- IMP-dev - salilab.org

[Bug 109] New: Add google native client compatibility
by bugzilla-daemon＠salilab.org 20 Jul '10

20 Jul '10

https://salilab.org/imp/bugs/show_bug.cgi?id=109 Summary: Add google native client compatibility Product: IMP Version: unspecified Platform: Other OS/Version: All Status: NEW Severity: enhancement Priority: P5 Component: kernel AssignedTo: drussel(a)SALILAB.ORG ReportedBy: drussel(a)SALILAB.ORG CC: imp-dev(a)salilab.org Estimated Hours: 0.0 And a test platform. -- Configure bugmail: https://salilab.org/imp/bugs/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

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Re: [IMP-dev] problem with current IMP
by Daniel Russel 13 Jul '10

13 Jul '10

Boost got upgraded on the Linux machines recently, and scons doesn't notice, leading to the compiler errors below. The easiest thing to do is to delete all the scons databases and things (rm .scons*). On Jul 13, 2010, at 7:18 PM, Keren Lasker <kerenl(a)salilab.org> wrote: > does not compile ... > not sure who made these recent changes: > > build/include/IMP/base_types.h:105: error: invalid application of 'sizeof' to incomplete type 'boost::STATIC_ASSERTION_FAILURE<false>' > In file included from build/include/IMP/VectorOfRefCounted.h:13, > from build/include/IMP/Object.h:18, > from build/include/IMP/Model.h:13, > from kernel/src/Model_dependencies.cpp:9: > build/include/IMP/base_types.h:105: error: invalid application of 'sizeof' to incomplete type 'boost::STATIC_ASSERTION_FAILURE<false>' > g++ -o modules/algebra/src/vector_search.os -c -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC \ > -Wall -Woverloaded-virtual -g -fvisibility=hidden -fPIC -DIMP_DATA_DIRECTORY=\"/usr/share/imp\" -DIMP_EXAMPLE_DIRECTORY=\"/usr/share/doc/imp/examples\" -DIM\ > PALGEBRA_EXPORTS -DGCC_VISIBILITY -Ibuild/include modules/algebra/src/vector_search.cpp > g++ -o build/src/algebra_link_0.os -c -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -Wall -Wo\ > verloaded-virtual -g -fvisibility=hidden -fPIC -DIMP_DATA_DIRECTORY=\"/usr/share/imp\" -DIMP_EXAMPLE_DIRECTORY=\"/usr/share/doc/imp/examples\" -DIMPALGEBRA_\ > EXPORTS -DGCC_VISIBILITY -Ibuild/include build/src/algebra_link_0.cpp > g++ -o build/src/algebra_link_1.os -c -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -Wall -Wo\ > verloaded-virtual -g -fvisibility=hidden -fPIC -DIMP_DATA_DIRECTORY=\"/usr/share/imp\" -DIMP_EXAMPLE_DIRECTORY=\"/usr/share/doc/imp/examples\" -DIMPALGEBRA_\ > EXPORTS -DGCC_VISIBILITY -Ibuild/include build/src/algebra_link_1.cpp > > can you please help? > > thanks, keren.

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automatic force field restraint setup
by Dave Barkan 12 Jul '10

12 Jul '10

Hi all, I was wondering if there is a quick way to set up force field restraints on a hierarchy of atoms generated by read_pdb()? Right now I have to explicitly set up three or four types of restraints myself (following the protocol in the charm_forcefield.py example in the atom module). This is likely to be re-implemented often and it would be nice if IMP provided an easy way to do this. Maybe less useful to others, but potentially to me, would be if you could specify a region of the protein to which to add the forcefield restraints (instead of the whole PDB you just read in). thanks, db

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changes to Model that presumably no one will notice
by Daniel Russel 22 Jun '10

22 Jun '10

I just checked in some changes to IMP::Model. I don't think anyone was using the features (and they are relatively new). - removed the function to evaluate the score on a subset of the particles. If you want to do that, I have a much more efficient way. Ask me. - move the dependency graph computations out of the model since the model is already doing lots of things and they don't need to be there. get_dependency_graph is now in the IMP namespace.

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rigid bodies
by Keren Lasker 17 Jun '10

17 Jun '10

hi - is there a way to remove a rigid body from a molecule ? thanks, keren.

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when scons complains about duplicate rules for a IMP_something.i
by Daniel Russel 16 Jun '10

16 Jun '10

The easiest thing to do, assuming you haven't changed any .i files, is to do rm kernel/pyext/*.i modules/*/pyext/*.i svn update That removes the .i files which were temporary files but being sloppily mixed in with input files. Sorry.

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Shiny new imp-users mailing list
by Ben Webb 20 Apr '10

20 Apr '10

Now that we have a public release of IMP that non-developers can use, there is a new imp-users mailing list. This is targeted at "users" of IMP, i.e. for discussion of and help with the use of IMP, as opposed to technical discussion of new features. Note that I did not automatically subscribe all the imp-dev people to imp-users. However, I suggest that you do subscribe to the imp-users list yourselves: http://salilab.org/imp/nightly/doc/html/maillists.html The non-technical amongst you might also want to unsubscribe from imp-dev at the same time! 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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[Bug 106] Out of memory in ConjugateGradients
by bugzilla-daemon＠salilab.org 20 Apr '10

20 Apr '10

https://salilab.org/imp/bugs/show_bug.cgi?id=106 --- Comment #4 from drussel(a)SALILAB.ORG 2010-04-20 13:02:33 PDT --- (In reply to comment #3) > If by "test bed" you mean a script which demonstrates the problem, the attached > memtest.py does exactly that. Yeah, I meant "now that we have" :-) > > If you want to explore other ways of solving the problem, you can chat with > Harianto Tjong over on imp-users, who I'm sure will be willing to help try > things out. -- Configure bugmail: https://salilab.org/imp/bugs/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

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[Bug 106] Out of memory in ConjugateGradients
by bugzilla-daemon＠salilab.org 20 Apr '10

20 Apr '10

https://salilab.org/imp/bugs/show_bug.cgi?id=106 --- Comment #3 from Ben Webb <ben(a)salilab.org> 2010-04-20 12:46:47 PDT --- If by "test bed" you mean a script which demonstrates the problem, the attached memtest.py does exactly that. If you want to explore other ways of solving the problem, you can chat with Harianto Tjong over on imp-users, who I'm sure will be willing to help try things out. -- Configure bugmail: https://salilab.org/imp/bugs/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

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[Bug 106] Out of memory in ConjugateGradients
by bugzilla-daemon＠salilab.org 20 Apr '10

20 Apr '10

https://salilab.org/imp/bugs/show_bug.cgi?id=106 --- Comment #2 from drussel(a)SALILAB.ORG 2010-04-20 12:43:28 PDT --- I see two easy ways forward: 1. convert the bad_alloc into a python-friendly exception with a nicer message. I'm not sure how useful this is as I suspect a general purpose optimizer and 100k particles and a nonbonded list can't be stably mixed with our current setup as it is likely to hit a tight configuration at some point. 2. convert the bad_alloc to a ModelException. Then if MC is being run, it can reject the conformation or CG run and try another so at least something can come out of it. But it makes the assumption that such a configuration would have a bad score. Slightly more involved, which I used to have in there is to reduce the slack in the NBL and try again. If we have a test bed, then I can experiment with that. -- Configure bugmail: https://salilab.org/imp/bugs/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are on the CC list for the bug.

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