[Bioclusters] Problems with mpiblast1.3

Mon Feb 7 09:33:18 EST 2005

Hi,

  I partially followed this thread, so I am not sure if you haven't done
that already. Did you check that the Blast does not crash when you run it
w/o mpi? I know that bad sequence inputs can cause BLAST to crash, or at
least used to.

  Eitan

--------------------
Eitan Rubin, PhD
Head of Bioinformatics
The Bauer Center for Genomics Research
Harvard University
Tel: 617-496-5649 Fax: 617-495-2196

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Today's Topics:

   1. Re: Problems with mpiblast1.3 (Aaron Darling)
   2. Re: Login & home directory strategies for PVM? (Tim Cutts)
   3. First CFP Int. Workshop on Natural Artificial Immune	Systems
      '05 (Simone Bassis)
   4. Re: Problems with mpiblast1.3 (Celeste vikram)

----------------------------------------------------------------------

Message: 1
Date: Sun, 06 Feb 2005 15:48:29 -0600
From: Aaron Darling <darling at cs.wisc.edu>
Subject: Re: [Bioclusters] Problems with mpiblast1.3
To: "Clustering,	compute farming & distributed computing in life
	science informatics"	<bioclusters at bioinformatics.org>,
mpiblast
	<mpiblast-users at lists.sourceforge.net>, celeste_tikoo at yahoo.com
Message-ID: <420690AD.7030307 at cs.wisc.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi, based on the call stack it looks like LAM is crashing during 
initialization (MPI_Init()).  I can't imagine why mpiblast would cause 
such behavior.  Do other parallel applications exhibit similar behavior?
Perhaps you need to clean your LAM environment after a previous crash?  
I think there's a program called lamclean or something.  Maybe somebody 
else could comment--I'm mostly an mpich user.

-Aaron

Celeste vikram wrote:

> Hi,
>  
> Sometimes I get some errors while running mpiblast1.3...Any help would 
> be appreciated.
>
----------------------------------------------------------------------------
------------------------------------
> MPI_Recv: process in local group is dead (rank 1, MPI_COMM_WORLD)
> Rank (1, MPI_COMM_WORLD): Call stack within LAM:
> Rank (1, MPI_COMM_WORLD):  - MPI_Recv()
> Rank (1, MPI_COMM_WORLD):  - MPI_Allreduce()
> Rank (1, MPI_COMM_WORLD):  - MPI_Comm_split()
> Rank (1, MPI_COMM_WORLD):  - MPI_Init()
> Rank (1, MPI_COMM_WORLD):  - main()
> MPI_Recv: process in local group is dead (rank 2, MPI_COMM_WORLD)
> Rank (2, MPI_COMM_WORLD): Call stack within LAM:
> Rank (2, MPI_COMM_WORLD):  - MPI_Recv()
> Rank (2, MPI_COMM_WORLD):  - MPI_Allreduce()
> Rank (2, MPI_COMM_WORLD):  - MPI_Comm_split()
> Rank (2, MPI_COMM_WORLD):  - MPI_Init()
> Rank (2, MPI_COMM_WORLD):  - main()
> MPI_Recv: process in local group is dead (rank 3, MPI_COMM_WORLD)
> Rank (3, MPI_COMM_WORLD): Call stack within LAM:
> Rank (3, MPI_COMM_WORLD):  - MPI_Recv()
> Rank (3, MPI_COMM_WORLD):  - MPI_Allreduce()
> Rank (3, MPI_COMM_WORLD):&n bsp; - MPI_Comm_split()
> Rank (3, MPI_COMM_WORLD):  - MPI_Init()
> Rank (3, MPI_COMM_WORLD):  - main()
>
----------------------------------------------------------------------------
-
> One of the processes started by mpirun has exited with a nonzero exit
> code.  This typically indicates that the process finished in error.
> If your process did not finish in error, be sure to include a "return
> 0" or "exit(0)" in your C code before exiting the application.
>  
> PID 17770 failed on node n0 (40.191.22.1) due to signal 15.
>
----------------------------------------------------------------------------
--------------------------
>  
> Thx,
> Cel
>
> ------------------------------------------------------------------------
> Do you Yahoo!?
> Yahoo! Search presents - Jib Jab's 'Second Term' 
>
<http://us.rd.yahoo.com/evt=30648/*http://movies.yahoo.com/movies/feature/ji
bjabinaugural.html> 
>
>
>------------------------------------------------------------------------
>
>_______________________________________________
>Bioclusters maillist  -  Bioclusters at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bioclusters
>  
>

------------------------------

Message: 2
Date: Mon, 7 Feb 2005 09:14:12 +0000
From: Tim Cutts <tjrc at sanger.ac.uk>
Subject: Re: [Bioclusters] Login & home directory strategies for PVM?
To: "Clustering,	compute farming & distributed computing in life
	science informatics"	<bioclusters at bioinformatics.org>
Message-ID: <9d2c2abe9606139fefdacdbfc41aaf84 at sanger.ac.uk>
Content-Type: text/plain; charset=US-ASCII; format=flowed

On 6 Feb 2005, at 11:04 am, Tony Travis wrote:

> Hello, Tim.
>
> We only have a 'small' 64-node cluster here :-)
>
> However, I've opted to use BOBCAT architecture:
>
> 	http://www.epcc.ed.ac.uk/bobcat/
>
> Although the original EPCC BOBCAT no longer exists, it's spirit lives 
> on in our RRI/BioSS cluster:
>
> 	http://bobcat.rri.sari.ac.uk
>
> The important thing is to have TWO completely separate private network 
> fabrics: One for DHCP/NFS, the other for IPC. The main problem we have 
> is that IPC (i.e. Inter Process Communication) can swamp the bandwidth 
> of a single network fabric and you rapidly lose control of the 
> cluster.

We don't have any IPC.  We don't run any parallel code.  Each job runs 
on a single CPU.  And NFS *still* causes problems, occasionally.  It 
really isn't a myth at this scale.  It's unusable.  For example, we 
have to make separate copies of the LSF binaries on all of the 
machines, because to do it the Platform-endorsed way, with everything 
NFS mounted, is a bit flakey.  The NFS contention from LSF's house 
keeping alone can be enough to break the cluster.

I suspect if you're running large parallel jobs, then the number of NFS 
operations involved is relatively low.  The issue for us is sometimes 
hundreds of jobs completing every minute, all trying to read some data 
files and then create three or four output files on an NFS mounted 
disk.  That's a lot of separate NFS operations, a large proportion of 
which are the particularly painful directory operations.  I plead with 
the users not to write code like this, but you know what users are 
like.

> I think there are some MYTHS about NFS and clusters around because of 
> the bandwidth contention on a single network fabric. The NFS network 
> traffic on our cluster is completely segregated from the IPC traffic 
> which is throttled by the bandwidth of its own network fabric. The 
> switches on the two network fabrics are NOT connected in any way...

Our approach is actually similar to yours; we're moving towards cluster 
filesystems like GPFS and Lustre, and in those cases, we run the 
cluster filesystem traffic over a second network.  It's actually a VLAN 
on the same switches, but that's not the performance problem you might 
think because the Extreme switches we use are fully non-blocking.  You 
can throw an absolutely obscene number of packets at them and they cope 
fine.  Even when a Ganglia bug caused a machine to emit thousands of 
multicast packets to all 1000 machines every second.  The ganglia 
daemons went into 100% CPU coping with the incoming packets, which made 
the cluster almost unusable, but the network itself was still going 
strong.

Tim

-- 
Dr Tim Cutts
Informatics Systems Group, Wellcome Trust Sanger Institute
GPG: 1024D/E3134233 FE3D 6C73 BBD6 726A A3F5  860B 3CDD 3F56 E313 4233

------------------------------

Message: 3
Date: Mon, 7 Feb 2005 13:33:52 +0100
From: Simone Bassis <bassis at dsi.unimi.it>
Subject: [Bioclusters] First CFP Int. Workshop on Natural Artificial
	Immune	Systems '05
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Apologies if you receive this more than once.
                         =================
                          Call for Papers

   International Workshop on Natural and Artificial Immune Systems (NAIS
 2005)

              Vietri sul Mare, Salerno, Italy, June 9-10, 2005

        http://siren.dsi.unimi.it/conferences/IMMUNE05/html/index.html

* Venue
   International Institute For Advanced Scientific Studies (IIASS),
   "E.R.Caianiello", Vietri sul Mare, (SA) Italy.
   http://www.iiassvietri.it/index.html
   http://www.iiassvietri.it/school2004/

* Important Dates
   Submission deadline:               March 25, 2005
   Acceptance/Rejection notification: April 25, 2005
   Camera-ready copy of papers:       June 6, 2005
   Workshop Date:                     June 9-10, 2005

* Aims and Scope
The workshop aims at catalyzing the interaction between modelers (computer
scientists, mathematicians and physicists), immunologists and biologists
interested in discussing the information processing mechanisms emerging in
 the functionalities of either natural or artificial immune systems.
The leading idea motivating this event is the attention to the various forms
 of "intelligent thinking" underlying the many attack/defense/adaptation
 strategies discovered in natural systems, such as tumor and virus escape
 mechanisms of animals and humans, or implemented in artificial systems.

This approach may reap several basic benefits of the original cybernetics
paradigm:
 -the emergence of the mind from chemical-physical reactions that can be
 studied and simulated,
 - the use of natural processing mechanisms for solving artificial problems,
 and the cross-fertilization of the natural and artificial research
 environments, -the adoption of comprehensive immune system models in the
 development of new therapeutic approaches.

Possible topics include, but are not limited to:
# Computational Immunology
# Immunological Computation
# Immunoinformatics
# modelling and simulation of immune systems
# model testing and game theory
# biological and immersive learning
# network security and artificial virus attacks
# comparisons between Artificial Immune Systems and other
 biologically-inspired paradigms
# theory and applications of Immunological Computing
# Immunocomputing

* Invited speakers
 -  Franco Celada, University of Genova, Italy
 -  Vincenzo Cutello, University of Catania, Italy
 -  Dipankar Dasgupta, University of Memphis, USA
 -  Doheon Lee, IBM-KAIST Bio-Computing Research Center, Korea
 -  John Timmis, Universityh of Kent, UK

* Conference Proceedings
The conference will feature both introductory tutorials and original
refereed
papers, to be published by an international publisher.
See details of electronic submission on the bottom of the web page:
http://siren.dsi.unimi.it/conferences/IMMUNE05/html/index.html

* Conference Chairs:
 - Bruno Apolloni, University of Milano, Italy.
   apolloni at dsi.unimi.it
 - Alberto Clivio, University of Milano, Italy.
   alberto.clivio at unimi.it
 - Vincenzo Cutello, University of Catania, Italy.
   cutello at dmi.unict.it
 - Giuseppe Nicosia, University of Catania, Italy.
   nicosia at dmi.unict.it

Programme Committee:
 - Franco Celada, University of Genova, Italy
 - Dipankar Dasgupta, University of Memphis, USA
 - Marco Gori, University of Siena, Italy
 - Doheon Lee, IBM-KAIST Bio-Computing Research Center, Korea
 - Piero Mussio, University of Milano, Italy
 - Anastasia Pagnoni, Unversity of Milano, Italy
 - John Timmis, Universityh of Kent, UK
 - Henry Linger, Monash University, Melbourne, Australia

* Getting Vietri Sul Mare
http://www.iiassvietri.it/school2004/getting_vietri.htm

* NAIS 2005 Conference Secretariats:
  - Department of Mathematics and Computer Science
    University of Catania,
    City University,
    V.le A. Doria 6, 95125 Catania, Italy
    Email: nais05 at dmi.unict.it
    Phone: +39-095-7383074
    Fax:   +39-095-330094

   or

  - Dip. di Scienze Dell'Informazione.
    University of Milano
    Via Comelico, 39
    20125 Milano, Italy
    Email: bassis at dsi.unimi.it
    Phone: +39-02-50316335
    Fax:   +39-02-50316228

* For additional information or questions, contact
  Alberto Clivio, University of Milano, Italy, alberto.clivio at unimi.it
  Giuseppe Nicosia, University of Catania, Italy, nicosia at dmi.unict.it

------------------------------

Message: 4
Date: Sun, 6 Feb 2005 23:20:54 -0800 (PST)
From: Celeste vikram <celeste_tikoo at yahoo.com>
Subject: Re: [Bioclusters] Problems with mpiblast1.3
To: Aaron Darling <darling at cs.wisc.edu>, "Clustering,	compute farming
	& distributed computing in life science informatics"
	<bioclusters at bioinformatics.org>, 	mpiblast
	<mpiblast-users at lists.sourceforge.net>
Message-ID: <20050207072054.16113.qmail at web61305.mail.yahoo.com>
Content-Type: text/plain; charset="us-ascii"

Thanks Aaron.

The program is called lamwipe but it doesn't help at all. I still run into
these errors very very frequently. On the rare occasions when mpiblast works
,it takes an awful lot of time !!

btw, Is mpich an alternative to lam-mpi ?

-Cel.

Aaron Darling <darling at cs.wisc.edu> wrote:
Hi, based on the call stack it looks like LAM is crashing during 
initialization (MPI_Init()). I can't imagine why mpiblast would cause 
such behavior. Do other parallel applications exhibit similar behavior?
Perhaps you need to clean your LAM environment after a previous crash? 
I think there's a program called lamclean or something. Maybe somebody 
else could comment--I'm mostly an mpich user.

-Aaron

Celeste vikram wrote:

> Hi,
> 
> Sometimes I get some errors while running mpiblast1.3...Any help would 
> be appreciated.
>
----------------------------------------------------------------------------
------------------------------------
> MPI_Recv: process in local group is dead (rank 1, MPI_COMM_WORLD)
> Rank (1, MPI_COMM_WORLD): Call stack within LAM:
> Rank (1, MPI_COMM_WORLD): - MPI_Recv()
> Rank (1, MPI_COMM_WORLD): - MPI_Allreduce()
> Rank (1, MPI_COMM_WORLD): - MPI_Comm_split()
> Rank (1, MPI_COMM_WORLD): - MPI_Init()
> Rank (1, MPI_COMM_WORLD): - main()
> MPI_Recv: process in local group is dead (rank 2, MPI_COMM_WORLD)
> Rank (2, MPI_COMM_WORLD): Call stack within LAM:
> Rank (2, MPI_COMM_WORLD): - MPI_Recv()
> Rank (2, MPI_COMM_WORLD): - MPI_Allreduce()
> Rank (2, MPI_COMM_WORLD): - MPI_Comm_split()
> Rank (2, MPI_COMM_WORLD): - MPI_Init()
> Rank (2, MPI_COMM_WORLD): - main()
> MPI_Recv: process in local group is dead (rank 3, MPI_COMM_WORLD)
> Rank (3, MPI_COMM_WORLD): Call stack within LAM:
> Rank (3, MPI_COMM_WORLD): - MPI_Recv()
> Rank (3, MPI_COMM_WORLD): - MPI_Allreduce()
> Rank (3, MPI_COMM_WORLD):&n bsp; - MPI_Comm_split()
> Rank (3, MPI_COMM_WORLD): - MPI_Init()
> Rank (3, MPI_COMM_WORLD): - main()
>
----------------------------------------------------------------------------
-
> One of the processes started by mpirun has exited with a nonzero exit
> code. This typically indicates that the process finished in error.
> If your process did not finish in error, be sure to include a "return
> 0" or "exit(0)" in your C code before exiting the application.
> 
> PID 17770 failed on node n0 (40.191.22.1) due to signal 15.
>
----------------------------------------------------------------------------
--------------------------
> 
> Thx,
> Cel
>
> ------------------------------------------------------------------------
> Do you Yahoo!?
> Yahoo! Search presents - Jib Jab's 'Second Term' 
> 
>
>
>------------------------------------------------------------------------
>
>_______________________________________________
>Bioclusters maillist - Bioclusters at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bioclusters
> 
>

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End of Bioclusters Digest, Vol 4, Issue 7
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