1.9. Blade Server Installations

The possible requirements for the machine learning project on the blade servers:

Current purpose - re-run just the steady state case without optimisation. Only require:

1.9.1. Proposed Run Script

module load python/anaconda3
source activate py3
of4

. $WM_PROJECT_DIR/bin/tools/RunFunctions

pyFoamClearCase.py . --processors-remove
/usr/local/Pointwise/PointwiseV18.0R2/pointwise -b Hydro_V18_wider.glf
rm -r 0
cp -r 0_orig 0
transformPoints -scale '(0.0254 0.0254 0.0254)'
renumberMesh -overwrite
cp system/controlDict_simple system/controlDict
decomposePar
runParallel potentialFoam
runParallel simpleFoam
reconstructPar -latestTime
pyFoamCopyLastToFirst.py . .
pyFoamClearCase.py . --processors-remove
cp system/controlDict_parcel system/controlDict
decomposePar
runParallel icoUncoupledKinematicParcelFoam

1.9.2. OS

uname -a
Linux cfd4 3.10.0-862.14.4.el7.x86_64 #1 SMP Tue Sep 25 14:32:52 CDT 2018 x86_64 x86_64 x86_64 GNU/Linux

1.9.3. Anaconda (Installed)

module load python/anaconda3
conda --version
conda 4.5.11

1.9.4. Python 3.x (Installed)

python -V
Python 3.5.4 :: Anaconda custom (64-bit)

  • Change to python 3 environment

conda search "^python$"
conda create –n py3 python=3.5.4 anaconda

Proceed ([y]/n)?

y

source activate py3

Can also remove conda environment (I didn’t do this)

conda remove -n py3 -all

1.9.4.1. pyFoam 0.6.6 (Installed)

pyFoamVersion.py
Python version: 2.7.5 (default, Jun 20 2019, 16:11:37)
pyFoam-Version: 0.6.10

  • (May have only been installed with Python 2.7.5)

pip install PyFoam==0.6.6

which pyFoamVersion.py
~/.conda/envs/py3/bin/pyFoamVersion.py

  • Alias to PyFoam version is not be needed as Python 3.5.4 environment is used

1.9.4.2. Numpy (Installed as 1.14.0 with Python 3.5.4)

python
import numpy
print (numpy.__version__)
1.14.0

1.9.4.3. Matplotlib (Installed as 2.1.2 with Python 3.5.4)

python
import matplotlib
print (matplotlib.__version__)
2.1.2

1.9.4.4. scipy (Installed as 1.0.0 with Python 3.5.4)

python
import scipy
print (scipy.__version__)
1.0.0

1.9.5. OpenFOAM 4.x (OK)

of4
foamVersion
OpenFOAM-4.x

1.9.6. Output of PATH

(OF:4.x) (py3) $ echo $PATH

/misc/OpenFOAM/ThirdParty-4.x/platforms/linux64Gcc/gperftools-svn/bin:
/misc/OpenFOAM/ThirdParty-4.x/platforms/linux64Gcc/ParaView-5.0.1/bin:
/home/links/apr207/OpenFOAM/apr207-4.x/platforms/linux64GccDPInt32Opt/bin:
/misc/OpenFOAM/site/4.x/platforms/linux64GccDPInt32Opt/bin:
/misc/OpenFOAM/OpenFOAM-4.x/platforms/linux64GccDPInt32Opt/bin:
/misc/OpenFOAM/OpenFOAM-4.x/bin:
/misc/OpenFOAM/OpenFOAM-4.x/wmake:
/usr/lib64/openmpi/bin:
/home/links/apr207/.conda/envs/py3/bin:
/usr/local/anaconda3/bin:
/usr/local/texlive/2017/bin/x86_64-linux:
/usr/lib64/qt-3.3/bin:
/usr/local/bin:
/usr/bin:
/usr/local/sbin:
/usr/sbin:
/opt/puppetlabs/bin:
/home/links/apr207/.local/bin:
/home/links/apr207/bin

1.9.7. Pointwise 18.0R1 (Installed as 18.0R2)

pointwise --help

  • No license, but can specify a license server and port

/usr/local/Pointwise/PointwiseV18.0R2/pointwise

  • Looks like 18.0R2 is installed (require Pointwise18.0R1)

ls -ls /usr/local/Pointwise/
4 drwxr-xr-x 9 root root 4096 Jan 25  2017 PointwiseV18.0R2

Obtain from John Stone: pw-V18.0R1-linux_x86_64-jre.sh (Not Available Online)

sh pw-V18.0R1-linux_x86_64-jre.sh
Next
Accept
/home/links/apr207/Pointwise/PointwiseV18.0R1 is installation directory
Run Pointwise
(Won't find license)
Specify license server
server: emps-pointwise
port: 2385

Add this to .bashrc:

# Pointwise alias for this version
alias pointwise="/home/links/apr207/Pointwise/PointwiseV18.0R1/pointwise"

1.9.10. Had to re-install OpenFOAM-4.x as OpenFOAM-4.x_blade_servers because lagrangian libraries are too complex

cp -rf OpenFOAM-4.x/ OpenFOAM-4.x_blade_servers

ln -s /usr/bin/mpicc.openmpi OpenFOAM-4.x_blade_servers/bin/mpicc ln -s /usr/bin/mpirun.openmpi OpenFOAM-4.x_blade_servers/bin/mpirun

source $HOME/OpenFOAM/OpenFOAM-4.x/etc/bashrc FOAMY_HEX_MESH=yes