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
Received on Thu Mar 24 2016 - 14:00:03 PDT
