<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,</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;">The one obvious difference I can see is that you have clang 6.0.0, while at least my Macbook pro says&nbsp;6.1.0.&nbsp;</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;">Could you check if there is any update available for the developer tools, and if so does that help?</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;">It is actually much better to use gcc since you will then also use all CPU cores. However, that requires patching a header file in /usr/include; I’ll dig up what I did there - we need to put it in the documentation anyway.</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:&nbsp;<span style="color:black">Carlo Camilloni</span> <a href="mailto:carlo.camilloni@gmail.com">&lt;carlo.camilloni@gmail.com&gt;</a><br>Reply:&nbsp;<span style="color:black">Carlo Camilloni</span> <a href="mailto:carlo.camilloni@gmail.com">&lt;carlo.camilloni@gmail.com&gt;&gt;</a><br>Date:&nbsp;<span style="color:black">16 Jul 2015 at 19:07:13</span><br>To:&nbsp;<span style="color:black">Erik Lindahl</span> <a href="mailto:erik.lindahl@gmail.com">&lt;erik.lindahl@gmail.com&gt;&gt;</a><br>Cc:&nbsp;<span style="color:black">gromacs.org_gmx-developers@maillist.sys.kth.se</span> <a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se">&lt;gromacs.org_gmx-developers@maillist.sys.kth.se&gt;&gt;</a>, <span style="color:black">gmx-developers@gromacs.org</span> <a href="mailto:gmx-developers@gromacs.org">&lt;gmx-developers@gromacs.org&gt;&gt;</a><br>Subject:&nbsp;<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 style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div></div><div>




<title></title>


Hi Erik,
<div class=""><br class=""></div>
<div class="">here it is:</div>
<div class=""><br class=""></div>
<div class=""><br class=""></div>
<div class="">
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">GROMACS version:&nbsp; &nbsp; VERSION 5.1-rc1</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">Precision:&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; single</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">Memory model: &nbsp; &nbsp; &nbsp; 64 bit</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">MPI library:&nbsp; &nbsp; &nbsp; &nbsp; none</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">OpenMP support: &nbsp; &nbsp; disabled</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">GPU support:&nbsp; &nbsp; &nbsp; &nbsp; enabled</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">OpenCL support: &nbsp; &nbsp; enabled</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">invsqrt routine:&nbsp; &nbsp;
gmx_software_invsqrt(x)</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">SIMD instructions:&nbsp; AVX_256</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">FFT library:&nbsp; &nbsp; &nbsp; &nbsp;
fftw-3.3.4-sse2-avx</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">RDTSCP usage: &nbsp; &nbsp; &nbsp; enabled</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">C++11 compilation:&nbsp; disabled</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">TNG support:&nbsp; &nbsp; &nbsp; &nbsp; enabled</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">Tracing support:&nbsp; &nbsp; disabled</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">Built on: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Thu 16 Jul
2015 09:34:14 BST</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">Built by: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; carlo@
[CMAKE]</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">Build OS/arch:&nbsp; &nbsp; &nbsp; Darwin 13.4.0
x86_64</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">Build CPU vendor: &nbsp; GenuineIntel</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">Build CPU brand:&nbsp; &nbsp; Intel(R) Xeon(R) CPU E5-1650
v2 @ 3.50GHz</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">Build CPU family: &nbsp; 6 &nbsp; Model: 62 &nbsp;
Stepping: 4</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c
htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt
pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">C compiler: &nbsp; &nbsp; &nbsp; &nbsp;
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
Clang 6.0.0.6000057</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">C compiler flags:&nbsp; &nbsp; -mavx&nbsp; &nbsp; -Wall
-Wno-unused -Wunused-value -Wunused-parameter
-Wno-unknown-pragmas&nbsp; -O3 -DNDEBUG</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">C++ compiler: &nbsp; &nbsp; &nbsp;
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
Clang 6.0.0.6000057</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">C++ compiler flags:&nbsp; -mavx&nbsp; &nbsp; -Wextra
-Wno-missing-field-initializers -Wpointer-arith -Wall
-Wno-unused-function -Wno-unknown-pragmas&nbsp; -O3 -DNDEBUG</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">Boost version:&nbsp; &nbsp; &nbsp; 1.58.0 (external)</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">OpenCL include dir:
/System/Library/Frameworks/OpenCL.framework</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">OpenCL library: &nbsp; &nbsp;
/System/Library/Frameworks/OPENCL.framework</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">OpenCL version: &nbsp; &nbsp; 1.2</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo; min-height: 14px;" class=""><br class=""></div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo; min-height: 14px;" class=""><br class=""></div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">Running on 1 node with total 12 logical cores, 2
compatible GPUs</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">Hardware detected:</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">&nbsp; CPU info:</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">&nbsp; &nbsp; Vendor: GenuineIntel</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">&nbsp; &nbsp; Brand:&nbsp; Intel(R) Xeon(R) CPU E5-1650 v2
@ 3.50GHz</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">&nbsp; &nbsp; Family:&nbsp; 6&nbsp; model: 62&nbsp;
stepping:&nbsp; 4</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">&nbsp; &nbsp; CPU features: aes apic avx clfsh cmov cx8
cx16 f16c htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm
pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt
x2apic</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">&nbsp; &nbsp; SIMD instructions most likely to fit this
hardware: AVX_256</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">&nbsp; &nbsp; SIMD instructions selected at GROMACS
compile time: AVX_256</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">&nbsp; GPU info:</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">&nbsp; &nbsp; Number of GPUs detected: 2</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">&nbsp; &nbsp; #0: name: AMD Radeon HD - FirePro D500
Compute Engine, vendor: AMD, device version: OpenCL 1.2 , stat:
compatible</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">&nbsp; &nbsp; #1: name: AMD Radeon HD - FirePro D500
Compute Engine, vendor: AMD, device version: OpenCL 1.2 , stat:
compatible</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class=""><br class=""></div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class="">Carlo</div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class=""><br class=""></div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class=""><br class=""></div>
<div style="margin: 0px; font-size: 12px; font-family: Menlo;" class=""><br class=""></div>
<div>
<blockquote type="cite" class="">
<div class="">On 16 Jul 2015, at 18:59, Erik Lindahl &lt;<a href="mailto:erik.lindahl@gmail.com" class="">erik.lindahl@gmail.com</a>&gt; wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; margin: 0px;" class="">Hi Carlo,</div>
<div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; margin: 0px;" class=""><br class=""></div>
<div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; margin: 0px;" class="">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 &amp;
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; margin: 0px;" class=""><br class=""></div>
<div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; margin: 0px;" class="">Cheers,</div>
<div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; margin: 0px;" class=""><br class=""></div>
<div id="bloop_customfont" style="font-family: Helvetica, Arial; font-size: 13px; margin: 0px;" class="">Erik</div>
<div class="airmail_ext_on" style=""><br class="">
From:&nbsp;<span style="" class="">Carlo Camilloni</span> <a href="mailto:carlo.camilloni@gmail.com" class="">&lt;carlo.camilloni@gmail.com&gt;</a><br class="">
Reply:&nbsp;<span style="" class=""><a href="mailto:gmx-developers@gromacs.org" class="">gmx-developers@gromacs.org</a></span> <a href="mailto:gmx-developers@gromacs.org" class="">&lt;gmx-developers@gromacs.org&gt;&gt;</a><br class="">
Date:&nbsp;<span style="" class="">16 Jul 2015 at
18:52:21</span><br class="">
To:&nbsp;<span style="" class=""><a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se" class="">gromacs.org_gmx-developers@maillist.sys.kth.se</a></span>
<a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se" class="">&lt;gromacs.org_gmx-developers@maillist.sys.kth.se&gt;&gt;</a><br class="">

Subject:&nbsp; <span style="" class="">Re: [gmx-developers] gromacs
5.1rc1 OpenCL problem with Parrinello-Rahman<br class=""></span></div>
<br class="">
<blockquote type="cite" class="clean_bq">
<div class="">
<div class=""></div>
<div class=""><span class="">Hi,<br class="">
<br class="">
I tested the OpenCL kernel on my macbook (nvidia gpu) and here it
produces the correct forces,<br class="">
so it could be a problem related to amd+osx, or maybe to some
specific compiler/os version<br class="">
<br class="">
Carlo<br class="">
<br class="">
<br class="">
&gt; On 15 Jul 2015, at 17:42, Carlo Camilloni &lt;<a href="mailto:carlo.camilloni@gmail.com" class="">carlo.camilloni@gmail.com</a>&gt; wrote:<br class="">
&gt;<br class="">
&gt; Hi,<br class="">
&gt;<br class="">
&gt; these are the tests that fail:<br class="">
&gt;<br class="">
&gt; FAILED. Check checkpot.out (12 errors), checkforce.out (3516
errors) file(s) in dd121 for dd121<br class="">
&gt; FAILED. Check checkpot.out (10 errors), checkforce.out (4027
errors) file(s) in nbnxn-energy-groups for
nbnxn-energy-groups<br class="">
&gt; FAILED. Check checkpot.out (26 errors), checkforce.out (2998
errors) file(s) in nbnxn-free-energy for
nbnxn-free-energy<br class="">
&gt; FAILED. Check checkpot.out (26 errors), checkforce.out (2998
errors) file(s) in nbnxn-free-energy-vv for
nbnxn-free-energy-vv<br class="">
&gt; FAILED. Check checkpot.out (11 errors), checkforce.out (4039
errors) file(s) in nbnxn-ljpme-geometric for
nbnxn-ljpme-geometric<br class="">
&gt; FAILED. Check checkpot.out (14 errors), checkforce.out (52
errors) file(s) in nbnxn-ljpme-LB for nbnxn-ljpme-LB<br class="">
&gt; FAILED. Check checkpot.out (14 errors), checkforce.out (52
errors) file(s) in nbnxn-ljpme-LB-geometric for
nbnxn-ljpme-LB-geometric<br class="">
&gt; FAILED. Check checkpot.out (10 errors), checkforce.out (4029
errors) file(s) in nbnxn-vdw-force-switch for
nbnxn-vdw-force-switch<br class="">
&gt; FAILED. Check checkpot.out (10 errors), checkforce.out (4032
errors) file(s) in nbnxn-vdw-potential-switch for
nbnxn-vdw-potential-switch<br class="">
&gt; 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 class="">
&gt; FAILED. Check checkpot.out (10 errors), checkforce.out (4027
errors) file(s) in nbnxn_pme for nbnxn_pme<br class="">
&gt; FAILED. Check checkpot.out (10 errors), checkforce.out (4027
errors) file(s) in nbnxn_pme_order5 for nbnxn_pme_order5<br class="">
&gt; FAILED. Check checkpot.out (10 errors), checkforce.out (4027
errors) file(s) in nbnxn_pme_order6 for nbnxn_pme_order6<br class="">
&gt; FAILED. Check checkpot.out (9 errors), checkforce.out (4028
errors) file(s) in nbnxn_rf for nbnxn_rf<br class="">
&gt; FAILED. Check checkpot.out (2 errors), checkforce.out (4
errors) file(s) in nbnxn_rzero for nbnxn_rzero<br class="">
&gt; FAILED. Check mdrun.out, md.log file(s) in nbnxn_vsite for
nbnxn_vsite<br class="">
&gt; FAILED. Check checkpot.out (13 errors), checkforce.out (15512
errors) file(s) in octahedron for octahedron<br class="">
&gt; FAILED. Check mdrun.out, md.log file(s) in position-restraints
for position-restraints<br class="">
&gt; FAILED. Check mdrun.out, md.log file(s) in pull_constraint for
pull_constraint<br class="">
&gt; FAILED. Check checkpot.out (10 errors), checkforce.out (4021
errors) file(s) in pull_cylinder for pull_cylinder<br class="">
&gt; FAILED. Check checkpot.out (11 errors), checkforce.out (39054
errors) file(s) in swap_x for swap_x<br class="">
&gt; FAILED. Check checkpot.out (11 errors), checkforce.out (39053
errors) file(s) in swap_y for swap_y<br class="">
&gt; FAILED. Check checkpot.out (12 errors), checkforce.out (39054
errors) file(s) in swap_z for swap_z<br class="">
&gt; 23 out of 60 complex tests FAILED<br class="">
&gt; FAILED. Check mdrun.out, md.log file(s) in expanded for
expanded<br class="">
&gt; FAILED. Check mdrun.out, md.log file(s) in transformAtoB for
transformAtoB<br class="">
&gt; 2 out of 10 freeenergy tests FAILED<br class="">
&gt;<br class="">
&gt;<br class="">
&gt; Carlo<br class="">
&gt;<br class="">
&gt;<br class="">
&gt;&gt;<br class="">
&gt;&gt;<br class="">
&gt;&gt; Message: 4<br class="">
&gt;&gt; Date: Wed, 15 Jul 2015 15:35:13 +0000<br class="">
&gt;&gt; From: Mark Abraham &lt;<a href="mailto:mark.j.abraham@gmail.com" class="">mark.j.abraham@gmail.com</a>&gt;<br class="">
&gt;&gt; To: <a href="mailto:gmx-developers@gromacs.org" class="">gmx-developers@gromacs.org</a>,<br class="">
&gt;&gt; <a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se" class="">gromacs.org_gmx-developers@maillist.sys.kth.se</a><br class="">
&gt;&gt; Subject: Re: [gmx-developers] gromacs 5.1rc1 OpenCL
problem with<br class="">
&gt;&gt; Parrinello-Rahman<br class="">
&gt;&gt; Message-ID:<br class="">
&gt;&gt; &lt;<a href="mailto:CAMNuMATveVRRyBBwn312xrY+w3M7deC2Hs3A7PZnaeugkw+VVA@mail.gmail.com" class="">CAMNuMATveVRRyBBwn312xrY+w3M7deC2Hs3A7PZnaeugkw+VVA@mail.gmail.com</a>&gt;<br class="">

&gt;&gt; Content-Type: text/plain; charset="utf-8"<br class="">
&gt;&gt;<br class="">
&gt;&gt; Hi,<br class="">
&gt;&gt;<br class="">
&gt;&gt; Thanks. If a difference of that magnitude can be seen,
then it should also<br class="">
&gt;&gt; show up when running the regressiontests (e.g.
cmake<br class="">
&gt;&gt; -DREGRESSIONTEST_DOWNLOAD=on and then make check) as a
failure<br class="">
&gt;&gt; of complex/nbnxn-ljpme-LB (which is the only P-R test that
can run on the<br class="">
&gt;&gt; GPU). If other tests fail, then the problem is actually
more widespread.<br class="">
&gt;&gt;<br class="">
&gt;&gt; It may be that there is some issue with some part of the
Mac+clang+OpenCL<br class="">
&gt;&gt; stack - we didn't target it during development, and at the
last minute when<br class="">
&gt;&gt; Erik was unexpectedly able to get it to compile. I don't
know if he got<br class="">
&gt;&gt; tests to pass. Erik?<br class="">
&gt;&gt;<br class="">
&gt;&gt; Mark<br class="">
&gt;&gt;<br class="">
&gt;&gt; On Wed, Jul 15, 2015 at 5:22 PM Carlo Camilloni
&lt;<a href="mailto:carlo.camilloni@gmail.com" class="">carlo.camilloni@gmail.com</a>&gt;<br class="">
&gt;&gt; wrote:<br class="">
&gt;&gt;<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt; Dear Mark and Szilard,<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt; thanks for your answer. I filed a bug in redmine but
in the meantime I was<br class="">
&gt;&gt;&gt; running more tests and I am a bit scared by what I
found:<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt; what I have done is the following I have performed a
single step run with<br class="">
&gt;&gt;&gt; gmx51-rc1 compiled with cuda, again clang and so
on<br class="">
&gt;&gt;&gt; and compared the forces on the first step with -nb cpu
or not (I am using<br class="">
&gt;&gt;&gt; -pforce 1), the forces are identical:<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt; ie.:<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt; cuda-gpu<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt; step 0 atom 1 x 3.940 5.612 2.226 force
1.90839e+03<br class="">
&gt;&gt;&gt; step 0 atom 2 x 3.852 5.659 2.211 force
4.24845e+02<br class="">
&gt;&gt;&gt; step 0 atom 3 x 3.979 5.665 2.303 force
6.89472e+02<br class="">
&gt;&gt;&gt; step 0 atom 4 x 3.992 5.610 2.139 force
7.42053e+02<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt; cpu:<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt; step 0 atom 1 x 3.940 5.612 2.226 force
1.90839e+03<br class="">
&gt;&gt;&gt; step 0 atom 2 x 3.852 5.659 2.211 force
4.24845e+02<br class="">
&gt;&gt;&gt; step 0 atom 3 x 3.979 5.665 2.303 force
6.89472e+02<br class="">
&gt;&gt;&gt; step 0 atom 4 x 3.992 5.610 2.139 force
7.42053e+02<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt; if I do the same test on the version compiled with
OpenCL<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt; cpu:<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt; (the former are done on my macbook pro avx2_256 this
latter on a MacPro<br class="">
&gt;&gt;&gt; avx_256, this should<br class="">
&gt;&gt;&gt; explain the small differences in the forces)<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt; step 0 atom 1 x 3.940 5.612 2.226 force
1.90838e+03<br class="">
&gt;&gt;&gt; step 0 atom 2 x 3.852 5.659 2.211 force
4.24848e+02<br class="">
&gt;&gt;&gt; step 0 atom 3 x 3.979 5.665 2.303 force
6.89470e+02<br class="">
&gt;&gt;&gt; step 0 atom 4 x 3.992 5.610 2.139 force
7.42043e+02<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt; opencl-gpu:<br class="">
&gt;&gt;&gt; step 0 atom 1 x 3.940 5.612 2.226 force
1.48597e+03<br class="">
&gt;&gt;&gt; step 0 atom 2 x 3.852 5.659 2.211 force
6.26942e+02<br class="">
&gt;&gt;&gt; step 0 atom 3 x 3.979 5.665 2.303 force
8.44032e+02<br class="">
&gt;&gt;&gt; step 0 atom 4 x 3.992 5.610 2.139 force
7.92786e+02<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt; I am afraid there is something wrong in OpenCL
kernels.<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt; I am using the topol-nvt-nogen.tpr I have uploaded on
redmine.<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt; Best,<br class="">
&gt;&gt;&gt; Carlo<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt;<br class="">
&gt;&gt;&gt; --<br class="">
&gt;&gt;&gt; Gromacs Developers mailing list<br class="">
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&gt;&gt; End of <a href="http://gromacs.org" class="">gromacs.org</a>_gmx-developers Digest, Vol 135, Issue
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&gt;&gt;
***********************************************************<br class="">

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</blockquote>
<div id="bloop_sign_1437065855198064128" class="bloop_sign">
<div style="font-family:helvetica,arial;font-size:13px" class="">
--&nbsp;<br class="">
<span style="font-family: 'helvetica Neue', helvetica;" class="">Erik Lindahl &lt;</span><a href="mailto:erik.lindahl@gmail.com" style="font-family: 'helvetica Neue', helvetica;" class="">erik.lindahl@gmail.com</a><span style="font-family: 'helvetica Neue', helvetica;" class="">&gt;&nbsp;</span><br style="font-family: 'helvetica Neue', helvetica;" class="">
<span style="font-family: 'helvetica Neue', helvetica;" class="">Professor of Biophysics, Dept. Biochemistry &amp; Biophysics,
Stockholm&nbsp;</span><span style="font-family: 'helvetica Neue', helvetica;" class="">University&nbsp;</span><br style="font-family: 'helvetica Neue', helvetica;" class="">
<span style="font-family: 'helvetica Neue', helvetica;" class="">Professor of Theoretical biophysics, Dept. Theoretical Physics,
Royal Inst.&nbsp;</span><span style="font-family: 'helvetica Neue', helvetica;" class="">Technology&nbsp;</span><br style="font-family: 'helvetica Neue', helvetica;" class="">
<span style="font-family: 'helvetica Neue', helvetica;" class="">Science for Life Laboratory, Box 1031, 17121 Solna,
Sweden</span></div>
</div>
</div>
</div>
</blockquote>
</div>
<br class=""></div>


</div></div></span></blockquote> <div id="bloop_sign_1437067027196130048" class="bloop_sign"><div style="font-family:helvetica,arial;font-size:13px">--&nbsp;<br><span style="font-family: 'helvetica Neue', helvetica;">Erik Lindahl &lt;</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;">&gt;&nbsp;</span><br style="font-family: 'helvetica Neue', helvetica;"><span style="font-family: 'helvetica Neue', helvetica;">Professor of Biophysics, Dept. Biochemistry &amp; Biophysics, Stockholm&nbsp;</span><span style="font-family: 'helvetica Neue', helvetica;">University&nbsp;</span><br style="font-family: 'helvetica Neue', helvetica;"><span style="font-family: 'helvetica Neue', helvetica;">Professor of Theoretical biophysics, Dept. Theoretical Physics, Royal Inst.&nbsp;</span><span style="font-family: 'helvetica Neue', helvetica;">Technology&nbsp;</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>