Re: [AMBER-Developers] 28 Mar release candidates for Amber11/AmberTools-1.4

From: case <>
Date: Tue, 30 Mar 2010 22:34:25 -0400

On Tue, Mar 30, 2010, Ben Roberts wrote:

> On Mac OS 10.6.2 with the Intel compilers (11.1.084) and their MKL libraries:

Thanks for the detailed reports. But I don't encourage others to follow
suit: by now there have been so many changes to the 28mar RC that it's
pointless to continue testing it. I'll issue an update soon.

Comments on what you found are below.

> Also, the tip5p test with PMEMD is missing these lines of output:
> EKCMT = 0.2373 VIRIAL = 15.5606 VOLUME = 0.0001
> Density = 0.0000
This has been seen lots, but is really low on the priority list.

> a symlink is made to the chamber directory.
Fixed in git.

> I second Dan's observation about numprocs.awk (which I resolved by
> linking to amber11/test/numprocs.awk) and testing the rism tests.
Fixed in git.

> Then, once the compilation was finished, with RISM, every single NAB
> test failed, with missing symbols:

This is weird, and not what I have seen. I'm assuming(?) you added -rismmpi
to the command line.

> * When running Make Clean before building in parallel, Make attempts to
> clean the directories sqm, rism, pbsa, blas, lapack and arpack - but
> because they don't exist (except in tools) and aren't preceded by a
> minus sign, it throws up its hands and quits.
fixed in git.

> * The test Run.dhfr.noboxinfo, though it passes, produces an MPI error.
Fixed in git.

> * On any number of CPUs, with the solvent cap test I put in rdparm.f,
> the test Run.pb_ivcap0 now fails. (Was I over-zealous by taking out
> PB as well as GB?) Also, this failure causes test.sander.BASIC to
> stop. Which is strange; I had thought "make -k" would be implied.

This test has been removed. The makefiles have all been updated to ensure
that all tests are run (make -k is indeed not enough).

> * On 2 CPUs, the test
> evb/malon_dbonds_umb_dg_UFF_3DG_qi_full_2D-PMF/Run.evb segfaults, as
> does evb/malon_dbonds_umb_dg_UFF_3DG_qi_full_corrF/Run.evb.

This is bug 129, I believe. There are a number of posts that indicate that
we are close to fixing this problem.

> * On 4 CPUs, the following tests failed:
> - ti_decomp/Run.ti_decomp (differences are attached)

> - neb-testcases/neb_gb_partial/Run.neb_gb_partial (cat: illegal option -- a)
> - neb-testcases/neb_gb_full/Run.neb_gb_full (cat: illegal option -- a)
> - neb-testcases/neb_explicit/Run.neb_explicit (cat: illegal option -- a)

Aaah...looks like the dacdif lines are messed up in the neb test cases; not
sure why nobody caught this before.

> - qmmm2/xcrd_build_test/Run.ortho_qmewald0 ("Non bond list
> overflow! Check MAXPR in locmem.f"), which stopped the QM/MM tests
> (surprisingly, again, considering -k)

needs to be looking into.


AMBER-Developers mailing list
Received on Tue Mar 30 2010 - 20:00:03 PDT
Custom Search