Hi there,
I'm a HPC systems administrator trying to setup Phenix and Rosetta for use with MR Rosetta. I find that the MR Rosetta test suite (phenix_regression.wizards.test_command_line_rosetta_quick) fails at test_fixed_model with the following error in Rosetta:
...
protocols.hybridization.CartesianHybridize: CYCLE 1
protocols.hybridization.CartesianHybridize: setting bonded weight = 0
protocols.hybridization.CartesianHybridize: setting bonded angle weight = 0
protocols.hybridization.CartesianHybridize: setting bonded length weight = 0
protocols.hybridization.CartesianHybridize: setting bonded torsion weight = 0
protocols.hybridization.CartesianHybridize: setting cst weight = 0
protocols.hybridization.CartesianHybridize: setting vdw weight = 0.1
ERROR: conformation.size() >= seqpos
ERROR:: Exit from: src/core/conformation/util.cc line: 308
protocols.jd2.JobDistributor:
...
The full log is attached.
We are running RHEL 6.3, Rosetta (2014.22.56873) was compiled with GCC 4.4.6 (no warnings). I've tried more recent versions of GCC which have resulted in compile warnings for Rosetta, and I've tried both binary and compiled versions of Phenix (1.9-1692). Rosetta unit tests seemed to all be ok.
If you believe this to be a Phenix issue, please let me know and I'll contact them
Cheers
| Attachment | Size |
|---|---|
 Error from test_fixed_model in phenix_regression.wizards.test_command_line_rosetta_quick | 16.14 KB |
Just an update in case this is of use to anyone else.
Using a previous release of Rosetta (3.5) and using GCC 4.4.6 works with Phenix 1.9-1692 on RHEL 6.3 and all tests pass on phenix_regression.wizards.test_command_line_rosetta_quick
However the following components of the integration test suite fail when Rosetta 3.5 is compiled with MPI support:
Running test_relax
------------------------------------------------------------
Numbers do not match: 6 1
Relaxed solutions 6
---
Relaxed solutions 1
------------------------------------------------------------
FAILED
See log files test_relax/test_relax.log test_relax/test_relax_current.log
=================================================================
Running test_relax_double
------------------------------------------------------------
Numbers do not match: 6 1
Relaxed solutions 6
---
Relaxed solutions 1
------------------------------------------------------------
------------------------------------------------------------
Numbers do not match: 6 1
Relaxed solutions 6
---
Relaxed solutions 1
------------------------------------------------------------
FAILED
See log files test_relax_double/test_relax_double.log test_relax_double/test_relax_double_current.log
=================================================================
Running test_relax_no_sol
------------------------------------------------------------
Numbers do not match: 6 1
Relaxed solutions 6
---
Relaxed solutions 1
------------------------------------------------------------
FAILED
See log files test_relax_no_sol/test_relax_no_sol.log test_relax_no_sol/test_relax_no_sol_current.log
A sample of the error logs have been attached.
Any help or suggestions are appreciated.