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.
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