mdlint

docs.it4i/anselm/software/mpi/mpi4py-mpi-for-python.md

@@ -20,7 +20,7 @@ $ ml av Python/
    Python/2.7.11-foss-2016a    Python/3.5.2-foss-2016a    Python/3.5.1
    Python/2.7.9-foss-2015g     Python/3.4.3-intel-2015b   Python/2.7.9
    Python/2.7.11-intel-2015b   Python/3.5.2
-   
+
 $ ml av OpenMPI/
 --------------------------------------- /apps/modules/mpi --------------------------
 OpenMPI/1.8.6-GCC-4.4.7-system   OpenMPI/1.8.8-GNU-4.9.3-2.25  OpenMPI/1.10.1-GCC-4.9.3-2.25
@@ -28,7 +28,8 @@ OpenMPI/1.8.6-GNU-5.1.0-2.25     OpenMPI/1.8.8-GNU-5.1.0-2.25  OpenMPI/1.10.1-GN
     OpenMPI/1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25   OpenMPI/2.0.2-GCC-6.3.0-2.27
 ```
 
-!!! Warning ""
+!!! Warning "Flavours"
+
     * modules Python/x.x.x-intel... - intel MPI
     * modules Python/x.x.x-foss...  - OpenMPI
     * modules Python/x.x.x - without MPI
@@ -37,8 +38,8 @@ OpenMPI/1.8.6-GNU-5.1.0-2.25     OpenMPI/1.8.8-GNU-5.1.0-2.25  OpenMPI/1.10.1-GN
 
 You need to import MPI to your python program. Include the following line to the python script:
 
-```cpp
-    from mpi4py import MPI
+```python
+from mpi4py import MPI
 ```
 
 The MPI4Py enabled python programs [execute as any other OpenMPI](Running_OpenMPI/) code.The simpliest way is to run
@@ -57,43 +58,43 @@ $ mpiexec python hello_world.py
 
 ### Hello World!
 
-```cpp
-    from mpi4py import MPI
+```python
+from mpi4py import MPI
 
-    comm = MPI.COMM_WORLD
+comm = MPI.COMM_WORLD
 
-    print "Hello! I'm rank %d from %d running in total..." % (comm.rank, comm.size)
+print "Hello! I'm rank %d from %d running in total..." % (comm.rank, comm.size)
 
-    comm.Barrier()   # wait for everybody to synchronize
+comm.Barrier()   # wait for everybody to synchronize
 ```
 
 ### Collective Communication With NumPy Arrays
 
-```cpp
-    from mpi4py import MPI
-    from __future__ import division
-    import numpy as np
+```python
+from mpi4py import MPI
+from __future__ import division
+import numpy as np
 
-    comm = MPI.COMM_WORLD
+comm = MPI.COMM_WORLD
 
-    print("-"*78)
-    print(" Running on %d cores" % comm.size)
-    print("-"*78)
+print("-"*78)
+print(" Running on %d cores" % comm.size)
+print("-"*78)
 
-    comm.Barrier()
+comm.Barrier()
 
-    # Prepare a vector of N=5 elements to be broadcasted...
-    N = 5
-    if comm.rank == 0:
-        A = np.arange(N, dtype=np.float64)    # rank 0 has proper data
-    else:
-        A = np.empty(N, dtype=np.float64)     # all other just an empty array
+# Prepare a vector of N=5 elements to be broadcasted...
+N = 5
+if comm.rank == 0:
+    A = np.arange(N, dtype=np.float64)    # rank 0 has proper data
+else:
+    A = np.empty(N, dtype=np.float64)     # all other just an empty array
 
-    # Broadcast A from rank 0 to everybody
-    comm.Bcast( [A, MPI.DOUBLE] )
+# Broadcast A from rank 0 to everybody
+comm.Bcast( [A, MPI.DOUBLE] )
 
-    # Everybody should now have the same...
-    print "[%02d] %s" % (comm.rank, A)
+# Everybody should now have the same...
+print "[%02d] %s" % (comm.rank, A)
 ```
 
 Execute the above code as:

docs.it4i/software/singularity.md

@@ -12,7 +12,7 @@ Singularity also allows you to leverage the resources of whatever host you are o
 Singularity can import, bootstrap, and even run Docker images directly from [Docker Hub](https://hub.docker.com/). You can easily run RHEL7 like this:
 
 ```console
-[hrb33@r33u01n865 ~]$ cat /etc/redhat-release 
+[hrb33@r33u01n865 ~]$ cat /etc/redhat-release
 CentOS release 6.7 (Final)
 [hrb33@r33u01n865 ~]$ ml Singularity
 [hrb33@r33u01n865 ~]$ singularity shell docker://centos:latest
@@ -23,8 +23,8 @@ Downloading layer: sha256:45a2e645736c4c66ef34acce2407ded21f7a9b231199d3b92d6c97
 Downloading layer: sha256:a3ed95caeb02ffe68cdd9fd84406680ae93d633cb16422d00e8a7c22955b46d4
 Singularity: Invoking an interactive shell within container...
 
-Singularity.centos:latest> cat /etc/redhat-release 
-CentOS Linux release 7.3.1611 (Core) 
+Singularity.centos:latest> cat /etc/redhat-release
+CentOS Linux release 7.3.1611 (Core)
 ```
 
 ## Creating Own Image from Docker Image
@@ -32,7 +32,7 @@ CentOS Linux release 7.3.1611 (Core)
 ```console
 hrb33@hrb33-toshiba:/$ cd /tmp/
 hrb33@hrb33-toshiba:/tmp$ sudo singularity create /tmp/c7.img
-[sudo] password for hrb33: 
+[sudo] password for hrb33:
 Creating a new image with a maximum size of 768MiB...
 Executing image create helper
 Formatting image with ext3 file system
@@ -49,7 +49,7 @@ No bootstrap definition passed, updating container
 Executing Prebootstrap module
 Executing Postbootstrap module
 Done.
-hrb33@hrb33-toshiba:/tmp$ sudo singularity shell --writable c7.img 
+hrb33@hrb33-toshiba:/tmp$ sudo singularity shell --writable c7.img
 Singularity: Invoking an interactive shell within container...
 
 Singularity.c7.img> mkdir /apps /scratch
@@ -68,10 +68,10 @@ Accessing /HOME and /SCRATCH Within Container
 ```console
 hrb33@hrb33-toshiba:/tmp$ ssh hrb33@login4.salomon
 
-                    _____       _                             
-                   / ____|     | |                            
-                  | (___   __ _| | ___  _ __ ___   ___  _ __  
-                   \___ \ / _` | |/ _ \| '_ ` _ \ / _ \| '_ \ 
+                    _____       _
+                   / ____|     | |
+                  | (___   __ _| | ___  _ __ ___   ___  _ __
+                   \___ \ / _` | |/ _ \| '_ ` _ \ / _ \| '_ \
                    ____) | (_| | | (_) | | | | | | (_) | | | |
                   |_____/ \__,_|_|\___/|_| |_| |_|\___/|_| |_|
 
@@ -80,7 +80,7 @@ hrb33@hrb33-toshiba:/tmp$ ssh hrb33@login4.salomon
 
 Last login: Fri Feb 10 14:38:36 2017 from 10.0.131.12
 [hrb33@login4.salomon ~]$ ml Singularity
-[hrb33@login4.salomon ~]$ singularity shell --bind /scratch --bind /apps --writable c7.img 
+[hrb33@login4.salomon ~]$ singularity shell --bind /scratch --bind /apps --writable c7.img
 Singularity: Invoking an interactive shell within container...
 
 Singularity.c7.img> ls /apps/ -l
@@ -124,5 +124,5 @@ drwx------   3 root root  4096 Aug 15  2016 backup
 drwxr-x---   2 root root  4096 Dec  5 10:34 sys
 drwxrwxrwt 154 root root 20480 Feb 14 14:03 temp
 drwxr-xr-x   4 root root  4096 Jan 25 10:48 work
-Singularity.c7.img> 
+Singularity.c7.img>
 ```