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
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Received on Thu Mar 24 2016 - 12:30:04 PDT
