id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8568 'overloadable' attribute missing rish.23@… Tristan Croll "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.dev202302242240 (2023-02-24 22:40:11 UTC) Description Trying to run Isolde simulation following the tutorial commands and 'overloadable' attribute is not present. Log: UCSF ChimeraX version: 1.6.dev202302242240 (2023-02-24) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show ISOLDE > set selectionWidth 4 Populating font family aliases took 236 ms. Replace uses of missing font family ""Carlito"" with one that exists to avoid this cost. > isolde tutorial > isolde demo cryo_em_intro modelOnly true startIsolde false 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb #1 --- Chain | Description | UniProt A B C | capsid protein VP1 | CAPSD_NVN68 9-520 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 51 residues in model #1 to IUPAC-IUB standards. 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb --- Chain | Description | UniProt 1.2/A 1.2/B 1.2/C | capsid protein VP1 | CAPSD_NVN68 9-520 Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205 > open 20205 fromDatabase emdb Opened emdb 20205 as #2, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at level 0.287, step 1, values float32 > clipper associate #2 toModel #1 Opened emdb 20205 as #1.1.1.1, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at step 1, values float32 > isolde start > set bgColor white > addh Summary of feedback from adding hydrogens to 6out.pdb #1.2 --- notes | Termini for 6out.pdb (#1.2) chain A determined from SEQRES records Termini for 6out.pdb (#1.2) chain B determined from SEQRES records Termini for 6out.pdb (#1.2) chain C determined from SEQRES records Chain-initial residues that are actual N termini: /B THR 9 Chain-initial residues that are not actual N termini: /A ASP 29, /C ASP 29 Chain-final residues that are actual C termini: /A SER 520 Chain-final residues that are not actual C termini: /B ALA 519, /C ALA 519 Missing OXT added to C-terminal residue /A SER 520 1438 hydrogen bonds Adding 'H' to /A ASP 29 Adding 'H' to /C ASP 29 /B ALA 519 is not terminus, removing H atom from 'C' /C ALA 519 is not terminus, removing H atom from 'C' 11439 hydrogens added > isolde restrain ligands #1 [Repeated 1 time(s)] > ui tool show ""Ramachandran Plot"" > select #1 22945 atoms, 23062 bonds, 1720 residues, 15 models selected > isolde sim start sel Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 320, in interceptRequest self._callback(info) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 93, in _intercept return interceptor(request_info, *args) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/help_viewer/tool.py"", line 320, in intercept chimerax_intercept(request_info, *args, session=self.session, File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 455, in chimerax_intercept session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 385, in thread_safe func(*args, **kw) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 446, in defer cxcmd(session, topic) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/widgets/htmlview.py"", line 464, in cxcmd run(session, cmd) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/cmd/cmd.py"", line 111, in isolde_sim isolde.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/isolde.py"", line 894, in start_sim sm.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 398, in start_sim sh.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1409, in start_sim self._prepare_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1367, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/app/simulation.py"", line 103, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index < bufferSize; index += get_local_size(0)) ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i < workGroupSize) ~~~~~~~~ ^ ~~~~~~~~~~~~~ openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i ~~~~~~~~ ^ ~~~~~~~~~~~~~ File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. > isolde sim start sel Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/__init__.py"", line 183, in run_provider toolbar_command(session, name) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/toolbar.py"", line 17, in toolbar_command run(session, 'isolde sim start sel') File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/cmd/cmd.py"", line 111, in isolde_sim isolde.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/isolde.py"", line 894, in start_sim sm.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 398, in start_sim sh.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1409, in start_sim self._prepare_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1367, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/app/simulation.py"", line 103, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index < bufferSize; index += get_local_size(0)) ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i < workGroupSize) ~~~~~~~~ ^ ~~~~~~~~~~~~~ openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i ~~~~~~~~ ^ ~~~~~~~~~~~~~ File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. > isolde sim start sel Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/__init__.py"", line 183, in run_provider toolbar_command(session, name) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/toolbar.py"", line 17, in toolbar_command run(session, 'isolde sim start sel') File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/cmd/cmd.py"", line 111, in isolde_sim isolde.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/isolde.py"", line 894, in start_sim sm.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 398, in start_sim sh.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1409, in start_sim self._prepare_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1367, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/app/simulation.py"", line 103, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index < bufferSize; index += get_local_size(0)) ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i < workGroupSize) ~~~~~~~~ ^ ~~~~~~~~~~~~~ openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i ~~~~~~~~ ^ ~~~~~~~~~~~~~ File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. > hide #!1.1 models > show #!1.1 models > hide #!1.1 models > hide #!1.2 models > hide #1.3 models > show #!1.2 models > select add #1.2 22945 atoms, 23062 bonds, 1720 residues, 11 models selected > isolde sim start sel Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/__init__.py"", line 183, in run_provider toolbar_command(session, name) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/toolbar.py"", line 17, in toolbar_command run(session, 'isolde sim start sel') File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/cmd/cmd.py"", line 111, in isolde_sim isolde.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/isolde.py"", line 894, in start_sim sm.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 398, in start_sim sh.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1409, in start_sim self._prepare_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1367, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/app/simulation.py"", line 103, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index < bufferSize; index += get_local_size(0)) ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i < workGroupSize) ~~~~~~~~ ^ ~~~~~~~~~~~~~ openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i ~~~~~~~~ ^ ~~~~~~~~~~~~~ File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. > hide #!1.2 models > show #!1.2 models > select add #1 22945 atoms, 23062 bonds, 1720 residues, 18 models selected > select add #1 22945 atoms, 23062 bonds, 1720 residues, 18 models selected > selwct #1 /B :322 Unknown command: selwct #1 /B :322 > select #1 /B :322 12 atoms, 11 bonds, 1 residue, 1 model selected > isolde sim start sel Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/__init__.py"", line 183, in run_provider toolbar_command(session, name) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/toolbar.py"", line 17, in toolbar_command run(session, 'isolde sim start sel') File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/cmd/cmd.py"", line 111, in isolde_sim isolde.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/isolde.py"", line 894, in start_sim sm.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 398, in start_sim sh.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1409, in start_sim self._prepare_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1367, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/app/simulation.py"", line 103, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index < bufferSize; index += get_local_size(0)) ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i < workGroupSize) ~~~~~~~~ ^ ~~~~~~~~~~~~~ openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i ~~~~~~~~ ^ ~~~~~~~~~~~~~ File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. > show #!1.1 models > select add #1.1 1304 atoms, 1300 bonds, 94 residues, 6 models selected > select subtract #1.1 1304 atoms, 1300 bonds, 94 residues, 1 model selected > select add #1.3 1304 atoms, 1300 bonds, 94 residues, 2 models selected > select add #1 22945 atoms, 23062 bonds, 1720 residues, 18 models selected > select add #1 22945 atoms, 23062 bonds, 1720 residues, 18 models selected > select add #1 22945 atoms, 23062 bonds, 1720 residues, 18 models selected > hide #!1 models > show #!1 models > select add #1 22945 atoms, 23062 bonds, 1720 residues, 18 models selected > select add #1.2 22945 atoms, 23062 bonds, 1720 residues, 18 models selected > select subtract #1.1 22945 atoms, 23062 bonds, 1720 residues, 13 models selected > select add #1.1 22945 atoms, 23062 bonds, 1720 residues, 18 models selected > select subtract #1.1.1 22945 atoms, 23062 bonds, 1720 residues, 14 models selected > select add #1.1.1 22945 atoms, 23062 bonds, 1720 residues, 18 models selected > select subtract #1.1.1 22945 atoms, 23062 bonds, 1720 residues, 14 models selected > isolde sim start sel Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/__init__.py"", line 183, in run_provider toolbar_command(session, name) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/toolbar.py"", line 17, in toolbar_command run(session, 'isolde sim start sel') File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/cmd/cmd.py"", line 111, in isolde_sim isolde.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/isolde.py"", line 894, in start_sim sm.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 398, in start_sim sh.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1409, in start_sim self._prepare_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1367, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/app/simulation.py"", line 103, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index < bufferSize; index += get_local_size(0)) ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i < workGroupSize) ~~~~~~~~ ^ ~~~~~~~~~~~~~ openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i ~~~~~~~~ ^ ~~~~~~~~~~~~~ File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. > isolde sim start sel Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/__init__.py"", line 183, in run_provider toolbar_command(session, name) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/toolbar.py"", line 17, in toolbar_command run(session, 'isolde sim start sel') File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/cmd/cmd.py"", line 111, in isolde_sim isolde.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/isolde.py"", line 894, in start_sim sm.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 398, in start_sim sh.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1409, in start_sim self._prepare_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1367, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/app/simulation.py"", line 103, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index < bufferSize; index += get_local_size(0)) ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i < workGroupSize) ~~~~~~~~ ^ ~~~~~~~~~~~~~ openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i ~~~~~~~~ ^ ~~~~~~~~~~~~~ File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. > select add #1.1 2849 atoms, 2886 bonds, 199 residues, 6 models selected > select subtract #1.1 2849 atoms, 2886 bonds, 199 residues, 1 model selected > hide #!1.1 models > show #!1.1 models > select add #1.2 22945 atoms, 23062 bonds, 1720 residues, 11 models selected > show #1.3 models > select add #1.3 22945 atoms, 23062 bonds, 1720 residues, 12 models selected > select subtract #1.3 22945 atoms, 23062 bonds, 1720 residues, 11 models selected > select add #1.3 22945 atoms, 23062 bonds, 1720 residues, 12 models selected > isolde sim start sel Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/__init__.py"", line 183, in run_provider toolbar_command(session, name) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/toolbar.py"", line 17, in toolbar_command run(session, 'isolde sim start sel') File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/cmd/cmd.py"", line 111, in isolde_sim isolde.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/isolde.py"", line 894, in start_sim sm.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 398, in start_sim sh.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1409, in start_sim self._prepare_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1367, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/app/simulation.py"", line 103, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index < bufferSize; index += get_local_size(0)) ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i < workGroupSize) ~~~~~~~~ ^ ~~~~~~~~~~~~~ openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i ~~~~~~~~ ^ ~~~~~~~~~~~~~ File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. > isolde sim start sel Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/toolbar/tool.py"", line 205, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 386, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py"", line 1289, in run_provider return cls._get_func(api, ""run_provider"")(session, name, mgr, **kw) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/__init__.py"", line 183, in run_provider toolbar_command(session, name) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/toolbar.py"", line 17, in toolbar_command run(session, 'isolde sim start sel') File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/cmd/cmd.py"", line 111, in isolde_sim isolde.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/isolde.py"", line 894, in start_sim sm.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 398, in start_sim sh.start_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1409, in start_sim self._prepare_sim() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1367, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/app/simulation.py"", line 103, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index < bufferSize; index += get_local_size(0)) ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i < workGroupSize) ~~~~~~~~ ^ ~~~~~~~~~~~~~ openmm.OpenMMException: Error compiling kernel: :31:6: error: redeclaration of 'atom_add' must have the 'overloadable' attribute void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous overload of function is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :31:6: error: conflicting types for 'atom_add' void atom_add(volatile __global unsigned long* p, long unsigned val) { ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:5815:21: note: previous declaration is here ulong __OVERLOAD__ atom_add(volatile __global ulong *p, ulong val); ^ :67:9: warning: 'make_short2' macro redefined #define make_short2(x...) ((short2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3188:9: note: previous definition is here #define make_short2(A,B) (short2)((A),(B)) ^ :68:9: warning: 'make_short3' macro redefined #define make_short3(x...) ((short3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3189:9: note: previous definition is here #define make_short3(A,B,C) (short3)((A),(B),(C)) ^ :69:9: warning: 'make_short4' macro redefined #define make_short4(x...) ((short4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3190:9: note: previous definition is here #define make_short4(A,B,C,D) (short4)((A),(B),(C),(D)) ^ :70:9: warning: 'make_int2' macro redefined #define make_int2(x...) ((int2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3200:9: note: previous definition is here #define make_int2(A,B) (int2)((A),(B)) ^ :71:9: warning: 'make_int3' macro redefined #define make_int3(x...) ((int3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3201:9: note: previous definition is here #define make_int3(A,B,C) (int3)((A),(B),(C)) ^ :72:9: warning: 'make_int4' macro redefined #define make_int4(x...) ((int4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3202:9: note: previous definition is here #define make_int4(A,B,C,D) (int4)((A),(B),(C),(D)) ^ :73:9: warning: 'make_float2' macro redefined #define make_float2(x...) ((float2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3224:9: note: previous definition is here #define make_float2(A,B) (float2)((A),(B)) ^ :74:9: warning: 'make_float3' macro redefined #define make_float3(x...) ((float3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3225:9: note: previous definition is here #define make_float3(A,B,C) (float3)((A),(B),(C)) ^ :75:9: warning: 'make_float4' macro redefined #define make_float4(x...) ((float4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3227:9: note: previous definition is here #define make_float4(A,B,C,D) (float4)((A),(B),(C),(D)) ^ :76:9: warning: 'make_double2' macro redefined #define make_double2(x...) ((double2) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3231:9: note: previous definition is here #define make_double2(A,B) (double2)((A),(B)) ^ :77:9: warning: 'make_double3' macro redefined #define make_double3(x...) ((double3) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3232:9: note: previous definition is here #define make_double3(A,B,C) (double3)((A),(B),(C)) ^ :78:9: warning: 'make_double4' macro redefined #define make_double4(x...) ((double4) (x)) ^ /System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/A/lib/clang/3.5/include/cl_kernel.h:3233:9: note: previous definition is here #define make_double4(A,B,C,D) (double4)((A),(B),(C),(D)) ^ :214:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' for (unsigned int index = thread; index ~~~~~ ^ ~~~~~~~~~~ :219:43: warning: comparison of integers of different signs: 'unsigned int' and 'int' if (thread%(i*2) == 0 && thread+i ~~~~~~~~ ^ ~~~~~~~~~~~~~ File ""/Users/anthonyrish/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/openmm/openmm.py"", line 2469, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) See log for complete Python traceback. OpenGL version: 4.1 ATI-4.9.51 OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0) OS Loader Version: 564.40.4~66 Software: System Software Overview: System Version: macOS 13.2 (22D49) Kernel Version: Darwin 22.3.0 Time since boot: 3 days, 10 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0000 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5300M: Chipset Model: AMD Radeon Pro 5300M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0043 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32207P1-020 Option ROM Version: 113-D32207P1-020 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.11.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.0.1 ChimeraX-AddCharge: 1.5.8 ChimeraX-AddH: 2.2.3 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.8 ChimeraX-AtomicLibrary: 10.0.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.20.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.dev202302242240 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3.3 ChimeraX-DockPrep: 1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.6.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.11 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.8 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.6.13 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.27.2 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.2 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.6 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.0.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.4 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.2.0 jupyterlab-widgets: 3.0.5 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 pandas: 1.5.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.0.0 prompt-toolkit: 3.0.37 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.2 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.2 python-dateutil: 2.8.2 pytz: 2022.7.1 pyzmq: 25.0.0 qtconsole: 5.4.0 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.0.2 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.9.0 typing-extensions: 4.5.0 urllib3: 1.26.14 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.5 zipp: 3.15.0 }}} " defect assigned normal Third Party all ChimeraX