Re: shared memory in computational chemistry
On Fri, 2007-04-06 at 15:39 -0700, Francesco Pietra wrote:
[context clipped]
> QUESTIONS:
> 1) How to set shmmax in debian?
shmmax is auto set on the Linux Kernel these days, you can set it but it
may or maynot be changed by the kernel itself.
But based on documentation of the default kernel VM and memory
management in the kernel lately, I may be mistaken here. I'll put reccs
further down.
> 2) Which is the upper limit for the hardware indicated
> abobe, should a relationship to the hardware be? (in
> fact, I can't predict the size of segments that will
> be tried to be allocated in the future i the MD
> simulations I am carrying out).
Pretty hefty hardware. Settings below.
> 3)What else - if anything - should be set besides
> shmmax.
Explanation
kernel.shmall
is the available memory for shared memory in 4K pages
kernel.shmmax
is the maximum size of one shared memory segment in byte
kernel.shmmni
is the maximum number of shared segments
kernel.sem
is the semaphore settings
kernel.msgmni
is the maximum number of queues system wide
kernel.msgmax
is the maximum size of messages in bytes
kernel.msgmnb
is the default size of queue in bytes
Your amount of memory: 16GB
Based on your amount and your architecture, my best guess for a somewhat
optimal setting. You may or may not see significant improvement. But,
you should "tweak" settings to see how things run.
kernel.sem = 250 256000 32 1024
kernel.msgmnb = 65536
kernel.msgmni = 1024
kernel.msgmax = 65536
kernel.shmmni = 4096
kernel.shmall = 4070400
kernel.shmmax = 16672358400
Put these lines in "/etc/systl.conf" and then perform:
"sysctl -p /etc/sysctl.conf"
These values are what I would typically use for an application server or
DB server with 16GB of memory, based on 50%-70% of memory usage by the
application, the rest for caching and system use.. I hope this helps,
remember, every machine in your cluster will need to have settings like
this, once you nail the problem of the dump.
You should also, read up on what these settings actually do, doing
things blindly can cause you greater harm than good. But if you trust
someone from a track record of "trustworthy advice" you may be able to
do that... but I always make sure before I use advice from people like
me that sound like they know what they are doing, but may in-fact not
know.
In general, these setting make a HORRIBLE desktop machine. As these
settings are aimed at application use rather than desktop response.
--
greg, greg@gregfolkert.net
I don't mow my lawn anymore. I just intimidate it into not growing.
Though it is quite hard to intimidate grass, it has been around a long time
and has quite an attitude about it.
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