- IMP-dev - salilab.org

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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Preparation for IMP 2.9.0 release
by Ben Webb 11 Jun '18

11 Jun '18

We're a little overdue for a new IMP stable release. Since there have been several applications of IMP published since the last stable release that currently only work with the nightly builds (e.g. NPC) and IMP 2.8 has some compilation issues with the latest CGAL and gcc, I'll be making a new release shortly - probably branching within a week or two and releasing at the end of this month. So now is a good time for any polishing, bug fixing, documentation fixes etc. (and a really bad time for any sweeping changes!) 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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IMP 2.8.0 release
by Ben Webb 16 Aug '17

16 Aug '17

IMP 2.8.0 is now available. This is a bugfix and minor update release. Most notably two new applications of IMP are now available, and the Anaconda and Windows pre-built binary packages are now MPI-enabled. This release also includes a number of bug fixes and performance improvements. Note that this will be the last release that includes packages for Ubuntu 12.04 (Precise Pangolin) since it has reached end of life. We will continue to provide packages for newer Ubuntu LTS releases. See https://integrativemodeling.org/2.8.0/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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Preparation for IMP 2.8.0 release
by Ben Webb 04 Aug '17

04 Aug '17

The develop branch of IMP is pretty stable right now, so I'd like to make a new release to add full support for recent systems such as SPB. I plan to branch for this early next week. Let me know if there are any urgent showstopper problems with IMP that we need to address before I do that. 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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IMP 2.7.0 release
by Ben Webb 13 Apr '17

13 Apr '17

IMP 2.7.0 is now available. This is a bugfix and major update release. Most notably we include a preview of mmCIF support for deposition of integrative models in PDB-dev (https://pdb-dev.rcsb.rutgers.edu/) see the IMP::pmi::mmcif module for more details. This release also includes a number of bug fixes and performance improvements. Note that this will be the last release that includes packages for RedHat Enterprise Linux 5 (and variants, such as CentOS 5), since RHEL 5 has reached end of life. See https://integrativemodeling.org/2.7.0/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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Upcoming joint IMP and NAMD/VMD workshop at UCSF next month
by Ben Webb 03 Nov '16

03 Nov '16

I just wanted to bring everyone's attention to a hands-on workshop that we'll be hosting next month (Dec 12-16) here at UCSF: https://www-s.ks.uiuc.edu/Training/Workshop/SanFrancisco2016/index.html This is a week long joint workshop in conjunction with the folks from TCBG at UIUC. Between us we'll be covering both IMP and TCBG tools such as NAMD and VMD. We'll have time to really look at a number of applications of IMP to biophysical systems in detail. This is a small workshop (25 attendees). Application deadline is Nov 18th. Please let me know if you have any questions about the workshop. 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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IMP 2.6.2 release
by Ben Webb 02 Jun '16

02 Jun '16

IMP 2.6.2 is now available. This corrects a few minor bugs and documentation issues in the previous release (2.6.1). In particular, we now provide packages for Ubuntu 16.04 (Xenial Xerus) and include a workaround for the buggy version of SWIG (3.0.8) included in that distribution. See https://integrativemodeling.org/2.6.2/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ 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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pointers and copy constructors / assignment operators
by Samuel Hanot 14 Apr '16

14 Apr '16

Hi all, I am currently implementing a restraint in C++ with the goal of providing similar functionality as the fuzzyRestraint in pmi/restraints/proteomics with better efficiency. I have come up with the following design (see code excerpts bellow): A pure virtual base FuzzyRestraint class that implements the interface. Several child classes that inherit from that and perform the fuzzy logic calculation (ie OR, AND, NOT). For example, given two restraints r1,r2, I could instantiate a FuzzyOr r3=r1|r2; My issue is the following: whenever I chain more that two operands (for example r=r1|r2|r3|r4), I get a segfault in the do_get_inputs. I believe this is due to the class containing pointers, but I didn't specify a copy constructor, assignment operator, and destructor to handle these operations without corrupting my memory/loosing information. I know if I was writing standard c++ that's what i'd have to do, but I admit that I am a bit lost when it comes to IMP due to the entanglement with python and automatic memory management. So my question is: 1/ Do you agree that my issue comes from that shallow copy ? 2/ Is there a functionality in IMP to handle such a case ? Thanks, sam hanot class IMPPMIEXPORT FuzzyRestraint; class IMPPMIEXPORT FuzzyOr; class IMPPMIEXPORT FuzzyRestraint : public Restraint { public: FuzzyRestraint(Model *m, std::string name) : Restraint(m, name) {} virtual double unprotected_evaluate(DerivativeAccumulator *) const = 0; virtual ModelObjectsTemp do_get_inputs() const = 0; FuzzyOr *operator|(FuzzyRestraint *r); IMP_OBJECT_METHODS(FuzzyRestraint); }; class IMPPMIEXPORT FuzzyOr : public FuzzyRestraint { FuzzyRestraint *r1_; FuzzyRestraint *r2_; public: FuzzyOr(Model *m, FuzzyRestraint *r1, FuzzyRestraint *r2) : FuzzyRestraint(m, "FuzzyOr %1%"), r1_(r1), r2_(r2) { std::cerr << "Creating FuzzyOr from " << r1_->get_name() << " (" << r1_ << ") " << r2_->get_name() << " (" << r2_ << ") " << ": " << get_name() << '\n'; } virtual double unprotected_evaluate(DerivativeAccumulator *) const IMP_OVERRIDE { Model *m(get_model()); double const a(r1_->unprotected_evaluate(nullptr)); double const b(r2_->unprotected_evaluate(nullptr)); return exp(-a) + exp(-b) - exp(-a - b); } virtual ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE { ModelObjectsTemp ret(r1_->get_inputs()); ModelObjectsTemp const tmp(r2_->get_inputs()); ret.insert(ret.end(), tmp.begin(), tmp.end()); return ret; } IMP_OBJECT_METHODS(FuzzyOr); }; FuzzyOr *FuzzyRestraint::operator|(FuzzyRestraint *r) { IMP_NEW(IMP::pmi::FuzzyOr, ret, (get_model(), this, r)); return ret.release(); }

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IMP 2.6.1 release
by Ben Webb 14 Apr '16

14 Apr '16

IMP 2.6.1 is now available. This corrects a few minor bugs and documentation issues in the previous release (2.6.0). See https://integrativemodeling.org/2.6.1/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ 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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gdp with IMP code?
by Charles Greenberg 01 Apr '16

01 Apr '16

Has anyone had success debugging IMP code with gdp? If so can you share? Thanks, Charles Greenberg Graduate student in biophysics @ UCSF Laboratory of Andrej Sali Cell: 561-531-9411

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