Linux for large scale sequencing?

Arne Elofsson arne at
Mon Feb 9 13:37:22 EST 1998

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Eugen Buehler <buehler at> writes:

> I would like to hear from anyone that is using Linux in
> a large scale sequencing project, particularly for programs like
> phred, phrap, the Staden package, acedb, blast, etc.  I compiled
> phrap on my new Dell at home and compared the time it took to
> assemble a relatively large (2700 sequences) project.  The results:
> Dell XPS Pentium II 300MHz, 64MB RAM, RH Linux 5.0:      11 minutes
> Sun Ultra2 Creator 3D, 300MHz, 128MB RAM, Solaris 2.5:   40 minutes
This differnce is too big. OK solaris is slower than linux but the
ultraII should be about  the same speed as a pentium II

> Both were compiled using gcc, optimized.  

You probably gain a factor of 2 or more using cc (-alotofflags) on
solarisand about 30 % using pgcc on linux.

> Considering the
> difference in price between these two machines, I'ld like to
> consider using PC's running Linux if we buy more workstations.
> Also of interest would be experiences people have networking
> between Solaris and Linux through NFS filesystems.

No problems, however NFS prestanda of linux is really bad (sometimes a
factor of 4 slower than on solaris). So write to local disks when you
write a lot of data


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              The more I use Windows, the more I love Linux
 Arne Elofsson     arne at
 Tel:+46(0)8-161553      Dept of Biochemistry, Stockholm University
 Fax:+46(0)8-153679	 10691 Stockholm, Sweden


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