Re: [GUSDEV] out of memory when loading taxonomy

[Jinal J. <jaj...@lb...>]

Hi Jian,

What are your ulimit settings? You can get it by typing "ulimit -a"



Thanks
--Jinal

On 5/31/06, Fernan Aguero <fe...@ii...> wrote:
>
> +----[ Jian Lu <jl...@vb...> (31.May.2006 10:45):
> |
> | Hi GUSDEV,
> |
> | When I was using GUS plug-in to load NCBI taxonomy, it failed. The error
> | message is 'Out of Memory'. My machine's RAM is 4G which should be
> | enough to hold the data. Any hint would be appreciated. Thanks,
> |
> | Jian
> |
> +----]
>
> Jian,
>
> can you post the exact error message (copy & paste)?
>
> Is it Perl running out of memory? Or is it the db
> (postgres/oracle)?
>
> Your box has 4Gb RAM, but this doesn't mean that all of this
> memory is available to the application.
>
> Are you running the plugin from one host and the db server
> in another host? If so, which one is 'getting out of
> memory'?
>
>
> What RDBMS are you using? Postgres? Oracle?
>
> Have you set up your RDBMS to use the extra available
> memory? Both Oracle and Postgres should be configured to use
> more memory, if it's available. The default configuration
> that (the one you get from a fresh install) would give you a
> horrid performance and will not make use of extra RAM.
>
>
> What OS are you using? Linux? FreeBSD?
>
> Have you tuned the OS? (through building a new kernel or
> modifying kernel tunables using sysctl or something
> similar?) Raising maxusers, maxfiles and/or a number of
> kernel parameters can give your app more room to scale if
> necessary.
>
>
> Is this a dedicated db server or is it running other
> applications alongside postgres or oracle? Even if you tune
> your db and OS to maximize the use of resources, running two
> or more apps that compete for the same resource will lead to
> degraded performance.
>
> As you can see, there are a number of steps that you should
> follow to make use of the available RAM and to optimize
> performance of your DB app.
>
> And we need more information about your setup to be able to
> guess what the problem might be.
>
> Fernan
>
> PS: I've succesfully loaded NCBI Taxonomy (in ~ 2hs) on
> PostgreSQL running on a spare box that was not particularly
> beefy (AMD Sempron, 1 Gb RAM, RAID-1 ATA100). But both the OS
> (FreeBSD) and the application (PostgresSQL) were tuned to
> maximize use of available resources.
>
>
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