make summit work

README.md

@@ -4,7 +4,7 @@
 
 <img src="https://github.com/UCL-CCS/TIES_MD/blob/main/TIES_MD/doc/source/_static/images/TIES_logov2.png" width="384">
 
-Please see our [documentation](https://UCL-CCS.github.io/TIES_MD/) for more information on `TIES MD` or our main [TIES](http://www.ties-service.org/) page for information on all TIES packages.
+Please see our [documentation](https://UCL-CCS.github.io/TIES_MD/) for more information on `TIES MD` or our main [TIES](http://www.ties-service.org/) page for information on all `TIES` packages.
 
 To install `TIES_MD` run:
 

TIES_MD/doc/source/HPC_submissions.rst

@@ -36,7 +36,7 @@ Here is an example of a submission script for a large system (≈100k atoms) run
     ties_dir=/hppfs/work/pn98ve/di67rov/test_TIES/study/prot/ties-l2-l1/com
 
     for stage in {0..3}; do
-    for lambda in 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 0.95 1.0;
+    for lambda in 0.00 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 0.95 1.0;
     do
             cd $ties_dir/replica-confs
             srun -N $nodes_per_namd -n $cpus_per_namd namd2 +replicas 5 --tclmain sim$stage-replicas.conf $lambda&

TIES_MD/doc/source/install.rst

@@ -4,23 +4,21 @@ Installation
 TIES MD
 -----------
 
-``TIES_MD`` can be installed with ``Conda`` on ``Linux-64`` and ``Linux-ppc64le`` machines. Assuming the user does not
-have Conda the steps to do this are as follows, starting with an install of ``Miniconda``::
+``TIES_MD`` can be installed with the ``Conda`` package manager. Assuming the user does not have ``Conda`` the
+steps to do this are as follows, starting with an install of ``Miniconda``::
 
     wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
     chmod +x Miniconda3-latest-Linux-x86_64.sh
     ./Miniconda3-latest-Linux-x86_64.sh -b -p $prefix
     export PATH="$prefix/bin:$PATH"
 
-
 Ensure the ``Miniconda`` used matches the platform on which you are running, for example use ``Miniconda3-latest-Linux-ppc64le.sh``
-for ``Linux-ppc64le`` machines, and that ``$prefix`` is set to some directory with read write permissions. We provide ``Conda`` installs for
-``Python 3.7/3.8/3.9`` on ``Linux-64`` and ``Python 3.7`` on ``Linux-ppc64le``. If required you can change your python version in ``Conda``
-using this command::
+for ``Linux-ppc64le`` machines, and that ``$prefix`` is set to some directory with read write permissions.
 
-    conda install python=3.7.3
+.. note::
+    If you are attempting a ``Linux-ppc64le`` read the final section of this page.
 
-Finally install ``TIES MD`` with::
+With ``Conda`` installed ``TIES MD`` can be installed with with::
 
     conda install -c conda-forge ties_md
 
@@ -32,7 +30,7 @@ for older ``OpenMM`` versions ``< 7.6`` this command was::
 
     python -m simtk.testInstallation
 
-In some instances the wrong version of ``OpenMM`` and ``CUDAtoolkit`` could be installed. If this has happend the above
+In some instances the wrong version of ``OpenMM`` and ``CUDAtoolkit`` could be installed. If this has happened the above
 test of ``OpenMM`` will produce an output which looks like::
 
     OpenMM Version: 7.7
@@ -88,9 +86,18 @@ TIES OpenMM linux-ppc64le
 --------------------------
 
 .. note::
-    There is no conda version of PyMABR 4.0 for linux-ppc64le FEP will not work until this is updated.
+    There is no version of PyMABR 4.0.1 for ``linux-ppc64le`` therefore FEP analysis will not work until this is updated.
+    To work around this FEP simulations can be run on ``linux-ppc64le`` but the result must be copied elsewhere for analysis.
+
+To use ``TIES_MD`` on ``linux-ppc64le`` skip the above install of ``TIES MD`` and instead run::
+
+    conda install -c ucl-ccs ties_md
+
+Then install OpenMM with::
+
+    conda install -c conda-forge openmm
 
-To use the OpenMM protocol in ``TIES_MD`` on ``linux-ppc64le`` a custom version of ``OpenMMTools`` is needed to perform the alchemical transformations
+And to use the OpenMM protocol a custom version of ``OpenMMTools`` is also needed to perform the alchemical transformations
 of the system and allow for thermodynamic integration calculations. In order to install the custom version of ``OpenMMTools`` run::
 
     mkdir openmmtools_install

devtools/conda-recipe/meta.yaml

@@ -11,8 +11,7 @@ build:
 
 requirements:
   build:
-    - python {{ python }} # [not ppc64le]
-    - python 3.7.3 # [ppc64le]
+    - python {{ python }}
     - setuptools
   run:
     - python
@@ -24,12 +23,11 @@ requirements:
     - numba
     - docopt
     - multiprocess
-    - openmm
     - cython
-    - ties_ana
     - mpiplus
     - scikit-learn
     - six
+    - openmm # [not ppc64le]
     - pymbar # [not ppc64le]
     - openmmtools # [not ppc64le]
 

docs/HPC_submissions.html

@@ -115,7 +115,7 @@ <h2>NAMD<a class="headerlink" href="#namd" title="Permalink to this heading">
 ties_dir=/hppfs/work/pn98ve/di67rov/test_TIES/study/prot/ties-l2-l1/com
 
 for stage in {0..3}; do
-for lambda in 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 0.95 1.0;
+for lambda in 0.00 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 0.95 1.0;
 do
         cd $ties_dir/replica-confs
         srun -N $nodes_per_namd -n $cpus_per_namd namd2 +replicas 5 --tclmain sim$stage-replicas.conf $lambda&amp;

docs/_sources/HPC_submissions.rst.txt

@@ -36,7 +36,7 @@ Here is an example of a submission script for a large system (≈100k atoms) run
     ties_dir=/hppfs/work/pn98ve/di67rov/test_TIES/study/prot/ties-l2-l1/com
 
     for stage in {0..3}; do
-    for lambda in 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 0.95 1.0;
+    for lambda in 0.00 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 0.95 1.0;
     do
             cd $ties_dir/replica-confs
             srun -N $nodes_per_namd -n $cpus_per_namd namd2 +replicas 5 --tclmain sim$stage-replicas.conf $lambda&

docs/_sources/install.rst.txt

@@ -4,26 +4,23 @@ Installation
 TIES MD
 -----------
 
-``TIES_MD`` can be installed with ``Conda`` on ``Linux-64`` and ``Linux-ppc64le`` machines. Assuming the user does not
-have Conda the steps to do this are as follows, starting with an install of ``Miniconda``::
+``TIES_MD`` can be installed with the ``Conda`` package manager. Assuming the user does not have ``Conda`` the
+steps to do this are as follows, starting with an install of ``Miniconda``::
 
     wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
     chmod +x Miniconda3-latest-Linux-x86_64.sh
     ./Miniconda3-latest-Linux-x86_64.sh -b -p $prefix
     export PATH="$prefix/bin:$PATH"
 
-
 Ensure the ``Miniconda`` used matches the platform on which you are running, for example use ``Miniconda3-latest-Linux-ppc64le.sh``
-for ``Linux-ppc64le`` machines, and that ``$prefix`` is set to some directory with read write permissions. We provide ``Conda`` installs for
-``Python 3.7/3.8/3.9`` on ``Linux-64`` and ``Python 3.7`` on ``Linux-ppc64le``. If required you can change your python version in ``Conda``
-using this command::
+for ``Linux-ppc64le`` machines, and that ``$prefix`` is set to some directory with read write permissions.
 
-    conda install python=3.7.3
+.. note::
+    If you are attempting a ``Linux-ppc64le`` read the final section of this page.
 
-Finally add ``conda-forge`` to your available conda channels and install ``TIES MD``::
+With ``Conda`` installed ``TIES MD`` can be installed with with::
 
-    conda config --add channels conda-forge
-    conda install ties_md
+    conda install -c conda-forge ties_md
 
 The install of ``OpenMM`` which was installed with ``TIES_MD`` can be verified by running::
 
@@ -33,7 +30,7 @@ for older ``OpenMM`` versions ``< 7.6`` this command was::
 
     python -m simtk.testInstallation
 
-In some instances the wrong version of ``OpenMM`` and ``CUDAtoolkit`` could be installed. If this has happend the above
+In some instances the wrong version of ``OpenMM`` and ``CUDAtoolkit`` could be installed. If this has happened the above
 test of ``OpenMM`` will produce an output which looks like::
 
     OpenMM Version: 7.7
@@ -89,9 +86,18 @@ TIES OpenMM linux-ppc64le
 --------------------------
 
 .. note::
-    There is no conda version of PyMABR 4.0 for linux-ppc64le FEP will not work until this is updated.
+    There is no version of PyMABR 4.0.1 for ``linux-ppc64le`` therefore FEP analysis will not work until this is updated.
+    To work around this FEP simulations can be run on ``linux-ppc64le`` but the result must be copied elsewhere for analysis.
+
+To use ``TIES_MD`` on ``linux-ppc64le`` skip the above install of ``TIES MD`` and instead run::
+
+    conda install -c ucl-ccs ties_md
+
+Then install OpenMM with::
+
+    conda install -c conda-forge openmm
 
-To use the OpenMM protocol in ``TIES_MD`` on ``linux-ppc64le`` a custom version of ``OpenMMTools`` is needed to perform the alchemical transformations
+And to use the OpenMM protocol a custom version of ``OpenMMTools`` is also needed to perform the alchemical transformations
 of the system and allow for thermodynamic integration calculations. In order to install the custom version of ``OpenMMTools`` run::
 
     mkdir openmmtools_install

docs/install.html

@@ -84,24 +84,22 @@
 <h1>Installation<a class="headerlink" href="#installation" title="Permalink to this heading"></a></h1>
 <section id="ties-md">
 <h2>TIES MD<a class="headerlink" href="#ties-md" title="Permalink to this heading"></a></h2>
-<p><code class="docutils literal notranslate"><span class="pre">TIES_MD</span></code> can be installed with <code class="docutils literal notranslate"><span class="pre">Conda</span></code> on <code class="docutils literal notranslate"><span class="pre">Linux-64</span></code> and <code class="docutils literal notranslate"><span class="pre">Linux-ppc64le</span></code> machines. Assuming the user does not
-have Conda the steps to do this are as follows, starting with an install of <code class="docutils literal notranslate"><span class="pre">Miniconda</span></code>:</p>
+<p><code class="docutils literal notranslate"><span class="pre">TIES_MD</span></code> can be installed with the <code class="docutils literal notranslate"><span class="pre">Conda</span></code> package manager. Assuming the user does not have <code class="docutils literal notranslate"><span class="pre">Conda</span></code> the
+steps to do this are as follows, starting with an install of <code class="docutils literal notranslate"><span class="pre">Miniconda</span></code>:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
 chmod +x Miniconda3-latest-Linux-x86_64.sh
 ./Miniconda3-latest-Linux-x86_64.sh -b -p $prefix
 export PATH=&quot;$prefix/bin:$PATH&quot;
 </pre></div>
 </div>
 <p>Ensure the <code class="docutils literal notranslate"><span class="pre">Miniconda</span></code> used matches the platform on which you are running, for example use <code class="docutils literal notranslate"><span class="pre">Miniconda3-latest-Linux-ppc64le.sh</span></code>
-for <code class="docutils literal notranslate"><span class="pre">Linux-ppc64le</span></code> machines, and that <code class="docutils literal notranslate"><span class="pre">$prefix</span></code> is set to some directory with read write permissions. We provide <code class="docutils literal notranslate"><span class="pre">Conda</span></code> installs for
-<code class="docutils literal notranslate"><span class="pre">Python</span> <span class="pre">3.7/3.8/3.9</span></code> on <code class="docutils literal notranslate"><span class="pre">Linux-64</span></code> and <code class="docutils literal notranslate"><span class="pre">Python</span> <span class="pre">3.7</span></code> on <code class="docutils literal notranslate"><span class="pre">Linux-ppc64le</span></code>. If required you can change your python version in <code class="docutils literal notranslate"><span class="pre">Conda</span></code>
-using this command:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">install</span> <span class="n">python</span><span class="o">=</span><span class="mf">3.7.3</span>
-</pre></div>
+for <code class="docutils literal notranslate"><span class="pre">Linux-ppc64le</span></code> machines, and that <code class="docutils literal notranslate"><span class="pre">$prefix</span></code> is set to some directory with read write permissions.</p>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>If you are attempting a <code class="docutils literal notranslate"><span class="pre">Linux-ppc64le</span></code> read the final section of this page.</p>
 </div>
-<p>Finally add <code class="docutils literal notranslate"><span class="pre">conda-forge</span></code> to your available conda channels and install <code class="docutils literal notranslate"><span class="pre">TIES</span> <span class="pre">MD</span></code>:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">config</span> <span class="o">--</span><span class="n">add</span> <span class="n">channels</span> <span class="n">conda</span><span class="o">-</span><span class="n">forge</span>
-<span class="n">conda</span> <span class="n">install</span> <span class="n">ties_md</span>
+<p>With <code class="docutils literal notranslate"><span class="pre">Conda</span></code> installed <code class="docutils literal notranslate"><span class="pre">TIES</span> <span class="pre">MD</span></code> can be installed with with:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">install</span> <span class="o">-</span><span class="n">c</span> <span class="n">conda</span><span class="o">-</span><span class="n">forge</span> <span class="n">ties_md</span>
 </pre></div>
 </div>
 <p>The install of <code class="docutils literal notranslate"><span class="pre">OpenMM</span></code> which was installed with <code class="docutils literal notranslate"><span class="pre">TIES_MD</span></code> can be verified by running:</p>
@@ -112,7 +110,7 @@ <h2>TIES MD<a class="headerlink" href="#ties-md" title="Permalink to this headin
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="o">-</span><span class="n">m</span> <span class="n">simtk</span><span class="o">.</span><span class="n">testInstallation</span>
 </pre></div>
 </div>
-<p>In some instances the wrong version of <code class="docutils literal notranslate"><span class="pre">OpenMM</span></code> and <code class="docutils literal notranslate"><span class="pre">CUDAtoolkit</span></code> could be installed. If this has happend the above
+<p>In some instances the wrong version of <code class="docutils literal notranslate"><span class="pre">OpenMM</span></code> and <code class="docutils literal notranslate"><span class="pre">CUDAtoolkit</span></code> could be installed. If this has happened the above
 test of <code class="docutils literal notranslate"><span class="pre">OpenMM</span></code> will produce an output which looks like:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">OpenMM</span> <span class="n">Version</span><span class="p">:</span> <span class="mf">7.7</span>
 <span class="n">Git</span> <span class="n">Revision</span><span class="p">:</span> <span class="mi">130124</span><span class="n">a3f9277b054ec40927360a6ad20c8f5fa6</span>
@@ -168,9 +166,18 @@ <h2>TIES MD<a class="headerlink" href="#ties-md" title="Permalink to this headin
 <h2>TIES OpenMM linux-ppc64le<a class="headerlink" href="#ties-openmm-linux-ppc64le" title="Permalink to this heading"></a></h2>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
-<p>There is no conda version of PyMABR 4.0 for linux-ppc64le FEP will not work until this is updated.</p>
+<p>There is no version of PyMABR 4.0.1 for <code class="docutils literal notranslate"><span class="pre">linux-ppc64le</span></code> therefore FEP analysis will not work until this is updated.
+To work around this FEP simulations can be run on <code class="docutils literal notranslate"><span class="pre">linux-ppc64le</span></code> but the result must be copied elsewhere for analysis.</p>
+</div>
+<p>To use <code class="docutils literal notranslate"><span class="pre">TIES_MD</span></code> on <code class="docutils literal notranslate"><span class="pre">linux-ppc64le</span></code> skip the above install of <code class="docutils literal notranslate"><span class="pre">TIES</span> <span class="pre">MD</span></code> and instead run:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">install</span> <span class="o">-</span><span class="n">c</span> <span class="n">ucl</span><span class="o">-</span><span class="n">ccs</span> <span class="n">ties_md</span>
+</pre></div>
+</div>
+<p>Then install OpenMM with:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">install</span> <span class="o">-</span><span class="n">c</span> <span class="n">conda</span><span class="o">-</span><span class="n">forge</span> <span class="n">openmm</span>
+</pre></div>
 </div>
-<p>To use the OpenMM protocol in <code class="docutils literal notranslate"><span class="pre">TIES_MD</span></code> on <code class="docutils literal notranslate"><span class="pre">linux-ppc64le</span></code> a custom version of <code class="docutils literal notranslate"><span class="pre">OpenMMTools</span></code> is needed to perform the alchemical transformations
+<p>And to use the OpenMM protocol a custom version of <code class="docutils literal notranslate"><span class="pre">OpenMMTools</span></code> is also needed to perform the alchemical transformations
 of the system and allow for thermodynamic integration calculations. In order to install the custom version of <code class="docutils literal notranslate"><span class="pre">OpenMMTools</span></code> run:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mkdir</span> <span class="n">openmmtools_install</span>
 <span class="n">cd</span> <span class="n">openmmtools_install</span>