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<div class="section" id="setting-up-musrfit-dks-high-speed-fitting-with-gpu-s">
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<span id="setup-dks"></span><span id="index-0"></span><h1>Setting up <tt class="docutils literal"><span class="pre">musrfit</span></tt> / <tt class="docutils literal"><span class="pre">DKS</span></tt>: High Speed Fitting with GPU’s<a class="headerlink" href="#setting-up-musrfit-dks-high-speed-fitting-with-gpu-s" title="Permalink to this headline">¶</a></h1>
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<p>In the years 2016/2017 we explored ways to speed up current fitting frameworks, especially <tt class="docutils literal"><span class="pre">musrfit.</span></tt>
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This allows now to analyze histogram sets of high field spectrometers like <tt class="docutils literal"><span class="pre">HAL-9500</span></tt> at PSI without
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the <em>error-prone</em> RRF fitting (see U. Locans and A. Suter,
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<a class="reference external" href="http://dx.doi.org/10.7566/JPSCP.21.011051">musrfit - Real Time Parameter Fitting Using GPU</a>, and the
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Memo from A. Suter, “Rotating Reference Frame Fits”, in the <tt class="docutils literal"><span class="pre">musrfit</span></tt> source code). At the same time
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it can help to speed-up elaborate global fits tremendously, and dealing properly with muonium. It also
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allows Apple macOS users to speed up their fitting code on the CPU. Currently it is not straight forward
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to get <tt class="docutils literal"><span class="pre">musrfit</span></tt> multi-threaded under macOS since Apple doesn’t be default support <tt class="docutils literal"><span class="pre">OpenMP</span></tt>. <tt class="docutils literal"><span class="pre">DKS</span></tt>
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enables <tt class="docutils literal"><span class="pre">musrfit</span></tt> to utilize <tt class="docutils literal"><span class="pre">OpenCL</span></tt> instead which is present on macOS by default.</p>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">Before you run into the shop to buy a gamer graphic card or a Tesla card, make sure that you have an
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appropriate server with a sufficiently strong power supply!</p>
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</div>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">However, the current <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> version doesn’t yet support all theory functions on the GPU.
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In case the theory function is not yet available for the GPU, <tt class="docutils literal"><span class="pre">musrfit</span></tt> will fall back to the CPU implementation.</p>
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</div>
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<p>Conceptually the setup of <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> is as following:</p>
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<ol class="arabic simple">
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<li>install the latest hardware driver for your graphic card.</li>
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<li>install the GPU SDK which enables number crunching (<tt class="docutils literal"><span class="pre">CUDA</span></tt> for NVIDIA, <tt class="docutils literal"><span class="pre">OpenCL</span></tt> for AMD)</li>
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<li>install <tt class="docutils literal"><span class="pre">DKS</span></tt></li>
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<li>install the <tt class="docutils literal"><span class="pre">musrfit</span></tt> version which is <tt class="docutils literal"><span class="pre">DKS</span></tt> ready</li>
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</ol>
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<p>In the following the description for the installation of <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> for the following systems will be discussed in some more detail:</p>
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<ul class="simple">
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<li>NVIDIA Tesla K40c</li>
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<li>AMD Graphic Card (Radeon R9 390X)</li>
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<li>macOS in order to get <tt class="docutils literal"><span class="pre">OpenCL</span></tt> support</li>
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</ul>
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<p>The usage of <tt class="docutils literal"><span class="pre">musrfit</span></tt> with GPU acceleration and <tt class="docutils literal"><span class="pre">OpenCL</span></tt> support is described in the
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<a class="reference internal" href="user-manual.html#user-manual"><em>User manual of the μSR data analysis software musrfit</em></a>. The additional
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<tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> are found <a class="reference internal" href="user-manual.html#msr-commands-block-dks"><em>here</em></a>.</p>
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<div class="section" id="setting-up-musrfit-dks-for-a-tesla-k40c-nvidia">
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<span id="index-1"></span><h2>Setting up <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> for a Tesla K40c (NVIDIA)<a class="headerlink" href="#setting-up-musrfit-dks-for-a-tesla-k40c-nvidia" title="Permalink to this headline">¶</a></h2>
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<p>It is assumed that the Tesla K40c is already physically installed on your system. For now I only
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will discuss to set it up for a Linux based system. In order to check that your operating systems
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see the card, enter the following command in the terminal:</p>
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<div class="highlight-bash"><div class="highlight"><pre><span></span>$ lspci <span class="p">|</span> grep NVIDIA
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</pre></div>
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</div>
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<p>The response should look something like</p>
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<div class="highlight-python"><div class="highlight"><pre><span></span>05:00.0 3D controller: NVIDIA Corporation GK110BGL [Tesla K40c] (rev a1)
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</pre></div>
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</div>
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<p>which means that the OS physically recognizes your card.</p>
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<div class="section" id="driver-installation-for-the-tesla-k40c">
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<h3>Driver Installation for the Tesla K40c<a class="headerlink" href="#driver-installation-for-the-tesla-k40c" title="Permalink to this headline">¶</a></h3>
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<p>Next, you will need to download and install the driver for your card. Select the proper operating system,
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card, etc. from the <a class="reference external" href="http://www.nvidia.com/Download/index.aspx?lang=en-us">NVIDIA download center</a>. At PSI
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we are running currently Red Hat Enterprise Linux 7.x (RHEL) for which we will get a <tt class="docutils literal"><span class="pre">rpm</span></tt> (something like
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<tt class="docutils literal"><span class="pre">nvidia-diag-driver-local-repo-rhel7-375.66-1.x86_64.rpm</span></tt>). Install it and make sure there is no conflict
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with the nouveau driver of the system.</p>
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</div>
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<div class="section" id="installation-of-cuda">
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<span id="index-2"></span><h3>Installation of CUDA<a class="headerlink" href="#installation-of-cuda" title="Permalink to this headline">¶</a></h3>
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<p>Download the <a class="reference external" href="https://developer.nvidia.com/cuda-downloads">CUDA SDK</a> form NVIDIA for your system. Again,
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for the RHEL 7.x this is an <tt class="docutils literal"><span class="pre">rpm</span></tt>. After the installation of the rpm you should reboot your machine.
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Afterwards you are ready for the installation of <tt class="docutils literal"><span class="pre">DKS</span></tt>.</p>
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</div>
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<div class="section" id="installation-of-dks">
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<span id="index-3"></span><h3>Installation of DKS<a class="headerlink" href="#installation-of-dks" title="Permalink to this headline">¶</a></h3>
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<p>For the following list of commands the <tt class="docutils literal"><span class="pre">'$'</span></tt> will be given as the command prompt. <em>Do not enter it!</em>
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Also some comments will be added starting with a <tt class="docutils literal"><span class="pre">'#'</span></tt> which can be omitted. They are only there to
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explain what is going on. <tt class="docutils literal"><span class="pre">DKS</span></tt> stands for Dynamical Kernel Scheduler and provides a thin interface
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allowing host applications to incorporate GPU’s and other hardware accelerators.</p>
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<p>Details can be found in the papers listed <a class="reference internal" href="cite.html#cite"><em>here</em></a>, or on the <a class="reference external" href="https://gitlab.psi.ch/uldis_l/DKS/wikis/home">DKS wiki page</a>.</p>
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<p>In brief the installation should be something like this:</p>
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<div class="highlight-bash"><div class="highlight"><pre><span></span><span class="c1"># go to whatever directory you would like to clone/install DKS</span>
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<span class="c1"># For macOS DKS will likely to got to $HOME/Applications to be consistent with the musrfit docu for macOS</span>
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$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps
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$ git clone https://gitlab.psi.ch/uldis_l/DKS.git
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$ <span class="nb">cd</span> DKS
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$ mkdir build
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$ <span class="nb">cd</span> build
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$ cmake ../ -DENABLE_MUSR<span class="o">=</span><span class="m">1</span> -DCMAKE_INSTALL_PREFIX<span class="o">=</span>../exec
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$ cmake --build ./ --clean-first
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$ make install
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</pre></div>
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</div>
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<p>Since <tt class="docutils literal"><span class="pre">DKS</span></tt> is installed in a non-standard path, a couple of additional small steps are required.
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This will be different for Linux compared to macOS.</p>
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<p>For <strong>Linux:</strong></p>
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<p>add the <tt class="docutils literal"><span class="pre">DKS</span></tt> library path to <tt class="docutils literal"><span class="pre">/etc/ld.so.conf.d/musrfit-x86_64.conf</span></tt> and execute as super user</p>
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<div class="highlight-bash"><div class="highlight"><pre><span></span>$ /sbin/ldconfig
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</pre></div>
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</div>
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<p>For <strong>macOS:</strong></p>
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<p>add the <tt class="docutils literal"><span class="pre">DKS</span></tt> path to <tt class="docutils literal"><span class="pre">$HOME/.profile</span></tt>:</p>
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<div class="highlight-bash"><div class="highlight"><pre><span></span><span class="nb">export</span> <span class="nv">DKS</span><span class="o">=</span><span class="nv">$HOME</span>/Applications/DKS/exec
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<span class="nb">export</span> <span class="nv">LD_LIBRARY_PATH</span><span class="o">=</span><span class="nv">$DKS</span>/lib:<span class="nv">$LD_LIBRARY_PATH</span>
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launchctl setenv DKS <span class="nv">$DKS</span>
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launchctl setenv LD_LIBRARY_PATH <span class="nv">$LD_LIBRARY_PATH</span>
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</pre></div>
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</div>
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</div>
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<div class="section" id="installation-of-musrfit-for-dks">
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<span id="musrfit-dks-install"></span><h3>Installation of musrfit for DKS<a class="headerlink" href="#installation-of-musrfit-for-dks" title="Permalink to this headline">¶</a></h3>
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<p>Most of the installation steps are the same as described for <tt class="docutils literal"><span class="pre">musrfit</span></tt> without GPU support.
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||
Here only the differences are explained. First checkout <tt class="docutils literal"><span class="pre">musrfit</span></tt>, then you will need to
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||
switch the working branch which is done by</p>
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<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps/musrfit
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$ git checkout dks6
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</pre></div>
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</div>
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<div class="section" id="install-via-cmake">
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<h4>Install via cmake<a class="headerlink" href="#install-via-cmake" title="Permalink to this headline">¶</a></h4>
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<p>There is on more configuration switch</p>
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<dl class="docutils">
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<dt><strong>-Ddks=<value></strong></dt>
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<dd>it allows to enable/disable <tt class="docutils literal"><span class="pre">DKS</span></tt> support. The default is <tt class="docutils literal"><span class="pre"><value>=1</span></tt>, <em>i.e.</em> enabled. To disable use <tt class="docutils literal"><span class="pre"><value>=0</span></tt>.</dd>
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</dl>
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<p>For a typical setup on a RHEL or macOS system it could look like this</p>
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<div class="highlight-bash"><div class="highlight"><pre><span></span>$ cmake ../ -DCMAKE_INSTALL_PREFIX<span class="o">=</span><span class="nv">$ROOTSYS</span> -DASlibs<span class="o">=</span><span class="m">1</span> -DBMWlibs<span class="o">=</span><span class="m">1</span> -Dnexus<span class="o">=</span><span class="m">1</span> -Ddks<span class="o">=</span><span class="m">1</span>
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</pre></div>
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</div>
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<p>After</p>
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<div class="highlight-bash"><div class="highlight"><pre><span></span>$ cmake --build ./ --clean-first -- -j8
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$ make install
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</pre></div>
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</div>
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<p>and updating the shared library lookup table (<em>only</em> needed for Linux)</p>
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<div class="highlight-bash"><div class="highlight"><pre><span></span>$ /sbin/ldconfig <span class="c1"># as superuser / root</span>
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</pre></div>
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</div>
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<p>you are done with the setup.</p>
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</div>
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</div>
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</div>
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<div class="section" id="setting-up-musrfit-dks-for-a-amd-graphic-card-radeon-r9-390x">
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<span id="index-4"></span><h2>Setting up <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> for a AMD Graphic Card (Radeon R9 390X)<a class="headerlink" href="#setting-up-musrfit-dks-for-a-amd-graphic-card-radeon-r9-390x" title="Permalink to this headline">¶</a></h2>
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||
<div class="section" id="driver-installation-for-an-amd-graphic-card-e-g-radeon-r9-390x">
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||
<h3>Driver Installation for an AMD Graphic Card, <em>e.g.</em> Radeon R9 390X<a class="headerlink" href="#driver-installation-for-an-amd-graphic-card-e-g-radeon-r9-390x" title="Permalink to this headline">¶</a></h3>
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<p>This will depend slightly on the AMD Card and operating system. Here I will summaries how it was done
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on a RHEL (Linux) system using a Radeon R9 390X.</p>
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<p>It is assumed that the Radeon R9 390X is already physically installed on your system. For now I only
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will discuss to set it up for a Linux based system. In order to check that your operating systems see
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the card, enter the following command in the terminal:</p>
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<div class="highlight-bash"><div class="highlight"><pre><span></span>$ lspci <span class="p">|</span> grep AMD
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</pre></div>
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</div>
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<p>The response should look something like</p>
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<div class="highlight-python"><div class="highlight"><pre><span></span>84:00.0 VGA compatible controller: Advanced Micro Devices, Inc. [AMD/ATI] Hawaii XT / Grenada XT [Radeon R9 290X/390X] (rev 80)
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</pre></div>
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</div>
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<p>which means that the OS physically recognizes your card.</p>
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<p>For RHEL7.x the AMDGPU-PRO driver should be used. It can be downloaded from <a class="reference external" href="http://support.amd.com/en-us/kb-articles/Pages/AMDGPU-PRO-RedHat-Install.aspx">AMD</a>. Unpack the driver</p>
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<div class="highlight-bash"><div class="highlight"><pre><span></span>$ tar -Jxvf amdgpu-pro-17.10-414273.tar.xz
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$ <span class="nb">cd</span> amdgpu-pro-17.10-414273
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</pre></div>
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</div>
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<p>Install the driver as root</p>
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<div class="highlight-bash"><div class="highlight"><pre><span></span>$ ./amdgpu-pro-install --compute -y
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</pre></div>
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</div>
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<p>Here I assume that the AMD graphic card is only used for computation. You need to add the following command
|
||
in order that the user <strong>blabla</strong> (change this to the appropriate user name) can access the GPU (otherwise
|
||
only root works):</p>
|
||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ /sbin/usermod -a -G video blabla
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</pre></div>
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</div>
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||
<p>Reboot the machine.</p>
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||
</div>
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||
<div class="section" id="amd-app-software-development-kit-sdk-to-enable-opencl-support">
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||
<h3>AMD APP Software Development Kit (SDK) to enable <tt class="docutils literal"><span class="pre">OpenCL</span></tt> support<a class="headerlink" href="#amd-app-software-development-kit-sdk-to-enable-opencl-support" title="Permalink to this headline">¶</a></h3>
|
||
<p>The AMD APP Software Development Kit (SDK) is a complete development platform created by AMD to allow you to
|
||
quickly and easily develop applications accelerated by AMD APP technology. The SDK provides samples, documentation,
|
||
and other materials to quickly get you started leveraging accelerated compute using <tt class="docutils literal"><span class="pre">OpenCL</span></tt> or <tt class="docutils literal"><span class="pre">C++</span> <span class="pre">AMP</span></tt> in your
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||
<tt class="docutils literal"><span class="pre">C/C++</span></tt> applications.</p>
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||
<p>Download the AMD APP SDK 3.0 from <a class="reference external" href="http://developer.amd.com/tools-and-sdks/opencl-zone/amd-accelerated-parallel-processing-app-sdk/">AMD-SDK</a>.</p>
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||
<p>Extract the installer</p>
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||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ tar -xvjf AMD-APP-SDKInstaller-v3.0.130.136-GA-linux64.tar.bz2
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||
</pre></div>
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||
</div>
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||
<p>Run the installer</p>
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||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ ./AMD-APP-SDK-v3.0.130.136-GA-linux64.sh
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||
</pre></div>
|
||
</div>
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||
<p>This will install the AMD APP SDK to <tt class="docutils literal"><span class="pre">/opt/AMDAPPSDK-3.0/</span></tt> where you can find the <tt class="docutils literal"><span class="pre">OpenCL</span></tt> include
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||
and library files, as well as documentation and sample code. The install guide for AMD OpenCL SDK can
|
||
be found at <a class="reference external" href="http://developer.amd.com/wordpress/media/2012/10/AMD_APP_SDK_InstallationNotes.pdf">AMD SDK Installation Notes</a>.</p>
|
||
</div>
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||
<div class="section" id="installation-of-dks-and-musrfit">
|
||
<h3>Installation of DKS and musrfit<a class="headerlink" href="#installation-of-dks-and-musrfit" title="Permalink to this headline">¶</a></h3>
|
||
<p>To install <tt class="docutils literal"><span class="pre">DKS</span></tt> and <tt class="docutils literal"><span class="pre">musrfit</span></tt> follow the instructions <a class="reference internal" href="#musrfit-dks-install"><em>above</em></a>.</p>
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||
</div>
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||
</div>
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||
<div class="section" id="setting-up-musrfit-dks-for-macos-for-opencl-support">
|
||
<span id="index-5"></span><h2>Setting up <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> for macOS for OpenCL support<a class="headerlink" href="#setting-up-musrfit-dks-for-macos-for-opencl-support" title="Permalink to this headline">¶</a></h2>
|
||
<p>Since Apple is not providing an out-of-the-box <tt class="docutils literal"><span class="pre">OpenMP</span></tt> support on their macOS compiler framework (Xcode),
|
||
typically <tt class="docutils literal"><span class="pre">musrfit</span></tt> is just running <em>single threaded</em>. Here <tt class="docutils literal"><span class="pre">DKS</span></tt> can help since it delivers <tt class="docutils literal"><span class="pre">OpenCL</span></tt>
|
||
support which is present on macOS. Hence, if you would like to run <tt class="docutils literal"><span class="pre">musrfit</span></tt> multi-threaded the easiest
|
||
way is to use <tt class="docutils literal"><span class="pre">DKS</span></tt>.</p>
|
||
<p>Since there is no graphic card involved, you do not need any graphic card driver of additional SDK.
|
||
The only thing you need <tt class="docutils literal"><span class="pre">DKS</span></tt> and the proper <tt class="docutils literal"><span class="pre">musrfit</span></tt> version.</p>
|
||
<p>The installation instruction for <tt class="docutils literal"><span class="pre">DKS/musrfit</span></tt> can be found <a class="reference internal" href="#musrfit-dks-install"><em>here</em></a>.</p>
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||
</div>
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<h3><a href="index.html">Table Of Contents</a></h3>
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||
<ul>
|
||
<li><a class="reference internal" href="#">Setting up <tt class="docutils literal"><span class="pre">musrfit</span></tt> / <tt class="docutils literal"><span class="pre">DKS</span></tt>: High Speed Fitting with GPU’s</a><ul>
|
||
<li><a class="reference internal" href="#setting-up-musrfit-dks-for-a-tesla-k40c-nvidia">Setting up <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> for a Tesla K40c (NVIDIA)</a><ul>
|
||
<li><a class="reference internal" href="#driver-installation-for-the-tesla-k40c">Driver Installation for the Tesla K40c</a></li>
|
||
<li><a class="reference internal" href="#installation-of-cuda">Installation of CUDA</a></li>
|
||
<li><a class="reference internal" href="#installation-of-dks">Installation of DKS</a></li>
|
||
<li><a class="reference internal" href="#installation-of-musrfit-for-dks">Installation of musrfit for DKS</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a class="reference internal" href="#setting-up-musrfit-dks-for-a-amd-graphic-card-radeon-r9-390x">Setting up <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> for a AMD Graphic Card (Radeon R9 390X)</a><ul>
|
||
<li><a class="reference internal" href="#driver-installation-for-an-amd-graphic-card-e-g-radeon-r9-390x">Driver Installation for an AMD Graphic Card, <em>e.g.</em> Radeon R9 390X</a></li>
|
||
<li><a class="reference internal" href="#amd-app-software-development-kit-sdk-to-enable-opencl-support">AMD APP Software Development Kit (SDK) to enable <tt class="docutils literal"><span class="pre">OpenCL</span></tt> support</a></li>
|
||
<li><a class="reference internal" href="#installation-of-dks-and-musrfit">Installation of DKS and musrfit</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a class="reference internal" href="#setting-up-musrfit-dks-for-macos-for-opencl-support">Setting up <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> for macOS for OpenCL support</a></li>
|
||
</ul>
|
||
</li>
|
||
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|
||
|
||
<h4>Previous topic</h4>
|
||
<p class="topless"><a href="setup-standard.html"
|
||
title="previous chapter">Setting up <tt class="docutils literal"><span class="pre">musrfit</span></tt> on Different Platforms</a></p>
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<h4>Next topic</h4>
|
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<p class="topless"><a href="musredit.html"
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title="next chapter"><tt class="docutils literal"><span class="pre">musredit</span></tt>: the GUI Based Interface to <tt class="docutils literal"><span class="pre">musrfit</span></tt></a></p>
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© Copyright 2019, Andreas Suter.
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Last updated on Jul 24, 2019.
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