<div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div dir="ltr" class="gmail_signature">On Thu, Apr 25, 2019 at 12:21 PM Mahmood Naderan <<a href="mailto:nt_mahmood@yahoo.com">nt_mahmood@yahoo.com</a>> wrote:<br></div></div></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div class="gmail-m_-852978352894065041ydpf4147f18yahoo-style-wrap" style="font-family:"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:16px"><div><div>Thanks Szilard,</div><div><br></div><div>I looked at that. It seems that it is a big GPU kernel and specific parts of it are executed using #ifdef macros and those are actually enabled whenever it is needed in <a href="http://nbnxn_cuda.cu" target="_blank">nbnxn_cuda.cu</a>.</div></div></div></div></blockquote><div><br></div><div>Not really. Combinations of LJ and Coulomb flavors as well input/output functionalities (force, force and energy, pruning) are all generated and compiled into the binary. Selection happens at runtime, see in nbnxn_cuda.cu:select_nbnxn_kernel().</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div class="gmail-m_-852978352894065041ydpf4147f18yahoo-style-wrap" style="font-family:"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:16px"><div><div>However, the names are still vague for me. For example, I assume that the FUNC_NAME is something like <span><span>ElecEw_VdwLJCombLB_F</span></span> but grepping even *LJComb* shows no match.</div></div></div></div></blockquote><div><br></div><div>It should show up; this a common component of the short-range pair interaction kernel over all architectures, CPU and GPU, so it will be all over the place in the nbnxn module. Try "git grep LJComb".</div><div><br></div><div>The CUDA kernel generation happens in src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div class="gmail-m_-852978352894065041ydpf4147f18yahoo-style-wrap" style="font-family:"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:16px"><div><div>Instead I see "<span>#ifndef LJ_COMB</span>". I would like to know which part of the kernel is used for <span><span><span>ElecEw_VdwLJCombLB_F?</span></span></span></div></div></div></div></blockquote><div><br></div><div>See the mapping of macros to filenames in the above file.</div><div><br></div><div>Let me know if something is still unclear.</div><div><br></div><div>Cheers,</div>--<br>Szilárd<br class="gmail-Apple-interchange-newline"><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div class="gmail-m_-852978352894065041ydpf4147f18yahoo-style-wrap" style="font-family:"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:16px"><div><div><br></div><div><br></div><div><br></div><div class="gmail-m_-852978352894065041ydpf4147f18signature">Regards,<br>Mahmood</div></div>
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On Thursday, April 25, 2019, 1:29:46 PM GMT+4:30, Szilárd Páll <<a href="mailto:pall.szilard@gmail.com" target="_blank">pall.szilard@gmail.com</a>> wrote:
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<div><div id="gmail-m_-852978352894065041yiv3132218080"><div><div dir="ltr"><div dir="ltr"><div>Hi Mahmood,</div><div><br clear="none"></div><div>The kernels are preprocessor-generated, including the kernel names (see NB_KERNEL_FUNC_NAME() macro); the common source code is in src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh.<br clear="none"></div><div><br clear="none"></div><div>Cheers,<br clear="none"></div><div><div><div class="gmail-m_-852978352894065041yiv3132218080gmail_signature" dir="ltr">--<br clear="none">Szilárd</div></div><br clear="none"></div></div></div><br clear="none"><div class="gmail-m_-852978352894065041yiv3132218080gmail_quote"><div class="gmail-m_-852978352894065041yiv3132218080yqt0801659908" id="gmail-m_-852978352894065041yiv3132218080yqt30938"><div class="gmail-m_-852978352894065041yiv3132218080gmail_attr" dir="ltr">On Wed, Apr 24, 2019 at 7:24 PM Mahmood <<a rel="nofollow" shape="rect" href="mailto:nt_mahmood@yahoo.com" target="_blank">nt_mahmood@yahoo.com</a>> wrote:<br clear="none"></div><blockquote class="gmail-m_-852978352894065041yiv3132218080gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div class="gmail-m_-852978352894065041yiv3132218080gmail-m_7309833779300565241ydp9338e8dayahoo-style-wrap" style="font-family:"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:16px"><div><div>Hi,</div><div><br clear="none"></div><div>How can I see the code of a GPU kernel named <span>nbnxn_kernel_ElecEw_VdwLJCombLB_F_cuda?</span></div><div><span><br clear="none"></span></div><div><span>That exists in src<span>/gromacs/mdlib/nbnxn_cuda/<a rel="nofollow" shape="rect" href="http://nbnxn_cuda.cu" target="_blank">nbnxn_cuda.cu</a></span> however, I can not find its implementation. <br clear="none"></span></div><div><span><br clear="none"></span></div><div><span>Can someone help?</span></div><div><span><br clear="none"></span></div><div><span><br clear="none"></span></div><div><br clear="none"></div><div class="gmail-m_-852978352894065041yiv3132218080gmail-m_7309833779300565241ydp9338e8dasignature">Regards,<br clear="none">Mahmood</div></div></div></div>-- <br clear="none">
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