I figure I'll throw my pointless little fix in the mix since it's easy
enough. When nab compiles mm_pbsa_nabnmode.nab, it creates
mm_pbsa_nabnmode.c which is not removed during a make clean, though it
probably should be. If, of course, you make it to the very end of
your priority list :).
Also, I'll test the flex issue tomorrow morning when I'm back on my
Ubuntu machine.
All the best,
Jason
On Tue, Mar 30, 2010 at 10:34 PM, case <case.biomaps.rutgers.edu> wrote:
> 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.
>
> ...thx....dac
>
>
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>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Mar 30 2010 - 21:00:05 PDT
