Error with coMD in VMD re GPUs

[roger99shi]

Hi,
I was running coMD in VMD 1.9.3. The following error pops up and kills the process.

can't read "::comd::gpus_present": no such variable
can't read "::comd::gpus_present": no such variable
while executing
"if {$::comd::gpus_present} {
set processes_per_run [expr {[llength [wsplit $::comd::gpus_selection1 ","]] + 1}]

if {[info exists ::comd::num_..."
(procedure "::comd::Prepare_system" line 220)
invoked from within

"::comd::Prepare_system"
invoked from within
".comdgui.main_frame.prepare.button invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 23)
invoked from within
"tk::ButtonUp .comdgui.main_frame.prepare.button"
(command bound to event)

I also tried 1.9.2 and even the ionization cannot complete.
Could you give me a clue about how to fix it? Many thanks!

[jamesmkrieger]

Can you try getting the latest CoMD from github please? I'm pretty sure I fixed this problem there.

If that doesn't work, let me know.

Best wishes
James

[roger99shi]

Tried the github version and the problem is fixed. However the following error appears:

'''
while executing
"exit"
invoked from within
"if {$status} {
set err_file [open "MD.log" a]
puts $err_file "ERROR: $output"
exit
}"
(file "/data/MD/LeverMD/MD/MD.tcl" line 110)
invoked from within
"source $tcl_file_name"
(procedure "::comd::Prepare_system" line 966)
invoked from within
"::comd::Prepare_system"
invoked from within
".comdgui.main_frame.prepare.button invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .comdgui.main_frame.prepare.button"
(command bound to event)

'''

If I continue and run the tcl, it seems nothing happened as shown before:

$ vmd -dispdev text -e MD.tcl
/programs/x86_64-linux/vmd/1.9.3/lib/vmd/vmd_LINUXAMD64: /lib64/libGL.so.1: no version information available (required by /programs/x86_64-linux/vmd/1.9.3/lib/vmd/vmd_LINUXAMD64)
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to [email protected]
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 32 CPUs detected.
Info) CPU features: SSE2 AVX
Info) Free system memory: 32GB (51%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 1 available CUDA accelerator:
Info) [0] GeForce GTX 760 6 SM_3.0 @ 1.03 GHz, 2.0GB RAM, KTO, AE1, ZCP
Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
Info) Compiling 1 OptiX shaders on 1 target GPU...
Info) Dynamically loaded 2 plugins in directory:
Info) /programs/x86_64-linux/vmd/1.9.3/lib/vmd/plugins/LINUXAMD64/molfile
MD_min0.sh
file20
1.2
/programs/x86_64-linux/system/sbgrid_bin/namd2
/programs/x86_64-linux/system/sbgrid_bin/python
file21
file21
Now running minimization 0
1
Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
Info) Exiting normally.
[ys89@bioc-c7320ld1 MD]$

Could you help me?

[roger99shi]

Just realized that I forgot to paste the log file and here is the error info:

---==## Mon Nov 25 11:05:02 EST 2019 #==---
Version: 1.0
Info: Logging started for setup of MD.
Solvation: Box padding 15 A in x, 15 A in y, 15 A in z.
Ionization: Initial PDB System has a total charge of -9.999980766326189 electrons.
Ionization: 10 sodium ions will be added to walker1.
Ionization: Initial PDB System is ionized to become neutral.
Ionization: Final PDB System has a total charge of -9.999980766326189 electrons.
Ionization: 10 sodium ions will be added to walker2.
Ionization: Final PDB System is ionized to become neutral.
Simulation: NAMD configuration files for minimization written in MD_walker1_min
and MD_walker2_min.
ERROR: ------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Unknown command-line option +devices

Charm++ fatal error:
FATAL ERROR: Unknown command-line option +devices

/programs/share/capsules/lib/job.sh: line 120: 20058 Aborted (core dumped) "$SB_EXECFILE" "$@"
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Unknown command-line option +devices

Charm++ fatal error:
FATAL ERROR: Unknown command-line option +devices

/programs/share/capsules/lib/job.sh: line 120: 20201 Aborted (core dumped) "$SB_EXECFILE" "$@"
ERROR: ------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Unknown command-line option +devices

Charm++ fatal error:
FATAL ERROR: Unknown command-line option +devices

/programs/share/capsules/lib/job.sh: line 120: 22959 Aborted (core dumped) "$SB_EXECFILE" "$@"
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Unknown command-line option +devices

Charm++ fatal error:
FATAL ERROR: Unknown command-line option +devices

/programs/share/capsules/lib/job.sh: line 120: 23086 Aborted (core dumped) "$SB_EXECFILE" "$@"

[jamesmkrieger]

I thought I fixed this problem too. Which NAMD version are you using?

[roger99shi]

I am using NAMD 2.13-multicore

[jamesmkrieger]

Ok. Thanks for that information. You probably want to use a version with CUDA for GPU acceleration (see https://www.ks.uiuc.edu/Research/namd/2.9/ug/node88.html) but I'll see if I can put in something to check for that anyhow.

…

> On Dec 3, 2019, at 8:35 AM, roger99shi ***@***.***> wrote:  I am using NAMD 2.13-multicore — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

[jamesmkrieger]

I should now have a fix for this in #64, which I will now merge. Please can you let me know if that fixes it. Sorry for the delay.

[jamesmkrieger]

I have just made and merged #66, which fixes an error I made creating #64. I will test whether this works myself now.