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
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Received on Thu Mar 24 2016 - 12:30:05 PDT
