[gmx-developers] gromacs 5.1rc1 OpenCL problem with Parrinello-Rahman

Carlo Camilloni carlo.camilloni at gmail.com
Wed Jul 15 17:43:02 CEST 2015 

Hi,

these are the tests that fail:

FAILED. Check checkpot.out (12 errors), checkforce.out (3516 errors) file(s) in dd121 for dd121
FAILED. Check checkpot.out (10 errors), checkforce.out (4027 errors) file(s) in nbnxn-energy-groups for nbnxn-energy-groups
FAILED. Check checkpot.out (26 errors), checkforce.out (2998 errors) file(s) in nbnxn-free-energy for nbnxn-free-energy
FAILED. Check checkpot.out (26 errors), checkforce.out (2998 errors) file(s) in nbnxn-free-energy-vv for nbnxn-free-energy-vv
FAILED. Check checkpot.out (11 errors), checkforce.out (4039 errors) file(s) in nbnxn-ljpme-geometric for nbnxn-ljpme-geometric
FAILED. Check checkpot.out (14 errors), checkforce.out (52 errors) file(s) in nbnxn-ljpme-LB for nbnxn-ljpme-LB
FAILED. Check checkpot.out (14 errors), checkforce.out (52 errors) file(s) in nbnxn-ljpme-LB-geometric for nbnxn-ljpme-LB-geometric
FAILED. Check checkpot.out (10 errors), checkforce.out (4029 errors) file(s) in nbnxn-vdw-force-switch for nbnxn-vdw-force-switch
FAILED. Check checkpot.out (10 errors), checkforce.out (4032 errors) file(s) in nbnxn-vdw-potential-switch for nbnxn-vdw-potential-switch
FAILED. Check checkpot.out (4 errors), checkforce.out (250 errors) file(s) in nbnxn-vdw-potential-switch-argon for nbnxn-vdw-potential-switch-argon
FAILED. Check checkpot.out (10 errors), checkforce.out (4027 errors) file(s) in nbnxn_pme for nbnxn_pme
FAILED. Check checkpot.out (10 errors), checkforce.out (4027 errors) file(s) in nbnxn_pme_order5 for nbnxn_pme_order5
FAILED. Check checkpot.out (10 errors), checkforce.out (4027 errors) file(s) in nbnxn_pme_order6 for nbnxn_pme_order6
FAILED. Check checkpot.out (9 errors), checkforce.out (4028 errors) file(s) in nbnxn_rf for nbnxn_rf
FAILED. Check checkpot.out (2 errors), checkforce.out (4 errors) file(s) in nbnxn_rzero for nbnxn_rzero
FAILED. Check mdrun.out, md.log file(s) in nbnxn_vsite for nbnxn_vsite
FAILED. Check checkpot.out (13 errors), checkforce.out (15512 errors) file(s) in octahedron for octahedron
FAILED. Check mdrun.out, md.log file(s) in position-restraints for position-restraints
FAILED. Check mdrun.out, md.log file(s) in pull_constraint for pull_constraint
FAILED. Check checkpot.out (10 errors), checkforce.out (4021 errors) file(s) in pull_cylinder for pull_cylinder
FAILED. Check checkpot.out (11 errors), checkforce.out (39054 errors) file(s) in swap_x for swap_x
FAILED. Check checkpot.out (11 errors), checkforce.out (39053 errors) file(s) in swap_y for swap_y
FAILED. Check checkpot.out (12 errors), checkforce.out (39054 errors) file(s) in swap_z for swap_z
23 out of 60 complex tests FAILED
FAILED. Check mdrun.out, md.log file(s) in expanded for expanded
FAILED. Check mdrun.out, md.log file(s) in transformAtoB for transformAtoB
2 out of 10 freeenergy tests FAILED


Carlo


> 
> 
> Message: 4
> Date: Wed, 15 Jul 2015 15:35:13 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-developers at gromacs.org,
> 	gromacs.org_gmx-developers at maillist.sys.kth.se
> Subject: Re: [gmx-developers] gromacs 5.1rc1 OpenCL problem with
> 	Parrinello-Rahman
> Message-ID:
> 	<CAMNuMATveVRRyBBwn312xrY+w3M7deC2Hs3A7PZnaeugkw+VVA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi,
> 
> Thanks. If a difference of that magnitude can be seen, then it should also
> show up when running the regressiontests (e.g. cmake
> -DREGRESSIONTEST_DOWNLOAD=on and then make check) as a failure
> of complex/nbnxn-ljpme-LB (which is the only P-R test that can run on the
> GPU). If other tests fail, then the problem is actually more widespread.
> 
> It may be that there is some issue with some part of the Mac+clang+OpenCL
> stack - we didn't target it during development, and at the last minute when
> Erik was unexpectedly able to get it to compile. I don't know if he got
> tests to pass. Erik?
> 
> Mark
> 
> On Wed, Jul 15, 2015 at 5:22 PM Carlo Camilloni <carlo.camilloni at gmail.com>
> wrote:
> 
>> 
>> Dear Mark and Szilard,
>> 
>> thanks for your answer. I filed a bug in redmine but in the meantime I was
>> running more tests and I am a bit scared by what I found:
>> 
>> what I have done is the following I have performed a single step run with
>> gmx51-rc1 compiled with cuda, again clang and so on
>> and compared the forces on the first step with -nb cpu or not (I am using
>> -pforce 1), the forces are identical:
>> 
>> ie.:
>> 
>> cuda-gpu
>> 
>> step 0  atom      1  x    3.940    5.612    2.226  force  1.90839e+03
>> step 0  atom      2  x    3.852    5.659    2.211  force  4.24845e+02
>> step 0  atom      3  x    3.979    5.665    2.303  force  6.89472e+02
>> step 0  atom      4  x    3.992    5.610    2.139  force  7.42053e+02
>> 
>> 
>> cpu:
>> 
>> step 0  atom      1  x    3.940    5.612    2.226  force  1.90839e+03
>> step 0  atom      2  x    3.852    5.659    2.211  force  4.24845e+02
>> step 0  atom      3  x    3.979    5.665    2.303  force  6.89472e+02
>> step 0  atom      4  x    3.992    5.610    2.139  force  7.42053e+02
>> 
>> if I do the same test on the version compiled with OpenCL
>> 
>> cpu:
>> 
>> (the former are done on my macbook pro avx2_256  this latter on a MacPro
>> avx_256, this should
>> explain the small differences in the forces)
>> 
>> step 0  atom      1  x    3.940    5.612    2.226  force  1.90838e+03
>> step 0  atom      2  x    3.852    5.659    2.211  force  4.24848e+02
>> step 0  atom      3  x    3.979    5.665    2.303  force  6.89470e+02
>> step 0  atom      4  x    3.992    5.610    2.139  force  7.42043e+02
>> 
>> opencl-gpu:
>> step 0  atom      1  x    3.940    5.612    2.226  force  1.48597e+03
>> step 0  atom      2  x    3.852    5.659    2.211  force  6.26942e+02
>> step 0  atom      3  x    3.979    5.665    2.303  force  8.44032e+02
>> step 0  atom      4  x    3.992    5.610    2.139  force  7.92786e+02
>> 
>> I am afraid there is something wrong  in OpenCL kernels.
>> 
>> I am using the topol-nvt-nogen.tpr I have uploaded on redmine.
>> 
>> Best,
>> Carlo
>> 
>> 
>> 
>> --
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