I just want to add that it's still safe to use igb8 model although the
tests are failed (since the tests are not updated for GPU).
Related discussion: http://archive.ambermd.org/201602/0190.html
cheers.
Hai
On Thu, Mar 24, 2016 at 4:48 PM, Guqin Shi <shi.293.osu.edu> wrote:
> After building DPFP and all tests passed except for igb8. Everything looks
> fine now. Thank you for all the help!
>
> 2016-03-24 15:29 GMT-04:00 Charles Lin <clin92.ucsd.edu>:
>
> > Running with SPFP should be fine for production runs. However, you'll
> get
> > slightly different rounding results based on GPU architecture. This
> should
> > be fine.
> >
> > DPFP has more precision so it will have the same results on all hardware.
> >
> > Charlie
> >
> > ________________________________________
> > From: Guqin Shi [shi.293.osu.edu]
> > Sent: Thursday, March 24, 2016 12:24 PM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] [AmberTools15 & Amber14 Installation] Make Test
> > Possible Failures Can Be Ignored or Not
> >
> > LOLs, thank you Charlie!!
> >
> > I did notice that DPFP is for debugging, not for production run. Is still
> > suggested to build cuda_DPFP even if it will not really used?
> >
> > -Guqin
> >
> > 2016-03-24 15:19 GMT-04:00 Charles Lin <clin92.ucsd.edu>:
> >
> > > Compile with -cuda_DPFP and then run the tests and they should all
> pass.
> > > Do note this will link pmemd.cuda to the DPFP version (slower) not the
> > SPFP
> > > version (faster). You're running with single precision which will have
> > > some round off errors.
> > >
> > > ________________________________________
> > > From: Guqin Shi [shi.293.osu.edu]
> > > Sent: Thursday, March 24, 2016 12:12 PM
> > > To: AMBER Mailing List
> > > Subject: [AMBER] [AmberTools15 & Amber14 Installation] Make Test
> Possible
> > > Failures Can Be Ignored or Not
> > >
> > > 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
> > _______________________________________________
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Mar 24 2016 - 15:30:04 PDT
