VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 24 2020 - 08:40:22 CST

Hi,
  We fixed an uninitialized flag issue with prior VMD test versions a
while back that could cause memory consumption on certain versions
of Linux. Please have your student download and install the latest
test version of VMD 1.9.4 and that should cure the issue.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 24, 2020 at 02:35:35PM +0100, Pawel Kedzierski wrote:
> 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

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> org;quoted-printable:Wroc=C5=82aw University of Technology, Faculty of Chemistry;Advanced Materials Engineering and Modelling Group
> adr;quoted-printable;quoted-printable;quoted-printable;quoted-printable:Wyb. Wyspia=C5=84skiego 27;;Politechnika Wroc=C5=82awska, Wydzia=C5=82 Chemiczny;Wroc=C5=82aw;dolno=C5=9Bl=C4=85skie;50-370;Poland
> email;internet:Pawel.Kedzierski_at_pwr.edu.pl
> tel;work:+48 71 3203200
> tel;fax:+48 71 3203364
> version:2.1
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> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/