Re: Daily cron stalls running NAMD outputs

From: Vlastimil Zíma (
Date: Wed Apr 01 2015 - 07:08:28 CDT

In progress:

I am very unsure about what causes the problem. Removal of the "apt" and
"mlocate" jobs seemed to resolve the issue. On the other hand, I tested the
cron itself by introduction of the "sleep 1" cron job which caused the
issue if it was accompanied by the rest of the jobs, but the "sleep" job
itself (removed all other corn jobs) didn't trigger the stalling. Neither
multiple (8) "sleep 0.2" jobs haven't trigger the problem.

I used following script to trigger the problem (for cycle with what I found
in /etc/crontab)

for I in $(seq 100); do echo -n "."; test -x /usr/sbin/anacron || ( cd / &&
run-parts --report /etc/cron.daily ); done; echo

I should also mention I run my NAMD from screen using following command

runnamd_cuda 20c_run.namd > 20c_run.output 2> 20c_run.error

where runnamd_cuda is following script

ulimit -c unlimited
namd2-mc-cuda +setcpuaffinity +idlepoll +p6 +devices 0 "$@"

The namd2-mc-cuda is compiled binary of namd with multicore and CUDA.


2015-04-01 10:04 GMT+02:00 Vlastimil Zíma <>:

> Hi everyone,
> I'm using NAMD2.9 on Debians equipped with GPU and I repetitively
> encounter wierd behaviour, namd is still running, but no new output i
> generated - restart files, dcd, not even the output redirected to a file. I
> noticed it usually happens at 6.24 in the morning which led me to discover
> that daily cron jobs are run at that time.
> Here is the list of my system daily crons
> apt
> aptitude
> bsdmainutils
> dpkg
> exim4-base
> logrotate
> man-db
> mlocate
> ntp
> passwd
> popularity-contest
> I'm not yet sure which one of those causes the NAMD output to stall
> neither what exactly causes the stalling. I was able to reproduce the
> problem on two of my machines so far.
> Does anybody had any similar issue?
> Vlastik

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:46 CST