. Enabled dependencies: Boost.FileSystem, Boost.ProgramOptions Disabled dependencies: OpenMM, Bullet, CGAL, ANN, OpenCV, NetCDF, modeller, FFTW3, GSL Enabled modules: em, kernel, domino, misc, statistics, container, display, saxs, system, core, algebra, restrainer, benchmark, atom, example Disabled modules: openmm, cgal, bullet, multifit, gsl, modeller, em2d Enabled applications: foxs, ligand_score, saxs_tools, em_tools Enabled systems: Groel, example_system R. Bryn Fenwick robert.fenwick(a)irbbarcelona.org Post-doctoral fellow Chemistry and Molecular Pharmacology Programme Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona Baldiri Reixac 10, 08028 Barcelona, SPAIN Tel. (+34) 9340 20460

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good coding habits
by Benjamin SCHWARZ 13 Jan '11

13 Jan '11

Hi list Trying to acquire good coding habits, I started a new personal module, now 1. I wonder if there is an IMP_WARN macro that would output some message under some condition, just like IMP_USAGE_CHECK() does but without aborting the application 2. I would like to write test case functions a. Is there a doc on how to write good test functions ? b. Where can I find the IMP.test.TestCase class, so that I can dissect it at will ? --Ben

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single_prot_fft_fit
by Benjamin SCHWARZ 14 Dec '10

14 Dec '10

Hi list, I am trying to run the single_prot_fft_fit software for some times now with no success. I looked into the code but could not find a quick fix. I would greatly appreciate if somebody could help me get the program running. The soft was built out of IMP svn 7513, and my command line is : /usr/local/IMPsvn/imp-latest/modules/multifit/bin/single_prot_fft_fit subCplx-18A.mrc 2 18 0.25 /home/schwarz/TFdata/struct-C-term.pdb 300 --n-hits 10 --output Cter--solutions.txt --sol taf6-Cter--fitted-solution- --cc-map Cter--fit-CC-map.map --local I have tried to run this soft on three machines : * Linux 2.6.32-21-generic #32-Ubuntu SMP Fri Apr 16 08:09:38 UTC 2010 x86_64 GNU/Linux The process simply stops after a few iteration, having received a SiGKILL signal according to gdb. * Linux 2.6.24-23-server #1 SMP Thu Nov 27 18:45:02 UTC 2008 x86_64 GNU/Linux Computation seems ok for 300 rotations, but when launched in more real conditions (12000 rotations), the machine becomes unstable apparently because the process asks more and more memory (43Gb at the time we had to restart the machine) * Linux hpc-n48 2.6.18-164.6.1.el5.centos.plus #1 SMP Wed Nov 4 09:31:39 EST 2009 x86_64 x86_64 x86_64 GNU/Linux The program stops on a Segmentation fault (core dumped) with the lowest bt level being : #0 0x00002aee817bfe3f in IMP::multifit::FFTFitting::get_correlation_hit_map() const () from /home/lbm/schwarz/BenInstalls/Installs/imp-latest/lib64/libimp_multifit.so --Ben

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import fails
by Robert Brynmor Fenwick 13 Dec '10

13 Dec '10

Hi, I have managed to build the python interface with swig, but fail to import IMP from python. I am rather sure that I have installed the modules, however I am unsure where I have to point my PYTHONPATH to pick them up. The other problem might be that I don't know which version of python the modules have been installed. How can I work out which version and the location of the python executable for which the modules were build? Many thanks, Bryn

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Re: [IMP-users] numerical bug
by Robert Brynmor Fenwick 13 Dec '10

13 Dec '10

Hi, I think that I have found a small numerical bug. I can not work out how to debug this as my knowledge of c++ is not what is needs to be. I encounter the error using the python interface with the latest nightly build. To reproduce the error you can play with the two files and code attached. The file that works with the code is 433.pdb. The file that fails is 434.pdb. The traceback appears as: Traceback (most recent call last): File "bug_case.py", line 30, in <module> surface_area = s.get_solvent_accessibility(IMP.core.XYZRs(particles)) File "/opt/imp/lib/python2.5/site-packages/IMP/saxs/__init__.py", line 428, in get_solvent_accessibility def get_solvent_accessibility(self, *args): return _IMP_saxs.SolventAccessibleSurface_get_solvent_accessibility(self, *args) _IMP.UsageException: Passed index not in grid (17, 2, 3) I suspect it is a numerical instability somewhere as I have a test case that fails where I can modify the file in two ways to create a file that works. A) I generate a sorter fail (434.cut) case by: tail -228 434.pdb > 434.cut B) This calculation will proceed if I generate a slightly shorter file (i.e. remove the first ten lines). This case is generated by: tail -218 434.pdb > 434.cut C) The strange part is the calculation will also proceed if the only the first 100 lines are used (i.e. keeping the part that I removed in B ) This case is generated by: tail -228 434.pdb | head -100 > 434.cut Any suggestions would be greatly appreciated. Bryn -- R. Bryn Fenwick robert.fenwick(a)irbbarcelona.org Post-doctoral fellow Chemistry and Molecular Pharmacology Programme Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona Baldiri Reixac 10, 08028 Barcelona, SPAIN Tel. (+34) 9340 20460

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imp scons install problem
by Benjamin SCHWARZ 25 Nov '10

25 Nov '10

Hi all, observed on Mac osX as well as Linux (2.6.18-164.6.1.el5.centos.plus x86_64) : when running scons install, only a tiny part of IMP is copied to the install dir : only the content of MacBook-Pro-de-Benjamin-SCHWARZ:lib schwarz$ ls /BenInstalls/imp-install/imp-fast-boost144/lib/python2.6/site-packages/IMP/ __init__.py atom cgal display example modeller statistics __init__.pyc benchmark container domino gsl restrainer algebra bullet core em misc saxs .h , .cpp as well as .so and .dylib are not copied. --Ben

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Error of using ConjugateOptimizer to optimize a Modeller model
by Jianlin Cheng 28 Oct '10

28 Oct '10

Hi, I was trying to use IMP's ConjugateOptimizer to optimize a Modeller model according to a small set of Modeller's restraints read from a file. The restraints seemed to be loaded successfully and the model could be evaluated on the restraints. However, when an ConjugateOptimizer was used to optimize the initial model according to the restraints, the program reported an error "There are no optimizeable degrees of freedom". Does anybody know how to solve the problem? Both the error message and the Python program are attached below. Thanks! Error Message: Traceback (most recent call last): File "test.py", line 35, in ? opt.optimize(100) File "/home/chengji/imp-dev/lib64/python2.4/site-packages/IMP/__init__.py", line 1695, in optimize def optimize(self, *args): return _IMP.Optimizer_optimize(self, *args) _IMP.ModelException: There are no optimizeable degrees of freedom. Python Code: import IMP.atom import IMP.container import modeller import IMP import IMP.modeller # Set up Modeller and build a model from a primary sequence e = modeller.environ() e.edat.dynamic_sphere = False e.libs.topology.read('${LIB}/top_heav.lib') e.libs.parameters.read('${LIB}/par.lib') modmodel = modeller.model(e) modmodel.build_sequence("AYVINDSCIACGACKPECPVNIIQGSIYAIDADSCIDCGSCASVCPVGAPNPED"); # Create an IMP model and load the model loader = IMP.modeller.ModelLoader(modmodel) m = IMP.Model() prot2 = loader.load_atoms(m); #read the restraints from a modeller restraint file restraints = loader.load_static_restraints_file("/home/chengji/imp-dev/share/doc/imp/examples/modeller/examples/my.rsr.small") #add restraints into the IMP model for r in restraints: m.add_restraint(r) # Finally, evaluate the score of the whole system (without derivatives) print m.evaluate(False) #use ConjugateGradients to optimize the model opt = IMP.core.ConjugateGradients() opt.set_model(m) opt.set_threshold(1e-5) opt.optimize(100)

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