VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Tue Nov 24 2020 - 07:35:35 CST

Dear VMD and FFTK developers,

Some of my students reported out-of-memory errors at the stage of
"Bonded Opt" optimization of bonding parameters in the FFTK plugin
available with VMD version 1.9.4a38. The error occurs after a few
iterations of running NAMD, with the message "can't fork child process",
presumably the namd2 process.

Unfortunately I have only seen this on the shared screen in ZOOM session
and I haven't though about making a screenshot, so I am reporting the
messages from memory. It does not seem to happen to everyone or in every
case. I did however checked the memory usage on the remote computer
while the error dialog was still shown.

The command `free` did not show anything unusual, `top` also reported
just a few percent of memory usage by VMD. The only value seemingly
unusual is the VIRT column showing allocation of 145GB of virtual memory.

   PID USER      PR  NI    VIRT    RES    SHR S  %CPU  %MEM     TIME+ COMMAND
27759 xxxxxxx   20   0  145,1g 298560  80348 S   0,0   7,6   0:07.46 vmd_LINUX+

The same optimization run just fine with VMD 1.9.4a8. The system is
Debian 10 GNU/Linux 64 bit.

If necessary, I can probably get the files to reproduce the problem.

Thank you,

Pawel