Error concerning PhenixInterface upon running rosetta.run_tests

2 posts / 0 new

I have successully compiled rosetta 2019.47.61047_bundle using 'rosetta.build_phenix_interface' command on a fedora 40 pc with gcc-12.3.0.

When I run 'rosetta.run_tests' I get the following error that apparently concerns PhenixInterface.

The same error occurs even with the most recent rosetta version on the website.

Any hint?

##############################################################################################################
#
# Rosetta crash log.
#

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2019.47+release.3d995b1
[COMMIT_DATE]: 2019-11-23T16:25:53.340829
[APPLICATION]: /usr/local/rosetta_src_2019.47.61047_bundle/main/source/bin/rosetta_scripts.python.linuxgccrelease
[MODE]: Release
[EXTRAS]: python
[OS]: GNU/Linux
[COMPILER]: GCC version "12.3.0"
[STDLIB]: libstdc++ version 20230508
[START_OPTIONS]
-in:file:s=1yjp_rosetta_in.pdb -out:nstruct=1 -out:suffix=_1 -run:preserve_header -parser:protocol=/usr/local/rosetta_src_2019.47.61047_bundle/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml -parser:script_vars=symmdef=1yjp_rosetta.symm bfactstrat=individual map_type=Auto -cryst:mtzfile=1yjp_rosetta_data.mtz -cryst:crystal_refine

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libcore.6.so(backtrace_string(int)+0x37) [0x148676316b87]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libutility.so(utility::excn::Exception::Exception(char const*, int, std::string const&)+0x7b) [0x148670e98cdb]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::string const&)+0xa2) [0x148670f4c9a2]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libutility.so(utility::exit(char const*, int, std::string const&, int)+0x34) [0x148670f4c564]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libcore.3.so(core::scoring::cryst::PhenixInterface::fitBfactors(core::pose::Pose&)+0x2003) [0x1486743bf1b3]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.4.so(protocols::cryst::FitBfactorsMover::apply(core::pose::Pose&)+0xa1) [0x14867980e381]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const&)+0x26e) [0x148676d8149e]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair, std::allocator<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair> > >)+0x3b) [0x148676d82b5b]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x1a6) [0x148676d83496]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const&)+0x26e) [0x148676d8149e]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::sequence_protocol(core::pose::Pose&, __gnu_cxx::__normal_iterator<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair const*, std::vector<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair, std::allocator<protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair> > >)+0x3b) [0x148676d82b5b]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&)+0x1a6) [0x148676d83496]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::string&, std::string&, unsigned long&, unsigned long&, bool)+0xd39) [0x148676f02c89]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x18b) [0x148676f0486b]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/build/src/release/linux/6.8/64/x86/gcc/12.3/python/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x49) [0x148676eec099]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/bin/rosetta_scripts.python.linuxgccrelease() [0x4025ed]
/lib64/libc.so.6(+0x2a088) [0x14867063d088]
/lib64/libc.so.6(__libc_start_main+0x8b) [0x14867063d14b]
/usr/local/rosetta_src_2019.47.61047_bundle/main/source/bin/rosetta_scripts.python.linuxgccrelease() [0x4028a5]

[END_BACKTRACE]

[FILE]: src/core/scoring/cryst/PhenixInterface.cc
[LINE]: 257
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: importing phenix.refine failed

[END_MESSAGE]
[END_CRASH_REPORT]

##############################################################################################################
#
# Rosetta crash log.
#

[END_OPTIONS]

[END_BACKTRACE]

[FILE]: src/protocols/jd2/JobDistributor.cc
[LINE]: 329
[START_MESSAGE]
1 jobs failed; check output for error messages

[END_MESSAGE]
[END_CRASH_REPORT]

Category:

Compilation

Post Situation:

Unsolved

Sat, 2024-06-15 08:02

vcalderone

Top

You get that error when Rosetta attempts to call phenix.refine though the Python interface, and that call fails for some reason. The error message from Phenix should be printed to the tracer output.

I'm not sure what that message is, but given this is a test case that should theoretically work, I imagine it's some issue with finding the proper function to call. Either the Phenix functions weren't properly compiled with the Rosetta version, or it could be that there's some version/call signature mismatch between what Rosetta is expecting and what the version of Phenix you're trying to use wants.

Mon, 2024-06-17 07:18

rmoretti

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Error concerning PhenixInterface upon running rosetta.run_tests