[phenixbb] Phenix-Rosetta integration tests fail with Rosetta MPI on RHEL 6.3

Terwilliger, Thomas Charles terwilliger at lanl.gov
Thu Sep 11 06:48:10 PDT 2014


i Sina,

Thanks for the question!   We have not tried Phenix mr_rosetta with Rosetta MPI so I am not too surprised that it did not work.  We have focused our effort on making it work with clusters using qsub and similar commands. Normally an individual Rosetta job does not take a really long time; rather it is the many Rosetta jobs that collectively take a long time.  Consequently using MPI to parallelize individual jobs seems to me to be likely to take about the same clock time as using many individual processors for separate jobs.  

I'll check on the Rosetta error that you mention separately.

All the best,
Tom T
  

  
________________________________________
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Sina Masoud-Ansari [s.ansari at auckland.ac.nz]
Sent: Wednesday, September 10, 2014 10:29 PM
To: phenixbb at phenix-online.org
Subject: [phenixbb] Phenix-Rosetta integration tests fail with Rosetta MPI      on RHEL 6.3

Hi there,

I'm wondering anyone has managed to successfully run Phenix with Rosetta
MPI on Red Hat Enterprise Linux 6.3 or similar?

I currently have a non-MPI build of Rosetta that passes all of the tests
in phenix_regression.wizards.test_command_line_rosetta_quick

However when running these tests with the MPI build of Rosetta the
following tests fail:

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

I have attempted to attach an archive of the logs.

I'm working with Rosetta 3.5, more recent versions of Rosetta fail other
tests in phenix_regression.wizards.test_command_line_rosetta_quick ,
please see https://www.rosettacommons.org/node/3721 for details.

Rosetta 3.5 was compiled with GCC 4.4.6 using OpenMPI 1.6.4

Any help or advice is appreciated.

--
Sina Masoud-Ansari
Centre for eResearch
409.G21 24 Symonds Street
University of Auckland

e: s.ansari at auckland.ac.nz
p: +64 9 3737599 ext 89369
w: http://www.eresearch.auckland.ac.nz



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