Linux for large scale sequencing?
Thomas.Sicheritz at molbio.uu.se
Wed Feb 11 17:08:58 EST 1998
Arne Elofsson <arne at elof.biokemi.su.se> writes:
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> Eugen Buehler <buehler at cbil.humgen.upenn.edu> 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
The NFS is a bit slower in the 2.0.x kernels but is completely rewritten in
the 2.1.x versions, - but investing in a fast ethercard instead of these
cheap ones people usually put in PC's should give you a 'normal' performance.
Sicheritz Ponten Thomas E. Department of Molecular Biology
Biomedical Center Uppsala University
BMC: +46 18 4714214 BOX 590 S-751 24 UPPSALA Sweden
Fax +46 18 557723 http://evolution.bmc.uu.se/~thomas
Molecular Tcl: http://evolution.bmc.uu.se/~thomas/tcl
Molecular Linux: http://evolution.bmc.uu.se/~thomas/mol_linux
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