- IMP-dev - salilab.org

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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dealing with scones issues
by Daniel Russel 28 Sep '11

28 Sep '11

I moved some files around in IMP. You probably won't notice, except that scons gets easily confused. If IMP won't build with odd messages about unfound dependencies, remove your .scons* files and, for good measure, your build directory.

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IMP-dev meeting tomorrow
by Dave Barkan 27 Sep '11

27 Sep '11

Hey all, No group meeting tomorrow, but for those who are interested, Ben will talk about the new IMP.parallel module. Let's go for normal group meeting time and place. thanks, dave

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problem running jobs on the cluster
by Keren Lasker 24 Sep '11

24 Sep '11

hi: running jobs on our shared cluster i am getting an error: "ImportError: libhdf5.so.6: cannot open shared object file: No such file or directory" things are running ok on baton2, the problem occurs on the nodes of the cluster. any idea how to resolve that? thanks, keren.

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another note about software on the cluster
by Daniel Russel 21 Sep '11

21 Sep '11

I have a build of gcc 4.6.1 in ~drussel/production. Max has been getting quite nice speedups for excluded volume computations from using it vs the native gcc version. If you are interested, ask Max for a config.py which has all the needed directories (it is slightly non-trivial).

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room today
by Dave Barkan 15 Sep '11

15 Sep '11

hey all, I forgot to make a room reservation, but let's try 3rd floor conference room in this building. Right now it is listed as having an all-day event, but no one is there currently. dave

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building imp faster on laptops
by Daniel Russel 15 Sep '11

15 Sep '11

You can greatly accelerate building IMP on your mac laptop (and reduce the chance of it saturating you I/O bus and making your machine temporarily useless) by sticking the build directory in a ram disk. The preferences panel "Esperance DV" helps make such a ram disk (and to save the contents back to disk when you log out). You need a ram disk of at least 1.2GB. And the ram disk seems to get paged to disk OK when I'm doing other things on my mac (so it is not permanently eating the memory).

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IMP dev Thursday
by Dave Barkan 15 Sep '11

15 Sep '11

Hey all, I am scheduling an IMP-dev meeting to talk about my peptide docking project. I'll go through how it works and what I still have to do. It will be a mini group meeting, but more focused on methods and ideas instead of results. This is for the final development and benchmarking push before I graduate :-) Andrej wants to come too and suggested Thursday at 12, hopefully that works for everyone. Thanks, Dave

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