I am an admin for a large University Cluster. We are testing the idea of moving the cluster over to Gentoo as it has awsome development tools for biology programs. As such I have built several ebuild files to compile as of yet non-included programs (lamarc, r-project, etc) I was very excited to see that somebody had already done the ncbi-tools package. However, it appears that this package doesn't make use of the 'mpi' use flag to compile in mpiBLAST. I have a working ebuild that is designed with out cluster in mind (no non-x86 support) but it should be easy to see how I was able to get mpiBLAST to patch and compile. I will try and attach the ebuild I am using once I have submitted the report. Reproducible: Always Steps to Reproduce:
Created attachment 72409 [details] The hobbled together version of ncbi I am using now.
The web site for mpiBLAST is here: http://mpiblast.lanl.gov/Downloads.Archive.html Also, would there be interest in including my custom ebuild scripts in the main repository? I have added oommf, r-project, s3 (Stochastic Spatial), lamarc, pdsh, and I am sure that there will be dozens more where these came from.
Hi Brady, I wanted to have a look at MPI blast during the week-end, but it seems the download site is down... I am definitely interested in including this in our NCBI tools distribution, however. If you can put the source archive for the package somewhere on the Web, I will mirror it on the Gentoo infrastructure.
(In reply to comment #3) > Hi Brady, > > I wanted to have a look at MPI blast during the week-end, but it seems the > download site is down... I am definitely interested in including this in our > NCBI tools distribution, however. If you can put the source archive for the > package somewhere on the Web, I will mirror it on the Gentoo infrastructure. I have placed it on our local web server here. The URL is: http://styx.ibest.uidaho.edu/mpiblast/mpiBLAST-1.4.0.tgz The ebuild I am using should have a semi understandable walktrogh on installation. There is also an included install file that should help. Thanks for your help with this issue! Sorry I forgot to check and see if mpiBLAST was available =)
Thanks for your work, Brady. Your patch is now in Portage, and MPI BLAST seems to work great. alpha, sparc: I had to drop ~sparc and ~alpha from the ebuild. The alpha team needs to add MPI to its profiles' use.mask since there is no MPI library available on this arch. The sparc team needs to set the default virtual/mpi for sparc to sys-cluster/lam-mpi since the default sys-cluster/mpich isn't available on sparc. Thanks in advance,
mpi use.mask'd and re-keyworded ncbi-tools. Cheers, Ferdy
Virtual was corrected on sparc, so I readded the keyword.
