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 [EMAIL PROTECTED] ------------------------------------------------------- This SF.Net email is sponsored by: Power Architecture Resource Center: Free content, downloads, discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl _______________________________________________ Oscar-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/oscar-devel
