IMP-users

imp-users@salilab.org

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273 discussions

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 29 Oct '10

29 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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Re: [IMP-users] installing within python version 2.6
by Ben Webb 11 Oct '10

11 Oct '10

On 10/8/10 4:17 PM, jeremy adler wrote: > Thanks for your help. I tried building it from the source into the > /usr/lib/python2.6 directory (after deleting everything from my previous > attempt). The follwoing files are placed there:\ > > _IMP_algebra.so _IMP_display.so _IMP_helper.so _IMP_saxs.so > _IMP_atom.so _IMP_domino.so _IMP_misc.so _IMP.so > _IMP_benchmark.so _IMP_em.so _IMP_modeller.so _IMP_statistics.so > _IMP_container.so _IMP_example.so _IMP_multifit.so > _IMP_core.so _IMP_gsl.so _IMP_restrainer.so > > Though nothing else is. When i try to import imp now it says the module > isnt there. Any advice? These are just the interfaces between Python and the underlying IMP C++ modules. There should also be a bunch of "real" Python files (.py extension) in the IMP subdirectory. These should also have been installed by "scons install" at the same time as those .so files above. Maybe they went in a different directory for some reason? Check the output from "scons install". Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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installing within python version 2.6
by jeremy adler 08 Oct '10

08 Oct '10

I have tried installing the version available for linux-it goes directly into the python v2.4 folder so I copied it to the v2.6 folder. I get the following error when i try to access IMP import IMP Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python2.6/IMP/__init__.py", line 25, in <module> _IMP = swig_import_helper() File "/usr/lib/python2.6/IMP/__init__.py", line 21, in swig_import_helper _mod = imp.load_module('_IMP', fp, pathname, description) ImportError: libimp.so: cannot open shared object file: No such file or directory The _IMP.so is present. Is there something else im missing? thanks Jeremy

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IMP svn compiling issues Mac OS X 10.6 fink-64
by Benjamin SCHWARZ 27 Sep '10

27 Sep '10

Hi list I try a compilation of IMP svn 6742 on Macbook laptop OS X 10.6 * Fink 64 bits installed (in /sw) with packages : cgal-4 fftw-3 boost1.35.python26 boost1.35.nopython gsl and graphviz * Ann hand installed in /usr/local * Modeller installed as most recent MAC dmg And I have several problems : 1.) the compilation process fails on cgal polyhedron compilation g++ -o modules/cgal/src/internal/polyhedrons.os -c -Os -fno-common -dynamic -I/BenInstalls/imp-install/imp-debug/include -I/opt/local/include -I/sw/include -Wall -Wno-deprecated -Woverloaded-virtual -g -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/BenInstalls/imp/src/build/include -I/usr/local/include -I/sw/include -I/usr/local/ann/ann_1.1.2/include /BenInstalls/imp/src/modules/cgal/src/internal/polyhedrons.cpp In file included from /sw/include/CGAL/Nef_3/SNC_items.h:26, from /sw/include/CGAL/Nef_3/Default_items.h:21, from /sw/include/CGAL/Nef_polyhedron_3.h:29, from /BenInstalls/imp/src/modules/cgal/src/internal/polyhedrons.cpp:8: /sw/include/CGAL/Nef_3/Halfedge.h: In member function 'typename Refs::Vector_3 CGAL::Halfedge_base<Refs>::vector() const': /sw/include/CGAL/Nef_3/Halfedge.h:110: error: 'ORIGIN' is not a member of 'CGAL' /usr/include/c++/4.2.1/bits/stl_function.h: In member function 'bool std::less<_Tp>::operator()(const _Tp&, const _Tp&) const [..] CGAL awful template insult [..] /BenInstalls/imp/src/modules/cgal/src/internal/polyhedrons.cpp:100: instantiated from here /usr/include/c++/4.2.1/bits/stl_function.h:227: error: no match for 'operator<' in '__x < __y' [..] a few lines with replacement propositions for this operator [..] Enabled dependencies: python, ANN, NetCDF, FFTW3, GSL, CGAL, Boost.ProgramOptions Disabled/unfound optional dependencies: Boost.FileSystem, ExampleLib, Bullet Enabled modules: kernel, cgal, algebra, core, container, atom, display, domino, em, example, misc, saxs, helper, statistics, gsl, modeller, restrainer, domino2, benchmark Disabled modules: em2d, multifit, bullet Errors building: modules/cgal/src/internal/polyhedrons.os 2.) I was then able to continue the compilation by disabling the cgal dependency (cgal="no" in the config.py). It then goes on quite a long time then crashes at link time on : g++ -o applications/saxs/profile.o -c -Os -fno-common -dynamic -I/BenInstalls/imp-install/imp-debug/include -I/opt/local/include -I/sw/include -Wall -Wno-deprecated -Woverloaded-virtual -g -Ibuild/include -I/BenInstalls/imp/src/build/include -I/usr/local/include -I/sw/include -I/usr/local/ann/ann_1.1.2/include /BenInstalls/imp/src/applications/saxs/profile.cpp g++ -o applications/saxs/foxs -g applications/saxs/profile.o applications/saxs/Gnuplot.o -Lbuild/lib -L/BenInstalls/imp/src/build/lib -L/usr/local/lib -L/sw/lib -L/usr/local/ann/ann_1.1.2/lib -L/BenInstalls/imp-install/imp-debug/lib -limp_saxs -limp_atom -limp_container -limp_core -limp_algebra -limp -lANN -lnetcdf_c++ -lboost_program_options ld: warning: directory '/BenInstalls/imp/src/build/lib' following -L not found ld: warning: directory '/BenInstalls/imp-install/imp-debug/lib' following -L not found Undefined symbols: "boost::program_options::options_description::options_description(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int)", referenced from: _main in profile.o ld: symbol(s) not found collect2: ld returned 1 exit status scons: *** [applications/saxs/foxs] Error 1 scons: building terminated because of errors. Any hint appreciated. --Ben Schwarz

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