26 Feb

New Cluster Build – Finishing Touches and Beta Launch

Boqueron

We are pleased to announce that our new cluster build has been making great strides lately and that we expect our new cluster to be up and running by sometime next week (finally!).  We can now reveal that the name of our new cluster will be Boqueron (pronounced boh-keh-ron) and that it will initially feature over 2200 computation cores, and 200 TB of /work space served over a 10Gbps and QDR Infiniband backbone.

Registered users should soon be receiving email messages with details on logging in to Boqueron.  When the cluster launches, however, you might notice that not all the software you used on Nanobio is readily available on Boqueron.  This is by design.  Instead of importing all the software on Nanobio that users may or may not actually use, we want you to request the software that you will actually use so that we can have a sort of clean slate with Boqueron.  In that sense, Boqueron’s launch will be like a sort of beta launch.

What this means for you

We need our users to request the software that they will actually use on Boqueron.  You can either wait until the launch of the new cluster to do so, or you can do so right now.  Just drop us a line at help@hpcf.upr.edu with the subject line

[Boqueron Software Request]

and we will queue your requested software for installation.  We can’t guarantee that all the requested software will be available at launch time, but the sooner you request it, the sooner it’ll be installed.

A note on license-based software

All software has a license of some sort.  However, some licenses are more restrictive than others.  These “more-restrictive-license” software is what I refer to as “license-based software”.  License-based software might take a bit longer to be available on Boqueron precisely because of their more restrictive and sometimes for-profit nature.  Some vendors will readily transfer our Nanobio licenses to be used on Boqueron, but others have much stricter processes and policies that will make their transfer over to Boqueron slower.  We ask for your patience with the availability of these software.

You might be wondering: “Well, why did you wait until the cluster was ready to launch to deal with the licenses?”  The answer is that we have to wait until out system is actually up and running before we can ask vendors to authorize it for running their software.  We can’t ask vendors to authorize a machine that doesn’t exist yet.

What software is currently available on Boqueron?

Just like in Nanobio, once you log in to Boqueron, you can run

$ module avail

to see what software is currently installed on Boqueron.  I will offer a preview, however, of software that is already installed so that you don’t have to request it.

gcc/5.1.0
openmpi/1.8.8
samtools 1.2
bcftools 1.2
bowtie2 2.2.6
boost (headers only) 1.59.0
python2 2.7.11
python3 3.5.1
pip2 7.1.2
jdk 1.8.0_65
R 3.2.3
trinityrnaseq 2.1.1
dsk 2.0.7
kanalyze 0.9.7
jellyfish 2.2.4
tophat 2.1.0
gatk/queue 3.5
trinotate 2.0.2
ncbi-blast+ 2.2.31
hmmer 3.1b2
signalp 4.1
tmhmm 2.0c
rnammer 1.2
Blast+ dbs:
 - SwissProt
 - Uniref90
HMMER dbs:
 - Pfam-A

Do you have documentation on Boqueron available?

Boqueron’s documentation is still a work in progress, but you are free to browse it if you wish to start becoming familiar with the new cluster.  It’s available here.

As always, we’d like to remind you that any dates we give for the new cluster are always subject to change.  That’s just the nature of working with computer resources.  Unforeseen circumstances always come up.  We thank you for your patience throughout this long process.  If you have any further questions or comments, feel free to contact us at help@hpcf.upr.edu.