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
==============================================================
export TESTsander='../../../bin/pmemd.MPI'; cd pmemdTI/pheMTI && ./Run.0
diffing out.0.save with out.0
PASSED
==============================================================
export TESTsander='../../../bin/pmemd.MPI'; cd pmemdTI/pheMTI && ./Run.1
diffing out.1.save with out.1
PASSED
==============================================================
export TESTsander='../../../bin/pmemd.MPI'; cd pmemdTI/pheMTI && ./Run.lambda0
diffing pheMTI0.out.save with pheMTI0.out
possible FAILURE: check pheMTI0.out.dif
==============================================================
export TESTsander='../../../bin/pmemd.MPI'; cd pmemdTI/pheMTI && ./Run.lambda1
diffing pheMTI1.out.save with pheMTI1.out
possible FAILURE: check pheMTI1.out.dif
==============================================================
export TESTsander='../../../bin/pmemd.MPI'; cd pmemdTI/sodium && ./Run.sodium
diffing md1.o.save with md1.o
possible FAILURE: check md1.o.dif
==============================================================
export TESTsander='../../../bin/pmemd.MPI'; cd pmemdTI/ti_ggcc && ./Run.test1
diffing out_icfe1_klambda_1_clambda_0.5.p1.save with
out_icfe1_klambda_1_clambda_0.5.p1
possible FAILURE: check out_icfe1_klambda_1_clambda_0.5.p1.dif
==============================================================
export TESTsander='../../../bin/pmemd.MPI'; cd pmemdTI/ti_ggcc &&
./Run.test2
diffing out_icfe1_klambda_6_clambda_0.5.p1.save with
out_icfe1_klambda_6_clambda_0.5.p1
possible FAILURE: check out_icfe1_klambda_6_clambda_0.5.p1.dif
==============================================================
......
Protein-Ligand complex test
diffing out.save with out
possible FAILURE: check out.dif
==============================================================
diffing restrt.save with restrt
PASSED
==============================================================
==============================================================
Solvation free energy test
diffing out.0.save with out.0
possible FAILURE: check out.0.dif
==============================================================
diffing restrt.0.save with restrt.0
PASSED
==============================================================
diffing out2.0.save with out2.0
possible FAILURE: check out2.0.dif
==============================================================
diffing restrt2.0.save with restrt2.0
PASSED
==============================================================
==============================================================
Dynamic lambda test
diffing out.0.save with out.0
possible FAILURE: check out.0.dif
==============================================================
diffing restrt.0.save with restrt.0
PASSED
==============================================================
==============================================================
Restrained complex test
diffing out.0.save with out.0
possible FAILURE: check out.0.dif
==============================================================
diffing restrt.0.save with restrt.0
PASSED
==============================================================
==============================================================
Using softcore electrostatics
diffing out.0.save with out.0
possible FAILURE: check out.0.dif
==============================================================
diffing restrt.0.save with restrt.0
PASSED
==============================================================
.....
==============================================================
export TESTsander='../../../bin/pmemd.MPI'; cd emil/emil_pmemd_tip3p
&& ./Run.emil EMIL
DO_PARALLEL is set: mpirun -np 4
diffing mdout.emil.0.1.save with mdout.emil.0.1
possible FAILURE: check mdout.emil.0.1.dif
==============================================================
diffing emil.log.0.1.save with emil.log.0.1
PASSED
==============================================================
diffing mdout.emil.0.5.save with mdout.emil.0.5
possible FAILURE: check mdout.emil.0.5.dif
==============================================================
diffing emil.log.0.5.save with emil.log.0.5
PASSED
==============================================================
diffing mdout.emil.0.9.save with mdout.emil.0.9
possible FAILURE: check mdout.emil.0.9.dif
==============================================================
diffing emil.log.0.9.save with emil.log.0.9
PASSED
==============================================================
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?
Huang
> From: David A Case <case.biomaps.rutgers.edu>
> Date: Tue, 8 Jul 2014 14:55:01 -0400
>
> On Tue, Jul 08, 2014, Blake Mertz wrote:
> >
> > I'm compiled the parallel version of Amber14 against gcc-4.7.4 and
> > openmpi-1.6.5-8 on a debian testing box (kernel 3.11), but when I ran the
> > tests, two groups failed, pmemdTI and emil_pmemd_tip3p. Here's some of the
> > difs:
>
> For what it may be worth to others: these are both failures to compute the
> components of DV/DL (in the section "DV/DL, AVERAGES").
>
> For Blake: what was your setting for DO_PARALLEL? Are there any other tests
> with similar diffs (i.e. a bunch of zeroes, as below)? Did you install
> openmpi yourself, or use something like a package manager?
>
> I don't think that anyone has reported failures in this test before. I can't
> get it to fail on any of my machines.
>
> ....dac
>
>
> >
> > possible FAILURE: check campTI.out.dif
> > /usr/local/src/amber14/test/pmemdTI/campTI
> > 339,342c339,342
> > < Etot = 0. EKtot = 0. EPtot = 4.3929
> > < BOND = 36.5819 ANGLE = -2.5879 DIHED =
> > -0.5307
> > < 1-4 NB = -0.0292 1-4 EEL = -85.1242 VDWAALS =
> > 2.5131
> > < EELEC = 53.5699 EHBOND = 0. RESTRAINT = 0.
> > ---
> > > Etot = 0. EKtot = 0. EPtot = 0.
> > > BOND = 0. ANGLE = 0. DIHED = 0.
> > > 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 0.
> > > EELEC = 0. EHBOND = 0. RESTRAINT = 0.
> > 345d344
> > < DV/DL = 4.3929
> >
> > and
> >
> > possible FAILURE: check mdout.emil.0.1.dif
> > /usr/local/src/amber14/test/emil/emil_pmemd_tip3p
> > 196,200c196,199
> > < Etot = 0. EKtot = 0. EPtot = 35484.36
> > < BOND = -248.06 ANGLE = -306.01 DIHED = -480.71
> > < 1-4 NB = -192.19 1-4 EEL = 4543.51 VDWAALS = -6625.23
> > < EELEC = 38793.07 EHBOND = 0. RESTRAINT = 0.
> > < DV/DL = 35484.36
> > ---
> > > Etot = 0. EKtot = 0. EPtot = 0.
> > > BOND = 0. ANGLE = 0. DIHED = 0.
> > > 1-4 NB = 0. 1-4 EEL = 0. VDWAALS = 0.
> > > EELEC = 0. EHBOND = 0. RESTRAINT = 0.
> >
> > I didn't find anything specific to these tests on the mailing list, so I
> > wasn't sure if how concerned I should be, since both of these tests deal
> > with FE calculations, which I don't need at the present moment. Thanks for
> > any help!
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Received on Tue Aug 19 2014 - 05:30:04 PDT
