AbinitioRelax crashed issue

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    • April 23, 2020 at 3:41 pm #3405
      Anonymous

        Hello

              I was trying to run AbinitioRelax for structure predictions with attached flags file. The program crashed with the message “Segmentation Fault”

         

        ##############################################################################################################

        #

        # Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/

        # or use the script Rosetta/main/source/scripts/python/public/report_crashes.py

        #

        [START_CRASH_REPORT]

        [ROSETTA_VERSION]: 2020.11+release.ce6f14f

        [COMMIT_DATE]: 2020-03-13T15:44:05.394556

        [APPLICATION]: membrane_abinitio2.mpi.linuxgccrelease

        [MODE]: Release

        [EXTRAS]: mpi (OpenMPI 4.0.2) 

        [OS]: GNU/Linux

        [COMPILER]: GCC version “8.3.0 20190222 (Cray Inc.)”

        [STDLIB]: libstdc++ version 20190222

        [START_OPTIONS]

         -in:path:database=/N/soft/cle6/rosetta/gnu/rosetta_bin_linux_2020.11.61179_bundle/main/database/ -in:file:native=./1elw.pdb -in:file:frag3=./aat000_03_05.200_v1_3 -in:file:frag9=./aat000_09_05.200_v1_3 -in:file:fasta=./1ELW.fasta -in:file:psipred_ss2=./t000_.psipred_ss2 -out:nstruct=1 -out:file:silent=./fold_silent.out -abinitio:relax -abinitio:use_filters -abinitio:increase_cycles=10 -abinitio:rg_reweight=0.5 -abinitio:rsd_wt_helix=0.5 -abinitio:rsd_wt_loop=0.5 -relax:fast

        [END_OPTIONS]

        [START_BACKTRACE]: RAW_LIBC

        /geode2/soft/hps/cle6/rosetta/gnu/rosetta_bin_linux_2020.11.61179_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/8.3/mpi/libutility.so(utility::save_crash_report(char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x23) [0x7fa05e7b3173]

        /geode2/soft/hps/cle6/rosetta/gnu/rosetta_bin_linux_2020.11.61179_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/8.3/mpi/libutility.so(utility::signal_handler(int)+0xd4) [0x7fa05e7b3284]

        /lib64/libc.so.6(+0x34ff0) [0x7fa05c002ff0]

        /geode2/soft/hps/cle6/rosetta/gnu/rosetta_bin_linux_2020.11.61179_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/8.3/mpi/libcore.2.so(core::conformation::Conformation::set_torsion(core::id::TorsionID const&, double)+0x17c) [0x7fa05ffa13dc]

        /geode2/soft/hps/cle6/rosetta/gnu/rosetta_bin_linux_2020.11.61179_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/8.3/mpi/libcore.6.so(core::fragment::BBTorsionSRFD::apply(core::kinematics::MoveMap const&, core::pose::Pose&, unsigned long) const+0x8a) [0x7fa0640f92ca]

        /geode2/soft/hps/cle6/rosetta/gnu/rosetta_bin_linux_2020.11.61179_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/8.3/mpi/libcore.6.so(core::fragment::FragData::apply(core::kinematics::MoveMap const&, core::pose::Pose&, unsigned long, unsigned long) const+0x72) [0x7fa064108232]

        /geode2/soft/hps/cle6/rosetta/gnu/rosetta_bin_linux_2020.11.61179_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/8.3/mpi/libprotocols.3.so(protocols::simple_moves::ClassicFragmentMover::apply_fragment(core::fragment::Frame const&, unsigned long, core::kinematics::MoveMap const&, core::pose::Pose&) const+0x12) [0x7fa066cad742]

        /geode2/soft/hps/cle6/rosetta/gnu/rosetta_bin_linux_2020.11.61179_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/8.3/mpi/libprotocols.3.so(protocols::simple_moves::ClassicFragmentMover::apply_frames(core::pose::Pose&, core::fragment::FrameList const&) const+0x78c) [0x7fa066caeabc]

        /geode2/soft/hps/cle6/rosetta/gnu/rosetta_bin_linux_2020.11.61179_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/8.3/mpi/libprotocols.3.so(protocols::simple_moves::ClassicFragmentMover::apply(core::pose::Pose&)+0xe5f) [0x7fa066cb4e1f]

        /geode2/soft/hps/cle6/rosetta/gnu/rosetta_bin_linux_2020.11.61179_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/8.3/mpi/libprotocols.1.so(protocols::moves::TrialMover::apply(core::pose::Pose&)+0x31) [0x7fa064a9a061]

        /geode2/soft/hps/cle6/rosetta/gnu/rosetta_bin_linux_2020.11.61179_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/8.3/mpi/libprotocols_b.6.so(protocols::abinitio::ClassicAbinitio::do_stage1_cycles(core::pose::Pose&)+0x4e5) [0x7fa06bf3bfe5]

        /geode2/soft/hps/cle6/rosetta/gnu/rosetta_bin_linux_2020.11.61179_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/8.3/mpi/libprotocols_b.6.so(protocols::abinitio::ClassicAbinitio::apply(core::pose::Pose&)+0x1034) [0x7fa06bf393d4]

        /geode2/soft/hps/cle6/rosetta/gnu/rosetta_bin_linux_2020.11.61179_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/8.3/mpi/libprotocols_b.6.so(protocols::abinitio::AbrelaxApplication::fold(core::pose::Pose&, std::shared_ptr<protocols::abinitio::Protocol>)+0xe58) [0x7fa06bf16ef8]

        /geode2/soft/hps/cle6/rosetta/gnu/rosetta_bin_linux_2020.11.61179_bundle/main/source/build/src/release/linux/4.4/64/x86/gcc/8.3/mpi/libprotocols_b.6.so(protocols::abinitio::AbrelaxApplication::run()+0xd7) [0x7fa06bf1f2a7]

        membrane_abinitio2.mpi.linuxgccrelease() [0x401bc5]

        /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fa05bfee735]

        membrane_abinitio2.mpi.linuxgccrelease() [0x401c59]

        [END_BACKTRACE]

        [FILE]: SIGSEGV

        [LINE]: 11

        [START_MESSAGE]

        Segmentation Fault

        [END_MESSAGE]

        [END_CRASH_REPORT]

         

         

         

         

         

         Could you help me to look at what is the issue of my project? 

         

        Thanks

        Xinhang

      • July 9, 2020 at 5:01 pm #15384
        Anonymous

          Segmentation faults are often hard to debug. Segfaults shouldn’t ever happen, but when they do they’re because something happened during the run which the programmer of the protocol thought would never realistically happen.

          One technique to getting a bit of a better information is to compile Rosetta with debug mode. (That is, with `mode=debug` versus `mode=release` on the scons command line). This turns on extra checks which makes the run slower, but can often give better information about what is going wrong. (Though it doesn’t always.)

          In your case, you do have a backtrace from the crash log. Reading the tea leaves, it looks like you have an issue in apply the fragments to the pose. In particular, it looks like a torsion it was expecting isn’t there.

          I’d recommend taking a closer look at your input files. In particular, checking to make sure that the fragment files you are using match up with the FASTA file you are using. (That is, the fragments are generated from the same fasta file you’re passing to AbinitoRelax.) It might also be worth it to take a look at the fragment & fasta files (with a text editor), to see if you can spot any obvious signs of corruption or truncation. While you’re at it, make sure that the psipred file is proper for your FASTA and isn’t corrupted either.

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