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IMP 2.6.1/CentOS-7/Ninja (only) building issue
by Tru Huynh 25 May '16

25 May '16

Hi, I am preparing the computer lab machine for a course this summer and I am running into a strange "ninja issue". [tru@optiplex7020 ninja]$ cmake ../imp-2.6.1 -DCMAKE_BUILD_TYPE=Release -G Ninja -DIMP_MAX_CHECKS=NONE -DCMAKE_INSTALL_PREFIX=/isb2016/imp-2.6.1 -DCMAKE_INCLUDE_PATH="/isb2016/Python-2.7.11;/isb2016/Python-2.7.11/include" -DCMAKE_LIBRARY_PATH="/isb2016/libTAU-1.0.1/lib;/isb2016/Python-2.7.11/lib" -DPYTHON_LIBRARY=/isb2016/Python-2.7.11/lib -DPYTHON_INCLUDE_DIR="/isb2016/Python-2.7.11;/isb2016/Python-2.7.11/include/python2.7" -DLIBTAU_INCLUDE_DIR="/isb2016/libTAU-1.0.1" CMake Error: CMake was unable to find a build program corresponding to "Ninja". CMAKE_MAKE_PROGRAM is not set. You probably need to select a different build tool. CMake Error: Error required internal CMake variable not set, cmake may be not be built correctly. Missing variable is: CMAKE_C_COMPILER_ENV_VAR CMake Error: Error required internal CMake variable not set, cmake may be not be built correctly. Missing variable is: CMAKE_C_COMPILER CMake Error: Could not find cmake module file:/home/tru/ISB2016/build/ninja/CMakeFiles/2.8.11/CMakeCCompiler.cmake CMake Error: Error required internal CMake variable not set, cmake may be not be built correctly. Missing variable is: CMAKE_CXX_COMPILER_ENV_VAR CMake Error: Error required internal CMake variable not set, cmake may be not be built correctly. Missing variable is: CMAKE_CXX_COMPILER CMake Error: Could not find cmake module file:/home/tru/ISB2016/build/ninja/CMakeFiles/2.8.11/CMakeCXXCompiler.cmake -- Configuring incomplete, errors occurred! [tru@optiplex7020 ninja]$ type ninja ninja is /isb2016/ninja-1.7.1/ninja ninja was built from source with "./configure.py --bootstrap". I tried Ninja 1.7.1 1.6.0 and 1.5.3 without success (same error). If I run the same command without the '-G Ninja', cmake completes properly and make -j8 completes without issue. [tru@optiplex7020 fast]$ cmake ../imp-2.6.1 -DCMAKE_BUILD_TYPE=Release -DIMP_MAX_CHECKS=NONE -DCMAKE_INSTALL_PREFIX=/isb2016/imp-2.6.1 -DCMAKE_INCLUDE_PATH="/isb2016/Python-2.7.11;/isb2016/Python-2.7.11/include" -DCMAKE_LIBRARY_PATH="/isb2016/libTAU-1.0.1/lib;/isb2016/Python-2.7.11/lib" -DPYTHON_LIBRARY=/isb2016/Python-2.7.11/lib -DPYTHON_INCLUDE_DIR="/isb2016/Python-2.7.11;/isb2016/Python-2.7.11/include/python2.7" -DLIBTAU_INCLUDE_DIR="/isb2016/libTAU-1.0.1" -- Running check_common_problems -- Running clean_build_dir -- Running setup_cmake -- GCC version: 4.8.5 -- Enabling g++ C++11 support -- GCC version: 4.8.5 -- No conversion issue -- Doxygen is /isb2016/doxygen-1.8.6/bin/doxygen, version 1.8.6 -- Running setup_doxygen -- Python binary is /isb2016/Python-2.7.11/bin/python (version 2.7.11) -- Found PythonLibs: /isb2016/Python-2.7.11/lib (Required is exact version "2.7.11") -- Running setup -- Running setup_all -- Running making containers -- Boost version: 1.53.0 -- Found the following Boost libraries: -- system -- filesystem -- thread -- program_options -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success ... Configuring module integrative_docking ...yes -- Running setup_swig_wrappers integrative_docking -- Running IMP.integrative_docking making all header -- Running setup_swig_dependencies -- Creating thread pool with 16 threads -- Running setup_imppy -- Configuring done -- Generating done -- Build files have been written to: /home/tru/ISB2016/build/fast [tru@optiplex7020 fast]$ nice make -j8 Scanning dependencies of target IMP.kmeans-all-header Scanning dependencies of target IMP.parallel-all-header Scanning dependencies of target IMP.kernel-all-header Scanning dependencies of target IMP.test-all-header ... Best regards Tru -- Dr Tru Huynh | http://www.pasteur.fr/research/bis mailto:tru@pasteur.fr | tel/fax +33 1 45 68 87 37/19 Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France

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IMP 2.6.2 release
by Ben Webb 25 May '16

25 May '16

IMP 2.6.2 is now available. This corrects a few minor bugs and documentation issues in the previous release (2.6.1). In particular, we now provide packages for Ubuntu 16.04 (Xenial Xerus) and include a workaround for the buggy version of SWIG (3.0.8) included in that distribution. See https://integrativemodeling.org/2.6.2/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

1 0

IMP 2.6.1 release
by Ben Webb 14 Apr '16

14 Apr '16

IMP 2.6.1 is now available. This corrects a few minor bugs and documentation issues in the previous release (2.6.0). See https://integrativemodeling.org/2.6.1/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

2 3

slow MC optimizer
by Joseph Eschweiler 14 Apr '16

14 Apr '16

Hello, I'm using the MC optimizer to optimize protein complexes represented by spheres. My script loops through various sets of restraints (either distance or MS-connectivity) and generates an ensemble of structures for each restraint set. My problem is that the speed of the optimizer changes drastically each time over the loop, and there is no correlation between the complexity of the restraint set and the speed of the optimizer. The speed usually varies between 10 and 30 models per second, but will sometimes slow to 1 model/10minutes forces me to terminate the script. I always initialize each optmization cycle with new random coordinates, so I know I'm not simply getting stuck in a local minima, and I know the restraint sets themselves are all fine since I could loop over the same restraint set many times and the speed would change unpredictably. I've also tried setting up a completely new model instance for each restraint set, which doesn't solve the problem either. for restraint set: for oc in range(self.optimization_cycles): for particle in self.system.ds: ## RANDOMIZE COORDINATES init_coors = IMP.algebra.get_random_vector_in(self.system.bb ) particle.set_coordinates(init_coors) T = self.initial_temperature for mc in range(self.mc_cool_cycles): ## DO THE ANNEALING MC T = 0.99*T self.optimizer.set_kt(T) self.optimizer.optimize(self.mc_cool_steps) Any input is greatly appreciated. Joe -- Joseph D. Eschweiler Ph.D. Candidate | Ruotolo Group Department of Chemistry University of Michigan

2 1

IMP 2.6.0 release
by Ben Webb 28 Mar '16

28 Mar '16

IMP 2.6.0 is now available. This is a bugfix and minor update release. Most notably we include most of the functionality of PMI2. This is an improved version of PMI that is faster than PMI1, more modular, and easier to use. See the IMP::pmi module docs for more information. This release also includes a number of bug fixes, most notably in the creation of sampled electron microscopy density maps. See the https://integrativemodeling.org/2.6.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ 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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how do I build working pmi rnapolii examples ?
by Isabelle Phan 25 Mar '16

25 Mar '16

Hello Ben, How do I install working examples for pmi rnapolii? I need to run the analysis on my model and could not match the IMP tutorial for rnapolii with my old code. They had diverged too much. So I installed 2.4.0 stable release. This does not seem to have working examples for rnapolii. The code only has modules/pmi/broken-examples/rnapolii I tried pulling from the development version, but that does not seem to include working examples either. Am grateful for any help, Isabelle

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MP.em.EnvelopeFitRestraint class
by Karine VOLTZ 05 Feb '16

05 Feb '16

Dear IMP-users, I have a question regarding the IMP.em.EnvelopeFitRestraint class: As a simple test I just tried to evaluate this restraint with an EM density map and a set of particles corresponding to each subunits that fill the map. As coordinates for each particle, I have assigned a random vector belonging to the boundingbox of the density map. Depending on the coordinates of the particles, sometimes the restraint is correctly calculated, sometimes I get the following error message: File "/usr/local/lib/IMP-python/IMP/kernel/__init__.py", line 2183, in evaluate return _IMP_kernel.Restraint_evaluate(self, *args) _IMP_base.UsageException: Usage check failure: The point is not part of the grid Context: fit_restraint::evaluate/fit_restraint scoring::evaluate/fit_restraint scoring::do_add_score_and_derivatives/fit_restraint::add_score_and_derivatives/fit_restraint::do_add_score_and_derivatives Can somebody explain me this error? Thank you Karine

2 1

Compiling IMP 2.5.0 on CentOS 7
by Novosielski, Ryan 02 Feb '16

02 Feb '16

Hi there, Having a heck of a time trying to compile IMP 2.5.0 and its dependencies. Hopefully someone can help. Note that below, the ones that do not say (CentOS 7.2) are in non-standard locations under /opt because we have to keep multiple versions of a lot of this stuff due to other software depending on it. I’m using: * GCC 4.8.5 (CentOS 7.2) * CMake 2.8.11 * Boost 1.60.00 * HDF5 1.8.16 (--with-parallel) * Python 2.7.11 * SWIG 2.0.10 (CentOS 7.2) * Modeller 9.16 * GSL 1.15 (CentOS 7.2) * OpenCV 2.3.1 * FFTW 3.3.3 (CentOS 7.2) * MVAPICH 2.1 * NumPy: 1.10.4, SciPy: 0.16.1, matplotlib: 1.5.1, biopython 1.66 First I had a very difficult time getting it to even detect OpenCV. My final solution was to set $PKG_CONFIG_PATH to include the pkgconfig directory for OpenCV 2.3.1 and to symlink opencv.pc (which was created by the build) to opencv22.pc (which is what IMP looks for for some reason). Note that the documentation mentions that 2.1-2.3 works, but it isn’t clear whether that’s actually true when a build failure claims 2.2 is not detected and that is the reason it won’t build em2d. OpenCV 2.2 doesn’t build properly on this environment, for a reason that I’m not quite sure of. As an aside, OpenCV 2.3.1 seems to require a very old version of CUDA that most people would not have, so one has to turn off CUDA support or get that very old version (which doesn’t support our hardware anyway). I then had difficulty with HDF5 not finding mpi.h. Apparently this is a common problem if you’ve built HDF5 parallel. My solution was setting the compilers to be mpicc/mpic++. At this point, I have to say I’m lost. Here is my cmake command line: cmake ../imp-2.5.0 -DCMAKE_BUILD_TYPE=Release -DPYTHON_LIBRARY=/opt/sw/packages/gcc-4.8.3/python/2.7.11/lib -DPYTHON_INCLUDE_DIR=/opt/sw/packages/gcc-4.8.3/python/2.7.11/include -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++ -DCMAKE_INSTALL_PREFIX=/opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost-1.60.0/imp/2.5.0 Doing a make with a high parallel number (eg. 24, 32) got me to a place where there were a number of errors on RMF/SWIG relating to not being able to find Python.h. It’s not clear whether that blocks the build, but it’s probably not good. The CMake command at the beginning reports that it found the expected version of Python (which didn’t work right unless I manually supplied it on the command line). It eventually fails for what I suspect is some other reason. Doing just a make fails on what looks like a problem with Boost. Perhaps Boost 1.60.0 isn’t supported? I don’t know what version to use instead, other than to assume 1.40.0 works since 1.40.0 or newer is required. Output as follows; your help is appreciated! Scanning dependencies of target IMP.statistics-lib [ 18%] Building CXX object modules/statistics/src/CMakeFiles/IMP.statistics-lib.dir/__/__/__/src/statistics_all.cpp.o In file included from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/functional/hash/extensions.hpp:24:0, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/functional/hash/hash.hpp:558, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/functional/hash.hpp:6, from /usr/src/imp-2.5.0-build/include/IMP/hash.h:17, from /usr/src/imp-2.5.0-build/include/IMP/statistics/statistics_config.h:162, from /usr/src/imp-2.5.0-build/include/IMP/statistics/ChiSquareMetric.h:11, from /usr/src/imp-2.5.0/modules/statistics/src/ChiSquareMetric.cpp:8, from /usr/src/imp-2.5.0-build/src/statistics_all.cpp:4: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp:446:25: error: ^Xice_not^Y is not a member of ^Xboost::type_traits^Y BOOST_STATIC_ASSERT(type_traits::ice_not<(is_same<Directed, bidirectionalS>::value)>::value); ^ /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/static_assert.hpp:70:55: note: in definition of macro ^XBOOST_STATIC_ASSERT^Y # define BOOST_STATIC_ASSERT( ... ) static_assert(__VA_ARGS__, #__VA_ARGS__) ^ /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp:446:89: error: ^X::value^Y has not been declared BOOST_STATIC_ASSERT(type_traits::ice_not<(is_same<Directed, bidirectionalS>::value)>::value); ^ /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/static_assert.hpp:70:55: note: in definition of macro ^XBOOST_STATIC_ASSERT^Y # define BOOST_STATIC_ASSERT( ... ) static_assert(__VA_ARGS__, #__VA_ARGS__) ^ /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp:446:89: note: suggested alternatives: BOOST_STATIC_ASSERT(type_traits::ice_not<(is_same<Directed, bidirectionalS>::value)>::value); ^ /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/static_assert.hpp:70:55: note: in definition of macro ^XBOOST_STATIC_ASSERT^Y # define BOOST_STATIC_ASSERT( ... ) static_assert(__VA_ARGS__, #__VA_ARGS__) ^ In file included from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/program_options/value_semantic.hpp:432:0, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/program_options/options_description.hpp:13, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/program_options.hpp:15, from /usr/src/imp-2.5.0-build/include/IMP/internal/Flag.h:13, from /usr/src/imp-2.5.0-build/include/IMP/Flag.h:13, from /usr/src/imp-2.5.0-build/include/IMP/internal/base_static.h:13, from /usr/src/imp-2.5.0-build/include/IMP/exception.h:16, from /usr/src/imp-2.5.0-build/include/IMP/Object.h:14, from /usr/src/imp-2.5.0-build/include/IMP/statistics/Metric.h:13, from /usr/src/imp-2.5.0-build/include/IMP/statistics/ChiSquareMetric.h:12, from /usr/src/imp-2.5.0/modules/statistics/src/ChiSquareMetric.cpp:8, from /usr/src/imp-2.5.0-build/src/statistics_all.cpp:4: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/program_options/detail/value_semantic.hpp:180:5: note: ^Xboost::program_options::value^Y value(T* v) ^ In file included from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/access.hpp:18:0, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/state.hpp:18, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/matcher/alternate_end_matcher.hpp:20, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/matchers.hpp:17, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/regex_primitives.hpp:22, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/xpressive_static.hpp:24, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/graphviz.hpp:34, from /usr/src/imp-2.5.0-build/include/IMP/internal/base_graph_utility.h:16, from /usr/src/imp-2.5.0-build/include/IMP/graph_macros.h:14, from /usr/src/imp-2.5.0-build/include/IMP/base_macros.h:24, from /usr/src/imp-2.5.0-build/include/IMP/base_utility.h:15, from /usr/src/imp-2.5.0-build/include/IMP/utility.h:13, from /usr/src/imp-2.5.0-build/include/IMP/algebra/VectorBaseD.h:16, from /usr/src/imp-2.5.0-build/include/IMP/algebra/VectorD.h:12, from /usr/src/imp-2.5.0-build/include/IMP/algebra/BoundingBoxD.h:12, from /usr/src/imp-2.5.0-build/include/IMP/algebra.h:10, from /usr/src/imp-2.5.0/modules/statistics/src/ChiSquareMetric.cpp:9, from /usr/src/imp-2.5.0-build/src/statistics_all.cpp:4: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/proto/traits.hpp:1161:5: note: ^Xboost::proto::value^Y value(Expr const &e) ^ In file included from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/access.hpp:18:0, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/state.hpp:18, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/matcher/alternate_end_matcher.hpp:20, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/matchers.hpp:17, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/regex_primitives.hpp:22, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/xpressive_static.hpp:24, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/graphviz.hpp:34, from /usr/src/imp-2.5.0-build/include/IMP/internal/base_graph_utility.h:16, from /usr/src/imp-2.5.0-build/include/IMP/graph_macros.h:14, from /usr/src/imp-2.5.0-build/include/IMP/base_macros.h:24, from /usr/src/imp-2.5.0-build/include/IMP/base_utility.h:15, from /usr/src/imp-2.5.0-build/include/IMP/utility.h:13, from /usr/src/imp-2.5.0-build/include/IMP/algebra/VectorBaseD.h:16, from /usr/src/imp-2.5.0-build/include/IMP/algebra/VectorD.h:12, from /usr/src/imp-2.5.0-build/include/IMP/algebra/BoundingBoxD.h:12, from /usr/src/imp-2.5.0-build/include/IMP/algebra.h:10, from /usr/src/imp-2.5.0/modules/statistics/src/ChiSquareMetric.cpp:9, from /usr/src/imp-2.5.0-build/src/statistics_all.cpp:4: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/proto/traits.hpp:294:16: note: ^Xboost::proto::result_of::value^Y struct value ^ In file included from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/access.hpp:18:0, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/state.hpp:18, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/matcher/alternate_end_matcher.hpp:20, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/core/matchers.hpp:17, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/regex_primitives.hpp:22, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/xpressive_static.hpp:24, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/graphviz.hpp:34, from /usr/src/imp-2.5.0-build/include/IMP/internal/base_graph_utility.h:16, from /usr/src/imp-2.5.0-build/include/IMP/graph_macros.h:14, from /usr/src/imp-2.5.0-build/include/IMP/base_macros.h:24, from /usr/src/imp-2.5.0-build/include/IMP/base_utility.h:15, from /usr/src/imp-2.5.0-build/include/IMP/utility.h:13, from /usr/src/imp-2.5.0-build/include/IMP/algebra/VectorBaseD.h:16, from /usr/src/imp-2.5.0-build/include/IMP/algebra/VectorD.h:12, from /usr/src/imp-2.5.0-build/include/IMP/algebra/BoundingBoxD.h:12, from /usr/src/imp-2.5.0-build/include/IMP/algebra.h:10, from /usr/src/imp-2.5.0/modules/statistics/src/ChiSquareMetric.cpp:9, from /usr/src/imp-2.5.0-build/src/statistics_all.cpp:4: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/proto/traits.hpp:824:16: note: ^Xboost::proto::functional::value^Y struct value ^ In file included from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/detail/detail_fwd.hpp:24:0, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/regex_primitives.hpp:21, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/xpressive_static.hpp:24, from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/graphviz.hpp:34, from /usr/src/imp-2.5.0-build/include/IMP/internal/base_graph_utility.h:16, from /usr/src/imp-2.5.0-build/include/IMP/graph_macros.h:14, from /usr/src/imp-2.5.0-build/include/IMP/base_macros.h:24, from /usr/src/imp-2.5.0-build/include/IMP/base_utility.h:15, from /usr/src/imp-2.5.0-build/include/IMP/utility.h:13, from /usr/src/imp-2.5.0-build/include/IMP/algebra/VectorBaseD.h:16, from /usr/src/imp-2.5.0-build/include/IMP/algebra/VectorD.h:12, from /usr/src/imp-2.5.0-build/include/IMP/algebra/BoundingBoxD.h:12, from /usr/src/imp-2.5.0-build/include/IMP/algebra.h:10, from /usr/src/imp-2.5.0/modules/statistics/src/ChiSquareMetric.cpp:9, from /usr/src/imp-2.5.0-build/src/statistics_all.cpp:4: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/xpressive/xpressive_fwd.hpp:134:12: note: ^Xboost::xpressive::value^Y struct value; ^ In file included from /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/bind.hpp:22:0, from /usr/src/imp-2.5.0-build/include/IMP/internal/container_helpers.h:19, from /usr/src/imp-2.5.0-build/include/IMP/internal/TupleRestraint.h:14, from /usr/src/imp-2.5.0-build/include/IMP/singleton_macros.h:15, from /usr/src/imp-2.5.0-build/include/IMP/macros.h:13, from /usr/src/imp-2.5.0-build/include/IMP/statistics/PartitionalClustering.h:13, from /usr/src/imp-2.5.0/modules/statistics/src/PartitionalClustering.cpp:7, from /usr/src/imp-2.5.0-build/src/statistics_all.cpp:8: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/bind/bind.hpp:118:25: note: ^Xboost::_bi::value^Y template<class T> class value ^ In file included from /usr/src/imp-2.5.0-build/include/IMP/statistics/internal/TrivialPartitionalClustering.h:14:0, from /usr/src/imp-2.5.0/modules/statistics/src/RecursivePartitionalClusteringEmbedding.cpp:9, from /usr/src/imp-2.5.0-build/src/statistics_all.cpp:10: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp: In instantiation of ^Xstatic boost::adj_mat_pm_helper<D, VP, EP, GP, A, Tag, boost::edge_property_tag>::type boost::adj_mat_pm_helper<D, VP, EP, GP, A, Tag, boost::edge_property_tag>::get_nonconst(boost::adjacency_matrix<D , VP, EP, GP, A>&, Tag) [with D = boost::undirectedS; VP = boost::no_property; EP = boost::property<boost::edge_weight_t, double, boost::property<boost::edge_ centrality_t, double> >; GP = boost::no_property; A = std::allocator<bool>; Tag = boost::edge_centrality_t; boost::adj_mat_pm_helper<D, VP, EP, GP, A, Tag, bo ost::edge_property_tag>::type = boost::function_property_map<boost::adj_mat_pm_helper<boost::undirectedS, boost::no_property, boost::property<boost::edge_weig ht_t, double, boost::property<boost::edge_centrality_t, double> >, boost::no_property, std::allocator<bool>, boost::edge_centrality_t, boost::edge_property_ta g>::lookup_property_from_edge<mpl_::bool_<false> >, boost::detail::matrix_edge_desc_impl<boost::undirected_tag, long unsigned int>, double&>; typename boost:: result_of<const boost::adj_mat_pm_helper<D, VP, EP, GP, A, Tag, boost::edge_property_tag>::lookup_property_from_edge<mpl_::bool_<false> >(const typename boost ::graph_traits<boost::adjacency_matrix<D, VP, EP, GP, A> >::edge_descriptor&)>::type = double&; typename boost::graph_traits<boost::adjacency_matrix<D, VP, EP , GP, A> >::edge_descriptor = boost::detail::matrix_edge_desc_impl<boost::undirected_tag, long unsigned int>]^Y: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp:1119:86: required from ^Xtypename boost::property_map<boost::ad jacency_matrix<D, VP, EP, GP, A>, Tag>::type boost::get(Tag, boost::adjacency_matrix<D, VP, EP, GP, A>&) [with D = boost::undirectedS; VP = boost::no_property ; EP = boost::property<boost::edge_weight_t, double, boost::property<boost::edge_centrality_t, double> >; GP = boost::no_property; A = std::allocator<bool>; T ag = boost::edge_centrality_t; typename boost::property_map<boost::adjacency_matrix<D, VP, EP, GP, A>, Tag>::type = boost::function_property_map<boost::adj_ma t_pm_helper<boost::undirectedS, boost::no_property, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_centrality_t, double> >, boost:: no_property, std::allocator<bool>, boost::edge_centrality_t, boost::edge_property_tag>::lookup_property_from_edge<mpl_::bool_<false> >, boost::detail::matrix_ edge_desc_impl<boost::undirected_tag, long unsigned int>, double&>]^Y /usr/src/imp-2.5.0/modules/statistics/src/internal/centrality_clustering.cpp:74:43: required from here /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp:1092:17: warning: unused parameter ^Xg^Y [-Wunused-parameter] static type get_nonconst(adjacency_matrix<D, VP, EP, GP, A>& g, Tag tag) { ^ /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp: In instantiation of ^Xstatic boost::adj_mat_pm_helper<D, VP, EP, GP, A, Tag, boost::edge_property_tag>::type boost::adj_mat_pm_helper<D, VP, EP, GP, A, Tag, boost::edge_property_tag>::get_nonconst(boost::adjacency_matrix<D , VP, EP, GP, A>&, Tag) [with D = boost::undirectedS; VP = boost::no_property; EP = boost::property<boost::edge_weight_t, double, boost::property<boost::edge_ centrality_t, double> >; GP = boost::no_property; A = std::allocator<bool>; Tag = boost::edge_weight_t; boost::adj_mat_pm_helper<D, VP, EP, GP, A, Tag, boost: :edge_property_tag>::type = boost::function_property_map<boost::adj_mat_pm_helper<boost::undirectedS, boost::no_property, boost::property<boost::edge_weight_t , double, boost::property<boost::edge_centrality_t, double> >, boost::no_property, std::allocator<bool>, boost::edge_weight_t, boost::edge_property_tag>::look up_property_from_edge<mpl_::bool_<false> >, boost::detail::matrix_edge_desc_impl<boost::undirected_tag, long unsigned int>, double&>; typename boost::result_o f<const boost::adj_mat_pm_helper<D, VP, EP, GP, A, Tag, boost::edge_property_tag>::lookup_property_from_edge<mpl_::bool_<false> >(const typename boost::graph_ traits<boost::adjacency_matrix<D, VP, EP, GP, A> >::edge_descriptor&)>::type = double&; typename boost::graph_traits<boost::adjacency_matrix<D, VP, EP, GP, A> > ::edge_descriptor = boost::detail::matrix_edge_desc_impl<boost::undirected_tag, long unsigned int>]^Y: /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp:1119:86: required from ^Xtypename boost::property_map<boost::ad jacency_matrix<D, VP, EP, GP, A>, Tag>::type boost::get(Tag, boost::adjacency_matrix<D, VP, EP, GP, A>&) [with D = boost::undirectedS; VP = boost::no_property ; EP = boost::property<boost::edge_weight_t, double, boost::property<boost::edge_centrality_t, double> >; GP = boost::no_property; A = std::allocator<bool>; T ag = boost::edge_weight_t; typename boost::property_map<boost::adjacency_matrix<D, VP, EP, GP, A>, Tag>::type = boost::function_property_map<boost::adj_mat_pm _helper<boost::undirectedS, boost::no_property, boost::property<boost::edge_weight_t, double, boost::property<boost::edge_centrality_t, double> >, boost::no_p roperty, std::allocator<bool>, boost::edge_weight_t, boost::edge_property_tag>::lookup_property_from_edge<mpl_::bool_<false> >, boost::detail::matrix_edge_des c_impl<boost::undirected_tag, long unsigned int>, double&>]^Y /usr/src/imp-2.5.0/modules/statistics/src/metric_clustering.cpp:25:39: required from here /opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost/1.60.0/include/boost/graph/adjacency_matrix.hpp:1092:17: warning: unused parameter ^Xg^Y [-Wunused-parameter] make[2]: *** [modules/statistics/src/CMakeFiles/IMP.statistics-lib.dir/__/__/__/src/statistics_all.cpp.o] Error 1 ake[1]: *** [modules/statistics/src/CMakeFiles/IMP.statistics-lib.dir/all] Error 2 make: *** [all] Error 2 -- ____ *Note: UMDNJ is now Rutgers-Biomedical and Health Sciences* || \\UTGERS |---------------------*O*--------------------- ||_// Biomedical | Ryan Novosielski - Senior Technologist || \\ and Health | novosirj(a)rutgers.edu - 973/972.0922 (2x0922) || \\ Sciences | OIRT/High Perf & Res Comp - MSB C630, Newark `'

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em.MapDistanceTransform class
by Karine VOLTZ 07 Jan '16

07 Jan '16

Dear IMP-users, I would like to use the em.MapDistanceTransform functionality of IMP but this class does not seem to be recognized as belonging to the em module. Can somebody give me information on the way to use this class? With my best wishes for 2016, Karine

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error during installation
by ashutosh srivastava 04 Jan '16

04 Jan '16

Dear IMP users I am trying to install IMP but I keep getting following error CMake Error at modules/atom/bin/cmake_install.cmake:42 (file): file INSTALL cannot find "/home/ashutosh/softwares/imp/bin/ligand_score". Call Stack (most recent call first): modules/atom/cmake_install.cmake:45 (include) cmake_install.cmake:8645 (include) I am installing imp-2.5.0 from source to local user (I dont have root permissions). I have installed SWIG and HDF5 also locally and passed their paths as environment variables. What could be the source of this error? Kindly let me know if any other detail is required. Thank you Best Regards Ashutosh

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