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Opened 5 years ago
Closed 5 years ago
#3201 closed defect (wontfix)
Out of memory error starting ISOLDE simulation
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 0.9 (2019-06-06) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.9 (2019-06-06) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /beegfs/cssb/user/yuanbiao/EscVC/ResolveCryoEM_43/DENMOD/denmod_map.ccp4 Opened denmod_map.ccp4, grid size 156,156,67, pixel 1.1, shown at level 0.779, step 1, values float32 > open /beegfs/cssb/user/yuanbiao/EscVC/ResolveCryoEM_43/DENMOD/EscVC_chainA_real_space_refined- coot-1.pdb Chain information for EscVC_chainA_real_space_refined-coot-1.pdb #2 --- Chain | Description A | No description available > toolshed show ISOLDE > set selectionWidth 4 Chain information for EscVC_chainA_real_space_refined-coot-1.pdb --- Chain | Description 2.3/A | No description available Done loading forcefield > addh Summary of feedback from adding hydrogens to EscVC_chainA_real_space_refined- coot-1.pdb #2.3 --- notes | No usable SEQRES records for EscVC_chainA_real_space_refined- coot-1.pdb (#2.3) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A SER 347 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 670 116 hydrogen bonds /A VAL 670 is not terminus, removing H atom from 'C' 2674 hydrogens added Traceback (most recent call last): File "/home/yuanbiao/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/isolde.py", line 2647, in _start_sim_or_toggle_pause self.start_sim() File "/home/yuanbiao/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/isolde.py", line 2677, in start_sim sm.start_sim() File "/home/yuanbiao/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 650, in start_sim sh.start_sim() File "/home/yuanbiao/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 1485, in start_sim self._prepare_sim() File "/home/yuanbiao/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 1447, in _prepare_sim integrator, platform, properties) File "/beegfs/cssb/group/marlov_grp/software/chimerax/0.9.1/lib/python3.7/site- packages/simtk/openmm/app/simulation.py", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File "/beegfs/cssb/group/marlov_grp/software/chimerax/0.9.1/lib/python3.7/site- packages/simtk/openmm/openmm.py", line 12231, in __init__ this = _openmm.new_Context(*args) Exception: Error initializing context: clCreateContext (-6) Exception: Error initializing context: clCreateContext (-6) File "/beegfs/cssb/group/marlov_grp/software/chimerax/0.9.1/lib/python3.7/site- packages/simtk/openmm/openmm.py", line 12231, in __init__ this = _openmm.new_Context(*args) See log for complete Python traceback. Traceback (most recent call last): File "/home/yuanbiao/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/isolde.py", line 2647, in _start_sim_or_toggle_pause self.start_sim() File "/home/yuanbiao/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/isolde.py", line 2677, in start_sim sm.start_sim() File "/home/yuanbiao/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 650, in start_sim sh.start_sim() File "/home/yuanbiao/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 1485, in start_sim self._prepare_sim() File "/home/yuanbiao/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 1447, in _prepare_sim integrator, platform, properties) File "/beegfs/cssb/group/marlov_grp/software/chimerax/0.9.1/lib/python3.7/site- packages/simtk/openmm/app/simulation.py", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File "/beegfs/cssb/group/marlov_grp/software/chimerax/0.9.1/lib/python3.7/site- packages/simtk/openmm/openmm.py", line 12231, in __init__ this = _openmm.new_Context(*args) Exception: Error initializing context: clCreateContext (-6) Exception: Error initializing context: clCreateContext (-6) File "/beegfs/cssb/group/marlov_grp/software/chimerax/0.9.1/lib/python3.7/site- packages/simtk/openmm/openmm.py", line 12231, in __init__ this = _openmm.new_Context(*args) See log for complete Python traceback. QWidget::repaint: Recursive repaint detected Traceback (most recent call last): File "/home/yuanbiao/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/isolde.py", line 2647, in _start_sim_or_toggle_pause self.start_sim() File "/home/yuanbiao/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/isolde.py", line 2677, in start_sim sm.start_sim() File "/home/yuanbiao/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 650, in start_sim sh.start_sim() File "/home/yuanbiao/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 1485, in start_sim self._prepare_sim() File "/home/yuanbiao/.local/share/ChimeraX/0.9/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 1447, in _prepare_sim integrator, platform, properties) File "/beegfs/cssb/group/marlov_grp/software/chimerax/0.9.1/lib/python3.7/site- packages/simtk/openmm/app/simulation.py", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File "/beegfs/cssb/group/marlov_grp/software/chimerax/0.9.1/lib/python3.7/site- packages/simtk/openmm/openmm.py", line 12231, in __init__ this = _openmm.new_Context(*args) Exception: Error initializing context: clCreateContext (-6) Exception: Error initializing context: clCreateContext (-6) File "/beegfs/cssb/group/marlov_grp/software/chimerax/0.9.1/lib/python3.7/site- packages/simtk/openmm/openmm.py", line 12231, in __init__ this = _openmm.new_Context(*args) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 440.33.01 OpenGL renderer: Quadro M6000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Out of memory error starting ISOLDE simulation |
comment:2 by , 5 years ago
| Resolution: | → wontfix |
|---|---|
| Status: | assigned → closed |
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clCreateContext error -6 corresponds to CL_OUT_OF_HOST_MEMORY. First time I've ever seen this one - can only surmise that this was run on a *very* lightweight machine. Will close this ticket - nothing much I can do about it - but I suppose in general it's about time I added some code to parse and explain the different OpenCL or CUDA errors.