clustalw-mpi from ubuntu server 12.04 doesn't work normally

[loïc lauréote]

Hi,

I have one bioinformatics question,
At lapaillasse some of us works on a beowulf cluster dedicated to bioinformatics.
So on our cluster we've got some package installed from ubuntu repository.
Testing our package we found something strange.
By comparing clustalw-mpi performance from 1  cpu to 4 cpu, we realized that something goes wrong.

config : clustalw-mpi 0.13 and openmpi 1.5

On a little dataset we found :

On a quadricore 3 gigahertz :
1 cpu = 51 secondes
4 cpu = 1m49 secondes


When you compile clustalw-mpi by yourself everything goes ok.


It is a normal beaviour, or did I miss something??

thx

[Josiah Zayner]

Your question will probably not receive many answers from this list and should instead be posted on a clustalw list. Further, not knowing anything about your cluster, what you ran, what parameters you ran the command with would make it extremely hard for anyone to make any assumption.

Just a cursory Search online shows that there apparently has been no work on that program in 8 years. Maybe try something else?

http://www.biostars.org/p/15102/

[ruphos]

Sounds like a combination of old software as Josiah mentioned and possibly also that the size of the dataset was too small to see performance increase over the additional resource overhead of creating / managing the additional threads. Take a look at MUSCLE as an alternative. http://www.drive5.com/muscle/

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[loïc lauréote]

ok thanks, this is not something about find an alternative but work for debugging clustalw-mpi. because i think on a real cluster this kind of lack of performance could be not visible, if there is a pb, this program have to be removed from the ubuntu repository.

2013/2/21 ruphos <apokr...@gmail.com>