Sorry. I should have said mpiBLAST requires *at least* four machines.
The config.xml is in the tarball in the repository. It looks like the
link to the repository was mangled by the period at the end of the
sentence in my last message. Here is the URL:
http://oscar-devel.cs.usd.edu/repository
I have also posted config.xml below.
<?xml version="1.0" encoding="ISO-8859-1"?>
<oscar>
<name>mpiblast</name>
<version>
<major>1</major>
<minor>4</minor>
<subversion>0</subversion>
<release>2</release>
<epoch>0</epoch>
</version>
<class>third-party</class>
<summary>Open Source Parallel BLAST</summary>
<license>GPL</license>
<group>Application</group>
<url>http://mpiblast.lanl.gov/</url>
<maintainer>
<name>Los Alamos National Laboratory</name>
</maintainer>
<packager>
<name>Doug Jennewein</name>
<email>[EMAIL PROTECTED]</email>
</packager>
<description>mpiBLAST is a freely available open source parallelization
of NCBI BLAST.
mpiBLAST segments the BLAST database and distributes it across cluster
nodes, permitting
BLAST queries to be processed on many nodes simultaneously. mpiBLAST is
based on MPI.
The current release runs under Linux and Windows, and will probably work
on other varieties
of Unix as well.
RPMs for mpiblast and the NCBI toolkit are provided by Joe Landman of
Scalable Informatics.</description>
<rpmlist>
<rpm>mpiblast_mpich-1.4.0-2oscar</rpm>
<rpm>mpiblast_lam-1.4.0-2oscar</rpm>
<rpm>NCBI-2.2.11-2oscar</rpm>
<rpm>mpiblast-oscar-wrapper-1.0-1oscar</rpm>
<rpm>mpiblast-modulefile-1.4.0-1oscar</rpm>
</rpmlist>
</oscar>
-Doug
John Mugler wrote:
Can you send me or post your config.xml file? There should be a
workaround for the install/uninstall package problem...basically, it
has to do with rpm dependancies and what you put in that file. And yes
the infrastructure is being overhauled to fix problems like that.
Are you hardcoded in some manner for 4 compute nodes? This doesn't sound
reasonable as an oscar cluster could be from 1 to N compute nodes.
-- John
On Wed, 28 Sep 2005, Doug Jennewein wrote:
I have been developing an OSCAR package for mpiBLAST using Joe
Landman's RPMs from http://downloads.scalableinformatics.com/. The
package includes the NCBI toolkit as well as mpiBLAST compiled for
both MPICH and LAM. A simple wrapper script is used to execute the
correct version for the currently-selected MPI implementation (based
on switcher settings). I have been testing with OSCAR 4.1 and FC2 and
have set up a repository at
http://oscar-devel.cs.usd.edu/repository. Any feedback from other
platforms would be greatly appreciated. mpiBLAST requires four
machines -- headnode + 3 compute nodes. Here are the issues I have
noticed so far:
1) The 'Install/Uninstall OSCAR Packages' button works for
uninstalling the package, but it fails when trying to re-install the
package. It says that the clients can't find the RPMs necessary to
install the package. According to Bernard this is because mpiBLAST
requires some other RPM which may not be installed on the
image/compute node, and there is no RPM repository to download and
install the necessary RPMs. He said that fundamental changes to the
OSCAR infrastructure are necessary to support that, and that such
changes are in the works for OSCAR 5.
2) When the clients try to mount /opt/mpiblast/shared they display an
error stating that the nfs server is down. After some experimenting
I am pretty sure that this has to do with running 'service nfs
restart' during post_install. I checked to ensure that the nfs and
portmap services were running on oscarserver and even restarted them,
but the clients still couldn't mount. The only way I can get the
clients to mount is to reboot oscarserver. Via google I found many
suggestions to append '-o nfsvers=2' to the mount command, but that
did not work. It looks like this might be an FC2-specific problem --
Bernard did not experience this problem on RHEL4.
--
Doug Jennewein
Research Analyst
Department of Computer Science
University of South Dakota
Vermillion, SD 57069
(605) 677-5388
(605) 677-6662 (fax)
[EMAIL PROTECTED]
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