Performance improvement in AbinitioRelax and relax 3.2 ???

[Anonymous]

I got the following benchmarks for AbinitioRelax and relax (version 3.2). The speed improvement I observed compared to 3.1 are so important that I am wondering if they are real. I would appreciate if someone could confirm that such improvement (3.2 vs 3.1) is really to be expected.

System : 90 residues protein

Protocols tested :

1. “AbinitioRelax -abinitio -out:nstruct 100”
2. “relax -relax” (3.1) or “relax -relax:thorough” (3.2) on above abinitio structures
3. “relax -relax:fast” on above abinitio structures

Benchmarks were all done on a single node (dual Intel Nahalem-EP at 2.8 GHz, 24 GB RAM, ), with a single process per node (i.e. yes, I am wasting 7 cores… until I get the pseudo-mpi version of Rosetta compiled).
Linux r107-n37 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux

All compiles were static, gcc=4.4.2, and included the following CCFLAGS
CCFLAGS = -pipe -ffor-scope -W -Wall -pedantic -Wno-long-long –param inline-unit-growth=1000 –param large-function-growth=50000 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=1133 -s -Wno-unused-variable

The following computation times are average user cpu time in seconds/structure for the above three protocols.

Rosetta 3.1 : 26.2 – 84.0 – 30.2
Rosetta 3.2 : 19.8 – 28.2 – 10.2

-abinitio (centroid): 24% faster with Rosetta-3.2
-relax:thorough (3.2) vs -relax (3.1) : 66% faster with Rosetta-3.2
-relax:fast : 66% faster with Rosetta-3.2

I realize from the docs that the relax protocols have changed significantly in 3.2, but 66% faster is amazing.
Also, does anyone know if -relax (default in 3.1 is “slow”) is the same as -relax:thorough (in 3.2)?
Even the generation of low-res decoys (AbinitioRelax -abinitio) is quite faster in 3.2… is that normal?

Finally, it appears now that the full-atom refinement (step 2) is must faster than the initial generation of decoys (10.2 sec vs 19.8 sec per structure). Is that real?

Although the results look fine, I would appreciate if someone would confirm that the full-atom refinement is not so compute-intensive in Rosetta-3.2. If so, this is really great!

Cheers,

Stéphane

[Anonymous]

I think the old relax ‘fast’ mode became the new standard. Someone in the Baker lab did a LOT of benchmarking and found that the fast protocol was equally effective for the same amount of awesome.

I think the benefits are all in relax, not in abinitio. Abinitio is pretty fast anyway.

I’ve asked around to confirm.

[Author]

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