Weird application behavior with linux-ck kernel

DarkSkyGhost · 2013-01-05 15:38:29

I have this weird thing happening.

Whenever I use molecular dynamics simulation and cpu's both cores are constantly loaded (but hdd gets written into briefly only at checkpoints every couple of minutes), almost all programs are responsive and working properly, dynamics program backs off when another program wants some cpu.

BUT, two programs have weird behaviour. One is ktorrent, another is clementine.

While using ck-k10 kernel, started ktorrent, launched simulation, dl/ul'ing immediately stopped. As soon as simulation was stopped, ktorrent started working normally. And as soon as simulation would be restarted, ktorrent would immediately stop. But system was more responsive and music playback wasn't stuttering.

Booted default kernel, launched simulation, started ktorrent, and it was dl/ul'ing properly. Although system was less responsive and more stuttery, especially music playback.

I tried playing with nice levels, setting simulation for lowest priority while setting ktorrent for highest, but to no avail.

Where do I go from here? Or is it just simply a trade - I get responsive system, but some things don't work, or I get less responsive system, but with everything working? Or do I have to manually compile kernel to lessen the drawbacks and make it more to my liking?

Could anyone point me in any direction where to dig deeper? I'd appreciate it.

graysky · 2013-01-05 15:46:03

I don't have any experience with either ktorrent or clementine, but I do compile while listing to mpd (pulseaudio) quite a bit. I also run the linux-ck package on my workstation. I haven't seen what you're describing while seeding with deluge and compiling and listening to music.

1) What is the molecular dynamics simulation package you speak of in your text (I am interested in reproducing)?
2) What nice level does it run at?
3) What are you using for audio (pulse or alsa or oss or...?)
4) What DE are you using (gnome, kde, e17 etc.)?

The fact that audio becomes choppy and system becomes unresponsive makes me think the cpu hogging app is not running at the correct nice level or is overly aggressive. I always `nice -19 makepkg ...` when I compile for example.

Last edited by graysky (2013-01-05 15:48:30)

DarkSkyGhost · 2013-01-05 16:09:05

1) GROMACS 4.5.5, compiled with double precision (use the --disable-float flag during configuration), patched with PLUMED (patch is probably irrelevant, wasn't using it at that time, but it's patched nonetheless). If you wish to reproduce, use this tutorial. You will need to go up to page 10 to prepare all files necessary for simulation.

2) Gromacs runs at default 0, as did KTorrent. Tried setting KTorrent at -19 (as I understand, it's highest priority), and mdrun_d at +19, but nothing changed.

3) ALSA, Asus Xonar D1.

4) KDE 4.9.5.

Audio becomes choppy and system gets unresponsive only with default kernel. On ck kernel, everything is smooth, except that clementime time to time hangs, continues playback until track ends, and revives only after a couple of minutes. KTorrent dl/ul stall, gui sometimes hangs (although I'm blaming the gui hang on massive 789 torrent number). Net browser, file browser, video playback (smplayer with vdpau) is completely normal.

Last edited by DarkSkyGhost (2013-01-05 16:14:51)

graysky · 2013-01-05 17:21:18

You shouldn't need to nice ktorrent I would think... what you are describing doesn't sound likean issue of ktorrent being CPU staved, but network staved which makes no sense to me. Is what you described 100 % reproducible? In other words, stop gromacs. THen ktorrent starts seeded. Start gromacs, then ktorrent stops seeding. Repeat. Repeat. Same result?

EDIT: Is there a PKGBUILD for gromacs?
EDIT2: Perhaps pulse-audio would solve your issues?

Last edited by graysky (2013-01-05 17:39:43)

brebs · 2013-01-05 17:51:59

Does ktorrent "nice" itself?

There's a current similar thread.

DarkSkyGhost · 2013-01-05 18:13:34

@graysky:

Yes, for me it is always reproducible.

With CK kernel, in a sequence:

I launch ktorrent.
KTorrent starts downloading torrent at high speed.
I launch gromacs.
Torrent download speed immediately starts dropping and comes to stop.
After some time peer list is lost. I can re-announce, get same peers, but it won't connect to them. Restarting torrent job have no effect. Neither does restarting KTorrent.
I stop gromacs.
KTorrent quickly gets peers and connects to them.
I Start gromacs.
Torrent stops downloading.
I stop gromacs.
Torrent starts downloading.

With default kernel, in a sequence:

I Launch KTorrent.
KTorrent starts downloading torrent at high speed.
I launch gromacs.
Torrent continues downloading.
I wait a couple of minutes.
I stop torrent.
I start torrent again.
KTorrent quickly connects and starts downloading.
I stop gromacs.
KTorrent continues downloading.
I start gromacs.
KTorrent doesn't lose connection and continues downloading.

With default kernel, I think I noticed, that when KTorrent is downloading and I launch gromacs, torrent download speed drops a little bit. If it is relevant, should I boot the default kernel and see if it drops and, if it does, by how much?

I think there is PKGBUILD for gromacs in AUR. But make sure you compile it with --disable-float.
I prepared the file for the job for you. Run it like this:

mdrun_d -deffnm md

About pulseaudio, I don't really care about the audio playback, I can substitute music with portable player. I'm more concerned with KTorrent.

@brebs:

If I understood you correctly, it launches with the niceness of 0.

I agree, the thread is similar. but:

I never had problems with watching videos and downloading torrents. Even when KTorrent is very active, I can watch videos without any delays. Even if the both video file and ktorrent jobs is in the same hdd.
I have set my hdds to maximum performance and loudest acoustic settings. It maybe helps. I am running smplayer with vdpau, with direct output to audio card, cache for local files is 50mb, double buffering, allows frame drop (but don't notice any drops).

I even can watch videos (both SD and 720p) when gromacs is running. No delays or stutter whatsoever(!).

I tried launching gromacs project on one hdd and download torrent on another hdd, but torrent job stops as well.

PRETTY IMPORTANT EDIT:

Launched KTorrent with niceness of -19 as super user. As previously, torrent stops as soon as gromacs is launched.

Tried deluge. WORKS PERFECTLY. Torrent download doesn't stop when gromacs is launched.

I guess it's KTorrent or KDE issue, not kernel-ck?

Last edited by DarkSkyGhost (2013-01-05 18:31:53)

brebs · 2013-01-05 19:32:23

Oh look, same issue. Sure looks like ktorrent does something weird.

I just grepped its sourcecode for "nice", but didn't find anything interesting.

graysky · 2013-01-05 19:42:05

DarkSkyGhost wrote:

Launched KTorrent with niceness of -19 as super user. As previously, torrent stops as soon as gromacs is launched.
Tried deluge. WORKS PERFECTLY. Torrent download doesn't stop when gromacs is launched.
I guess it's KTorrent or KDE issue, not kernel-ck?

That was my contention all along. Deluge is a very nice product. Just switch and be happy.

DarkSkyGhost · 2013-01-05 19:55:27

Uh. Will take a long time to migrate 800 torrents. Oh well.

I guess this issue is kind of solved.

Thanks to both of you for your time

Arch Linux

#1 2013-01-05 15:38:29

Weird application behavior with linux-ck kernel

#2 2013-01-05 15:46:03

Re: Weird application behavior with linux-ck kernel

#3 2013-01-05 16:09:05

Re: Weird application behavior with linux-ck kernel

#4 2013-01-05 17:21:18

Re: Weird application behavior with linux-ck kernel

#5 2013-01-05 17:51:59

Re: Weird application behavior with linux-ck kernel

#6 2013-01-05 18:13:34

Re: Weird application behavior with linux-ck kernel

#7 2013-01-05 19:32:23

Re: Weird application behavior with linux-ck kernel

#8 2013-01-05 19:42:05

Re: Weird application behavior with linux-ck kernel

#9 2013-01-05 19:55:27

Re: Weird application behavior with linux-ck kernel

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