<html><head><style>body{font-family:Helvetica,Arial;font-size:13px}</style></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Hi Carlo,</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">IIRC, I managed to get it working on a Mac Pro with AMD Firepro D300 GPUs. Please post the contents of the top of your logfile (where it says everything about the compilers & config), and mention what hardware you tried it on - then we’ll see if we can reproduce it.</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Cheers,</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Erik</div> <div class="airmail_ext_on" style="color:black"><br>From: <span style="color:black">Carlo Camilloni</span> <a href="mailto:carlo.camilloni@gmail.com"><carlo.camilloni@gmail.com></a><br>Reply: <span style="color:black">gmx-developers@gromacs.org</span> <a href="mailto:gmx-developers@gromacs.org"><gmx-developers@gromacs.org>></a><br>Date: <span style="color:black">16 Jul 2015 at 18:52:21</span><br>To: <span style="color:black">gromacs.org_gmx-developers@maillist.sys.kth.se</span> <a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se"><gromacs.org_gmx-developers@maillist.sys.kth.se>></a><br>Subject: <span style="color:black"> Re: [gmx-developers] gromacs 5.1rc1 OpenCL problem with Parrinello-Rahman <br></span></div><br> <blockquote type="cite" class="clean_bq"><span><div><div></div><div>Hi,
<br>
<br>I tested the OpenCL kernel on my macbook (nvidia gpu) and here it produces the correct forces,
<br>so it could be a problem related to amd+osx, or maybe to some specific compiler/os version
<br>
<br>Carlo
<br>
<br>
<br>> On 15 Jul 2015, at 17:42, Carlo Camilloni <carlo.camilloni@gmail.com> wrote:
<br>>
<br>> Hi,
<br>>
<br>> these are the tests that fail:
<br>>
<br>> FAILED. Check checkpot.out (12 errors), checkforce.out (3516 errors) file(s) in dd121 for dd121
<br>> FAILED. Check checkpot.out (10 errors), checkforce.out (4027 errors) file(s) in nbnxn-energy-groups for nbnxn-energy-groups
<br>> FAILED. Check checkpot.out (26 errors), checkforce.out (2998 errors) file(s) in nbnxn-free-energy for nbnxn-free-energy
<br>> FAILED. Check checkpot.out (26 errors), checkforce.out (2998 errors) file(s) in nbnxn-free-energy-vv for nbnxn-free-energy-vv
<br>> FAILED. Check checkpot.out (11 errors), checkforce.out (4039 errors) file(s) in nbnxn-ljpme-geometric for nbnxn-ljpme-geometric
<br>> FAILED. Check checkpot.out (14 errors), checkforce.out (52 errors) file(s) in nbnxn-ljpme-LB for nbnxn-ljpme-LB
<br>> FAILED. Check checkpot.out (14 errors), checkforce.out (52 errors) file(s) in nbnxn-ljpme-LB-geometric for nbnxn-ljpme-LB-geometric
<br>> FAILED. Check checkpot.out (10 errors), checkforce.out (4029 errors) file(s) in nbnxn-vdw-force-switch for nbnxn-vdw-force-switch
<br>> FAILED. Check checkpot.out (10 errors), checkforce.out (4032 errors) file(s) in nbnxn-vdw-potential-switch for nbnxn-vdw-potential-switch
<br>> FAILED. Check checkpot.out (4 errors), checkforce.out (250 errors) file(s) in nbnxn-vdw-potential-switch-argon for nbnxn-vdw-potential-switch-argon
<br>> FAILED. Check checkpot.out (10 errors), checkforce.out (4027 errors) file(s) in nbnxn_pme for nbnxn_pme
<br>> FAILED. Check checkpot.out (10 errors), checkforce.out (4027 errors) file(s) in nbnxn_pme_order5 for nbnxn_pme_order5
<br>> FAILED. Check checkpot.out (10 errors), checkforce.out (4027 errors) file(s) in nbnxn_pme_order6 for nbnxn_pme_order6
<br>> FAILED. Check checkpot.out (9 errors), checkforce.out (4028 errors) file(s) in nbnxn_rf for nbnxn_rf
<br>> FAILED. Check checkpot.out (2 errors), checkforce.out (4 errors) file(s) in nbnxn_rzero for nbnxn_rzero
<br>> FAILED. Check mdrun.out, md.log file(s) in nbnxn_vsite for nbnxn_vsite
<br>> FAILED. Check checkpot.out (13 errors), checkforce.out (15512 errors) file(s) in octahedron for octahedron
<br>> FAILED. Check mdrun.out, md.log file(s) in position-restraints for position-restraints
<br>> FAILED. Check mdrun.out, md.log file(s) in pull_constraint for pull_constraint
<br>> FAILED. Check checkpot.out (10 errors), checkforce.out (4021 errors) file(s) in pull_cylinder for pull_cylinder
<br>> FAILED. Check checkpot.out (11 errors), checkforce.out (39054 errors) file(s) in swap_x for swap_x
<br>> FAILED. Check checkpot.out (11 errors), checkforce.out (39053 errors) file(s) in swap_y for swap_y
<br>> FAILED. Check checkpot.out (12 errors), checkforce.out (39054 errors) file(s) in swap_z for swap_z
<br>> 23 out of 60 complex tests FAILED
<br>> FAILED. Check mdrun.out, md.log file(s) in expanded for expanded
<br>> FAILED. Check mdrun.out, md.log file(s) in transformAtoB for transformAtoB
<br>> 2 out of 10 freeenergy tests FAILED
<br>>
<br>>
<br>> Carlo
<br>>
<br>>
<br>>>
<br>>>
<br>>> Message: 4
<br>>> Date: Wed, 15 Jul 2015 15:35:13 +0000
<br>>> From: Mark Abraham <mark.j.abraham@gmail.com>
<br>>> To: gmx-developers@gromacs.org,
<br>>>         gromacs.org_gmx-developers@maillist.sys.kth.se
<br>>> Subject: Re: [gmx-developers] gromacs 5.1rc1 OpenCL problem with
<br>>>         Parrinello-Rahman
<br>>> Message-ID:
<br>>>         <CAMNuMATveVRRyBBwn312xrY+w3M7deC2Hs3A7PZnaeugkw+VVA@mail.gmail.com>
<br>>> Content-Type: text/plain; charset="utf-8"
<br>>>
<br>>> Hi,
<br>>>
<br>>> Thanks. If a difference of that magnitude can be seen, then it should also
<br>>> show up when running the regressiontests (e.g. cmake
<br>>> -DREGRESSIONTEST_DOWNLOAD=on and then make check) as a failure
<br>>> of complex/nbnxn-ljpme-LB (which is the only P-R test that can run on the
<br>>> GPU). If other tests fail, then the problem is actually more widespread.
<br>>>
<br>>> It may be that there is some issue with some part of the Mac+clang+OpenCL
<br>>> stack - we didn't target it during development, and at the last minute when
<br>>> Erik was unexpectedly able to get it to compile. I don't know if he got
<br>>> tests to pass. Erik?
<br>>>
<br>>> Mark
<br>>>
<br>>> On Wed, Jul 15, 2015 at 5:22 PM Carlo Camilloni <carlo.camilloni@gmail.com>
<br>>> wrote:
<br>>>
<br>>>>
<br>>>> Dear Mark and Szilard,
<br>>>>
<br>>>> thanks for your answer. I filed a bug in redmine but in the meantime I was
<br>>>> running more tests and I am a bit scared by what I found:
<br>>>>
<br>>>> what I have done is the following I have performed a single step run with
<br>>>> gmx51-rc1 compiled with cuda, again clang and so on
<br>>>> and compared the forces on the first step with -nb cpu or not (I am using
<br>>>> -pforce 1), the forces are identical:
<br>>>>
<br>>>> ie.:
<br>>>>
<br>>>> cuda-gpu
<br>>>>
<br>>>> step 0 atom 1 x 3.940 5.612 2.226 force 1.90839e+03
<br>>>> step 0 atom 2 x 3.852 5.659 2.211 force 4.24845e+02
<br>>>> step 0 atom 3 x 3.979 5.665 2.303 force 6.89472e+02
<br>>>> step 0 atom 4 x 3.992 5.610 2.139 force 7.42053e+02
<br>>>>
<br>>>>
<br>>>> cpu:
<br>>>>
<br>>>> step 0 atom 1 x 3.940 5.612 2.226 force 1.90839e+03
<br>>>> step 0 atom 2 x 3.852 5.659 2.211 force 4.24845e+02
<br>>>> step 0 atom 3 x 3.979 5.665 2.303 force 6.89472e+02
<br>>>> step 0 atom 4 x 3.992 5.610 2.139 force 7.42053e+02
<br>>>>
<br>>>> if I do the same test on the version compiled with OpenCL
<br>>>>
<br>>>> cpu:
<br>>>>
<br>>>> (the former are done on my macbook pro avx2_256 this latter on a MacPro
<br>>>> avx_256, this should
<br>>>> explain the small differences in the forces)
<br>>>>
<br>>>> step 0 atom 1 x 3.940 5.612 2.226 force 1.90838e+03
<br>>>> step 0 atom 2 x 3.852 5.659 2.211 force 4.24848e+02
<br>>>> step 0 atom 3 x 3.979 5.665 2.303 force 6.89470e+02
<br>>>> step 0 atom 4 x 3.992 5.610 2.139 force 7.42043e+02
<br>>>>
<br>>>> opencl-gpu:
<br>>>> step 0 atom 1 x 3.940 5.612 2.226 force 1.48597e+03
<br>>>> step 0 atom 2 x 3.852 5.659 2.211 force 6.26942e+02
<br>>>> step 0 atom 3 x 3.979 5.665 2.303 force 8.44032e+02
<br>>>> step 0 atom 4 x 3.992 5.610 2.139 force 7.92786e+02
<br>>>>
<br>>>> I am afraid there is something wrong in OpenCL kernels.
<br>>>>
<br>>>> I am using the topol-nvt-nogen.tpr I have uploaded on redmine.
<br>>>>
<br>>>> Best,
<br>>>> Carlo
<br>>>>
<br>>>>
<br>>>>
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<br></div></div></span></blockquote> <div id="bloop_sign_1437065855198064128" class="bloop_sign"><div style="font-family:helvetica,arial;font-size:13px">-- <br><span style="font-family: 'helvetica Neue', helvetica;">Erik Lindahl <</span><a href="mailto:erik.lindahl@gmail.com" style="font-family: 'helvetica Neue', helvetica;">erik.lindahl@gmail.com</a><span style="font-family: 'helvetica Neue', helvetica;">> </span><br style="font-family: 'helvetica Neue', helvetica;"><span style="font-family: 'helvetica Neue', helvetica;">Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm </span><span style="font-family: 'helvetica Neue', helvetica;">University </span><br style="font-family: 'helvetica Neue', helvetica;"><span style="font-family: 'helvetica Neue', helvetica;">Professor of Theoretical biophysics, Dept. Theoretical Physics, Royal Inst. </span><span style="font-family: 'helvetica Neue', helvetica;">Technology </span><br style="font-family: 'helvetica Neue', helvetica;"><span style="font-family: 'helvetica Neue', helvetica;">Science for Life Laboratory, Box 1031, 17121 Solna, Sweden</span></div></div></body></html>