Thank you, Ross.
I will go ahead and check that.
Best,
Guqin
2016-03-24 15:22 GMT-04:00 Ross Walker <ross.rosswalker.co.uk>:
> Hi Guqin,
>
> This is normal - roundoff differences are often seen with SPFP. This will
> be fixed in the upcoming AMBER 16 so the test suite is more robust for
> GPUs. The IGB 8 issue is because changes were made with an update but the
> test output was never updated. You can safely ignore these issues.
>
> If you want to be sure compile with -cuda_DPFP and do cd
> $AMBERHOME/test;./test_amber_cuda.sh DPFP (the GB8 test will still fail
> but the other roundoff differences should go).
>
> All the best
> Ross
>
> > On Mar 24, 2016, at 12:12, Guqin Shi <shi.293.osu.edu> wrote:
> >
> > Hi all,
> >
> > I've just upgraded to AmberTools15 and recompiled everything following a
> > tutorial kindly written by Jason Swails. (
> > http://jswails.wikidot.com/installing-amber14-and-ambertools14)
> >
> > I did:
> > make test.serial
> > make test.parallel
> > everything went well. No comparison diff.
> >
> > then I did:
> > make test.cuda
> > ./test_amber_cuda_parallel.sh
> > Around half of tests showed comparison diffs, which is expected for cuda.
> > Most of them are round errors as I could tell.
> >
> > However, there are some "possible failures" which I am not sure if I can
> > safely ignore them or not. Below is part of them:
> >
> > ======================================================================
> >
> > possible FAILURE: check irest1_ntt0_igb8_ntc2.out.dif
> > /usr/local/amber14/test/cuda/gb_ala3
> > 53c53
> > < Frozen or restrained atoms:
> >> gb_alpha_hnu = 0.53705, gb_beta_hnu = 0.36286, gb_gamma_hnu
> > = 0.11670
> > 54c54
> > < ibelly = 0, ntr = 0
> >> gb_alpha_cnu = 0.33167, gb_beta_cnu = 0.19684, gb_gamma_cnu
> > = 0.09342
> > 55c55
> > < Molecular dynamics:
> >> gb_alpha_nnu = 0.68631, gb_beta_nnu = 0.46319, gb_gamma_nnu
> > = 0.13872
> > 56c56
> > < nstlim = 20, nscm = 50, nrespa = 1
> >> gb_alpha_onu = 0.60634, gb_beta_onu = 0.46301, gb_gamma_onu
> > = 0.14226
> > 57c57
> > < t = 0., dt = 0.00050, vlimit = -1.00000
> >> gb_alpha_pnu = 0.41836, gb_beta_pnu = 0.29005, gb_gamma_pnu
> > = 0.10642
> > 58c58
> > < SHAKE:
> >> Frozen or restrained atoms:
> > 59c59
> > < ntc = 2, jfastw = 0
> >> ibelly = 0, ntr = 0
> > 60c60
> > < tol = 0.00001
> >> Molecular dynamics:
> > 61c61
> > <
> >
> --------------------------------------------------------------------------------
> >> nstlim = 20, nscm = 50, nrespa = 1
> > 62c62
> > < 3. ATOMIC COORDINATES AND VELOCITIES
> >> t = 0., dt = 0.00050, vlimit = -1.00000
> > 63c63
> > <
> >
> --------------------------------------------------------------------------------
> >> SHAKE:
> > 64c64
> > < ACE
> >> ntc = 2, jfastw = 0
> > 65c65
> > < begin time read from input coords = 1050.000 ps
> >> tol = 0.00001
> > 66c66
> > < Number of triangulated 3-point waters found: 0
> >>
> >
> --------------------------------------------------------------------------------
> > 67c67
> > <
> >
> --------------------------------------------------------------------------------
> >> 3. ATOMIC COORDINATES AND VELOCITIES
> > 68c68
> > < 4. RESULTS
> >>
> >
> --------------------------------------------------------------------------------
> > 69c69
> > <
> >
> --------------------------------------------------------------------------------
> >> ACE
> > 70c70
> > < NSTEP = 1 TIME(PS) = 1050.001 TEMP(K) = 337.60 PRESS
> > = 0.
> >> begin time read from input coords = 1050.000 ps
> > 71c71
> > < Etot = 21.0035 EKtot = 32.8726 EPtot =
> > -11.8690
> >> Number of triangulated 3-point waters found: 0
> > 72c72
> > < BOND = 3.0496 ANGLE = 15.6236 DIHED =
> > 25.7299
> >>
> >
> --------------------------------------------------------------------------------
> >
> > ======================================================================
> >
> > I didn't really see what the failure is or is it related to round errors
> or
> > not. Anybody can help look at that? Can I safely ignore them? I can also
> > upload full .diff file if needed.
> >
> > Thanks for your time!
> > Guqin
> >
> > --
> > Guqin SHI
> > The Ohio State University
> > College of Pharmacy
> > 500 W. 12th Ave.
> > Columbus, OH, 43210
> > (614)688-3531
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Guqin SHI
The Ohio State University
College of Pharmacy
500 W. 12th Ave.
Columbus, OH, 43210
(614)688-3531
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Received on Thu Mar 24 2016 - 12:30:09 PDT
