Slashdot Mirror
Swap Performance in Linux
GizmoDuck writes "I'm working in a computational chemistry lab, and we find ourselves using memory and CPU hogs like Amber and Gaussian. The CPU hogging isn't a problem, thanks to Condor, but when submitting one of the jobs that request (and pretty much require) all the physical RAM in the machines, Linux promptly starts swapping so hard that the mouse pointer in X stops moving, NFS and NIS halt, and things don't get back to normal for five minutes. I've tried toying a bit with the settings in /proc/sys/vm/kswapd to no avail. I've done some poking around on the 'net looking for answers. Faster disks and swap partitions at the beginning of the drive aren't really an option at this point. I haven't found a good solution yet. I was wondering if the /. community has any input on how to keep the system from locking during periods of necessarily high swap activity?"
Maybe try out the preemptible kernel patch?
My personal experience is that it has helped my workstation's interactive performance noticeably for big ass c++ compiles and periods of lots of disk activity (big apt-get dist-upgrades). Thankfully, I'm no longer doing the big ass c++ compiles, so it's not as big of an issue as it used to be :)
It should improve interactive performance (i.e., your mouse will start moving again :) ) when load is high. Also, running your background process nice'ed will be helpful.
You might also consider a crazy idea of having swap file on NFS -- you'll get (if your network is decent) almost the same bandwidth as you get when accessing (older) disk, but much higher latency (this will put your background process in disadvantage compared to your interactive processes).
Hope this helps.
Paul B.
If your program(s) push Linux to the point where it actually runs out of available RAM faster than it can free it up, then "all hell breaks loose". It has to swap something out, and just about every program is eligible to be swapped out. That includes GPM (if you are on a virtual console) or X (if you are in X Windows). You need to account for all of these things to determine your RAM needs. Add up the memory usage of all your active programs, plus the buffer demands they have doing disk I/O, plus the kernel, and you need that much RAM. If the program is doing a LOT if disk/file writes, you can expect the buffer demands to be the majority of this, too (because the kernel believes what you just wrote you might soon want to read back, so it tries to keep lots of it in RAM even if that means swapping out GPM and X).
now we need to go OSS in diesel cars
Is switching to FreeBSD an option? The virtual memory management there is much better than in Linux under stress.
The best way to handle this(or at least the best way I handled a similar situation) is to combine Robert Love's Preempt patch and Ingo's Scheduler.
They will significant increase high load user performance, keeps the system from running away with itself. If your feeling really, adventuresome you could also throw in Rik's Rmap VM...I have done very little testing with it, but I hear alot of reports that it helps.
there are all available in the authors respective directories on Kernel.org riel,rml,mingo
Power Corrupts,Absolute Power Corrupts Absolutely, leaving one person(group)in charge is absolutely corrupt.
Unfortunately, you're out of luck. The current linux VM (in later 2.4 series) is fine for low to medium load systems but falls apart on high load systems. The previous VM (early 2.4 series) is a good design but isn't really ready for production.
I would suggest buying more RAM (it's cheap) if you aren't already maxed at 4 gigs (x86). Alternatively switch to FreeBSD which has a very stable efficient VM. Any source should recompile without too much trouble and it can run linux binaries at almost full speed!
Best slashdot comment
Did you miss all the 2.4 Linux VM Stories?
I suggest build/installing the latest kernel with the aa VM (the default VM, since 2.4.10). If you still have VM (Swap) problems then go get the latest rmap VM patch and try that.
The kernel VM (Virtual Machine) is what manages memory and sawp, btw.
And if u did miss all the VM stories, a summery:
at the start of 2.4 a new fancy mv was put in to action, using something known as reverse mapping. this was very clever but it wasn't quite ready and there were teathing troubles then suddenly (2.4.10) Linus switched VM to one similar to that of 2.3 (with some updates and a few features from the previous 2.4 VM) This started a big fight, which caused concerns (such that it may split the linux comunity)
which is better i dont know some swer by one other swer the other. but unless ur using RH 2.4.9 kernel i would not recommend a pre 2.4.10 kernel.
however you may need to experiment which is best the VM now in 2.4 (to stay) or rmap, u should try both and see
steps
Install 2.4.[17,18,19]
try it
if it fails u try the rmap patch
Do you really have to be using the machine while it's calculating? If not, what about shutting down X and any other memory-hogging system components? Unlike on Windows you do have the option of turning off that expensive GUI.
Note to ACs: I usually delete AC replies without reading them. If you want to talk to me, log in.
Why don't you submit yhis query to the computational chemistry mailing list (see CCL)
Those people may be able to give you some sensible suggestions, especially with respect to those particular peices of software.
I believe that you can restrict the amount of memory that Gaussian uses via its keywords. When it requires more, it will handle the dumping of data to disk itself. Read the manual - I haven't used gaussian since g94 was the current version so can't remember..
How big is your AMBER simulation? I think I would run a smaller system... or even better... buy some more RAM given that it is dirt cheap nowadays.
AMBER's memory use is a bit heavy - you may have better luck with another MD package. Maybe NAMD? (Although I'd still vote for the "buy more RAM" option)
With that as a given, if your app needs all available memory, run top and lsmod to see what's using your memory and remove everything you don't need (usually by deleting the links to those processes in the /etc/???/rc5.d directory).
If you can't remove it, scale it down. For example /etc/inittab lists off the different virtual terminals that appear when you press ctrl-alt and a function key. If you never use this feature, try reducing this down to 1 or 2 terminals. Leave some behind just in case you need them later. To do this, just comment the higher numbered lines that look like this;
6:2345:respawn:/sbin/mingetty tty6
(NOTE: Removing these lines might not make any difference -- it all depends on the distribution.)
As for X (assuming you need it and are using XFree), try removing any Load lines in the modules section that you don't need and scaling down the display size, background images, and color depth. Another big area of savings is changing the window manager. FVWM usually is installed, and while it is ugly it is also fairly light weight when compaired to KDE, Gnome, and other popular full-featured WMS.
While these steps alone won't eliminate the speed problems -- the other comments might solve that -- the time you spend waiting might be cut way down.
A firewall can not protect you from yourself. Turn off what you do not need. Do not use the firewall to do your work.
You could try hdparm -u 1 which unmasks interrupts when the disk interrupt service routine is active. This often allows your mouse to continue moving even if the disk is busy dealing with swap. It's not perfect but it helps a lot. As others have suggested, also try the preemptible kernel patch but keep backups!
Scroogle