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<div class="section" id="installation">
<span id="start-guide"></span><h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
<div class="section" id="prerequisites">
<h2>Prerequisites<a class="headerlink" href="#prerequisites" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div><table border="1" class="docutils">
<colgroup>
<col width="22%" />
<col width="43%" />
<col width="35%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>MPI C++ compiler</td>
<td> </td>
<td>C++11 and MPI-3 support</td>
</tr>
<tr class="row-even"><td>GNU Libtool</td>
<td><a class="reference external" href="https://www.gnu.org/software/libtool">https://www.gnu.org/software/libtool</a></td>
<td> </td>
</tr>
<tr class="row-odd"><td>GNU Autoconf</td>
<td><a class="reference external" href="https://www.gnu.org/software/autoconf">https://www.gnu.org/software/autoconf</a></td>
<td>Version 2.69 or newer</td>
</tr>
<tr class="row-even"><td>GNU Automake</td>
<td><a class="reference external" href="https://www.gnu.org/software/automake">https://www.gnu.org/software/automake</a></td>
<td> </td>
</tr>
<tr class="row-odd"><td>Boost C++ Libraries</td>
<td><a class="reference external" href="http://www.boost.org">http://www.boost.org</a></td>
<td>Version 1.53.0 or newer</td>
</tr>
<tr class="row-even"><td>BLAS</td>
<td><a class="reference external" href="http://www.netlib.org/blas">http://www.netlib.org/blas</a></td>
<td>Use optimized BLAS</td>
</tr>
<tr class="row-odd"><td>LAPACK</td>
<td><a class="reference external" href="http://www.netlib.org/lapack">http://www.netlib.org/lapack</a></td>
<td>Use optimized LAPACK</td>
</tr>
<tr class="row-even"><td>ScaLAPACK</td>
<td><a class="reference external" href="http://www.netlib.org/scalapack">http://www.netlib.org/scalapack</a></td>
<td>Use optimized ScaLPACK</td>
</tr>
</tbody>
</table>
</div></blockquote>
<p>Intel MKL is strongly recommended for BLAS, LAPACK, and ScaLAPACK (distributed for free for academic users)</p>
</div>
<div class="section" id="downloading-the-source">
<h2>Downloading the source<a class="headerlink" href="#downloading-the-source" title="Permalink to this headline">¶</a></h2>
<p>The simplest approach is to just download and extract the tarball containing the most recent BAGEL release:</p>
<pre class="literal-block">
$ wget <a class="reference external" href="https://github.com/nubakery/bagel/archive/v">https://github.com/nubakery/bagel/archive/v</a>1.1.1.tar.gz
$ tar xvf bagel-1.1.1.tar.gz
$ cd bagel
</pre>
<p>Alternatively, you can clone the git repository:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ git clone https://github.com/nubakery/bagel.git
$ cd bagel
</pre></div>
</div>
<p>The SMITH3 code generator can be downloaded in a similar manner from <a class="reference external" href="https://github.com/nubakery/">the NUBakery GitHub page</a>.</p>
</div>
<div class="section" id="build-bagel">
<h2>Build BAGEL<a class="headerlink" href="#build-bagel" title="Permalink to this headline">¶</a></h2>
<ul>
<li><p class="first">Automake</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ glibtoolize (or, libtoolize)
$ aclocal
$ autoconf
$ autoheader
$ automake -a
</pre></div>
</div>
</li>
<li><p class="first">Create an object directory</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ mkdir obj
$ cd obj
</pre></div>
</div>
</li>
<li><p class="first">Configure</p>
<p>A minimal set of configure options is</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ export BOOST_ROOT=/path/to/boost
$ export LD_LIBRARY_PATH=$BOOST_ROOT/lib:$LD_LIBRARY_PATH
$ ../configure --enable-mkl --with-boost=$BOOST_ROOT
</pre></div>
</div>
<dl class="docutils">
<dt>Configure options:</dt>
<dd><div class="first last line-block">
<div class="line"><code class="docutils literal notranslate"><span class="pre">--with-mpi=value</span></code> turns on MPI, where “value” can be “mvapich”, “intel”, or “openmpi”.
However, Open MPI is not recommended.</div>
<div class="line"><code class="docutils literal notranslate"><span class="pre">--enable-mkl</span></code> turns on MKL extensions, such as efficient matrix transposition. MKL libraries are automatically detected.</div>
<div class="line"><code class="docutils literal notranslate"><span class="pre">--with-boost=/path/to/boost</span></code> specifies the BOOST library to be used.</div>
<div class="line"><code class="docutils literal notranslate"><span class="pre">--disable-scalapack</span></code> will disable the use of ScaLapack (parallel Lapack) which is not recommended.</div>
<div class="line"><code class="docutils literal notranslate"><span class="pre">--disable-smith</span></code> will disable the code generated by SMITH which is not recommended.</div>
<div class="line"><code class="docutils literal notranslate"><span class="pre">--with-include</span></code> can be used to specifically include paths.</div>
<div class="line"><code class="docutils literal notranslate"><span class="pre">--with-libxc</span></code> turns on the interface to libxc.</div>
<div class="line"><code class="docutils literal notranslate"><span class="pre">CXXFLAGS=-DNDEBUG</span></code> deactivates the debugging mode. <strong>It is absolutely essential to specify this for release builds</strong>.</div>
<div class="line"><code class="docutils literal notranslate"><span class="pre">CXXFLAGS=-DCOMPILE_J_ORB</span></code> allows the inclusion of <em>j</em>-type atomic basis functions.</div>
</div>
</dd>
</dl>
<p>Example (Release build on the Shiozaki group’s cluster)</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ export BOOST_ROOT=/usr/local/boost/boost_1_64_0_gcc-7.1.0
$ export LD_LIBRARY_PATH=$BOOST_ROOT/lib:$LD_LIBRARY_PATH
$ ../configure CXXFLAGS="-DNDEBUG -O3 -mavx" --enable-mkl --with-boost=$BOOST_ROOT --with-mpi=intel
</pre></div>
</div>
</li>
<li><p class="first">Compile</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ make -j4
$ make install
</pre></div>
</div>
</li>
<li><p class="first">Test run</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ BAGEL path_to_bagel/test/benzene_svp_mp2.json
</pre></div>
</div>
<p>Also there is a suite of test programs. To run this, in obj</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ cd bagel/obj
$ make check
$ cd src
$ ./TestSuite --log_level=all
</pre></div>
</div>
<p>One of the tests (ASD-DMRG) is meant to fail.</p>
</li>
<li><p class="first">Additional Notes</p>
<ul>
<li><p class="first">Configuring without MKL</p>
<div class="line-block">
<div class="line">If MKL is not available, the path to cblas headers may need to be included as a configure option
(e.g., ‘–with-include=-I/usr/path/to/cblas’). One may also add “LDFLAGS=-lcblas” as an option.
Furthermore, if relativistic calculations fail without MKL, users may consider reconfiguring and recompiling with -DZDOT_RETURN in CXXFLAGS.</div>
</div>
</li>
<li><p class="first">Compiling on small machines</p>
<div class="line-block">
<div class="line">Some files in BAGEL require several GB of RAM to compile. This is generally not a problem for clusters, but on personal computers the
compilation will occasionally fail. Compiling with one thread (make -j1) and not using -DCOMPILE_J_ORB may help.</div>
</div>
</li>
</ul>
</li>
</ul>
</div>
</div>
</div>
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<li class="toctree-l1 current"><a class="reference internal" href="../user-manual.html"><strong>BAGEL user manual</strong></a><ul class="current">
<li class="toctree-l2 current"><a class="reference internal" href="quickstart.html">First steps with BAGEL</a></li>
<li class="toctree-l2"><a class="reference internal" href="../molecule/molecule-toc.html">Molecule specification</a></li>
<li class="toctree-l2"><a class="reference internal" href="../scf/scf.html">Self-consistent field</a></li>
<li class="toctree-l2"><a class="reference internal" href="../ci/ci_methods.html">Configuration interaction</a></li>
<li class="toctree-l2"><a class="reference internal" href="../multi/multi.html">Multiconfiguration self-consistent field</a></li>
<li class="toctree-l2"><a class="reference internal" href="../pt2/pt2.html">Perturbation theory</a></li>
<li class="toctree-l2"><a class="reference internal" href="../smith/smith.html">SMITH3-generated code</a></li>
<li class="toctree-l2"><a class="reference internal" href="../grad/grad.html">Nuclear gradients and related functionalities</a></li>
<li class="toctree-l2"><a class="reference internal" href="../asd/asd.html">Active space decomposition method</a></li>
<li class="toctree-l2"><a class="reference internal" href="../miscellaneous/misc.html">Miscellaneous features</a></li>
<li class="toctree-l2"><a class="reference internal" href="../supp_info/supp_info.html">Supplementary information</a></li>
<li class="toctree-l2"><a class="reference internal" href="../author.html">Author contributions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../funding.html">Funding and citation</a></li>
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