![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Last modified 3 years ago
#8568 assigned defect
'overloadable' attribute missing
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: 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: <program source>: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);
^
<program source>: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);
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
~~~~~ ^ ~~~~~~~~~~
<program source>: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: <program source>: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);
^
<program source>: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);
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
~~~~~ ^ ~~~~~~~~~~
<program source>: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: <program source>: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);
^
<program source>: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);
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
~~~~~ ^ ~~~~~~~~~~
<program source>: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: <program source>: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);
^
<program source>: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);
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
~~~~~ ^ ~~~~~~~~~~
<program source>: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: <program source>: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);
^
<program source>: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);
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
~~~~~ ^ ~~~~~~~~~~
<program source>: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: <program source>: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);
^
<program source>: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);
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
~~~~~ ^ ~~~~~~~~~~
<program source>: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: <program source>: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);
^
<program source>: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);
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
~~~~~ ^ ~~~~~~~~~~
<program source>: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: <program source>: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);
^
<program source>: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);
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
~~~~~ ^ ~~~~~~~~~~
<program source>: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: <program source>: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);
^
<program source>: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);
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
^
<program source>: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))
~~~~~ ^ ~~~~~~~~~~
<program source>: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
Change History (2)
comment:1 by , 3 years ago
| Platform: | → all |
|---|---|
| Project: | → ChimeraX |
comment:2 by , 3 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → 'overloadable' attribute missing |
Note:
See TracTickets
for help on using tickets.
Thanks for reporting this! I checked in with the OpenMM team, and this is a known bug (https://github.com/openmm/openmm/issues/3855) affecting older Intel GPUs that is fixed in OpenMM 8.0. ChimeraX is currently using 8.0.0beta, but will be updating to the 8.0 release soon, with the planned migration to Python 3.11. Once that happens this problem should go away.