Thank Jason for the reply.
The compiler was gcc (Debian 4.9.1-4) 4.9.1.
The problem could be associated with the compiler. These days, I use
gcc 4.8, and almost everything is OK. The exception is:
===================================================================
possible FAILURE: check mdout.pbsa_decres.dif
/home/qshuang/.local/amber14/test/sander_pbsa_decres
1320c1320
< Total surface charge -5.9357
> Total surface charge -5.9270
1321c1321
< Reaction field energy -2007.5763
> Reaction field energy -1609.3322
1322c1322
< Cavity solvation energy 38.8528
> Cavity solvation energy 39.1489
1324c1324
< 1 -3.0345E+3 1.6433E+1 8.6691E+1 C 1030
> 1 -2.6359E+3 1.6488E+1 8.6861E+1 C 1030
1326c1326
< VDWAALS = -546.2276 EEL = -4637.2832 EPB = -2007.5763
> VDWAALS = -546.2276 EEL = -4637.2832 EPB = -1609.3322
1328c1328
< ECAVITY = 38.8528 EDISPER = 0.
> ECAVITY = 39.1489 EDISPER = 0.
1332c1332
< 1 -3.0345E+3 1.6433E+1 8.6691E+1 C 1030
> 1 -2.6360E+3 1.6488E+1 8.6861E+1 C 1030
.............................
1563c1563
< BDC 46 7.292 -1.777 -10.137 -0.362 0.
> BDC 46 7.292 -1.777 -10.137 1.035 0.
1564c1564
< BDC 47 11.405 -2.431 -14.597 3.828 0.
> BDC 47 11.405 -2.431 -14.597 5.180 0.
1565c1565
< BDC 48 8.706 -1.390 -12.134 -2.052 0.
> BDC 48 8.706 -1.390 -12.134 -0.257 0.
1566c1566
< BDC 49 5.771 0.197 -9.574 0.041 0.
> BDC 49 5.771 0.197 -9.574 2.894 0.
1567c1567
< BDC 50 7.482 -1.515 2.838 -6.288 0.
> BDC 50 7.482 -1.515 2.838 -5.536 0.
1568c1568
< BDC 51 11.960 -0.284 -7.838 -4.120 0.
> BDC 51 11.960 -0.284 -7.838 -2.004 0.
1569c1569
< BDC 52 7.142 -1.721 -5.027 -8.712 0.
> BDC 52 7.142 -1.721 -5.027 -5.727 0.
.............................
1592c1592
< BDC 75 7.492 -0.795 3.788 -7.440 0.
> BDC 75 7.492 -0.795 3.788 -5.399 0.
1593c1593
< BDC 76 7.328 -1.602 -33.516 -44.142 0.
> BDC 76 7.328 -1.602 -33.516 -51.973 0.
### Maximum absolute error in matching lines = 3.99e+02 at line 1324 field 2
### Maximum relative error in matching lines = 6.96e+01 at line 1566 field 6
---------------------------------------
===================================================================
The version is Amber 14.05 and AmberTools 14.10.
If compiling Amber 14 without update, this failure disappears (and
everything is OK). I don't konw if it is a new bug or is due to
out-of-date test data.
Huang
> From: Jason Swails <jason.swails.gmail.com>
> Date: Tue, 19 Aug 2014 08:41:30 -0400
>
> On Tue, 2014-08-19 at 20:15 +0800, Huang wrote:
> > I encounter the same situation when `make test` Amber14, for a serial
> > version. Here is the setting of my platform:
> > Intel(R) Xeon(R) CPU E7310 . 1.60GHz
> > Debian jessie/sid
> > gcc (Debian 4.9.1-4) 4.9.1
> > mpirun (Open MPI) 1.6.5
> >
> > I also do `make test` for a parallel version with DO_PARALLEL='mpirun
> > -np2', and more module reports similar failure.
> > Thus bin/pmemd.MPI is also broken. Failed modules are:
> >
> > export TESTsander='../../../bin/pmemd.MPI'; cd pmemdTI/campTI && ./Run.campTI
> > diffing campTI.out.save with campTI.out
> > possible FAILURE: check campTI.out.dif
> > ==============================================================
> > ......
> >
> > ==============================================================
> >
> >
> > I guess Dr Case is right, since all differences are around the section
> > "DV/DL, AVERAGES".
> >
> > What can I do to fix the error, or to obtain more specific information?
>
> Make sure you've updated Amber 14 to the latest version. You can do
> this by recompiling. If you are asked to update your installation
> during the configure step, you need to recompile Amber in serial and
> parallel. If not, it's fine.
>
> Also, you should look at the dif files that the output suggests you look
> at. For instance, see where it says "check mdout.emil.0.9.dif" -- look
> at that file. If the differences appear very small, then it's not
> really a problem, it's just round-off error.
>
> Also, what compilers are you using?
>
> HTH,
> Jason
>
> --
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Received on Mon Aug 25 2014 - 03:00:05 PDT
