IMP-dev

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869 discussions

IMP 2.9.0 release
by Ben Webb 03 Jul '18

03 Jul '18

IMP 2.9.0 is now available. This is a bugfix and major update release. Most notably a number of new applications of IMP are now available, including the elucidation of the structure of the entire yeast nuclear pore complex. This release also includes a number of bug fixes and performance improvements. See https://integrativemodeling.org/2.9.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Correctly setting non-default temperatures in Brownian dynamics simulations
by Barak Raveh 02 Jul '18

02 Jul '18

This note is for advanced BD (and possibly MD) users only - it is not relevant if you simulate IMP at the default IMP temperature (297.15 K). The issue if you do simulations at non-default temperature is that the particles diffusion coefficients scale with T according to the equations of Brownian However, The BrownianDynamics class relies on whatever diffusion coefficients were set by the Diffusion decorator, regardless of the simulation temperature. Therefore, to simulate correctly at non-default temperatures, one must do two things: (1) Call BrownianDynamics::set_temperature() (2) Update the diffusion coefficients for all particles to scale with temperature - e.g. D is 10% higher at 330 K than at 300 K. I will update the IMP documentation to explain this subtlety. Let me know if you think we should change the code behavior. Perhaps we can add code to automatically update D, but it's also risky and could lead to unexpected behavior. Barak

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sample profiling output + sample profiling of python script
by Barak Raveh 20 Jun '18

20 Jun '18

1) Some people are getting weird results from gperftools/pperf (and I'm happy to help unweird them :). I attach profiling.pdf, a sample output of gperftools so you know how it should look like when it works, in this case for a python IMP script that spends most of its time in the C++ section of the code. You will see 60% of the running time is spent in BrownianDynamics::do_step, of these 45% in score evaluation, of which 16% are spent preparing for score evaluation, 22% in the score evaluation itself, and 6% in post-evaluation tasks. Another 33% are spent in updating optimizer states (in this particular example, which is optimizer state intensive). 2) If most of your running time is not in the C++ parts of the code, you could profile the python code itself. There are many tools available. One easy option to profile a python script at the function level is cProfile (documentation https://docs.python.org/2/library/profile.html). If you just want to quickly start, here is a sample file that uses cProfile. There are other profilers that work for line-by-line profiling of python scripts, or for parallel runs import cProfile def ho(): for i in range(10): pass def hi(): for i in range(1000): ho() def he(): for i in range(10000): hi() if __name__ == '__main__': cProfile.run('he()')

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Re: [IMP-dev] profiling IMP files on Unix
by Barak Raveh 20 Jun '18

20 Jun '18

A general note - my experience is with profiling C++ heavy runs (even if bound by python) that are serial (working on one CPU each). There are good solutions for profiling the python script itself (the time spent performing actual python operations, not just calling IMP binary libraries). I can elaborate more if relevant (but test what I sent first!). Also, profiling parallel programs might work but I’m not sure - start with profiling serial runs before trying parallel, if possible. On Tue, Jun 19, 2018 at 12:52 PM Barak Raveh <barak.raveh(a)gmail.com> wrote: > This is for binary files or python files on unix machines, examples are > given in bash. > I haven't profiled Mac files though I think Charles has. Only profile > files in fast mode - no point in profiling debug builds! > > > *Profiling python IMP files:* > > 1) Use the CPU_PROFILE flag to specify an output .prof file (on some > systems you might also need to add LD_PRELOAD=/usr/lib64/libprofiler.so - > probably not): > > $ CPUPROFILE=./barak.prof /home/barak/imp_git/fast/setup_environment.sh > python expensive_test_statistics_from_simulation_data.py &> LOG > > 2) Use "pprof --pdf <path-to-python-binary> <path-to-.prof-file>" to print > to PDF format - perhaps the process id will be appended to the output > profile file. Use "--gv", "--txt" or some of the other pprof options if you > like. > > pprof --pdf /usr/bin/python barak.prof_31784 > 31784.pdf > > > *Profiling binary IMP files:* > > 1) Run your binary IMP program as you usually would, but with the > --cpu_profile flag. > (this is a generic IMP flag, which will create a .prof file with > profiling information. The default .prof file will be created in the > current folder, or edit CPU_PROFILE to change the path of the output .prof > file). > > 2) Use "pprof --pdf <path-to-binary-IMP-file> <path-to-.prof-file>" to > print to PDF format. Use "--gv", "--txt" or some of the other pprof > options if you like. > > > *Comments:* > > 1) Documentation of gperftools https://github.com/gperftools/gperftools > > 2) See also possibly partially updated IMP page on profiling > https://github.com/salilab/imp/blob/4941f4e11403bac687a64b273f80f1ccc70b352… > > 3) Try "pprof --help" for some interesting options > > > -- -- Barak

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Fwd: profiling IMP files on Unix
by Barak Raveh 19 Jun '18

19 Jun '18

---------- Forwarded message ---------- From: Barak Raveh <barak.raveh(a)gmail.com> Date: Tue, Jun 19, 2018 at 12:52 PM Subject: profiling IMP files on Unix To: Sali Lab <salilab(a)salilab.org> This is for binary files or python files on unix machines, examples are given in bash. I haven't profiled Mac files though I think Charles has. Only profile files in fast mode - no point in profiling debug builds! *Profiling python IMP files:* 1) Use the CPU_PROFILE flag to specify an output .prof file (on some systems you might also need to add LD_PRELOAD=/usr/lib64/libprofiler.so - probably not): $ CPUPROFILE=./barak.prof /home/barak/imp_git/fast/setup_environment.sh python expensive_test_statistics_from_simulation_data.py &> LOG 2) Use "pprof --pdf <path-to-python-binary> <path-to-.prof-file>" to print to PDF format - perhaps the process id will be appended to the output profile file. Use "--gv", "--txt" or some of the other pprof options if you like. pprof --pdf /usr/bin/python barak.prof_31784 > 31784.pdf *Profiling binary IMP files:* 1) Run your binary IMP program as you usually would, but with the --cpu_profile flag. (this is a generic IMP flag, which will create a .prof file with profiling information. The default .prof file will be created in the current folder, or edit CPU_PROFILE to change the path of the output .prof file). 2) Use "pprof --pdf <path-to-binary-IMP-file> <path-to-.prof-file>" to print to PDF format. Use "--gv", "--txt" or some of the other pprof options if you like. *Comments:* 1) Documentation of gperftools https://github.com/gperftools/gperftools 2) See also possibly partially updated IMP page on profiling https://github.com/salilab/imp/blob/4941f4e11403bac687a64b273f80f1 ccc70b3522/doc/manual/profiling.md 3) Try "pprof --help" for some interesting options -- Barak

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Poll for Profiling results meeting
by Daniel Saltzberg 19 Jun '18

19 Jun '18

Hi all, We're going to try and meet in the first half of August to go over the IMP profiling results. Please fill in the doodle poll! https://doodle.com/poll/zwuggidx2fxegpni Best, -Daniel -- Daniel Saltzberg Post-doctoral Scholar University of California at San Francisco Lab of Andrej Sali (www.salilab.org) T: 415.514.4258 *Mailing Address:* UCSF MC 2552, Mission Bay, Byers Hall 1700 4th Street, Suite 503B San Francisco, CA 94158-2330 saltzberg(a)salilab.org ds229(a)bu.edu

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Re: [IMP-dev] IMP Efficiency Comm
by Daniel Saltzberg 18 Jun '18

18 Jun '18

Hi all, Just a reminder that we will have a meeting to discuss strategies for making IMP more efficient at 11AM Pacific tomorrow. For those in the office, we will be in MH 1405. You can join virtually using the salilab Zoom link; https://ucsf.zoom.us/my/ salilab *Agenda:* 1) Introduction. Scope of these meetings. 2) IMP efficiency projects. - Discuss status of and plans for completing: a) IncrementalScoringFunction (Issue 959 <https://github.com/salilab/imp/issues/959>) b) Parallelization of Replicas c) GPU accelleration 3) Additional projects to consider. 4) Schedule next/recurring meetings. Cheers, -Daniel On Sun, Jun 17, 2018 at 5:27 PM, Chemmama, Ilan <Ilan.Chemmama(a)ucsf.edu> wrote: > Next Tuesday at 11AM PST works for me as well. > Best, > Ilan > > On Jun 15, 2018, at 10:16 AM, Ignacia Echeverria <iecheverria(a)gmail.com> > wrote: > > Next Tuesday works for me. > Best, > Ignacia > > On Thu, Jun 14, 2018 at 9:25 AM Daniel Saltzberg <ds229(a)bu.edu> wrote: > >> I like the idea of involving the entire IMP community, however, my >> initial goals for this meeting were not quite as large as Barak suggested! >> In that case, let's push the meeting off until next week so that we give >> people enough time to schedule and myself enough time to prepare a more >> focused agenda. >> >> I'll suggest next *Tuesday, June 19th at 11AM Pacific Time.* The meeting >> will go no longer than an hour and a half. >> >> For those new to this email thread, we are interested in identifying >> specific areas in IMP where efficiency and functionality can be >> significantly improved with a moderate amount of effort and task these >> projects to individuals or small groups. Some issues we discussed at the >> retreat are: >> >> * Scoring efficiency - Make IncrementalScoringFunction work with current >> restraints (EM, EV) >> * Parallelization of individual replicas >> * Parallelizing propagation of moves within coarse grained representation >> of rigid bodies. >> * Identification of GPU-friendly computations >> >> The purpose of this meeting and subsequent ones will be to discuss the >> root causes of these issues, discuss general strategies for solving them, >> document them/improve the documentation in github issues and assign people >> to work on them outside of the meeting. >> >> Cheers, >> -Daniel >> >> On Tue, Jun 12, 2018 at 11:33 PM, Dina Schneidman <duhovka(a)gmail.com> >> wrote: >> >>> agree with Barak. morning is best >>> >>> On Jun 12, 2018 11:52 PM, "Barak Raveh" <barak.raveh(a)gmail.com> wrote: >>> >>> I think it's great if we can get all IMP developers including in Europe >>> and Asia on board, at least for the first meeting. IMP development could >>> benefit a lot from collaboration among the various IMP labs, and this could >>> also support future collaboration among IMP labs. >>> >>> The timezone is an issue - my recollection is that we have developers in >>> Spain (+8 hours), France (+9 hours), Israel (+10 hours), possibly in >>> Germany (+9 hours - Jan Kosinski at EMBL, Heidelberg may be interested). If >>> I didn't forget anyone (Ben?) - a morning meeting here (say 10 or 11 am) >>> could allow them to join in the European/ME evening. >>> >>> >>> On Mon, Jun 11, 2018 at 10:36 AM, Ben Webb <ben(a)salilab.org> wrote: >>> >>>> On 6/8/18 4:44 PM, Daniel Saltzberg wrote: >>>> >>>>> We had a good discussion at the retreat about how improving the >>>>> reliability and efficiency in IMP is critical for our current and future >>>>> goals in structural modeling. To do this, we proposed a periodic meeting to >>>>> discuss problems/inefficiencies in IMP, identify the root causes and >>>>> collectively design the best ways to fix them. >>>>> >>>> >>>> The best place for such discussion is the existing IMP developers' >>>> mailing list (cc'd): >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> There are several people outside of the lab who are IMP developers and >>>> so may be interested in joining these meetings. They're not on the lab >>>> mailing list but are (or can be) on imp-dev. >>>> >>>> I suggest we have our first meeting next week...say Thursday 2PM? (or >>>>> Ben, whatever day you plan to be in). We can decide on a recurring time >>>>> then. >>>>> >>>> >>>> If you want to have physical meetings as well, that's fine, although >>>> Fridays are better for me. 2pm's probably not a great time if anybody from >>>> Europe or Asia will be joining though. >>>> >>>> Ben >>>> -- >>>> ben(a)salilab.org https://salilab.org/~ben/ >>>> "It is a capital mistake to theorize before one has data." >>>> - Sir Arthur Conan Doyle >>>> >>> >>> >>> >>> -- >>> Barak >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev(a)salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> >> >> >> -- >> >> >> Daniel Saltzberg >> Post-doctoral Scholar >> University of California at San Francisco >> Lab of Andrej Sali (www.salilab.org) >> >> T: 415.514.4258 >> >> *Mailing Address:* >> UCSF MC 2552, >> Mission Bay, Byers Hall >> 1700 4th Street, Suite 503B >> <https://maps.google.com/?q=1700+4th+Street,+Suite+503B+%0D%0ASan+Francisco,…> >> San Francisco, CA 94158-2330 >> >> saltzberg(a)salilab.org >> ds229(a)bu.edu >> > > > -- > --------------------------------------- > Ignacia Echeverria > Postdoctoral Scholar > Department of Bioengineering and Therapeutic Sciences > University of California, San Francisco > http://salilab.org/~ignacia > ---------------------------------------- > > > -- Daniel Saltzberg Post-doctoral Scholar University of California at San Francisco Lab of Andrej Sali (www.salilab.org) T: 415.514.4258 *Mailing Address:* UCSF MC 2552, Mission Bay, Byers Hall 1700 4th Street, Suite 503B San Francisco, CA 94158-2330 saltzberg(a)salilab.org ds229(a)bu.edu

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Fwd: Re: IMP Efficiency Comm
by Ben Webb 18 Jun '18

18 Jun '18

-------- Forwarded Message -------- Subject: Re: [IMP-dev] IMP Efficiency Comm Date: Thu, 14 Jun 2018 09:24:54 -0700 From: Daniel Saltzberg <ds229(a)bu.edu> To: Dina Schneidman <duhovka(a)gmail.com> CC: Barak Raveh <barak.raveh(a)gmail.com>, List for IMP development <imp-dev(a)salilab.org>, Ben Webb <ben(a)salilab.org>, SaliLab Mail <salilab(a)salilab.org> I like the idea of involving the entire IMP community, however, my initial goals for this meeting were not quite as large as Barak suggested! In that case, let's push the meeting off until next week so that we give people enough time to schedule and myself enough time to prepare a more focused agenda. I'll suggest next *Tuesday, June 19th at 11AM Pacific Time.* The meeting will go no longer than an hour and a half. For those new to this email thread, we are interested in identifying specific areas in IMP where efficiency and functionality can be significantly improved with a moderate amount of effort and task these projects to individuals or small groups. Some issues we discussed at the retreat are: * Scoring efficiency - Make IncrementalScoringFunction work with current restraints (EM, EV) * Parallelization of individual replicas * Parallelizing propagation of moves within coarse grained representation of rigid bodies. * Identification of GPU-friendly computations The purpose of this meeting and subsequent ones will be to discuss the root causes of these issues, discuss general strategies for solving them, document them/improve the documentation in github issues and assign people to work on them outside of the meeting. Cheers, -Daniel On Tue, Jun 12, 2018 at 11:33 PM, Dina Schneidman <duhovka(a)gmail.com <mailto:duhovka@gmail.com>> wrote: agree with Barak. morning is best On Jun 12, 2018 11:52 PM, "Barak Raveh" <barak.raveh(a)gmail.com <mailto:barak.raveh@gmail.com>> wrote: I think it's great if we can get all IMP developers including in Europe and Asia on board, at least for the first meeting. IMP development could benefit a lot from collaboration among the various IMP labs, and this could also support future collaboration among IMP labs. The timezone is an issue - my recollection is that we have developers in Spain (+8 hours), France (+9 hours), Israel (+10 hours), possibly in Germany (+9 hours - Jan Kosinski at EMBL, Heidelberg may be interested). If I didn't forget anyone (Ben?) - a morning meeting here (say 10 or 11 am) could allow them to join in the European/ME evening. On Mon, Jun 11, 2018 at 10:36 AM, Ben Webb <ben(a)salilab.org <mailto:ben@salilab.org>> wrote: On 6/8/18 4:44 PM, Daniel Saltzberg wrote: We had a good discussion at the retreat about how improving the reliability and efficiency in IMP is critical for our current and future goals in structural modeling. To do this, we proposed a periodic meeting to discuss problems/inefficiencies in IMP, identify the root causes and collectively design the best ways to fix them. The best place for such discussion is the existing IMP developers' mailing list (cc'd): https://salilab.org/mailman/listinfo/imp-dev <https://salilab.org/mailman/listinfo/imp-dev> There are several people outside of the lab who are IMP developers and so may be interested in joining these meetings. They're not on the lab mailing list but are (or can be) on imp-dev. I suggest we have our first meeting next week...say Thursday 2PM? (or Ben, whatever day you plan to be in). We can decide on a recurring time then. If you want to have physical meetings as well, that's fine, although Fridays are better for me. 2pm's probably not a great time if anybody from Europe or Asia will be joining though. Ben -- ben(a)salilab.org <mailto:ben@salilab.org> https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle -- Barak _______________________________________________ IMP-dev mailing list IMP-dev(a)salilab.org <mailto:IMP-dev@salilab.org> https://salilab.org/mailman/listinfo/imp-dev <https://salilab.org/mailman/listinfo/imp-dev> -- Daniel Saltzberg Post-doctoral Scholar University of California at San Francisco Lab of Andrej Sali (www.salilab.org <http://www.salilab.org>) T: 415.514.4258 _ _ _/Mailing Address:/_ UCSF MC 2552, Mission Bay, Byers Hall 1700 4th Street, Suite 503B San Francisco, CA 94158-2330 saltzberg(a)salilab.org <mailto:saltzberg@salilab.org> ds229(a)bu.edu <mailto:ds229@bu.edu>

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Re: [IMP-dev] IMP Efficiency Comm
by Barak Raveh 14 Jun '18

14 Jun '18

Technically, this was Ben's (awesome) idea to include everyone :) Just to gauge the level of interest of IMP developers outside of UCSF - who wants to join besides Dina? On Thu, Jun 14, 2018 at 9:24 AM, Daniel Saltzberg <ds229(a)bu.edu> wrote: > I like the idea of involving the entire IMP community, however, my initial > goals for this meeting were not quite as large as Barak suggested! In that > case, let's push the meeting off until next week so that we give people > enough time to schedule and myself enough time to prepare a more focused > agenda. > > I'll suggest next *Tuesday, June 19th at 11AM Pacific Time.* The meeting > will go no longer than an hour and a half. > > For those new to this email thread, we are interested in identifying > specific areas in IMP where efficiency and functionality can be > significantly improved with a moderate amount of effort and task these > projects to individuals or small groups. Some issues we discussed at the > retreat are: > > * Scoring efficiency - Make IncrementalScoringFunction work with current > restraints (EM, EV) > * Parallelization of individual replicas > * Parallelizing propagation of moves within coarse grained representation > of rigid bodies. > * Identification of GPU-friendly computations > > The purpose of this meeting and subsequent ones will be to discuss the > root causes of these issues, discuss general strategies for solving them, > document them/improve the documentation in github issues and assign people > to work on them outside of the meeting. > > Cheers, > -Daniel > > On Tue, Jun 12, 2018 at 11:33 PM, Dina Schneidman <duhovka(a)gmail.com> > wrote: > >> agree with Barak. morning is best >> >> On Jun 12, 2018 11:52 PM, "Barak Raveh" <barak.raveh(a)gmail.com> wrote: >> >> I think it's great if we can get all IMP developers including in Europe >> and Asia on board, at least for the first meeting. IMP development could >> benefit a lot from collaboration among the various IMP labs, and this could >> also support future collaboration among IMP labs. >> >> The timezone is an issue - my recollection is that we have developers in >> Spain (+8 hours), France (+9 hours), Israel (+10 hours), possibly in >> Germany (+9 hours - Jan Kosinski at EMBL, Heidelberg may be interested). If >> I didn't forget anyone (Ben?) - a morning meeting here (say 10 or 11 am) >> could allow them to join in the European/ME evening. >> >> >> On Mon, Jun 11, 2018 at 10:36 AM, Ben Webb <ben(a)salilab.org> wrote: >> >>> On 6/8/18 4:44 PM, Daniel Saltzberg wrote: >>> >>>> We had a good discussion at the retreat about how improving the >>>> reliability and efficiency in IMP is critical for our current and future >>>> goals in structural modeling. To do this, we proposed a periodic meeting to >>>> discuss problems/inefficiencies in IMP, identify the root causes and >>>> collectively design the best ways to fix them. >>>> >>> >>> The best place for such discussion is the existing IMP developers' >>> mailing list (cc'd): >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> There are several people outside of the lab who are IMP developers and >>> so may be interested in joining these meetings. They're not on the lab >>> mailing list but are (or can be) on imp-dev. >>> >>> I suggest we have our first meeting next week...say Thursday 2PM? (or >>>> Ben, whatever day you plan to be in). We can decide on a recurring time >>>> then. >>>> >>> >>> If you want to have physical meetings as well, that's fine, although >>> Fridays are better for me. 2pm's probably not a great time if anybody from >>> Europe or Asia will be joining though. >>> >>> Ben >>> -- >>> ben(a)salilab.org https://salilab.org/~ben/ >>> "It is a capital mistake to theorize before one has data." >>> - Sir Arthur Conan Doyle >>> >> >> >> >> -- >> Barak >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev(a)salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> >> > > > -- > > > Daniel Saltzberg > Post-doctoral Scholar > University of California at San Francisco > Lab of Andrej Sali (www.salilab.org) > > T: 415.514.4258 > > *Mailing Address:* > UCSF MC 2552, > Mission Bay, Byers Hall > 1700 4th Street, Suite 503B > <https://maps.google.com/?q=1700+4th+Street,+Suite+503B+San+Francisco,+CA+94…> > San Francisco, CA 94158 > <https://maps.google.com/?q=1700+4th+Street,+Suite+503B+San+Francisco,+CA+94…> > -2330 > > saltzberg(a)salilab.org > ds229(a)bu.edu > -- Barak

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Re: [IMP-dev] IMP Efficiency Comm
by Ben Webb 12 Jun '18

12 Jun '18

On 6/8/18 4:44 PM, Daniel Saltzberg wrote: > We had a good discussion at the retreat about how improving the > reliability and efficiency in IMP is critical for our current and future > goals in structural modeling. To do this, we proposed a periodic meeting > to discuss problems/inefficiencies in IMP, identify the root causes and > collectively design the best ways to fix them. The best place for such discussion is the existing IMP developers' mailing list (cc'd): https://salilab.org/mailman/listinfo/imp-dev There are several people outside of the lab who are IMP developers and so may be interested in joining these meetings. They're not on the lab mailing list but are (or can be) on imp-dev. > I suggest we have our first meeting next week...say Thursday 2PM? (or > Ben, whatever day you plan to be in). We can decide on a recurring time > then. If you want to have physical meetings as well, that's fine, although Fridays are better for me. 2pm's probably not a great time if anybody from Europe or Asia will be joining though. Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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