id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1673 Linux flavor ABI incompatibility tic20@… Conrad Huang "Relevant part of traceback below. The offending line in rota.cpp is innocuous: Rotamer::Rotamer(Residue *res, Rota_Mgr *mgr): _residue(res), _mgr(mgr) { auto rname = res->name(); // segfault Seems a straightforward case of ABI incompatibility. As far as I'm aware the ToolShed doesn't have the ability to serve different binaries for different Linux flavours. How is progress going on a controlled environment for building in Linux? #0 0x00007fffedd2532b in std::basic_string, std::allocator >::basic_string(std::string const&) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6 #1 0x00007fff3faf0419 in isolde::Rotamer::Rotamer (this=0x7f01480, res=0x79b5670, mgr=0x561c4d0) at src/validation/rota.cpp:39 #2 0x00007fff3faf0d3b in isolde::Rota_Mgr::new_rotamer (this=0x561c4d0, residue=0x79b5670) at src/validation/rota.cpp:150 #3 0x00007fff3faf0e3b in isolde::Rota_Mgr::get_rotamer (this=this@entry=0x561c4d0, residue=) at src/validation/rota.cpp:169 #4 0x00007fff3fb2863c in rota_mgr_get_rotamer (mgr=0x561c4d0, residue=0x7c7d3d0, n=229) at src/validation/rota_ext.h:167 #5 0x00007ffff270ae40 in ffi_call_unix64 () from /usr/lib/x86_64-linux-gnu/libffi.so.6 Forwarded email below. I've asked him if he can run GDB on it to get a full traceback, but it looks like my bundles built against the CentOS .rpm build are incompatible with the Ubuntu .deb. -------- Original Message -------- Subject: Isolde Crash on Ubuntu 16.04 Date: 2019-02-01 10:22 From: Hubert Santuz To: tic20@cam.ac.uk Hi Tristan Croll, I'm trying to use your tool Isolde with ChimeraX 0.8 on an Ubuntu 16.04. I successfully installed both ChimeraX and Isolde from package framework. Unfortunately, when I press the ""load demo"" button, ChimeraX instantly crashed with a segmentation fault : Fatal Python error: Segmentation fault Current thread 0x00007fca1c729700 (most recent call first): File ""/ibpc/sablons/santuz/.local/share/ChimeraX/0.8/site-packages/chimerax/isolde/molobject.py"", line 1371 in get_rotamers File ""/ibpc/sablons/santuz/.local/share/ChimeraX/0.8/site-packages/chimerax/isolde/validation/rota_annotation.py"", line 110 in track_whole_model File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/graphics/drawing.py"", line 228 in __setattr__ File ""/ibpc/sablons/santuz/.local/share/ChimeraX/0.8/site-packages/chimerax/isolde/validation/rota_annotation.py"", line 75 in __init__ File ""/ibpc/sablons/santuz/.local/share/ChimeraX/0.8/site-packages/chimerax/isolde/session_extensions.py"", line 206 in get_rota_annotator File ""/ibpc/sablons/santuz/.local/share/ChimeraX/0.8/site-packages/chimerax/isolde/isolde.py"", line 2328 in _change_selected_model File ""/ibpc/sablons/santuz/.local/share/ChimeraX/0.8/site-packages/chimerax/isolde/isolde.py"", line 970 in _update_model_list File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/triggerset.py"", line 130 in invoke File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/triggerset.py"", line 190 in activate File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/triggerset.py"", line 325 in activate_trigger File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/models.py"", line 456 in add File ""/ibpc/sablons/santuz/.local/share/ChimeraX/0.8/site-packages/chimerax/clipper/symmetry.py"", line 430 in __init__ File ""/ibpc/sablons/santuz/.local/share/ChimeraX/0.8/site-packages/chimerax/clipper/symmetry.py"", line 145 in get_symmetry_handler File ""/ibpc/sablons/santuz/.local/share/ChimeraX/0.8/site-packages/chimerax/isolde/isolde.py"", line 2314 in _change_selected_model File ""/ibpc/sablons/santuz/.local/share/ChimeraX/0.8/site-packages/chimerax/isolde/isolde.py"", line 970 in _update_model_list File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/triggerset.py"", line 130 in invoke File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/triggerset.py"", line 190 in activate File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/triggerset.py"", line 325 in activate_trigger File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/models.py"", line 456 in add File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/models.py"", line 602 in open File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/commands/open.py"", line 62 in handle_unknown_kw File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/core/commands/open.py"", line 117 in open File ""/ibpc/sablons/santuz/.local/share/ChimeraX/0.8/site-packages/chimerax/isolde/isolde.py"", line 3107 in load_demo_data File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/chimerax/ui/gui.py"", line 227 in event_loop File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/ChimeraX_main.py"", line 715 in init File ""/usr/lib/ucsf-chimerax/lib/python3.6/site-packages/ChimeraX_main.py"", line 807 in File ""/usr/lib/ucsf-chimerax/lib/python3.6/runpy.py"", line 85 in _run_code File ""/usr/lib/ucsf-chimerax/lib/python3.6/runpy.py"", line 193 in _run_module_as_main Segmentation fault (core dumped) I have the same behavior, when I have already a pdb loaded and when I hit the button ""Isolde"". Do you have an idea to solve this ? Thanks, Hubert -- Hubert Santuz UPR 9080 - Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique 13, rue Pierre et Marie Curie, 75005 Paris Tél: 01 58 41 51 32" defect closed major 1.0 Tool Shed fixed Greg Couch Eric Pettersen all ChimeraX