Merge branch 'master' of gitlab.mpib-berlin.mpg.de:lip-support/tardis-doc

.pages.sh

+#!/bin/bash
+set -e
+
+SRC=$1
+DST=$2
+
+cd $1
+make html
+cd -
+mkdir -p $2
+cp -r $1/_build/html/. $2
+exit 0

introduction/index.rst

@@ -19,11 +19,11 @@ Tardis
    :width: 60%
 
 Some technical facts:
-    + **608** Intel® Xeon® CPU E5-2670 CPU cores inside 32 Dell m620 blade servers
-    + **R**:sub:`max` = 5.1 TFlops, **R**:sub:`peak` = 12.6 TFlops
-    + **3.2TB** total amount of memory
-    + **256 GB** RAM on 6 of those nodes
-    + **32 TB** of attached NFS storage
+    + **712** Intel® Xeon® CPU E5-2670 CPU cores(no HT) inside 42 Dell m6x0 blade servers
+    + **R**:sub:`max` = 9.9 TFlops, **R**:sub:`peak` = 14.8 TFlops
+    + **6.4TB** total amount of memory
+    + **32TB** of attached NFS storage
+    + **4.1TB** experimental glusterfs storage
     + simple 2-level fat tree network with a theoretical bisection bandwidth of **40GB/s**
 
 

introduction/login.rst

@@ -48,7 +48,7 @@ in Nautilus:
 
 Open the following URL in your file manager (CTRL-L) ::
 
-   ssh://<YOUR_USERNAME>@tardis.mpib-berlin.mpg.de/home/mpib/``
+   ssh://YOUR_USERNAME@tardis.mpib-berlin.mpg.de/home/mpib/
 
 Mac OSX
 ^^^^^^^

make

@@ -14,3 +14,4 @@ while true ; do
     WATCHSOURCE="**/*.rst *.rst"
     $MAKEFUNC
 done
+

software/fsl.rst

 FSL
 ===
 
+We are automatically following the FSL 5 release history of `Neurodebian <http://neuro.debian.net>`_.
+
+To use FSL in your jobs, activate it like this:
+
+.. code-block:: bash
+
+   source /etc/fsl/5.0/fsl.sh
+
+Afterwards the :file:`PATH` variable should be set correctly.
+
 
 FIX
 ---
 
-We have set up a running version of [FSL
-Fix](http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX). Currently it is not using
-FSL's internal qsub so it only makes sense to parallelize over a number of
-subjects. Example:
+We have set up a running version of `FSL Fix <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX>`_.
+Currently it is not using FSL's internal qsub so it only makes sense to
+parallelize over a number of subjects. Example:
 
 .. code-block:: bash
 

software/r.rst

@@ -105,8 +105,23 @@ Timings:
        user  system elapsed
     107.442   0.052   7.20
 
+Alternatively you can use `%dopar%` and `foreach`:
 
-If you want to unroll the vector operation of the whole cluster, have a look at
+.. code-block:: r
+
+    library(doMC)
+    library(gmp)
+
+    cores <- Sys.getenv("PBS_NUM_PPN")
+    cores <- if (cores == '') 1 else as.numeric(cores)
+    registerDoMC(cores)
+
+    foreach(i=seq(1,16)) %dopar% {
+        factorize(matrix(as.bigz(2**521)-1))
+    }
+
+
+If you want to unroll the vector operation to the whole cluster, have a look at
 the  `batchjobs`_ package.
 
 .. _batchjobs: https://cran.r-project.org/web/packages/BatchJobs/index.html