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#6585 closed defect (nonchimerax)

/usr/local/cuda/bin/nvcc: not found

Reported by:	shashank.chavali@…	Owned by:	Tristan Croll
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:	Tom Goddard
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-4.15.0-175-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
I had installed ISOLDE on ChimeraX1.2 and tried to simulate a single residue. The follow error showed and I am not sure how to proceed from here:
simtk.openmm.OpenMMException: Error launching CUDA compiler: 32512
sh: 1: /usr/local/cuda/bin/nvcc: not found


File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/simtk/openmm/openmm.py", line 17752, in __init__
this = _openmm.new_Context(*args)

I'd appreciate any help on this,

Best,
Shashank

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/shashank/Downloads/cryosparc_P15_J718__localfilter.mrc format mrc

Opened cryosparc_P15_J718__localfilter.mrc as #1, grid size 450,450,450, pixel
1.15, shown at level 0.0716, step 2, values float32  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.2.2-cp38-cp38-manylinux_2_17_x86_64.whl  
Successfully installed ChimeraX-Clipper-0.16.0 ChimeraX-ISOLDE-1.2.2  
Installed ChimeraX-Clipper (0.16.0)  
Installed ChimeraX-ISOLDE (1.2.2)  

> volume #1 step 1

> volume #1 level 0.07

> open /home/shashank/Desktop/ranked_myo1c.pdb

Chain information for ranked_myo1c.pdb #2  
---  
Chain | Description  
A | No description available  
  

> set bgColor white

> select #2

12970 atoms, 13108 bonds, 793 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-109.69,0,1,0,308.87,0,0,1,289.61

> view matrix models #2,1,0,0,0.30977,0,1,0,203.92,0,0,1,244.82

> view matrix models
> #2,0.37338,0.1573,-0.91425,-21.749,-0.1085,0.98616,0.12536,206.06,0.92131,0.052388,0.38528,236.07

> view matrix models
> #2,0.91985,-0.38704,-0.06382,12.707,-0.19369,-0.30666,-0.9319,234.61,0.34111,0.86958,-0.35705,193.59

> view matrix models
> #2,-0.36381,-0.91369,0.18114,31.193,-0.22418,-0.10286,-0.9691,226.73,0.90409,-0.39318,-0.1674,242.95

> view matrix models
> #2,-0.38826,-0.79205,0.47108,31.437,0.036793,-0.52409,-0.85086,244.29,0.92082,-0.31302,0.23263,246.53

> view matrix models
> #2,-0.38826,-0.79205,0.47108,70.276,0.036793,-0.52409,-0.85086,267.66,0.92082,-0.31302,0.23263,179.9

> view matrix models
> #2,-0.52328,-0.81023,0.26404,67.201,-0.54723,0.081976,-0.83296,244.72,0.65324,-0.58036,-0.48628,177.06

> view matrix models
> #2,-0.52328,-0.81023,0.26404,173.08,-0.54723,0.081976,-0.83296,196.1,0.65324,-0.58036,-0.48628,227.99

> view matrix models
> #2,-0.52328,-0.81023,0.26404,184.91,-0.54723,0.081976,-0.83296,246.05,0.65324,-0.58036,-0.48628,242.54

> view matrix models
> #2,0.37594,-0.85516,-0.3569,179.42,-0.60383,-0.51823,0.60567,289.95,-0.7029,-0.012187,-0.71119,214.67

> view matrix models
> #2,0.23073,-0.95447,-0.1891,185.14,-0.70539,-0.29794,0.64316,282.46,-0.67022,-0.015008,-0.74201,214.38

> view matrix models
> #2,0.19605,-0.96693,-0.16313,185.89,-0.73953,-0.25504,0.62294,280.52,-0.64394,-0.0014905,-0.76507,213.62

> view matrix models
> #2,0.14369,-0.98111,-0.12951,186.76,-0.78618,-0.19266,0.58721,277.6,-0.60107,0.017444,-0.79901,212.54

> view matrix models
> #2,0.12974,-0.98469,-0.11642,187.05,-0.78964,-0.17362,0.58849,276.94,-0.59969,0.015575,-0.80008,212.6

> view matrix models
> #2,-0.23627,-0.96908,-0.071116,186.08,-0.96782,0.22818,0.10613,254.52,-0.086621,0.093904,-0.99181,208.38

> view matrix models
> #2,-0.27675,-0.9588,-0.064127,185.7,-0.95784,0.26988,0.098525,252.96,-0.077159,0.08869,-0.99307,208.57

> view matrix models
> #2,-0.67378,-0.734,0.085213,178.9,-0.71022,0.67512,0.19949,241.03,-0.20395,0.073892,-0.97619,208.97

> ~select #2

Nothing selected  

> select #2

12970 atoms, 13108 bonds, 793 residues, 1 model selected  

> view matrix models
> #2,-0.52798,-0.82356,-0.20731,177.86,-0.4811,0.49122,-0.72612,233.51,0.69984,-0.28364,-0.65557,229.51

> view matrix models
> #2,-0.52798,-0.82356,-0.20731,82.291,-0.4811,0.49122,-0.72612,249.07,0.69984,-0.28364,-0.65557,166.17

> view matrix models
> #2,-0.8136,-0.5418,0.21095,78.109,-0.4528,0.36284,-0.81445,252.28,0.36473,-0.75816,-0.54053,183.71

> view matrix models
> #2,-0.8136,-0.5418,0.21095,179.9,-0.4528,0.36284,-0.81445,236.03,0.36473,-0.75816,-0.54053,253.72

> view matrix models
> #2,-0.8136,-0.5418,0.21095,176.42,-0.4528,0.36284,-0.81445,256.74,0.36473,-0.75816,-0.54053,252.09

> fitmap #2 inMap #1

Fit molecule ranked_myo1c.pdb (#2) to map cryosparc_P15_J718__localfilter.mrc
(#1) using 12970 atoms  
average map value = 0.0558, steps = 344  
shifted from previous position = 21  
rotated from previous position = 36.6 degrees  
atoms outside contour = 8795, contour level = 0.07  
  
Position of ranked_myo1c.pdb (#2) relative to
cryosparc_P15_J718__localfilter.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.93151618 -0.19845082 0.30478667 190.89657777  
-0.29137306 -0.09433990 -0.95194631 266.23320232  
0.21766807 -0.97556000 0.03005592 246.09406645  
Axis -0.18228235 0.67249899 -0.71729927  
Axis point 70.68629630 244.29743594 0.00000000  
Rotation angle (degrees) 176.28622098  
Shift along axis -32.27861093  
  

> set bgColor black

> ui mousemode right translate

> ui mousemode right "translate selected models"

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.93152,-0.19845,0.30479,191.3,-0.29137,-0.09434,-0.95195,265.86,0.21767,-0.97556,0.030056,247.17

> view matrix models
> #2,-0.93152,-0.19845,0.30479,191.03,-0.29137,-0.09434,-0.95195,266.08,0.21767,-0.97556,0.030056,245

> fitmap #2 inMap #1

Fit molecule ranked_myo1c.pdb (#2) to map cryosparc_P15_J718__localfilter.mrc
(#1) using 12970 atoms  
average map value = 0.05767, steps = 824  
shifted from previous position = 7.3  
rotated from previous position = 10.4 degrees  
atoms outside contour = 8754, contour level = 0.07  
  
Position of ranked_myo1c.pdb (#2) relative to
cryosparc_P15_J718__localfilter.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.87150011 -0.16625697 0.46135260 193.01834011  
-0.43246822 -0.18299701 -0.88288357 259.68953239  
0.23121169 -0.96895345 0.08758106 243.97587663  
Axis -0.23758332 0.63527034 -0.73483724  
Axis point 75.58056267 224.19830556 0.00000000  
Rotation angle (degrees) 169.56405284  
Shift along axis -60.16743961  
  

> clipper associate #1 toModel #2

Opened cryosparc_P15_J718__localfilter.mrc as #1.1.1.1, grid size 450,450,450,
pixel 1.15, shown at level 0.146, step 1, values float32  
Chain information for ranked_myo1c.pdb  
---  
Chain | Description  
1.2/A | No description available  
  

> ui tool show ISOLDE

> set selectionWidth 4

Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

> undo

> fitmap #1.2 inMap #1.1.1.1

Fit molecule ranked_myo1c.pdb (#1.2) to map
cryosparc_P15_J718__localfilter.mrc (#1.1.1.1) using 12970 atoms  
average map value = 0.03367, steps = 76  
shifted from previous position = 13  
rotated from previous position = 6.7 degrees  
atoms outside contour = 12970, contour level = 0.14588  
  
Position of ranked_myo1c.pdb (#1.2) relative to
cryosparc_P15_J718__localfilter.mrc (#1.1.1.1) coordinates:  
Matrix rotation and translation  
0.99667592 -0.00368178 0.08138525 -23.56719876  
0.01049085 0.99646124 -0.08339630 26.81485303  
-0.08079020 0.08397288 0.99318755 2.78411939  
Axis 0.71683755 0.69459292 0.06070098  
Axis point 0.00000000 -6.95623646 306.00110645  
Rotation angle (degrees) 6.70407410  
Shift along axis 1.90055285  
  

> ui mousemode right translate

> select clear

> select clear

Traceback (most recent call last):  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2726, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2780, in start_sim  
sm.start_sim()  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim  
sh.start_sim()  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim  
self._prepare_sim()  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1561, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/simtk/openmm/app/simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 17752, in __init__  
this = _openmm.new_Context(*args)  
simtk.openmm.OpenMMException: Error launching CUDA compiler: 32512  
sh: 1: /usr/local/cuda/bin/nvcc: not found  
  
  
simtk.openmm.OpenMMException: Error launching CUDA compiler: 32512  
sh: 1: /usr/local/cuda/bin/nvcc: not found  
  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 17752, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  

> ui tool show Log

Traceback (most recent call last):  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2726, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2780, in start_sim  
sm.start_sim()  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim  
sh.start_sim()  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim  
self._prepare_sim()  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1561, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/simtk/openmm/app/simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 17752, in __init__  
this = _openmm.new_Context(*args)  
simtk.openmm.OpenMMException: Error launching CUDA compiler: 32512  
sh: 1: /usr/local/cuda/bin/nvcc: not found  
  
  
simtk.openmm.OpenMMException: Error launching CUDA compiler: 32512  
sh: 1: /usr/local/cuda/bin/nvcc: not found  
  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 17752, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1165, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1961, in
update_dihedral_restraints  
force.update_targets(restraints.sim_indices,  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1371, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1371, in
update_targets  
f(int(self.this), n, pointer(ind), pointer(params))  
  
See log for complete Python traceback.  
  

> select clear

> select clear

> select #2:288

Nothing selected  

> select #1.2:288

15 atoms, 14 bonds, 1 residue, 1 model selected  
Traceback (most recent call last):  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2726, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2780, in start_sim  
sm.start_sim()  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim  
sh.start_sim()  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim  
self._prepare_sim()  
File "/home/shashank/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1561, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/simtk/openmm/app/simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 17752, in __init__  
this = _openmm.new_Context(*args)  
simtk.openmm.OpenMMException: Error launching CUDA compiler: 32512  
sh: 1: /usr/local/cuda/bin/nvcc: not found  
  
  
simtk.openmm.OpenMMException: Error launching CUDA compiler: 32512  
sh: 1: /usr/local/cuda/bin/nvcc: not found  
  
  
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 17752, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3 (Core Profile) Mesa 20.0.8
OpenGL renderer: llvmpipe (LLVM 10.0.0, 256 bits)
OpenGL vendor: VMware, Inc.
Manufacturer: ASUS
Model: All Series
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 Intel(R) Core(TM) i7-6900K CPU @ 3.20GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G         31G         19G        1.4G         12G         29G
	Swap:           64G        5.3G         59G

Graphics:
	05:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1070] [10de:1b81] (rev a1)	
	Subsystem: NVIDIA Corporation GP104 [GeForce GTX 1070] [10de:119d]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

Change History (4)

comment:1 by Eric Pettersen, 4 years ago

Cc:	Tom Goddard added
Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → /usr/local/cuda/bin/nvcc: not found

comment:2 by Tristan Croll, 4 years ago

Looks like your CUDA installation is corrupt/incomplete. OpenMM has found the CUDA *libraries* (otherwise the CUDA platform wouldn't be enabled), but the nvcc executable (used to compile CUDA code) isn't in the expected location. Try reinstalling CUDA 11.2.

Also, is there any reason you're using 1.2 and not 1.3?

in reply to: 3 ; follow-up: 3 comment:3 by shashank.chavali@…, 4 years ago

Thanks very much for your reply! I had issues installing the chimerax 1.3 version but turns out I was trying to install it on the wrong ubuntu version. Now I have the right version installed and ISOLDE is working properly.

Thanks again,

Best,
Shashank
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, April 11, 2022 2:57 PM
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Chavali, Shashank <shashank.chavali@yale.edu>; tic20@cam.ac.uk <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #6585: /usr/local/cuda/bin/nvcc: not found

#6585: /usr/local/cuda/bin/nvcc: not found
-----------------------------------------+---------------------------
          Reporter:  shashank.chavali@…  |      Owner:  Tristan Croll
              Type:  defect              |     Status:  assigned
          Priority:  normal              |  Milestone:
         Component:  Third Party         |    Version:
        Resolution:                      |   Keywords:
        Blocked By:                      |   Blocking:
Notify when closed:                      |   Platform:  all
           Project:  ChimeraX            |
-----------------------------------------+---------------------------

Comment (by Tristan Croll):

 Looks like your CUDA installation is corrupt/incomplete. OpenMM has found
 the CUDA *libraries* (otherwise the CUDA platform wouldn't be enabled),
 but the `nvcc` executable (used to compile CUDA code) isn't in the
 expected location. Try reinstalling CUDA 11.2.

 Also, is there any reason you're using 1.2 and not 1.3?

--
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ChimeraX Issue Tracker

comment:4 by Tristan Croll, 4 years ago

Resolution:	→ nonchimerax
Status:	assigned → closed

Great! Will go ahead and close this ticket then.

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