Updated hardware requirements Gmod servers

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Updated hardware requirements Gmod servers

Michael Dondrup
Dear all,


In my project I am responsible for establishing
a model-organism database with a genome browser  (e.g. Gbrowse2) and likely a CHADO
database using Postgres on Linux server as a back-end. We are still in the process of
specifying the system and features (see [1]) so requirements can change.

Are there any (updated) hardware specifications or recommendations for a GMOD system based on
GBrowse and CHADO?

I am aware of  examples [2,3]. Is there a more recent overview of hardware specs and what are people actually using?

Key data: the organism has about 500 Mbase genome-size, which is in about 100 scaffolds atm,
gene-predictions will be available soon. 3 to 4 similar genomes will be made available in the system.
There are about 30 project users who will also annotate, but I have no idea what is going to happen when the site will
go public on the net.

We will need web-servers, database-servers, and storage.
The idea I picked up is to divide the system into two identical stacks,
one for the master curation database, and one for the public version which is a read-only dump of the master DB.
I will start with a small test-stack first and a handful of test-users to get an impression for how the system scales.

I know that my question is quite hard to answer, but we need to acquire server hardware pretty soon.
Any suggestions will help.

Thank you very much
Michael

[1]: http://biostar.stackexchange.com/questions/17099/what-is-your-experience-with-gmod-tools-or-alternatives
[2]: http://flybase.org/forums/viewtopic.php?f=14&t=112
[3]: http://wiki.wormbase.org/index.php/WormBase_Infrastructure


Michael Dondrup
Post-doctoral researcher
The Sea Lice Research Centre
University of Bergen
Thormøhlensgate 55, N-5008 Bergen,
Norway








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Re: Updated hardware requirements Gmod servers

Josh Goodman
Hi Michael,

In general I would try to get as much memory and the fastest disks
that you can.  I would recommend at least 32 GB of RAM and preferably
more depending on your budget.  For disks you might want to consider
using 2x solid state drives (SSDs) in a RAID 1 configuration for your
PostgreSQL database, but that can get expensive.  The
postgresql-performance mailing list has lots of info on what SSDs work
best for Pg.  Then I would supplement that with standard SAS drives in
a RAID 5 for a total size of 1-2 TB.  For CPUs I would go with a
typical setup of dual quad or six core chips.

FlyBase has been able to buy systems such as this (minus the SSDs) for
around $4k USD.  SSDs would probably add another $1-2k depending on
the size and type you go with.

It is hard to give you specifics without more information, but
hopefully this will help guide you in the right direction.

Cheers,
Josh

On Tue, Feb 14, 2012 at 9:14 AM, Michael Dondrup <[hidden email]> wrote:

> Dear all,
>
>
> In my project I am responsible for establishing
> a model-organism database with a genome browser  (e.g. Gbrowse2) and likely a CHADO
> database using Postgres on Linux server as a back-end. We are still in the process of
> specifying the system and features (see [1]) so requirements can change.
>
> Are there any (updated) hardware specifications or recommendations for a GMOD system based on
> GBrowse and CHADO?
>
> I am aware of  examples [2,3]. Is there a more recent overview of hardware specs and what are people actually using?
>
> Key data: the organism has about 500 Mbase genome-size, which is in about 100 scaffolds atm,
> gene-predictions will be available soon. 3 to 4 similar genomes will be made available in the system.
> There are about 30 project users who will also annotate, but I have no idea what is going to happen when the site will
> go public on the net.
>
> We will need web-servers, database-servers, and storage.
> The idea I picked up is to divide the system into two identical stacks,
> one for the master curation database, and one for the public version which is a read-only dump of the master DB.
> I will start with a small test-stack first and a handful of test-users to get an impression for how the system scales.
>
> I know that my question is quite hard to answer, but we need to acquire server hardware pretty soon.
> Any suggestions will help.
>
> Thank you very much
> Michael
>
> [1]: http://biostar.stackexchange.com/questions/17099/what-is-your-experience-with-gmod-tools-or-alternatives
> [2]: http://flybase.org/forums/viewtopic.php?f=14&t=112
> [3]: http://wiki.wormbase.org/index.php/WormBase_Infrastructure
>
>
> Michael Dondrup
> Post-doctoral researcher
> The Sea Lice Research Centre
> University of Bergen
> Thormøhlensgate 55, N-5008 Bergen,
> Norway
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

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