I forwarded this to imp-dev since I am not super familiar with the MD support int IMP. My guess is that the velocities are not being added before the OptimizerState is called.
As for the other questions, the general error handler function is now IMP::base::handle_error (and is now documented). You can also do "catch throw" in gdb to break any time there is an exception, but this is a bit annoying when reading pdbs as exceptions are thrown over missing/unknown atoms.
On Tue, Jun 26, 2012 at 12:15 PM, Dave Barkan dbarkan@salilab.org wrote:
> ** > Hey Daniel, > > I am getting an IMP usage exception when I try to use a > VelocityScalingOptimizerState (output run from gdb): > > Traceback (most recent call last): > File "generateTrajectories.py", line 56, in <module> > p.runMolecularDynamics() > File > "/trombone1/home/dbarkan/IMP/impBuildFour/imp/debug/build/lib/IMP/pepdock/peptideDocker.py", > line 107, in runMolecularDynamics > self.mdHandler.runMdStage(i) > File > "/trombone1/home/dbarkan/IMP/impBuildFour/imp/debug/build/lib/IMP/pepdock/md.py", > line 59, in runMdStage > > self.mdOptimizer.optimize(self.schedule.getStepCountForMdStage(stageNumber)) > File > "/trombone1/home/dbarkan/IMP/impBuildFour/imp/debug/build/lib/IMP/__init__.py", > line 3049, in optimize > return _IMP.Optimizer_optimize(self, *args) > _IMP.UsageException: Usage check failure: Can't get attribute that is not > there > Context: MD 0::optimize/simulate > > WARNING No frames were saved to file "HierarchySaveLink0" even though > objects were added. > WARNING Object "HierarchySaveLink0" was never used. See the IMP::Object > documentation for an explanation. > WARNING Object "lj_flex_flex" was never used. See the IMP::Object > documentation for an explanation. > [Inferior 1 (process 40694) exited with code 01] > > I can use other OptimizerStates without seeing this error. > VelocityScalingOptimizerState was working before but stopped after I > changed some of my code (no IMP updates) around so I am probably not > initializing something correctly. > > I tried running it with gdb but it appears to exit without allowing me to > see the backtrace (it says 'no stack' when I type backtrace). Previously I > was able to set a breakpoint when a usage exception was occurring by typing > > break IMP::internal::assert_fail > > before running gdb. But that seems to no longer work: > > (gdb) break IMP::internal::assert_fail > Function "IMP::internal::assert_fail" not defined. > Make breakpoint pending on future shared library load? (y or [n]) > > So my questions: > > 1. Does anything immediately stand out to you with the error? > 2. Can I get gdb to stop upon the Usage Exception with the stack in memory > so I can track down the error? > > Thanks, > Dave >
I figured out the problem, not sure if it's a bug or not.
In my system some atoms are fixed and some are flexible. The ones that are fixed I call
atom.set_coordinates_are_optimized(0)
which prevents them from moving in MD.
Then I create the optimizer and velocity scaler as such:
mdOptimizer = IMP.atom.MolecularDynamics(model) vsos = IMP.atom.VelocityScalingOptimizerState(IMP.atom.get_leaves(protein), 0, 0) vsIndex = mdOptimizer.add_optimizer_state(vsos) vsos.set_temperature(100.0) . . .
mdOptimizer.optimize(100) #throws exception
The error comes if I call set_coordinates_are_optimized(0) *after* creating the VelocityScalingOptimizerState. If I call set_coordinates_are_optimized(0) before creating vsos, it works fine.
dave
On 6/26/12 1:12 PM, Daniel Russel wrote: > I forwarded this to imp-dev since I am not super familiar with the MD > support int IMP. My guess is that the velocities are not being added > before the OptimizerState is called. > > As for the other questions, the general error handler function is now > IMP::base::handle_error (and is now documented). You can also do > "catch throw" in gdb to break any time there is an exception, but this > is a bit annoying when reading pdbs as exceptions are thrown over > missing/unknown atoms. > > On Tue, Jun 26, 2012 at 12:15 PM, Dave Barkan <dbarkan@salilab.org > mailto:dbarkan@salilab.org> wrote: > > Hey Daniel, > > I am getting an IMP usage exception when I try to use a > VelocityScalingOptimizerState (output run from gdb): > > Traceback (most recent call last): > File "generateTrajectories.py", line 56, in <module> > p.runMolecularDynamics() > File > "/trombone1/home/dbarkan/IMP/impBuildFour/imp/debug/build/lib/IMP/pepdock/peptideDocker.py", > line 107, in runMolecularDynamics > self.mdHandler.runMdStage(i) > File > "/trombone1/home/dbarkan/IMP/impBuildFour/imp/debug/build/lib/IMP/pepdock/md.py", > line 59, in runMdStage > > self.mdOptimizer.optimize(self.schedule.getStepCountForMdStage(stageNumber)) > File > "/trombone1/home/dbarkan/IMP/impBuildFour/imp/debug/build/lib/IMP/__init__.py", > line 3049, in optimize > return _IMP.Optimizer_optimize(self, *args) > _IMP.UsageException: Usage check failure: Can't get attribute that > is not there > Context: MD 0::optimize/simulate > > WARNING No frames were saved to file "HierarchySaveLink0" even > though objects were added. > WARNING Object "HierarchySaveLink0" was never used. See the > IMP::Object documentation for an explanation. > WARNING Object "lj_flex_flex" was never used. See the IMP::Object > documentation for an explanation. > [Inferior 1 (process 40694) exited with code 01] > > I can use other OptimizerStates without seeing this error. > VelocityScalingOptimizerState was working before but stopped after > I changed some of my code (no IMP updates) around so I am probably > not initializing something correctly. > > I tried running it with gdb but it appears to exit without > allowing me to see the backtrace (it says 'no stack' when I type > backtrace). Previously I was able to set a breakpoint when a usage > exception was occurring by typing > > break IMP::internal::assert_fail > > before running gdb. But that seems to no longer work: > > (gdb) break IMP::internal::assert_fail > Function "IMP::internal::assert_fail" not defined. > Make breakpoint pending on future shared library load? (y or [n]) > > So my questions: > > 1. Does anything immediately stand out to you with the error? > 2. Can I get gdb to stop upon the Usage Exception with the stack > in memory so I can track down the error? > > Thanks, > Dave > >
In various cases non-optimized particles are skipped (for efficiency since they won't be moved anyway). It sounds like you introduce an inconsistency between the particles the optimizer state skips and the particles the MD optimizer skips (and since the optimizer adds the velocities, you get an error). I guess that could be fixed by the optimizer state adding velocities itself, but I think the ultimate answer is "Don't do it, it isn't really what you want anyway" :-)
On Tue, Jun 26, 2012 at 4:01 PM, Dave Barkan dbarkan@salilab.org wrote:
> ** > I figured out the problem, not sure if it's a bug or not. > > In my system some atoms are fixed and some are flexible. The ones that are > fixed I call > > atom.set_coordinates_are_optimized(0) > > which prevents them from moving in MD. > > Then I create the optimizer and velocity scaler as such: > > mdOptimizer = IMP.atom.MolecularDynamics(model) > vsos = > IMP.atom.VelocityScalingOptimizerState(IMP.atom.get_leaves(protein), 0, 0) > vsIndex = mdOptimizer.add_optimizer_state(vsos) > vsos.set_temperature(100.0) > . > . > . > > mdOptimizer.optimize(100) #throws exception > > The error comes if I call set_coordinates_are_optimized(0) *after* > creating the VelocityScalingOptimizerState. If I call > set_coordinates_are_optimized(0) before creating vsos, it works fine. > > dave > > On 6/26/12 1:12 PM, Daniel Russel wrote: > > I forwarded this to imp-dev since I am not super familiar with the MD > support int IMP. My guess is that the velocities are not being added before > the OptimizerState is called. > > As for the other questions, the general error handler function is now > IMP::base::handle_error (and is now documented). You can also do "catch > throw" in gdb to break any time there is an exception, but this is a bit > annoying when reading pdbs as exceptions are thrown over missing/unknown > atoms. > > On Tue, Jun 26, 2012 at 12:15 PM, Dave Barkan dbarkan@salilab.org wrote: > >> Hey Daniel, >> >> I am getting an IMP usage exception when I try to use a >> VelocityScalingOptimizerState (output run from gdb): >> >> Traceback (most recent call last): >> File "generateTrajectories.py", line 56, in <module> >> p.runMolecularDynamics() >> File >> "/trombone1/home/dbarkan/IMP/impBuildFour/imp/debug/build/lib/IMP/pepdock/peptideDocker.py", >> line 107, in runMolecularDynamics >> self.mdHandler.runMdStage(i) >> File >> "/trombone1/home/dbarkan/IMP/impBuildFour/imp/debug/build/lib/IMP/pepdock/md.py", >> line 59, in runMdStage >> >> self.mdOptimizer.optimize(self.schedule.getStepCountForMdStage(stageNumber)) >> File >> "/trombone1/home/dbarkan/IMP/impBuildFour/imp/debug/build/lib/IMP/__init__.py", >> line 3049, in optimize >> return _IMP.Optimizer_optimize(self, *args) >> _IMP.UsageException: Usage check failure: Can't get attribute that is not >> there >> Context: MD 0::optimize/simulate >> >> WARNING No frames were saved to file "HierarchySaveLink0" even though >> objects were added. >> WARNING Object "HierarchySaveLink0" was never used. See the IMP::Object >> documentation for an explanation. >> WARNING Object "lj_flex_flex" was never used. See the IMP::Object >> documentation for an explanation. >> [Inferior 1 (process 40694) exited with code 01] >> >> I can use other OptimizerStates without seeing this error. >> VelocityScalingOptimizerState was working before but stopped after I >> changed some of my code (no IMP updates) around so I am probably not >> initializing something correctly. >> >> I tried running it with gdb but it appears to exit without allowing me to >> see the backtrace (it says 'no stack' when I type backtrace). Previously I >> was able to set a breakpoint when a usage exception was occurring by typing >> >> break IMP::internal::assert_fail >> >> before running gdb. But that seems to no longer work: >> >> (gdb) break IMP::internal::assert_fail >> Function "IMP::internal::assert_fail" not defined. >> Make breakpoint pending on future shared library load? (y or [n]) >> >> So my questions: >> >> 1. Does anything immediately stand out to you with the error? >> 2. Can I get gdb to stop upon the Usage Exception with the stack in >> memory so I can track down the error? >> >> Thanks, >> Dave >> > > >
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Daniel Russel -
Dave Barkan