R Installation Procedure

The following procedures will lead to a working R installation (complete with rsnow and rmpi):

0) Wherever you see the word 'version' in the following instructions, replace it with the applicable version number
1) Download the latest R from here
2) Uncompress
3) type

$ ./configure --prefix=/usr/local/R-version CFLAGS=-O3 FFLAGS=-O3 && make && sudo make install

4) R should now be successfully installed in /usr/local/R-version
5) Download the latest snow and rmpi from here
6) Install snow like this:

$ sudo /usr/local/R-version/bin/R CMD INSTALL snow_version.tar.gz

7) Now install Rmpi

sudo /usr/local/R-version/bin/R CMD INSTALL rmpi_version.tar.gz --configure-args="--with-mpi=/usr/local/lam-version CC=mpicc"

8) All done, should be good to go.

Long time no update . . .

We haven't updated the blog in a few months, but I assure you, we have been quite busy. Hopefully we can post our updates here (if we remember them!).

On the new cluster, I recompiled the linux kernel and exluded the ethernet driver for the ethernet port that contains the management card. We decided to use both ethernet ports since we have the management card installed. It is possible to have the management card and linux use the same ethernet port, but it requires a software solution that would probably break quite easily.

It was necessary to exclude the ethernet driver because merely disabling that ethernet card within linux worked only for that one machine; as soon as we imaged the other machines, it was reenabled. Sometimes, as well, eth0 would show up as eth1, and eth1 would show up as eth0. Headaches all around.

With that change, the 'new' cluster is completely ready to go (outside of software being installed). And so is the old cluster, which our senior capstone course is actively working on. One group is working on things related to BLAST, and one group is working on R.

One issue at the moment that we are running into is that we cannot seem to compile WWWBLAST. It doesn't happen when we do ncbi/make/makedis.csh, as per the instructions. So we're tracking that down. There are precompiled binaries around, but they are for every platform except ppc-linux (there's ppc64 linux though . . . ).

Rmpi and whatnot is just getting up and running, so we'll be able to propogate this new software soon.