On Mon, Apr 12, 2010 at 9:04 AM, case <case.biomaps.rutgers.edu> wrote:
>
> 4. Dan: can we get a current picture of what cygwin is doing?
>
>
Results for CYGWIN serial have been posted on the wiki. Most of the problems
seem to be with either sleap or pbsa. I suspect the pbsa issues could be
more problems with CYGWIN's small stack size as all the pbsa failures seem
to happen at the allocation stage.
General note: errors are over-counted, occasionally 1 error will generate 2
error messages, e.g.:
cd pbsa_tsr && ./Run.tsrb.min
> ./Run.tsrb.min: Program error
> make: *** [test.pbsa] Error 1
>
The way that the error counting is currently set up (grep "[Ee]rror" | wc
-l) counts this as two errors. Note that this line:
make: Target `test.serial' not remade because of errors.
>
is also counted as an error in the error log. Errors such as this:
cd pdbent; ./Run.pdbent2
> ./Run.pdbent2: line 13: 768 Aborted (core dumped)
> ../../../exe/sleap < leap.in > pdbent2.out 2>&1
> cat: mdl_1hpv.mol2: No such file or directory
> diffing mdl_1hpv.mol2.save with mdl_1hpv.mol2
> possible FAILURE: check mdl_1hpv.mol2.dif
>
are not counted as errors, merely failures.
Here are the details of the tests and failures:
RC 08apr10
System: CYGWIN_NT-5.1 1.7.2 i686 on Athlon 64 X2 4400+
Compilers: GNU 4.3.4
./configure -noX11 -cygwin gnu
test_at_serial
212 file comparisons passed
2 file comparisons failed
3 tests experienced errors
Two of the three errors are from sleap, which result in the 2 failed file
comparisons:
* $AMBERHOME/AmberTools/test/sleap/pdbent/Run.pdbent2 Fails on loading
1hpv.pdb (stack is dumped)
* $AMBERHOME/AmberTools/test/sleap/amoeba/Run.amoeba_sol Fails on solvateoct
hpv WATBOX 4.0 (stack is dumped)
Remaining error is from the pbsa_tsr test:
Number of triangulated 3-point waters found: 0
>
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> SA Bomb in sa_arc(): Allocates aborted 0 0
> 5014 0 0
>
>
test_amber_serial
416 file comparisons passed
1 file comparison failed
5 tests experienced errors
Failure is from mmpbsa_py: looks like everything below this line in
FINAL_RESULTS_MMPBSA.dat is cut off ( i.e. the "POISSON BOLTZMANN:"
section). Here are the last 3 lines:
RESULT OF ALANINE SCANNING: (D231A MUTANT:) DELTA DELTA G binding =
> -0.0925 +/- 5.6721
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
>
Here are the errors:
* cd sander_pbsa_tsr && ./Run.tsrb.min
>From the output:
SA Bomb in sa_arc(): Allocates aborted 0 0
> 5014 0 0
>
Looks like the same error as in the AmberTools test.
* cd ../src/mm_pbsa/Examples && ./Run.mmpbsa.test
Crashes on TEST: 02_MMPBSA_Stability:
Calc PBSA
> /home/Dan/Amber/Release-Cantidate/amber11-08apr10/bin/sander -O -i
> pbsa_com.in -o pbsa_com.1.out -c ../01_GenerateSnapshots/test_com.crd.1 -p
> ../test_com_mbondi2.prmtop not successful
> For details see:
> http://ambermd.org/Questions/mm_pbsa.html#pbsa_command_not_successful
>
Same error in output:
SA Bomb in sa_arc(): Allocates aborted 0 5014
> 5014 0 0
>
-Dan
--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
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Received on Mon Apr 12 2010 - 12:30:02 PDT
