Cygwin Update:
CYGWIN_NT-5.1 1.7.2 i686 on Athlon 64 X2 4400+; GNU 4.3.4; RC 14apr10
./configure -noX11 -cygwin [-mpi] gnu
Errors are over-counted. Maybe using "Program error" as the grep search key
would be better?
test_at_serial: The sleap/pdbent/ and sleap/amoeba tests still fail for me
with segfaults. Could it be that these are stack-limited?
test_at_parallel: Everything works.
test_amber_serial: mmpbsa_py/ fails at PB step, and
../src/mm_pbsa/Examples/Run.mmpbsa.test fails at 02_MMPBSA_Stability, both
with "SA Bomb in sa_arc(): Allocates aborted" messages. Perhaps these could
be fixed like the pbsa_tsr tests (adding maxarcdot=8000 to pb namelist)?
test_amber_parallel: Multiple failures with 2 threads. The 5 EVB tests that
failed before because of the stack limit still fail: I get "unlimit: Command
not found."; the stack cannot be resized in Cygwin easily so these tests
should just not run if the stack cannot be resized.
There are 11 PMEMD errors but they are certainly related to the mpich2-1.2.1
issue that has been discussed - I am currently compiling mpich2-1.0.7 to
test that instead. Also, it appears that the cd chamber/md_engine/dhfr_cmap
&& ./Run.dhfr_charmm.md test is run twice in the Makefile - looks like one
of the runs should be cd chamber/md_engine/dhfr_cmap &&
./Run.dhfr_charmm.min.
The only error without explanation so far is rem_hybrid, which segfaults -
not sure why yet.
All other problems are round-off related and are listed on the wiki-page.
-Dan
On Fri, Apr 16, 2010 at 9:20 PM, Ben Roberts <roberts.qtp.ufl.edu> wrote:
>
> On 16/4/2010, at 5:51 p.m., Ben Roberts wrote:
>
> >
> > On 16/4/2010, at 11:28 a.m., Ben Roberts wrote:
> >
> >> Hi all,
> >>
> >> On my Mac (Snow Leopard 10.6.2, Intel compilers 11.1.084), I get this
> now:
> >>
>
> And finally, for the Amber parallel tests:
>
> Sander.RISM.MPI is now generated, and the 3D-RISM tests pass.
>
> With 2 CPUs:
>
> 385 file comparisons passed
> 2 file comparisons failed
> 0 tests experienced errors
>
> possible FAILURE: check evbout.dif
>
> /Applications/Amber11/2010-04-14/amber11/test/evb/malon_dbonds_umb_dg_UFF_3DG_qi_full_corrF
> 158c158
> < 0.00396164 19.38711526 -515.49226027
> > 0.00395165 19.38711410 -515.49223224
> ### Maximum absolute error in matching lines = 9.99e-06 at line 158 field 1
> ### Maximum relative error in matching lines = 2.53e-03 at line 158 field 1
>
> Plus the customary TIP5P diff.
>
> With 4 CPUs:
>
> 343 file comparisons passed
> 1 file comparison failed
> 0 tests experienced errors
>
> where the failure is the TIP5P diff.
>
> With 8 CPUs:
>
> Finished parallel test suite for Amber 11 at Fri 16 Apr 2010 20:21:36 EDT.
> 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 README for details.
>
> 315 file comparisons passed
> 3 file comparisons failed
> 18 tests experienced errors
>
> The errors included:
>
> cd PIMD/full_cmd_water/equilib && ./Run.full_cmd
> cd PIMD/full_cmd_water/restart && ./Run.full_cmd
> cd PIMD/full_nmpimd_water && ./Run.full_pimd
> cd PIMD/full_pimd_amoeba && ./Run.full_pimd_amoeba
> cd PIMD/full_pimd_ntp_water && ./Run.full_pimd_ntp
>
> These ones behaved strangely - they started running in some kind of endless
> loop. For example, the first one ran for 45 minutes before I intervened and
> killed it from the command line. After that, I got considerably less
> patient, and would kill them after a minute or two.
>
> cd qmmm2/xcrd_build_test/ && ./Run.ortho_qmewald0
> cd qmmm2/xcrd_build_test/ && ./Run.truncoct_qmewald0
>
> These two failed with this error:
> * NB pairs <num> <number> exceeds capacity ( 185750)
> 3
> SIZE OF NONBOND LIST = 185750
> SANDER BOMB in subroutine nonbond_list
> Non bond list overflow!
> check MAXPR in locmem.f
>
> (where <num> is a three-digit number and <number> is a six-digit number
> marginally bigger than 185,750)
>
> The ncsu/smd2 test (which contributed two of the failures) failed with
> "Must have more residues than processors!". In this case, with seven
> residues present, I guess that means a maximum of six processors. I've
> prepared a patch for the run.sh script ($AMBERHOME/test/ncsu/smd2/run.sh),
> which I've attached.
>
> The other failure is our old friend TIP5P.
>
> Cheers,
> Ben
>
>
>
> _______________________________________________
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> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
>
--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
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Received on Fri Apr 16 2010 - 19:30:02 PDT
