Re: [AMBER-Developers] Amber test concerns

From: B. Lachele Foley <>
Date: Thu, 20 Jan 2011 01:24:24 +0000

There have been a number of major changes lately with sleap. The tests might not be keeping up. Our group is testing the changes now. So far, they're looking good. As soon as we lay off Wei for a day or two, he'll probably fix the tests. I'll be sure to give that test a thorough check, tho. Is this behavior different on x86_64 than elsewhere?

:-) Lachele

Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA

From: Jason Swails []
Sent: Wednesday, January 19, 2011 6:12 PM
To: AMBER Developers Mailing List
Subject: [AMBER-Developers] Amber test concerns


I've tested both Amber and AmberTools from a recent git checkout and I've
summarized what I think the major issues are below:

Linux x86_64:

AmberTools (serial):

sleap/glycam && ./Run.test1 -- n.pdb is completely different now, and
there's another proton attached somewhere as well. Is this an intentional

Amber (serial):

sander_pbsa_ipb2 && ./Run.110D.min -- some numbers are significantly
different, but it may be benign
rism3d/ala && ./Run.ala.hnc && ./Run.ala.pse1 -- exits in error with sander
printing the message [ ERROR> solvcut must > 0. ]

Amber (parallel, 2 threads):

All sander.RISM.MPI tests failed with the message [ Fatal error in
MPI_Comm_rank: Invalid communicator, error stack: ]
All EVB tests failed with the error messages:
rank 1 in job 616 Batman_45773 caused collective abort of all ranks
  exit status of rank 1: killed by signal 11
rank 0 in job 616 Batman_45773 caused collective abort of all ranks
  exit status of rank 0: killed by signal 9

(This has been happening for a long time with the EVB tests -- even with the
Amber 11 release)

I'll follow up with relevant (different) Mac OS X failures later.

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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Received on Wed Jan 19 2011 - 17:30:05 PST
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