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 - 12:30:03 PDT
