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<div class="section" id="binary-distribution">
<span id="sec-conda"></span><h1>Binary Distribution<a class="headerlink" href="#binary-distribution" title="Permalink to this headline">¶</a></h1>
<p><span class="sc">Psi4</span> is available as a pre-compiled binary for Linux architectures
(Mac coming soon) through <a class="reference external" href="https://store.continuum.io/cshop/anaconda/">Continuum Analytics</a>, the company that produces
<a class="reference external" href="http://docs.continuum.io/anaconda/index.html">Anaconda Python</a> (a
full-fledged scientific python environment with package manager <a class="reference external" href="http://conda.pydata.org/index.html">conda</a>) and, more particularly, <a class="reference external" href="http://conda.pydata.org/miniconda.html">Miniconda</a> (a lightweight python
distribution with same package manger <a class="reference external" href="http://conda.pydata.org/index.html">conda</a>). Some nice features for us:</p>
<ul class="simple">
<li>cross-platform (Linux only at present)</li>
<li>no root, administrator, or sudo access required</li>
<li>built with high-performance math libraries</li>
<li>lightweight software stack (<100 MB w/o <span class="sc">Psi4</span>; <500 MB including <span class="sc">Psi4</span>)</li>
<li>updated nightly so new features accessible</li>
<li>standardizes python distribution so no need to find/install libpython packages</li>
<li>add-ons (plugins, extra features requiring Fortran compiler, etc.) can be made available as conda packages</li>
</ul>
<p>The <span class="sc">Psi4</span> binary repository is at <a class="reference external" href="https://anaconda.org/psi4">Anaconda (formerly Binstar)</a>.</p>
<p>For commands to get a default installation, go to <a class="reference internal" href="#sec-quickconda"><span>Quick Installation</span></a>.
For more flexibility and a detailed explanation, go to
<a class="reference internal" href="#sec-slowconda"><span>Detailed Installation of Miniconda</span></a> and <a class="reference internal" href="#sec-slowpsi4"><span>Detailed Installation of Psi4</span></a>.</p>
<div class="section" id="quick-installation">
<span id="sec-quickconda"></span><h2>Quick Installation<a class="headerlink" href="#quick-installation" title="Permalink to this headline">¶</a></h2>
<p>Sequence of commands to get you to a working <span class="sc">Psi4</span> on Linux. Installs
Miniconda into <code class="docutils literal"><span class="pre">$HOME/miniconda</span></code> and the <span class="sc">Psi4</span> executable into the
main conda environment at <code class="docutils literal"><span class="pre">$HOME/miniconda/bin/psi4</span></code>.</p>
<div class="highlight-bash"><div class="highlight"><pre>>>> bash
>>> curl -O <span class="s2">"http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh"</span>
>>> bash Miniconda-latest-Linux-x86_64.sh -b -p <span class="nv">$HOME</span>/miniconda <span class="c"># agrees to conda's license terms</span>
>>> <span class="nb">echo</span> <span class="s2">"export PATH=</span><span class="nv">$HOME</span><span class="s2">/miniconda/bin:\$PATH"</span> >> ~/.bashrc
<span class="c"># log out, log back in so conda in path</span>
>>> conda update --yes --all
>>> conda config --add channels http://conda.anaconda.org/psi4
>>> conda install --yes psi4
>>> psi4 <span class="s2">"</span><span class="k">$(</span>dirname <span class="k">$(</span>which psi4<span class="k">))</span><span class="s2">"</span>/../share/psi/samples/scf1/input.dat -o stdout <span class="c"># test installation. works b/c PSI_SCRATCH defaults to /tmp</span>
</pre></div>
</div>
<p>That last command tested that <code class="docutils literal"><span class="pre">psi4</span></code> is in your path, and it’s finding
all the libraries it needs. Now you need only specify a scratch directory
(see <a class="reference internal" href="external.html#sec-psirc"><span>Scratch Files and the ~/.psi4rc File</span></a>) by replacing the placeholder in the following:</p>
<div class="highlight-bash"><div class="highlight"><pre>>>> <span class="nb">echo</span> <span class="s2">"export PSI_SCRATCH=/path/to/existing/writable/local-not-network/directory/for/scratch/files"</span> >> ~/.bashrc
<span class="c"># log out, log back in so variable takes effect</span>
</pre></div>
</div>
<p>All done!</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Above commands use bash for installation and set up your environment for bash at runtime. To use csh at runtime, follow the on-screen directions at the end of the installation or consult step 7 below.</p>
</div>
</div>
<div class="section" id="detailed-installation-of-miniconda">
<span id="sec-slowconda"></span><h2>Detailed Installation of Miniconda<a class="headerlink" href="#detailed-installation-of-miniconda" title="Permalink to this headline">¶</a></h2>
<ol class="arabic simple" start="0">
<li>Sanity check. If you already have Miniconda or Anaconda, skip to step 5. The whole installation takes ~5 min; reading this page takes far longer.</li>
<li>Get <code class="docutils literal"><span class="pre">bzip2</span></code>. You’ll need this slightly exotic command so run <code class="docutils literal"><span class="pre">which</span></code> to test for availability, and install from <code class="docutils literal"><span class="pre">yum</span></code>, source, <em>etc.</em> if unavailable. You’ll also need an internet connection for downloading; computers behind a firewall or with restricted login domains are eligible. So long as you can ssh <em>into</em> the computer to an account with write permissions and can connect to the internet <em>from</em> the computer, all is well.</li>
</ol>
<div class="highlight-bash"><div class="highlight"><pre><span class="c"># check</span>
>>> which bzip2
/usr/bin/bzip2
>>> curl -O <span class="s2">"http://psicode.org/psi4manual/master/introduction.html"</span>
>>> ls -1
introduction.html
</pre></div>
</div>
<ol class="arabic simple" start="2">
<li>Get Miniconda installer script. Either issue the command below or download from <a class="reference external" href="http://conda.pydata.org/miniconda.html">http://conda.pydata.org/miniconda.html</a> by clicking on the appropriate link for your OS. If you already have or would prefer to use Anaconda rather than Miniconda, that’s fine. Locate or install Anaconda, check that <code class="docutils literal"><span class="pre">conda</span></code> is in your path, and skip to step 4.</li>
</ol>
<div class="highlight-bash"><div class="highlight"><pre>>>> curl -O <span class="s2">"http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh"</span>
<span class="c"># check</span>
>>> ls -1
Miniconda-latest-Linux-x86_64.sh
</pre></div>
</div>
<ol class="arabic simple" start="3">
<li>Install Miniconda. Execute the script and answer its questions, particularly your choice of installation location. You may need to replace the filename below with the correct filename for the OS/version of installer you downloaded. Execute with <code class="docutils literal"><span class="pre">bash</span></code> regardless of <code class="docutils literal"><span class="pre">csh</span></code>/<code class="docutils literal"><span class="pre">bash</span></code> shell. If you’re a <code class="docutils literal"><span class="pre">bash</span></code> user, it’s convenient to agree to its offer to prepend <code class="docutils literal"><span class="pre">conda</span></code> commands to your <span class="target" id="index-0"></span><a class="reference internal" href="external.html#envvar-PATH"><code class="xref std std-envvar docutils literal"><span class="pre">PATH</span></code></a> in <code class="docutils literal"><span class="pre">~/.bashrc</span></code>. If you’re a <code class="docutils literal"><span class="pre">csh</span></code>/<code class="docutils literal"><span class="pre">tcsh</span></code> user, it’s convenient to do the same by hand to your <code class="docutils literal"><span class="pre">~/.tcshrc</span></code>: <code class="docutils literal"><span class="pre">setenv</span> <span class="pre">PATH</span> <span class="pre">/path/to/miniconda/bin:${PATH}</span></code>. Further directions assume that the <code class="docutils literal"><span class="pre">conda</span></code> command is in your path; you may have to log out and log back in for <code class="docutils literal"><span class="pre">which</span> <span class="pre">conda</span></code> to return correctly.</li>
</ol>
<div class="highlight-bash"><div class="highlight"><pre>>>> bash Miniconda-latest-Linux-x86_64.sh
<span class="c"># check</span>
>>> which conda
/path/to/miniconda/bin/conda
</pre></div>
</div>
<ol class="arabic simple" start="4">
<li>Update conda. This updates the package manager itself.</li>
</ol>
<div class="highlight-bash"><div class="highlight"><pre>>>> conda update conda
</pre></div>
</div>
</div>
<div class="section" id="detailed-installation-of-psifour">
<span id="sec-slowpsi4"></span><h2>Detailed Installation of <span class="sc">Psi4</span><a class="headerlink" href="#detailed-installation-of-psifour" title="Permalink to this headline">¶</a></h2>
<ol class="arabic simple" start="5">
<li>Subscribe to <span class="sc">Psi4</span>. Subscribe to our channel at <a class="reference external" href="http://anaconda.org/psi4">http://anaconda.org/psi4</a> that contains the <span class="sc">Psi4</span> package and several dependency packages. Make sure this shows up in your <code class="docutils literal"><span class="pre">~/.condarc</span></code> file.</li>
</ol>
<div class="highlight-bash"><div class="highlight"><pre>>>> conda config --add channels http://conda.anaconda.org/psi4
<span class="c"># check</span>
>>> cat ~/.condarc
channels:
- http://conda.anaconda.org/psi4
- defaults
</pre></div>
</div>
<ol class="arabic simple" start="6">
<li>Install <span class="sc">Psi4</span>. You can install into the main conda environment so that whenever commands <code class="docutils literal"><span class="pre">conda</span></code> or (Ana/Miniconda’s) <code class="docutils literal"><span class="pre">python</span></code> are available, then <code class="docutils literal"><span class="pre">psi4</span></code> is available, too.</li>
</ol>
<div class="highlight-bash"><div class="highlight"><pre>>>> conda install psi4
<span class="c"># check</span>
>>> which psi4
/path/to/miniconda/bin/psi4
</pre></div>
</div>
<p>Or, you can install into a <a class="reference external" href="http://conda.pydata.org/docs/faq.html#environments">conda environment</a> that places <span class="sc">Psi4</span> and its dependencies (including python) into a sandbox unaffected by any other software installed in Ana/Miniconda. This is recommended for developers to avoid interference between multiple versions (including github/conda versions) or to test python versions, <em>etc.</em>. If your main conda is not python=2.7, then <span class="sc">Psi4</span> <em>must</em> be installed into a conda environment. In practical terms, installing into a conda environment means you can turn <span class="sc">Psi4</span>‘s availability on/off by switching conda environments without turning on/off the whole Ana/Miniconda installation. Below, <span class="sc">Psi4</span> is installed into an environment called <code class="docutils literal"><span class="pre">p4env</span></code>. Then the environment is activated, removing the main Ana/Miniconda <code class="docutils literal"><span class="pre">bin</span></code> and adding <code class="docutils literal"><span class="pre">envs/p4env/bin</span></code> to <span class="target" id="index-1"></span><a class="reference internal" href="external.html#envvar-PATH"><code class="xref std std-envvar docutils literal"><span class="pre">PATH</span></code></a>. The activate command only works in <code class="docutils literal"><span class="pre">bash</span></code>, so <code class="docutils literal"><span class="pre">csh</span></code>/<code class="docutils literal"><span class="pre">tcsh</span></code> will need corresponding adjustments.</p>
<div class="highlight-bash"><div class="highlight"><pre>>>> conda create -n p4env psi4
>>> <span class="nb">source </span>activate p4env
<span class="c"># check</span>
>>> which psi4
/path/to/miniconda/envs/p4env/bin/psi4
</pre></div>
</div>
<p>The output for either of the installation commands above looks like the following. It checks what packages are needed, gets your approval for downloading them, fetches and installs them, prints out some useful information, and runs a <span class="sc">Psi4</span> test case to check that all’s well.</p>
<div class="highlight-bash"><div class="highlight"><pre>>>> conda install psi4
Fetching package metadata: ......
Solving package specifications: .
Package plan <span class="k">for</span> installation in environment /path/to/miniconda:
The following packages will be downloaded:
package <span class="p">|</span> build
---------------------------<span class="p">|</span>-----------------
psi4-0.1.12 <span class="p">|</span> py27_g60a9afd 31.4 MB
The following NEW packages will be INSTALLED:
psi4: 0.1.12-py27_g60a9afd
Fetching packages ...
psi4-0.1.12-py 100% <span class="p">|</span><span class="c">################################################################################| Time: 0:00:01 32.49 MB/s</span>
Extracting packages ...
<span class="o">[</span> COMPLETE <span class="o">]</span> <span class="p">|</span><span class="c">##################################################################################################| 100%</span>
Linking packages ...
Thank you <span class="k">for</span> installing psi4. Additional resources:
Website: www.psicode.org
Inputs: /path/to/miniconda/share/psi/samples
Manual: bit.ly/psi4manual
GitHub: https://github.com/psi4/psi4public/wiki
Binstar: https://binstar.org/psi4
Runtime Environment Diagnostic: /path/to/miniconda/share/psi/scripts/setenv.py
For csh/tcsh <span class="nb">command</span>-line use, add to shell or ~/.tcshrc file:
setenv PATH /path/to/miniconda/bin:<span class="nv">$PATH</span>
setenv PSI_SCRATCH /path/to/existing/writable/local-not-network/disk/for/scratch/files
For sh/bash <span class="nb">command</span>-line use, add to shell or ~/.bashrc file:
<span class="nb">export </span><span class="nv">PATH</span><span class="o">=</span>/path/to/miniconda/bin:<span class="nv">$PATH</span>
<span class="nb">export </span><span class="nv">PSI_SCRATCH</span><span class="o">=</span>/path/to/existing/writable/local-not-network/disk/for/scratch/files
Nuclear Repulsion Energy..........................................PASSED SAPT0 Eelst.......................................................PASSED SAPT0 Eexch.......................................................PASSED SAPT0 Eind........................................................PASSED SAPT0 Edisp.......................................................PASSED SAPT0 Etotal......................................................PASSED
<span class="o">[</span> COMPLETE <span class="o">]</span> <span class="p">|</span><span class="c">##################################################################################################| 100%</span>
</pre></div>
</div>
<ol class="arabic simple" start="7">
<li>Configure environment. Preceeding steps have placed <code class="docutils literal"><span class="pre">conda</span></code> and <code class="docutils literal"><span class="pre">psi4</span></code> in your <span class="target" id="index-2"></span><a class="reference internal" href="external.html#envvar-PATH"><code class="xref std std-envvar docutils literal"><span class="pre">PATH</span></code></a>, either permanently through rc-files or temporarily in this terminal session. You can keep or undo these changes. For general psi4 use, you must enable the <code class="docutils literal"><span class="pre">psi4</span></code> executable to be found through any of:</li>
</ol>
<blockquote>
<div><ol class="arabic simple">
<li>prepending to <span class="target" id="index-3"></span><a class="reference internal" href="external.html#envvar-PATH"><code class="xref std std-envvar docutils literal"><span class="pre">PATH</span></code></a> in shell, <code class="docutils literal"><span class="pre">~/.bashrc</span></code>, <code class="docutils literal"><span class="pre">~/.tcshrc</span></code>, or PBS <code class="docutils literal"><span class="pre">cmd</span></code> file</li>
<li>activating the conda environment (p4env above) in shell, <code class="docutils literal"><span class="pre">~/.bashrc</span></code>, or PBS <code class="docutils literal"><span class="pre">cmd</span></code> file</li>
<li>supplying full path to executable (shell or PBS <code class="docutils literal"><span class="pre">cmd</span></code> file)</li>
</ol>
</div></blockquote>
<p>Similarly, the scratch directory (see <a class="reference internal" href="external.html#sec-psirc"><span>Scratch Files and the ~/.psi4rc File</span></a>) must be specified through:</p>
<blockquote>
<div><ol class="arabic simple">
<li>defining <span class="target" id="index-4"></span><a class="reference internal" href="external.html#envvar-PSI_SCRATCH"><code class="xref std std-envvar docutils literal"><span class="pre">PSI_SCRATCH</span></code></a> in shell, <code class="docutils literal"><span class="pre">~/.bashrc</span></code>, <code class="docutils literal"><span class="pre">~/.tcshrc</span></code>, or PBS <code class="docutils literal"><span class="pre">cmd</span></code> file</li>
</ol>
</div></blockquote>
<p>Suitable values for these variables have been printed to screen during installation (see last codeblock in step 6).</p>
</div>
<div class="section" id="useful-commands">
<h2>Useful Commands<a class="headerlink" href="#useful-commands" title="Permalink to this headline">¶</a></h2>
<ul>
<li><p class="first">Update to latest <span class="sc">Psi4</span> version</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">conda</span> <span class="n">update</span> <span class="n">psi4</span>
</pre></div>
</div>
</li>
<li><p class="first">Install into a conda environment “p4env” instead of “root”. Second command only works on bash; for csh/tsch, <code class="docutils literal"><span class="pre">setenv</span> <span class="pre">PATH</span> <span class="pre">/path/to/miniconda/envs/p4env/bin:$PATH</span></code> instead. This creates a sandbox with just <span class="sc">Psi4</span> and python (loaded as dependency).</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">conda</span> <span class="n">create</span> <span class="o">-</span><span class="n">y</span> <span class="o">-</span><span class="n">n</span> <span class="n">p4env</span> <span class="n">psi4</span>
<span class="gp">>>> </span><span class="n">source</span> <span class="n">activate</span> <span class="n">p4env</span>
</pre></div>
</div>
</li>
<li><p class="first">Install a particular <span class="sc">Psi4</span> version</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">conda</span> <span class="n">install</span> <span class="n">psi4</span><span class="o">=</span><span class="mf">0.1</span><span class="o">.</span><span class="mi">12</span>
</pre></div>
</div>
</li>
<li><p class="first">Uninstall <span class="sc">Psi4</span> from current environment</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">conda</span> <span class="n">remove</span> <span class="n">psi4</span>
</pre></div>
</div>
</li>
</ul>
</div>
<div class="section" id="troubleshooting">
<h2>Troubleshooting<a class="headerlink" href="#troubleshooting" title="Permalink to this headline">¶</a></h2>
<ul>
<li><p class="first">If the target computer doesn’t have libc >= 2.7 (released c.2007; for reference, 2.10 is newer than 2.7; unlike most libraries, libc generally not available in multiple versions on a computer), the <span class="sc">Psi4</span> conda package won’t work.</p>
<div class="highlight-python"><div class="highlight"><pre># unsuitable computer
>>> ldd --version
ldd (GNU libc) 2.5
# suitable computer
>>> ldd --version
ldd (GNU libc) 2.17
</pre></div>
</div>
</li>
<li><p class="first">It is of greatest importance that the <span class="sc">Psi4</span> executable be linked against conda libpython.so <em>not</em> against any system libpython.so. This is arranged by setting <code class="docutils literal"><span class="pre">RPATH</span></code> to seek libraries relative to executable (thanks, conda binary relocation routine!). The conda <span class="sc">Psi4</span> executable is not vulnerable to interference from your <code class="docutils literal"><span class="pre">LD_LIBRARY_PATH</span></code> settings. Below shows a well-linked executable.</p>
<blockquote>
<div><ul class="simple">
<li>no libraries “not found”</li>
<li>fundamental libraries like libc, ld-linux, pthreads found system libraries to link against</li>
<li>libpython linked against conda python <em>not</em> system python</li>
<li>libm is linked against conda <em>or</em> system</li>
<li>blas, c++, and gcc libraries are absent because statically linked</li>
</ul>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">conda</span> <span class="n">install</span> <span class="n">conda</span><span class="o">-</span><span class="n">build</span> <span class="c"># needed for next command</span>
<span class="gp">>>> </span><span class="n">conda</span> <span class="n">inspect</span> <span class="n">linkages</span> <span class="n">psi4</span>
<span class="go">python-2.7.9-2:</span>
<span class="go"> libpython2.7.so.1.0 (lib/libpython2.7.so.1.0)</span>
<span class="go">system-5.8-1:</span>
<span class="go"> libm.so.6 (lib/libm.so.6)</span>
<span class="go">system:</span>
<span class="go"> libc.so.6 (/lib64/libc.so.6)</span>
<span class="go"> libdl.so.2 (/lib64/libdl.so.2)</span>
<span class="go"> libpthread.so.0 (/lib64/libpthread.so.0)</span>
<span class="go"> librt.so.1 (/lib64/librt.so.1)</span>
<span class="go"> libutil.so.1 (/lib64/libutil.so.1)</span>
<span class="go"> linux-vdso.so.1 ()</span>
<span class="go">not found:</span>
</pre></div>
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