September 2011 - IMP-dev

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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can a restraint be in more than one restraintset?
by Keren Lasker 08 Sep '11

08 Sep '11

does it mean the restraint is going to be evaluated twice?

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recently in IMP
by Daniel Russel 08 Sep '11

08 Sep '11

- The RMF base support (stuff in the ::RMF namespace), has been moved to a new module, simply called RMF (no IMP). Now the functionality should be called like RMF.open_rmf_file() and headers include like \c RMF/RootHandle.h. This most was done in order to make the spin off of the RMF library as transparent as possible when it occurs later. - to work around various issues with ref counting pointers and compiler eccentricities, we added emulation of the C++0x \c nullptr. You should prefer that to \c NULL in \imp code that you want to run cross platform. - IMP::IntsList, IMP::FloatsList and IMP::StringsList have been added to replace the various scattered solutions for passing such types. - ::RMF::HDF5DataSetD is now templated on the dimension. Typedefs have been provided for the basic types so you can create an ::RMF::HDF5IndexDataSet2D now. - Various low level classes of IMP::rmf have been moved to the plain old ::RMF namespace as pat of cleaning things up to separate the RMF low level library from \imp. This include ::RMF::HDF5DataSetD. - IMP::Restraint::get_decomposition() and IMP::Restraint::get_current_decomposition() changed to return a single Restraint, instead of a list. This makes it easier to propagate the weight and maximum reliably. - \imp now supports usage of restraints without adding them to the IMP::Model scoring function. To do this, do IMP::Restraint::set_model(), passing the model. The restraint can then be evaluated. - IMP::domino::DominoSampler does not use the IMP::domino::OptimizeRestraints restraint optimization by default. Instead, if it is asked to create the IMP::domino::RestraintScoreSubsetFilterTable, it decomposes the restraints first (via IMP::create_decomposition()). This avoids several bugs and very fragile code. - the IMP::core::DiameterRestraint was ignoring the radii of the particles involved and so was giving artifically low scores. It now is on the actual diameter of this molecule. - the IMP::core::MonteCarlo optimizers now support incremental evaluation. This can be a lot faster when only a few particles are moved each step. - all the plural types in IMP have moved to bounds checked vectors when using debug builds with gcc. If you get a non-imp error about an invalid access, it is probably some code that walks off the end of an array. Please report it. - RMF::KeyCategory was renamed to RMF::Category - The deprecated constructors for various rmf/hdf5 things from files have been removed. Now use the methods RMF::open_rmf_file(), RMF::create_rmf_file(), RMF::open_rmf_file_read_only(), RMF::open_hdf5_file(), RMF::create_hdf5_file(). - RMF:: broke backward compatibility in order to accelerate loading times of files and use a more compact storage for strings. - The IMP::core::MoverBase was changed to move it off of the IMP::SingletonContainer. This resulted in the IMP::core::BallMover and IMP::core::NormalMover having new constructors. Now create them from a list of particles, a list of float keys and a radius/standard deviation. This removes some complexity and inefficiencies as well is removes some scope for errors. - Temp and non-temp decorator lists have been merged in C++. This was done to simplifity code since no one was using the non-temp variants. Now all decorator lists are temp (non-reference counted) variants. - restraints and restraint sets are now evaluated only using "canonical" weights. That is, each restraint has one weight for the model (the total over all the restraint sets it is contained in and will always be evaluated with that weight). This allows the evaluation of simple restraints to be faster. - The IMP_LIST() macros have been changed slightly. If your usage needs to take action upon addition, removal or changes to the list, use the IMP_LIST_ACTION() variant in your header. The IMP_LIST_IMPL() macro no longer takes the actions, and the last three (generally empty arguments) will have to be removed from the call to get it to work. This is needed to move towards more flexible and efficient passing of lists of values.

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::rmf -> ::RMF
by Daniel Russel 01 Sep '11

01 Sep '11

Sorry I forgot to send this earlier. I had to rename the non-IMP rmf namespace to RMF to get around some bugs in old versions of swig. So now IMP RMF functionality is in ::IMP::rmf and non-imp functionality is in ::RMF.

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