October 2011 - IMP-dev

newton method
by Yannick Spill 26 Oct '11

26 Oct '11

Hi there, I was about to write a Newton optimizer (that uses the Hessian) and I came across the quasi-newton optimizer in the IMP gsl module. It says it's not well tested. Has anyone been using it lately? How is it? Should I code a true Newton optimizer? thanks! Yannick

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Get particle by name
by Davide Baù 23 Oct '11

23 Oct '11

Hi, I've searched about this but did not find an answer. I'd like to know if it's possible to get a particle (from, e.g., a ListSingletonContainer) using its name instead of its index. Thanks, Davide

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Problem compiling IMP trunk on a Mac with Lion
by Davide Baù 13 Oct '11

13 Oct '11

Hi all, I have a problem trying to compile the latest IMP build (r11272) on a MBP updated to Lion. I got the latest version of IMP (svn co http://svn.salilab.org/imp/trunk) but I'm not able to compile it (Errors building: tools/imppy.sh). Does anyone knows if it depends on the IMP version I'm trying to compile? Davide > scons: *** [tools/imppy.sh] KeyError : 'kernel' > Traceback (most recent call last): > File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/scons-2.0.1/SCons/Action.py", line 1046, in execute > result = self.execfunction(target=target, source=rsources, env=env) > File "/usr/src/imp/r11272/scons_tools/imppy.py", line 61, in builder_script_file > if data.get(env).modules['kernel'].external: > KeyError: 'kernel' > scons: building terminated because of errors. > > > IMP configuration: > boost ='yes' > boostlibs ='' > boostversion ='104601' > boostlibsuffix ='-mt' > endian ='little' > boost_programoptions='yes' > boost_programoptionslibs='boost_program_options-mt' > build ='fast' > prefix ='/usr' > local ='True' > pythonpath ='/usr/src/imp/r11272' > libpath ='/opt/local/lib' > ldlibpath ='/usr/src/imp/r11272' > swigpath ='/usr/src/imp/r11272' > datapath ='/usr/src/imp/r11272' > cxxcompiler ='g++' > cxxflags='-isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wmissing-prototypes -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' > pythoncxxflags ='-isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wno-deprecated -Winit-self -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' > bincxxflags='-isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' > shliblinkflags =' -dynamiclib -headerpad_max_install_names' > arliblinkflags ='' > binlinkflags ='-headerpad_max_install_names' > pythonlinkflags =' -bundle -bundle -flat_namespace -undefined suppress -headerpad_max_install_names' > rpath ='True' > static ='False' > pythonsosuffix ='.so' > pkgconfig ='True' > path ="/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/opt/local/bin:/usr/local/git/bin:/Users/dbau/Work/scripts:/Users/dbau/Work/scripts/ucsf:/Users/dbau/Work/scripts/tools:/Users/dbau/Work/scripts/IMP:/Users/dbau/Scripts:/opt/local/bin:/usr/bin:/bin:/usr/local/git/bin:/usr/src/android-sdk-mac_x86/platforms:/usr/src/android-sdk-mac_x86/tools:/usr/src/android-sdk-mac_x86/platform-tools" > python ="python" > > > Enabled dependencies: Boost, Boost.ProgramOptions > > Disabled modules: em, core, container, saxs, multifit, modules, example_system_local, rmf, atom, em2d > > Disabled applications: rmf_tools, ligand_score, saxs_tools, Groel, nup84, multifit, em_tools, example_system, rnapii, foxs > > Errors building: > tools/imppy.sh

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