[Bioclusters] RE: non linear scale-up issues?
David Gayler
bioclusters@bioinformatics.org
Mon, 10 May 2004 19:36:57 -0500
Thanks for the feedback,
I am aware of United Devices. They seem to have a very good solution and it
is multi-platform too. I am interested in any pain points you have with
their or similar technology? Are there features or functionality you would
like to see that are missing, specifically geared towards bioinformatics
research?
If I understand you, you are saying that this is a good example of where
grid technology is delivering on the promise. It is pretty clear that when
the problem is 'embarrassingly parallel', enterprise grid (cycle stealing)
solutions (like UD's) can be an intelligent way to use one's current IT
infrastructure investment. I guess what I am looking for is what could be
made better.
Also, what do you mean by standards folks? Are you talking about Globus
Toolkit and its ever evolving architecture (now mainly web-service based)?
What do you see as the threat with this?
IMHO, MPI is just fine for clusters with good links where security is of no
or little concern, however it really isn't made for loosely coupled networks
and cycle stealing scenarios. It certainly never has had security in mind.
These are the kind of things that, if not baked into the technology, can
turn your Grid nodes into a security risk and ultimately a bunch of zombies
waiting to be used for a DDOS attack or worse. Once that happens, trying to
trust or even keep your Grid could be a tough political battle.
On Sun, 9 May 2004, Rayson Ho wrote:
> UD: http://www.grid.org/stats/
>
> 325,033 years of CPU time collected
he he :-) Rayson knows his stuff, as do United Devices. You will not see
mpi any where near this 300k+ CPU years. Good point.
> BOINC: http://boinc.berkeley.edu
This looks great. Classic 'grid hype' this certainly is not. Good stuff.
Thanks for sending on the link, I really hope that the standards folk keep
the hell away from this. If they do it may have a real chance...
Best regards,
J.
--
James Cuff, D. Phil.
Group Leader, Applied Production Systems
The Broad Institute. 320 Charles Street, Cambridge,
MA. 02141-2023. Tel: 617-252-1925 Fax: 617-258-0903
-----Original Message-----
From: bioclusters-admin@bioinformatics.org
[mailto:bioclusters-admin@bioinformatics.org] On Behalf Of
bioclusters-request@bioinformatics.org
Sent: Monday, May 10, 2004 11:01 AM
To: bioclusters@bioinformatics.org
Subject: Bioclusters digest, Vol 1 #483 - 4 msgs
When replying, PLEASE edit your Subject line so it is more specific
than "Re: Bioclusters digest, Vol..." And, PLEASE delete any
unrelated text from the body.
Today's Topics:
1. non linear scale-up issues? (David Gayler)
2. Re: MPI clustalw (Tim Cutts)
3. Re: non linear scale-up issues? (Rayson Ho)
4. Re: non linear scale-up issues? (James Cuff)
--__--__--
Message: 1
From: "David Gayler" <dag_project@sbcglobal.net>
To: <bioclusters@bioinformatics.org>
Date: Sun, 9 May 2004 12:22:59 -0500
Subject: [Bioclusters] non linear scale-up issues?
Reply-To: bioclusters@bioinformatics.org
Hi,
I am a newbie and not a bio guy, but rather a computer science guy.
I am interested in why you are seeing these kind of horrible non-linear
Scale-out numbers. Please excuse my ignorance, but is the problem that there
are dependencies between jobs and this doesn't scale? What exactly is the
relationship of this problem to MPI? I just have to wonder if figuring out a
better way to divide and conquer has any merit. I am interested in y'alls
feedback as my company is working on a Windows .NET based Grid solution and
we want to focus on the bioinformatics community. It seems to me that a lot
of researchers spend time worrying about getting faster results
(understandably), however it doesn't seem like there is much in the way of
cycle-stealing grid software solutions that are flexible, secure, and easy
to use. I want to know what is missing currently to get these faster results
reliably, despite hardware faults, etc.
I am aware of Condor (free), DataSynapse, Platform Computing, and others. I
am interested in knowing what is, if anything, lacking in these solutions.
Thanks in advance.
-----Original Message-----
From: bioclusters-admin@bioinformatics.org
[mailto:bioclusters-admin@bioinformatics.org] On Behalf Of
bioclusters-request@bioinformatics.org
Sent: Sunday, May 09, 2004 11:01 AM
To: bioclusters@bioinformatics.org
Subject: Bioclusters digest, Vol 1 #482 - 1 msg
When replying, PLEASE edit your Subject line so it is more specific
than "Re: Bioclusters digest, Vol..." And, PLEASE delete any
unrelated text from the body.
Today's Topics:
1. Re: MPI clustalw (Guy Coates)
-- __--__--
Message: 1
Date: Sun, 9 May 2004 11:17:16 +0100 (BST)
From: Guy Coates <gmpc@sanger.ac.uk>
To: bioclusters@bioinformatics.org
Subject: [Bioclusters] Re: MPI clustalw
Reply-To: bioclusters@bioinformatics.org
> example web servers and services where you need rapid response for
> single, or small numbers of jobs.
We (well, the ensembl-ites) do run a small amount of mpi-clustalw. The
algorithm scales OK for small alignment (but they run quickly, so why
bother?) but is horrible for large alignments.
These are figures for an alignment of a set of 9658 sequences, running on
Dual 2.8GHz PIV machines with gigabit.
Ncpus Runtime Efficiency
---- ------- -----------
2 28:21:33 1
4 19:49:05 0.72
8 14:49:02 0.48
10 14:09:41 0.4
16 13:37:36 0.26
24 13:00:30 0.18
32 12:48:39 0.14
48 12:48:39 0.09
64 11:19:40 0.08
96 11:30:09 0.05
128 11:13:28 0.04
However, although the scaling is horrible, it does at least bring the
runtime down to something more manageable. MPI clustalw only gets run for
the alignments that the single CPU version chokes on. It may not be
pretty, but at least you do get an answer, eventually. Horses for courses
and all that.
>
> Guy/Tim - did you ever deploy that HMMer PVM cluster we talked about
> for the Pfam web site?
>
It's on the ever-expanding list of things to do. So, does anyone here have
any opinions/experience on the PVM verison of HMMer?
Guy
--
Guy Coates, Informatics System Group
The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
Tel: +44 (0)1223 834244 ex 7199
-- __--__--
_______________________________________________
Bioclusters maillist - Bioclusters@bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bioclusters
End of Bioclusters Digest
--__--__--
Message: 2
From: Tim Cutts <tjrc@sanger.ac.uk>
Subject: Re: [Bioclusters] MPI clustalw
Date: Sun, 9 May 2004 19:10:45 -0300
To: bioclusters@bioinformatics.org
Reply-To: bioclusters@bioinformatics.org
On 6 May 2004, at 10:30 pm, James Cuff wrote:
> Guy/Tim - did you ever deploy that HMMer PVM cluster we talked about
> for the Pfam web site?
That's still a watch this space. The PFAMers are still talking about
doing some MPI/PVM stuff. Like you, I am still a sceptic.
Having said that, some of the EBI chaps are running MPI clustalw -- not
sure which one -- on the IBM blades, and claim to be getting decent
performance out of it. That's GBit interconnect, as you know, and we
limit them to 10 CPUs (i.e. 5 machines) per job. Haven't got as far as
getting it to schedule sensibly with the network topology. LSF has a
useful looking sc_topology.so mbschd plugin, but I've not found any
docs for it yet.
Tim
-
Dr Tim Cutts
Informatics Systems Group
Wellcome Trust Sanger Institute
Hinxton, Cambridge, CB10 1SA, UK
--__--__--
Message: 3
Date: Sun, 9 May 2004 17:00:50 -0700 (PDT)
From: Rayson Ho <raysonlogin@yahoo.com>
Subject: Re: [Bioclusters] non linear scale-up issues?
To: bioclusters@bioinformatics.org
Reply-To: bioclusters@bioinformatics.org
UD: http://www.grid.org/stats/
325,033 years of CPU time collected
BOINC: http://boinc.berkeley.edu
Will be used by the next generation of SETI@home and other research
projects.
Rayson
--- David Gayler <dag_project@sbcglobal.net> wrote:
> however it doesn't seem like there is much in the
> way of
> cycle-stealing grid software solutions that are flexible, secure, and
> easy
> to use. I want to know what is missing currently to get these faster
> results
> reliably, despite hardware faults, etc.
>
> I am aware of Condor (free), DataSynapse, Platform Computing, and
> others. I
> am interested in knowing what is, if anything, lacking in these
> solutions.
>
> Thanks in advance.
>
> -----Original Message-----
> From: bioclusters-admin@bioinformatics.org
> [mailto:bioclusters-admin@bioinformatics.org] On Behalf Of
> bioclusters-request@bioinformatics.org
> Sent: Sunday, May 09, 2004 11:01 AM
> To: bioclusters@bioinformatics.org
> Subject: Bioclusters digest, Vol 1 #482 - 1 msg
>
> When replying, PLEASE edit your Subject line so it is more specific
> than "Re: Bioclusters digest, Vol..." And, PLEASE delete any
> unrelated text from the body.
>
>
> Today's Topics:
>
> 1. Re: MPI clustalw (Guy Coates)
>
> -- __--__--
>
> Message: 1
> Date: Sun, 9 May 2004 11:17:16 +0100 (BST)
> From: Guy Coates <gmpc@sanger.ac.uk>
> To: bioclusters@bioinformatics.org
> Subject: [Bioclusters] Re: MPI clustalw
> Reply-To: bioclusters@bioinformatics.org
>
> > example web servers and services where you need rapid response for
> > single, or small numbers of jobs.
>
> We (well, the ensembl-ites) do run a small amount of mpi-clustalw.
> The
> algorithm scales OK for small alignment (but they run quickly, so why
> bother?) but is horrible for large alignments.
>
> These are figures for an alignment of a set of 9658 sequences,
> running on
> Dual 2.8GHz PIV machines with gigabit.
>
> Ncpus Runtime Efficiency
> ---- ------- -----------
> 2 28:21:33 1
> 4 19:49:05 0.72
> 8 14:49:02 0.48
> 10 14:09:41 0.4
> 16 13:37:36 0.26
> 24 13:00:30 0.18
> 32 12:48:39 0.14
> 48 12:48:39 0.09
> 64 11:19:40 0.08
> 96 11:30:09 0.05
> 128 11:13:28 0.04
>
> However, although the scaling is horrible, it does at least bring the
> runtime down to something more manageable. MPI clustalw only gets run
> for
> the alignments that the single CPU version chokes on. It may not be
> pretty, but at least you do get an answer, eventually. Horses for
> courses
> and all that.
>
>
> >
> > Guy/Tim - did you ever deploy that HMMer PVM cluster we talked
> about
> > for the Pfam web site?
> >
>
> It's on the ever-expanding list of things to do. So, does anyone here
> have
> any opinions/experience on the PVM verison of HMMer?
>
>
> Guy
> --
> Guy Coates, Informatics System Group
> The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
> Tel: +44 (0)1223 834244 ex 7199
>
>
>
>
> -- __--__--
>
> _______________________________________________
> Bioclusters maillist - Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
>
>
> End of Bioclusters Digest
>
> _______________________________________________
> Bioclusters maillist - Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
__________________________________
Do you Yahoo!?
Win a $20,000 Career Makeover at Yahoo! HotJobs
http://hotjobs.sweepstakes.yahoo.com/careermakeover
--__--__--
Message: 4
Date: Sun, 9 May 2004 22:16:13 -0400 (EDT)
From: James Cuff <jcuff@broad.mit.edu>
To: bioclusters@bioinformatics.org
Subject: Re: [Bioclusters] non linear scale-up issues?
Reply-To: bioclusters@bioinformatics.org
On Sun, 9 May 2004, Rayson Ho wrote:
> UD: http://www.grid.org/stats/
>
> 325,033 years of CPU time collected
he he :-) Rayson knows his stuff, as do United Devices. You will not see
mpi any where near this 300k+ CPU years. Good point.
> BOINC: http://boinc.berkeley.edu
This looks great. Classic 'grid hype' this certainly is not. Good stuff.
Thanks for sending on the link, I really hope that the standards folk keep
the hell away from this. If they do it may have a real chance...
Best regards,
J.
--
James Cuff, D. Phil.
Group Leader, Applied Production Systems
The Broad Institute. 320 Charles Street, Cambridge,
MA. 02141-2023. Tel: 617-252-1925 Fax: 617-258-0903
--__--__--
_______________________________________________
Bioclusters maillist - Bioclusters@bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bioclusters
End of Bioclusters Digest