Thank you for the reply and questions.
I have 8 cores. I used 8 processors earlier.
I reran 'make test' this afternoon with 4 processors.
I obtained a different result.
The tests ran to completion without hanging.
The 'mwabmd' test case would not run because it required 8 threads.
Perhaps these new results help pinpoint the problem.
1) which mpi am I using?
/opt/local/bin/mpicc --version
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin14.5.0
Thread model: posix
/opt/local/bin/mpif90 --version
GNU Fortran (MacPorts gcc49 4.9.4_1) 4.9.4
Copyright (C) 2015 Free Software Foundation, Inc.
2) what was my $DO_PARALLEL environment variable?
export DO_PARALLEL='mpirun -np 8; make test
When I reran it this afternoon with 4 processors,
export DO_PARALLEL='mpirun -np 4'; make test
"""
.
.
.
==============================================================
diffing save.pmemd/work.txt with work.txt
PASSED
==============================================================
>>>>>>> doing 'mwabmd'
This test case (/Users/blaine-mooers/software/Amber16/test/nfe/mwabmd) requires 8 mpi threads.
Not running test, exiting .....
Finished parallel test suite for Amber 17 at Sat Apr 22 15:06:52 CDT 2017.
Some tests require 4 threads to run, while some will not
run with more than 2. Please run further parallel tests with the
appropriate number of processors. See /Users/blaine-mooers/software/Amber16/test/README.
164 file comparisons passed
0 file comparisons failed
2 tests experienced an error
Test log file saved as /Users/blaine-mooers/software/Amber16/logs/test_amber_parallel/2017-04-22_15-03-50.log
No test diffs to save!
Summary of AmberTools parallel tests:
915 file comparisons passed
0 file comparisons failed
0 tests experienced errors
Test log file saved as /Users/blaine-mooers/software/Amber16/logs/test_at_parallel/2017-04-22_14-43-02.log
No test diffs to save!
"""
Best regards,
Blaine
Blaine Mooers, Ph.D.
Assistant Professor
Department of Biochemistry and Molecular Biology, College of Medicine
University of Oklahoma Health Sciences Center
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Faculty webpage X-ray lab (LBSF) Molecular Graphics Links Small Angle Scattering
office: (405) 271-8300 lab: (405) 271-8313 e-mail: blaine-mooers.ouhsc.edu
________________________________________
From: David Case [david.case.rutgers.edu]
Sent: Friday, April 21, 2017 8:42 PM
To: AMBER Mailing List
Subject: Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10
On Fri, Apr 21, 2017, Mooers, Blaine H.M. (HSC) wrote:
> I installed amber17tools and amber16 on a Mac OS X 10.10 with macports python 2.7.13
>
> ./configure -mpi -macAccelerate --with-python /opt/local/bin/python
The key here is probably neither python nor pnetcdf, but MPI: which mpi
are you using?
> I got a warning about needing parallel netcdf, which is not in macports.
Sigh...we need to reword this. Most users will never need parallel netcdf
support, and cpptraj.MPI will build fine without it. But I agree that the
message currently emitted is not very clear about that.
>
> After passing 731 file comparisons, the following message was printed
> and the program hung for several hours.
> """
> Testing AMD with IPS
This is a serious problem, that was not encountered during our testing.
In addition to reporting on what mpi you are using, let us know what
your DO_PARALLEL environment variable was. We'll have to try to reproduce
this problem.
Thanks for the report....dac
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Received on Sat Apr 22 2017 - 14:30:02 PDT
