Member Site › Forums › Rosetta 3 › Rosetta 3 – General › Successful installation on OpenSuse11.1 – tests?
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Anonymous.
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August 19, 2010 at 7:30 am #654
Anonymous
I’ve got Rosetta 3.1 installed and running on my computer, and knowing (by experience,) that 2.3.x can’t install, how might I go about testing this build?
Running the benchmark python script gives no errors, and the Rosetta_demo downloads don’t have sample output files to compare my outputs with.
(mini-benchmark output)
benchmark: {
‘core_scoring_Score’:57.543596,
‘protocols_moves_SmallMover’:91.449715,
‘protocols_moves_ShearMover’:93.425838,
‘protocols_optimization_Minimizer_dfpmin’:173.554847,
‘protocols_optimization_Minimizer_dfpmin_armijo’:221.641852,
‘protocols_optimization_Minimizer_dfpmin_armijo_nonmonotone’:218.325644,
‘protocols_docking_DockingLowRes’:485.906367,
‘protocols_docking_DockingHighRes’:299.194699,
‘protocols_ligand_docking_LigandDockProtocol’:70.752422,
}thanks,
Poker. -
August 19, 2010 at 2:02 pm #4576
Anonymous
Your timing benchmarks are reasonable.
You can run the unit tests, and they should all pass. Compile them with “scons cat=test mode=release” and run them with “test/run.py -database (path)” from the main rosetta directory.
The integration tests do not ship with results because the actual results change from machine to machine – Rosetta is not deeply numerically stable against 32/64 bits and processor architectures. If you want, I can send you a copy of what they look like on my machine, but basically you can do this: compile with “scons bin mode=release” then cd test/integration and run “integration.py -d (database path)” to run the tests. You can then poke around in the ref directory created and look at the results; if they seem “complete” then you’re good. The integration tests are timed to run in less than a minute so they rarely give a “real” trajectory, but they should give complete trajectories which at least try out all parts of a protocol and print some result.
There are also scientific tests in test/scientific. I don’t know how to run them but they have instructions built in; post again if you need help with them and I’ll ask around.
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August 20, 2010 at 5:40 am #4579
Anonymous
Okay.
Some extra information:
– The final compile command is as follows, as the python interpreter cannot identify the openSuse distribution of gcc (installed with Yast, so its version identifier is different)
– scons bin mode=release -cxx=gcc -cxx_ver=4.3– I did run the unit tests, all 526 of 526 passes (although I did note that there was a lot of warnings in the tests about not being able to find atoms from whatever).
e.g.
“core.io.pdb.file_data: [ WARNING ] can’t find atom for res 188 atom CG1 (trying to set temp)”– those messages also appear in the integration, but otherwise most appears to have run and have spit out results.
“core.io.pdb.file_data: [ WARNING ] can’t find atom for res 71 atom 2HD2 (trying to set temp)”Running scientific tests now…
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August 20, 2010 at 1:32 pm #4580
Anonymous
Those warnings can be safely ignored. It’s a symptom of imperfectly prepared PDBs, not a flaw in your compilation.
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August 23, 2010 at 4:32 am #4582
Anonymous
Oh good. Scientific tests have also passed – don’t expect any more problems with the comparison run. So, it would seem that previous problems of 2.3.x with Suse was an unknown compiler/OS specific bug.
For future information:
– run log on Rosetta3.1/OpenSuse11.1 build using GCC (SUSE Linux) 4.3.2 and Python 2.6.– Scons version: v1.1.0.d20081104.r3765
– Two results are for single thread and -j2:
sequence_recovery:
the identity for all positions is: 32.9% / 33.4%
hydrophobic non-polar amino acids (VAL,ILE,LEU,MET,PHE,GLY,ALA,PRO,TRP,TYR): 45.4% / 46.3%
polar uncharged amino acid except CYS (SER,THR,ASN,GLN): 20.4% / 18.9%
negative charged amino acid(ASP,GLU): 19.8% / 20.4%
positive charged amino acid(ARG,LYS,HIS): 14.7% / 16.1%rna_denovo:
FARNA, 25th percentile rms (50 decoys): 2.39 / 2.40 [should be less than 3.00]
Hi-res refine, 25th percentile rms (50 decoys): 2.34 / 2.22 [should be less than 2.75]rna_design:
no base pairs, seq. recovery: 0.41 / 0.39 [should be more than 0.30]
Watson/Crick bp, seq. recovery: 0.44 / 0.43 [should be more than 0.35]
non-Watson/Crick bp, seq. recovery: 0.78 / 0.74 [should be more than 0.70]
all RNA, seq. recovery: 0.53 / 0.51 [should be more than 0.45]
All tests passed.
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