Update Linux MPI sample (Azure-Samples#254)

* Update Linux MPI sample

* Update based on feedback.

* fix travis-ci own issue

.gitattributes

@@ -1,3 +1,4 @@
 * text=auto
 # Set the default behavior of Linux shell scripts to lf
 *.sh text eol=lf
+Python/Batch/article_samples/mpi/data/* text eol=lf

.travis.yml

@@ -2,7 +2,6 @@ language: python
 cache: pip
 python:
   - 2.7
-  - 3.3
   - 3.4
   - 3.5
   # disable pypy until travis upgrades to at least pypy2.6 due to cryptography
@@ -11,6 +10,9 @@ python:
   #- pypy3
 addons:
   apt:
+    config:
+      retries: true
+    update: true  
     packages:
       - oracle-java8-installer
 env:

Python/Batch/article_samples/mpi/README.md

@@ -0,0 +1,25 @@
+## Azure Batch Python Article Samples
+
+### Configuring the samples
+In order to run the Python samples, they must be updated with Azure Batch
+and Azure Storage credentials. 
+
+### Setting up the Python environment
+In order to run the samples, you will need a Python interpreter compatible
+with version 2.7 or 3.3+. You will also need to install the
+[Azure Batch](https://pypi.python.org/pypi/azure-batch) and
+[Azure Storage](https://pypi.python.org/pypi/azure-storage) python packages.
+Installation can be performed using the [requirements.txt](./requirements.txt)
+file via the command `pip install -r requirements.txt`
+
+### MPI sample
+The MPI sample is an introduction to running an MPI command in Azure Batch in a
+Linux environment. It creates a pool with RDMA enabled virtual machines (You can
+use STANDARD_A8 to replace the virtual machine size if you don't have enough
+core quota). It submits a job to the pool, and then submits a task which 
+performs a simple MPI pingpong command. The files required by the task are
+automatically uploaded to Azure Storage and then downloaded onto the nodes via
+Batch resource files. When the task is done, the console output of the MPI
+pingpong command is uploaded back to Azure Storage.
+
+For more details on MPI/RDMA, visit [here](https://docs.microsoft.com/en-us/azure/virtual-machines/linux/classic/rdma-cluster).

Python/Batch/article_samples/mpi/data/application-cmd

@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+#Command script to run pingpong performance testing on multiple machines as MPI task on Azure Batch.
+#Usage: application-cmd [nodes]
+
+#For more details of MPI/RDMA, visit: https://docs.microsoft.com/en-us/azure/virtual-machines/linux/classic/rdma-cluster
+
+#Use the intel mpi exists in CentOS-HPC 7.4 image
+source /opt/intel/impi/5.1.3.223/bin64/mpivars.sh
+#prepare environment variables for intel mpi to use RDMA
+export I_MPI_FABRICS=shm:dapl
+export I_MPI_DAPL_PROVIDER=ofa-v2-ib0
+export I_MPI_DYNAMIC_CONNECTION=0
+
+# Run mpi application with appropriate parameters
+mpirun -n $1 -ppn 1 -hosts $AZ_BATCH_HOST_LIST IMB-MPI1 pingpong

Python/Batch/article_samples/mpi/data/coordination-cmd

@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+#Command script to run pingpong performance testing on multiple machines as MPI task on Azure Batch.
+#Usage: coordination-cmd
+
+#For more details of MPI/RDMA, visit: https://docs.microsoft.com/en-us/azure/virtual-machines/linux/classic/rdma-cluster
+
+#Prepare environment

Python/Batch/article_samples/mpi/data/linux/openfoam/application-cmd

@@ -1,43 +1,7 @@
-#!/usr/bin/env bash
-#Command script to run OpenFoam application on multiple machines as MPI task on Azure Batch.
-#Usage: application [nodes] [cores_per_node] [CFD iterations]
-
-#prepare environment variables for intel mpi and openfoam
-mnt=$4
-source /opt/intel/impi/5.1.3.181/bin64/mpivars.sh
-export MPI_ROOT=$I_MPI_ROOT
-export FOAM_INST_DIR=$mnt/share/OpenFOAM
-source $mnt/share/OpenFOAM/OpenFOAM-2.3.x/etc/bashrc
+source /opt/intel/impi/5.1.3.223/bin64/mpivars.sh
 export I_MPI_FABRICS=shm:dapl
 export I_MPI_DAPL_PROVIDER=ofa-v2-ib0
 export I_MPI_DYNAMIC_CONNECTION=0
-export LD_LIBRARY_PATH=$mnt/share/OpenFOAM/intel64_lin:$LD_LIBRARY_PATH
-# total number of processes is number of nodes multipled by number of processes per node
-(( numProc = $1 * $2 ))
-
-#prepare decomposition mesh as per total number of nodes, processes and number of iterations for openfoam
-cd $mnt/share/OpenFOAM/motorBike
-echo $numProc
-sed -i.bak "s/SUB1/$numProc/g" system/decomposeParDict
-sed -i.bak2 "s/SUB2/$1/g" system/decomposeParDict
-sed -i.bak "s/SUB1/$3/g" system/controlDict
-decomposePar
-ls -d processor* | xargs -I {} rm -rf ./{}/0
-ls -d processor* | xargs -I {} cp -r 0.org ./{}/0
 
 # Run mpi application with appropriate parameters
-mpirun -np $numProc -ppn $2 --host $5 -wdir $mnt/share/OpenFOAM/motorBike simpleFoam -parallel
-
-# process the output
-reconstructPar -latestTime
-foamToVTK -latestTime
-
-# prepare the output and compress it as result
-cp $4/genimages.py VTK/
-cp $4/stdout.txt VTK/
-cp $4/stderr.txt VTK/
-cd VTK
-mv motorBike*/*.vtk .
-mmv "*:*.vtk" "#1#2.vtk"
-mmv "*%*.vtk" "#1#2.vtk"
-tar -czf $4/VTK.tgz ../VTK/
+mpirun -n $1 -ppn `nproc` --host $AZ_BATCH_HOST_LIST IMB-MPI1 pingpong