Dear experts,
I am studying the tutorial "Spin-orbit transport calculations: Bi2Se3 topological insulator thin-film device" and want to reproduce the results of the tutorial. I downloaded the script "electrode1.py" and ran it on my local computer using ATK2016 with the default setting of the Job manager. It took me a long time (nearly 5 days) to get the result. The configuration of my computer is :
Intel Core (TM) i7 6700 CPU, quad core, 3.4 GHz, 16GB RAM
Since it took to too long time, I want to run it on the computer cluster of our university using MPI process to speedup the calculation. Because of the license of ATK, only ATK2015 can be used on the cluster. I modified some parts of the script "electrod1.py" using ATK2015 and submitted it to the cluster using these MPI settings:
Number of Nodes: 8
Tasks per Node: 2
memory per CPU =16GB
as some other's suggestion, I disabled the threading calculation using "export OMP_NUM_THREADS=1, export OMP_DYNAMIC=FALSE" and set 16 MPI processes to run the calculation.
(Please see the attached files: electrode1gkm_argo5.py is the python file for calculation and elelctrode1gkm_argo5.sh (txt) is the file for submitting the job to the cluster.)
Now the calculation has been running on the cluster for 2D21hrs, much slower than I expected.
What I want to ask is: Is there anything wrong with my MPI setting or the scripts? Why it's almost no use for speeding up the calculation?
Thank you very much for your kind reply!