0.8.2

sequenceserver
#1

People,

I made another point release that:

* Makes sure SequenceServer always "jumps" to the result. Previously
SS would forget if you scrolled up to the search form and BLASTed
again; SS expected you to click back button before re-BLASTing.
* Lets you find out version number of SequenceSever installed by
running `sequenceserver -v`.
* Tightens dependency constraints, so we don't fail at runtime because
SS is seeing an incompatible version of its dependencies.

To update:

$ gem install sequenceserver

Let me know if you run into an issue with either of the fixes,
especially the last two.

Again, this was scheduled for 0.9.0, but I thought it would be better
to publish it as a minor release for you all to see instead of letting
the changes rot in the git repo till 0.9.0 is out.

Cheers!

#2

I just updated to 0.8.2 (mostly because I WANTED that multiprocessor support that came out in 0.8.1). The startup script I had been using to launch 0.8.0 didn’t work until I gave full read/write permissions to the Gemfile.lock in the new 0.8.2 directory - but I have to say it’s FANTASTIC seeing the increased speed of searching! Thanks, Anurag!

#3

Hi Anurag,

Upgraded from 0.8.0 to 0.8.2 without problems and I agree with wolfgang.rumpf, the speed-up is nice (nothing like throwing 30 cores at a BLAST+ search).

Cheers,

Halocaridina

#4

Okay, now I’m salivating. How did you get 30 cores to work together for BLAST? I’m assuming you have multiple boxes, and not just one ginormous box that somehow has 30 cores in it?

#5

Hi Wolfgang,

Its a single rack-mounted box running Scientific Linux 6.1 (a RHEL clone) with the following hardware layout:

/0/4 processor Intel(R) Xeon(R) CPU E7- 8870 @ 2.40GHz
/0/4/5 memory 640KiB L1 cache
/0/4/6 memory 2560KiB L2 cache
/0/4/7 memory 30MiB L3 cache
/0/8 processor Intel(R) Xeon(R) CPU E7- 8870 @ 2.40GHz
/0/8/9 memory 640KiB L1 cache
/0/8/a memory 2560KiB L2 cache
/0/8/b memory 30MiB L3 cache
/0/c processor Intel(R) Xeon(R) CPU E7- 8870 @ 2.40GHz
/0/c/d memory 640KiB L1 cache
/0/c/e memory 2560KiB L2 cache
/0/c/f memory 30MiB L3 cache
/0/10 processor Intel(R) Xeon(R) CPU E7- 8870 @ 2.40GHz
/0/10/11 memory 640KiB L1 cache
/0/10/12 memory 2560KiB L2 cache
/0/10/13 memory 30MiB L3 cache
/0/1b memory 256GiB System Memory

/0/100/7/0/2.3.0 disk 11TB MR9265-8i

Spec sheet for the Intel E7- 8870 is here:

http://ark.intel.com/products/53580/Intel-Xeon-Processor-E7-8870-(30M-Cache-2_40-GHz-6_40-GTs-Intel-QPI)

Each E7- 8870 has 10 cores/20 threads, so 40 cores/80 threads max can be thrown at any single job. Most of the work that the box does is RAM-intensive (Illumina assemblies de novo), so I decided to devote 3/4 of the 40 cores toward BLAST+.

Also compiled BLAST+ 2.2.26 from source using the following flags:

./configure --with-mt --prefix=/usr/local/genome/ncbi-blast-2.2.26+

Cheers,

Halocaridina