Moved CUDA out to TOC root. Separated software by MD and ML categories.

jade-hpc-gpu · Oct 10, 2017 · 5671d40 · 5671d40
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diff --git a/software/libs/cuda.rst → cuda.rst b/software/libs/cuda.rst → cuda.rst
@@ -88,10 +88,3 @@ Useful presentations at NVIDIA's 2017 GTC conference contain:
 * `NCCL 2.0 <http://on-demand.gputechconf.com/gtc/2017/presentation/s7155-jeaugey-nccl.pdf>`_
 * `Multi-GPU Programming <http://on-demand.gputechconf.com/gtc/2017/presentation/s7142-jiri-kraus-multi-gpu-programming-models.pdf>`_
 * `The Making of Saturn-V <http://on-demand.gputechconf.com/gtc/2017/presentation/s7750-louis-capps-making-of-dgx-saturnv.pdf>`_
-
-
-.. toctree::
-    :maxdepth: 2
-    :glob:
-
-    learn/index
diff --git a/index.rst b/index.rst
@@ -52,9 +52,8 @@ JADE hardware consists of:
    :maxdepth: -1
    :hidden:
 
-
    jade/index
    software/index
-   cuda/index
+   cuda
    more_info
    troubleshooting
diff --git a/jade/connecting.rst b/jade/connecting.rst
@@ -17,7 +17,7 @@ After starting MobaXterm you should see something like this:
    :width: 50%
    :align: center
 
-Click *Start local terminal* and if you see something like the following then please continue to :ref:`ssh`.
+Click *Start local terminal* and if you see something like the following then please continue to :ref:`ssh-connection`.
 
 .. image:: /images/mobaxterm-terminal.png
    :width: 50%
@@ -36,16 +36,16 @@ Linux and macOS (OS X) both typically come with a command-line SSH client pre-in
 If you are using macOS and want to be able to run graphical applications on the clusters then
 you need to install the latest version of the `XQuartz <https://www.xquartz.org/>`_ *X Windows server*.
 
-Open a terminal (e.g. *Gnome Terminal* on Linux or *Terminal* on macOS) and then go to :ref:`ssh`.
+Open a terminal (e.g. *Gnome Terminal* on Linux or *Terminal* on macOS) and then go to :ref:`ssh-connection`.
 
-.. _ssh:
+.. _ssh-connection:
 
 Establishing a SSH connection
 -----------------------------
 
-Once you have a terminal open, run the following command to log into one of the JADE front-end nodes:
-::
-    ssh -l $USER jade.hartree.stfc.ac.uk
+Once you have a terminal open, run the following command to log into one of the JADE front-end nodes: ::
+
+  ssh -l $USER jade.hartree.stfc.ac.uk
 
 Here you need to replace ``$USER`` with your username (e.g. ``te1st-test``)
 
@@ -68,4 +68,3 @@ Here you need to replace ``$USER`` with your username (e.g. ``te1st-test``)
     You **should not** run applications on the login nodes.
     Running ``srun`` gives you an interactive terminal
     on one of the many worker nodes in the cluster.
-
diff --git a/jade/index.rst b/jade/index.rst
@@ -10,9 +10,9 @@ The JADE facility consists of 2 head nodes and 22 NVIDIA `DGX-1 <https://www.sca
 
 Users get accounts on the system by following the directions in the **Getting an account** section, on the left.
 
-New users must provide a public SSH key and are given a user ID on JADE.  Using this ID, they will then be able to login to one of the head nodes by using an SSH command like
-::
-   ssh -l account_name jade.hartree.stfc.ac.uk
+New users must provide a public SSH key and are given a user ID on JADE.  Using this ID, they will then be able to login to one of the head nodes by using an SSH command like ::
+
+  ssh -l account_name jade.hartree.stfc.ac.uk
 
 Further details are in the section **Connecting to the cluster using SSH**.
 

diff --git a/jade/pi-projectmanager.rst b/jade/pi-projectmanager.rst
@@ -46,8 +46,7 @@ After creating a group, users can be added to a project.
 
 **To add users:**
 
-  1. Provide your users with the **project name**, **project signup code** (see above section) and signup instruction for regular users at:
-    `http://jade-hpc.readthedocs.io/en/latest/jade/getting-account.html <http://jade-hpc.readthedocs.io/en/latest/jade/getting-account.html>`_
+  1. Provide your users with the **project name**, **project signup code** (see above section) and signup instruction for regular users at: `http://jade-hpc.readthedocs.io/en/latest/jade/getting-account.html <http://jade-hpc.readthedocs.io/en/latest/jade/getting-account.html>`_
   2. Once a user has requested to join a project, there will be a "New Project Management Requests" box. Click the `Process` button and `Accept` (or `Reject`) the new member.
   3. The PI can now add the member to the a **group** previously created.
   4. Click on `Administer` for the Project then choose `Project Group Administration`.
@@ -63,8 +62,7 @@ Project groups and shared file system area
 ------------------------------------------
 
 
-Each Project group maps to a Unix group, and each Project group member's home file system is set up under a directory group structure. The example below starts from a user's home directory and shows that all other members of the Project group are assigned home directories as "peer" directories.
-::
+Each Project group maps to a Unix group, and each Project group member's home file system is set up under a directory group structure. The example below starts from a user's home directory and shows that all other members of the Project group are assigned home directories as "peer" directories. ::
   -bash-4.1$ pwd
   /gpfs/home/training/jpf03/jpf26-jpf03
   -bash-4.1$ cd ..

diff --git a/jade/scheduler/index.rst b/jade/scheduler/index.rst
@@ -8,7 +8,7 @@ Introduction
 
 Running software on the JADE system is accomplished via batch jobs, *i.e.* in an unattended, non-interactive manner.  Typically a user logs in to the JADE login nodes, prepares a job script and submits it to the job queue.
 
-Jobs on JADE are managed by the `Slurm <https://slurm.schedmd.com>`_ batch system, which is in charge of:
+Jobs on JADE are managed by the `Slurm batch system <https://slurm.schedmd.com>`_ , which is in charge of:
 
 * allocating the computer resources requested for the job,
 * running the job and

diff --git a/software/development/index.rst b/software/development/index.rst
diff --git a/software/index.rst b/software/index.rst
@@ -33,6 +33,5 @@ The following are the available applications, libraries and development tools on
     :maxdepth: 2
     :glob:
 
-    apps/index
-    libs/index
-    development/index
+    molecular-dynamics/index
+    machine-learning/index
diff --git a/software/libs/index.rst b/software/libs/index.rst
diff --git a/software/apps/caffe.rst → software/machine-learning/caffe.rst b/software/apps/caffe.rst → software/machine-learning/caffe.rst
@@ -7,12 +7,12 @@ Caffe
 
    :URL: http://caffe.berkeleyvision.org/
 
-`Caffe <http://caffe.berkeleyvision.org/>`_ is a Deep Learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (`BVLC <http://bvlc.eecs.berkeley.edu/>`_) and by community contributors.
+`Caffe <http://caffe.berkeleyvision.org/>`__ is a Deep Learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (`BVLC <http://bvlc.eecs.berkeley.edu/>`_) and by community contributors.
 
 The Caffe Docker Container
 --------------------------
 
-Caffe is available on JADE through the use of a `Docker container <https://docker.com>`_. For more information on JADE's use of containers, see :ref:`containers`.
+Caffe is available on JADE through the use of a `Docker container <https://docker.com>`__. For more information on JADE's use of containers, see :ref:`containers`.
 
 
 Using Caffe Interactively

diff --git a/software/machine-learning/index.rst b/software/machine-learning/index.rst
@@ -0,0 +1,11 @@
+.. _machine-learning:
+
+Machine Learning
+================
+
+
+.. toctree::
+    :maxdepth: 1
+    :glob:
+
+    ./*
diff --git a/software/apps/tensorflow.rst → software/machine-learning/tensorflow.rst b/software/apps/tensorflow.rst → software/machine-learning/tensorflow.rst
@@ -10,7 +10,7 @@ Tensorflow
 TensorFlow is an open source software library for numerical computation using data flow graphs. Nodes in the graph represent mathematical operations, while the graph edges represent the multidimensional data arrays (tensors) communicated between them. The flexible architecture allows you to deploy computation to one or more CPUs or GPUs in a desktop, server, or mobile device with a single API. TensorFlow was originally developed by researchers and engineers working on the Google Brain Team within Google's Machine Intelligence research organization for the purposes of conducting machine learning and deep neural networks research, but the system is general enough to be applicable in a wide variety of other domains as well.
 
 Tensorflow Docker Container
------------------------
+---------------------------
 
 Tensorflow is available on JADE through the use of a `Docker container <https://docker.com>`_. For more information on JADE's use of containers, see :ref:`containers`.
 

diff --git a/software/apps/theano.rst → software/machine-learning/theano.rst b/software/apps/theano.rst → software/machine-learning/theano.rst
diff --git a/software/apps/torch.rst → software/machine-learning/torch.rst b/software/apps/torch.rst → software/machine-learning/torch.rst
diff --git a/software/apps/gromacs.rst → software/molecular-dynamics/gromacs.rst b/software/apps/gromacs.rst → software/molecular-dynamics/gromacs.rst
diff --git a/software/molecular-dynamics/index.rst b/software/molecular-dynamics/index.rst
@@ -0,0 +1,11 @@
+.. _molecular-dynamics:
+
+Molecular Dynamics
+==================
+
+
+.. toctree::
+    :maxdepth: 1
+    :glob:
+
+    ./*
diff --git a/software/apps/namd.rst → software/molecular-dynamics/namd.rst b/software/apps/namd.rst → software/molecular-dynamics/namd.rst