ISOLDE: implicit solvent applied twice if CUDA fails and falls back to OpenCL

[richard_walsh@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.45.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
When running the isolde plugin the model "runs" out of the density in some places. No previous issues withcurrent map model before recent upgrades.

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /nfs/userdocs/sch/walsh/Documents/for_tristan.cxs

Opened extradens_C2_J108_sharp.mrc as #1.1.1.1, grid size 360,360,360, pixel
1.06, shown at level 0.874, step 1, values float32  
Restoring stepper: Fixed-active-1-Hwithsomesim-coot-0.pdb  
Log from Thu Jan 13 09:24:11 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /nfs/userdocs/sch/walsh/Documents/Fixed-active-1-Hwithsomesim-
> coot-0.pdb

Chain information for Fixed-active-1-Hwithsomesim-coot-0.pdb #1  
---  
Chain | Description  
1 M | No description available  
2 N | No description available  
A O | No description available  
B P | No description available  
C Q | No description available  
D R | No description available  
E S | No description available  
F T | No description available  
G U | No description available  
H V | No description available  
I W | No description available  
J X | No description available  
K Y | No description available  
L Z | No description available  
a b | No description available  
  

> open /nfs/userdocs/sch/walsh/Documents/extradens_C2_J108_sharp.mrc

Opened extradens_C2_J108_sharp.mrc as #2, grid size 360,360,360, pixel 1.06,
shown at level 0.306, step 2, values float32  

> addh

Summary of feedback from adding hydrogens to Fixed-active-1-Hwithsomesim-
coot-0.pdb #1  
---  
notes | No usable SEQRES records for Fixed-active-1-Hwithsomesim-coot-0.pdb
(#1) chain 1; guessing termini instead  
No usable SEQRES records for Fixed-active-1-Hwithsomesim-coot-0.pdb (#1) chain
2; guessing termini instead  
No usable SEQRES records for Fixed-active-1-Hwithsomesim-coot-0.pdb (#1) chain
A; guessing termini instead  
No usable SEQRES records for Fixed-active-1-Hwithsomesim-coot-0.pdb (#1) chain
B; guessing termini instead  
No usable SEQRES records for Fixed-active-1-Hwithsomesim-coot-0.pdb (#1) chain
C; guessing termini instead  
25 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /1 PHE 21, /2 THR 34, /A HIS
15, /B THR 10, /C ILE 10, /D PHE 18, /E SER 13, /F ASN 4, /G THR 5, /H THR 20,
/I THR 30, /J ASP 3, /K MET 1, /L THR 75, /M PHE 21, /N THR 34, /O HIS 15, /P
THR 10, /Q ILE 10, /R PHE 18, /S SER 13, /T ASN 4, /U THR 5, /V THR 20, /W THR
30, /X ASP 3, /Y MET 1, /Z THR 76, /a PRO 127, /b PRO 127  
Chain-initial residues that are not actual N termini: /A ASP 192, /C LEU 52,
/C VAL 126, /C GLU 183, /C LYS 208, /D SER 62, /D ARG 127, /E LYS 32, /E VAL
140, /O ASP 192, /Q LEU 52, /Q VAL 126, /Q GLU 183, /Q LYS 208, /R SER 62, /R
ARG 127, /S LYS 32, /S VAL 140, /a ALA 144, /a SER 194, /a ALA 207, /b ALA
144, /b SER 194, /b ALA 207  
Chain-final residues that are actual C termini: /1 ASP 241, /B LEU 250, /C GLN
243, /D GLN 243, /F ILE 234, /G ASN 247, /H LEU 215, /J ASP 205, /L GLY 286,
/M ASP 241, /P LEU 250, /Q GLN 243, /R GLN 243, /T ILE 234, /U ASN 247, /V LEU
215, /X ASP 205, /Z GLY 287  
Chain-final residues that are not actual C termini: /2 THR 263, /A GLU 250, /A
SER 189, /C ARG 49, /C SER 123, /C ASN 178, /C VAL 203, /D ARG 48, /D THR 121,
/E ALA 248, /E PHE 22, /E LEU 119, /I ILE 249, /K PHE 195, /N THR 263, /O GLU
250, /O SER 189, /Q ARG 49, /Q SER 123, /Q ASN 178, /Q VAL 203, /R ARG 48, /R
THR 121, /S ALA 248, /S PHE 22, /S LEU 119, /W ILE 249, /Y PHE 195, /a PRO
229, /a GLN 139, /a PRO 179, /a PRO 202, /b PRO 229, /b GLN 139, /b PRO 179,
/b PRO 202  
6234 hydrogen bonds  
/2 THR 263 is not terminus, removing H atom from 'C'  
/A GLU 250 is not terminus, removing H atom from 'C'  
/E ALA 248 is not terminus, removing H atom from 'C'  
/I ILE 249 is not terminus, removing H atom from 'C'  
/K PHE 195 is not terminus, removing H atom from 'C'  
7 messages similar to the above omitted  
2 hydrogens added  
  

> clipper associate #2 toModel #1

Opened extradens_C2_J108_sharp.mrc as #1.1.1.1, grid size 360,360,360, pixel
1.06, shown at level 0.874, step 1, values float32  
Chain information for Fixed-active-1-Hwithsomesim-coot-0.pdb  
---  
Chain | Description  
1.2/1 1.2/M | No description available  
1.2/2 1.2/N | No description available  
1.2/A 1.2/O | No description available  
1.2/B 1.2/P | No description available  
1.2/C 1.2/Q | No description available  
1.2/D 1.2/R | No description available  
1.2/E 1.2/S | No description available  
1.2/F 1.2/T | No description available  
1.2/G 1.2/U | No description available  
1.2/H 1.2/V | No description available  
1.2/I 1.2/W | No description available  
1.2/J 1.2/X | No description available  
1.2/K 1.2/Y | No description available  
1.2/L 1.2/Z | No description available  
1.2/a 1.2/b | No description available  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Done loading forcefield  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error launching CUDA compiler: 32512  
sh: /usr/local/cuda/bin/nvcc: No such file or directory  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error launching CUDA compiler: 32512  
sh: /usr/local/cuda/bin/nvcc: No such file or directory  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /nfs/userdocs/sch/walsh/Documents/for_tristan.cxs includeMaps true

Taking snapshot of stepper: Fixed-active-1-Hwithsomesim-coot-0.pdb  

——— End of log from Thu Jan 13 09:24:11 2022 ———

opened ChimeraX session  

> select /I:200@CA

1 atom, 1 residue, 1 model selected  

> select /I:200@CA

1 atom, 1 residue, 1 model selected  

> select up

11 atoms, 10 bonds, 1 residue, 1 model selected  

> isolde start

> set selectionWidth 4

Done loading forcefield  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error launching CUDA compiler: 32512  
sh: /usr/local/cuda/bin/nvcc: No such file or directory  
  

ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  




OpenGL version: 3.3.0 NVIDIA 450.80.02
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            31G         24G        1.1G        399M        5.3G        5.6G
	Swap:          2.0G        891M        1.1G

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P4000] [10de:1bb1] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11a3]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
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[Tristan Croll]

OK, I see the problem. There's something wrong with your CUDA installation, which is triggering a bug when ISOLDE automatically falls back to using OpenCL instead: the implicit solvent correction term ends up being added twice. You can avoid that for now by either:

• correcting your CUDA installation (preferred - for best startup performance go with CUDA 11.2 - that's the version OpenMM was compiled against). OpenMM expects to find it in /usr/local/cuda - you may need to create a symbolic link to the versioned directory (/usr/local/cuda-{version}). It should still work with any CUDA 11.x, but startup will be slightly slower because it instead has to use the command-line nvcc.
• switching ISOLDE to use OpenCL by default - in the "Experience level" drop-down menu at bottom right of the ISOLDE panel switch to "Advanced", then choose "OpenCL" in the cyan drop-down menu that appears on the "Sim settings" tab.

One thing that's confusing me a bit - the fallback code is supposed to switch ISOLDE to using OpenCL by default for the remainder of the session, but that's not what I see in the log:

Error launching CUDA compiler: 32512  
sh: /usr/local/cuda/bin/nvcc: No such file or directory  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error launching CUDA compiler: 32512  
sh: /usr/local/cuda/bin/nvcc: No such file or directory  
  

ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

Is there any chance you closed and restarted ISOLDE between those two log entries?

[Tristan Croll]

SBGRID are fixing the CUDA library error, and the bug in ISOLDE's fallback mechanism will be fixed for the next release.