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
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Received on Thu Mar 24 2016 - 12:30:07 PDT
