Monte Carlo tutorials failing on 2018.2

[Benjamin H]

Hello,


Could you please help?

Running version 2018.2 of Linux binary, all tests passed after extraction.

Attempting to follow along the Monte Carlo tutorial: http://chryswoods.com/intro_to_mc/part2/intro.html


$SIRE/bin/python test_install.py passed correctly.

$SIRE/bin/python rigidbody.py failed with the following error:

Block 1

Block 1, Move 1
Traceback (most recent call last):
File "rigidbody.py", line 102, in <module>
mcMove(i, j)
File "rigidbody.py", line 39, in mcMove
random_water = waterbox[ MolIdx(water_id) ].molecule()
UserWarning: Exception 'SireError::program_bug' thrown by the thread 'master'.
There is a problem - the parent forcefield of cljff (4) is null!
Thrown from FILE: /home/chris/Sire/corelib/src/libs/SireFF/ffmolgroup.cpp, LINE: 144, FUNCTION: void SireFF::detail::FFMolGroupPvt::assertNotNull() const
__Backtrace__
( 0) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Qt/../../../../../lib/libSireError.so.2018 ([0x7f53734a9c7e] ++0x2e)
-- SireError::getBackTrace()

( 1) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Qt/../../../../../lib/libSireError.so.2018 ([0x7f53734a6a16] ++0x86)
-- SireError::exception::exception(QString, QString)

( 2) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Units/../../../../../lib/libSireFF.so.2018 ([0x7f536e680892] ++0x202)
-- SireFF::detail::FFMolGroupPvt::assertNotNull() const

( 3) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Units/../../../../../lib/libSireFF.so.2018 ([0x7f536e680a76] ++0x26)
-- SireFF::FFMolGroup::FFMolGroup(SireFF::detail::FFMolGroupPvt const&)

( 4) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Units/../../../../../lib/libSireFF.so.2018 ([0x7f536e680b01] ++0x21)
-- SireFF::detail::FFMolGroupPvt::clone() const

( 5) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Qt/../../../../../lib/libSireBase.so.2018 ([0x7f5374529532] ++0x32)
-- SireBase::PropPtrBase::PropPtrBase(SireBase::Property const&)

( 6) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Units/../../../../../lib/libSireMol.so.2018 ([0x7f536e11d0a4] ++0xa4)
-- SireMol::MolGroupsBase::selectAll() const

( 7) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Units/../../../../../lib/libSireMol.so.2018 ([0x7f536e11d1c9] ++0x9)
-- SireMol::MolGroupsBase::groups() const

( 8) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Units/../../../../../lib/libSireMol.so.2018 ([0x7f536e122d5b] ++0x4b)
-- SireMol::MolGroupsBase::getMoleculeNumber(SireMol::MolIdx) const

( 9) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Units/../../../../../lib/libSireMol.so.2018 ([0x7f536e12344b] ++0x3b)
-- SireMol::MolGroupsBase::map(SireMol::MolIdx) const

( 10) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Units/../../../../../lib/libSireMol.so.2018 ([0x7f536e163ad7] ++0x27)
-- SireMol::MolIdx::map(SireMol::MolGroupsBase const&) const

( 11) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Units/../../../../../lib/libSireMol.so.2018 ([0x7f536e1242be] ++0x2e)
-- SireMol::MolGroupsBase::at(SireMol::MolID const&) const

( 12) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Units/../../../../../lib/libSireMol.so.2018 ([0x7f536e124679] ++0x9)
-- SireMol::MolGroupsBase::operator[](SireMol::MolID const&) const

( 13) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/System/../../../../../lib/libSireSystem.so.2018 ([0x7f536746fe29] ++0x9)
-- SireSystem::System::operator[](SireMol::MolID const&) const

/home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/System/_System.so(+0xf3e4b) [0x7f53677d2e4b]
( 15) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Qt/../../../../../lib/libboost_python.so ([0x7f537428813d] ++0x30d)
-- boost::python::objects::function::call(_object*, _object*) const

/home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Qt/../../../../../lib/libboost_python.so(+0x2c278) [0x7f5374288278]
( 17) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Qt/../../../../../lib/libboost_python.so ([0x7f537427ef1b] ++0x4b)
-- boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const

/home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Error/_Error.so(+0x250d) [0x7f5371f8b50d]
( 19) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Qt/../../../../../lib/libboost_python.so ([0x7f537427eefa] ++0x2a)
-- boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const

/home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Error/_Error.so(+0x24cb) [0x7f5371f8b4cb]
( 21) /home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Qt/../../../../../lib/libboost_python.so ([0x7f537427ecef] ++0x2f)
-- boost::python::handle_exception_impl(boost::function0<void>)

/home/ec2-user/sire.app/lib/python3.5/site-packages/Sire/Qt/../../../../../lib/libboost_python.so(+0x2a309) [0x7f5374286309]
( 23) /home/ec2-user/sire.app/bin/python ([0x565245f3789a] ++0x3a)
-- PyObject_Call

/home/ec2-user/sire.app/bin/python(+0x148e4f) [0x565245f7fe4f]
( 25) /home/ec2-user/sire.app/bin/python ([0x565245f3789a] ++0x3a)
-- PyObject_Call

/home/ec2-user/sire.app/bin/python(+0x15e150) [0x565245f95150]
( 27) /home/ec2-user/sire.app/bin/python ([0x565245fda4da] ++0x110a)
-- PyEval_EvalFrameEx

( 28) /home/ec2-user/sire.app/bin/python ([0x565245fd9e90] ++0xac0)
-- PyEval_EvalFrameEx

( 29) /home/ec2-user/sire.app/bin/python ([0x565245fe403d] ++0x20d)
-- PyEval_EvalCodeEx

( 30) /home/ec2-user/sire.app/bin/python ([0x565245fe4f5c] ++0x1c)
-- PyEval_EvalCode

/home/ec2-user/sire.app/bin/python(+0x20a454) [0x565246041454]
( 32) /home/ec2-user/sire.app/bin/python ([0x565246042ac1] ++0xa1)
-- PyRun_FileExFlags

( 33) /home/ec2-user/sire.app/bin/python ([0x565246042cde] ++0x1de)
-- PyRun_SimpleFileExFlags

( 34) /home/ec2-user/sire.app/bin/python ([0x5652460433c2] ++0x602)
-- Py_Main

( 35) /home/ec2-user/sire.app/bin/python ([0x565245f0e871] ++0xe1)
-- main

( 36) /lib64/libc.so.6 ([0x7f537b8833d5] ++0xf5)
-- __libc_start_main

/home/ec2-user/sire.app/bin/python(+0x1af808) [0x565245fe6808]
__EndTrace__
Exception 'SireError::program_bug' thrown by the thread 'master'.
There is a problem - the parent forcefield of cljff (4) is null!
Thrown from FILE: /home/chris/Sire/corelib/src/libs/SireFF/ffmolgroup.cpp, LINE: 144, FUNCTION: void SireFF::detail::FFMolGroupPvt::assertNotNull() const



The same error occured running montecarlo.py from the mc_moves EMBO2014 examples: https://chryswoods.com/embo2014/Monte_Carlo.html

Problem was replicated for 2018.2 Linux binaries on Ubuntu 16.04 and RHEL 7.5, as well as OS X binary on 10.11.


Thank you!

BGSH

[Christopher Woods]

  Hi Ben,

Thanks for highlighting this. It looks like changes in API of Sire since 2014 have broken this tutorial. We will investigate this and will fix the tutorial.

  Best wishes,

  Christopher

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