Getting Started with OpenMX for ISC25 SCC
- Ophir Maor
- Gerardo Cisneros Stoianowski
- Taisuke Ozaki (Unlicensed)
- David Jaekyu Cho
Overview
OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT) , norm-conserving pseudopotentials and pseudo-atomic localized basis functions.
Website: https://www.openmx-square.org/index.html
Build
Download the version 3.9 and keep the data folder, DFT_DATA19.
wget https://www.openmx-square.org/openmx3.9.tar.gz
tar xfp openmx3.9.tar.gz
cd openmx3.9
rm -rf sourceDownload and extract the version 3.962, .
tar xfp source3.962.tar.gz
cd source3.962Note: don’t use the v3.9.9, but the 3.962 in the competition.
Edit the makefile for the compilers and MPI on the system you will be using. The following shows the differences between the modified makefile and the original one:
$ diff makefile makefile.orig
9,12c9,12
< # MKLROOT = /opt/intel/mkl
< CC = mpicc -O3 -march=core-avx2 -ip -no-prec-div -qopenmp -I${MKLROOT}/include/fftw -diag-disable=10441
< FC = mpif90 -O3 -march=core-avx2 -ip -no-prec-div -qopenmp -diag-disable=10441
< LIB= -mkl -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64
---
> MKLROOT = /opt/intel/mkl
> CC = mpicc -O3 -xHOST -ip -no-prec-div -qopenmp -I/opt/intel/mkl/include/fftw/
> FC = mpif90 -O3 -xHOST -ip -no-prec-div -qopenmp
> LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_openmpi_lp64 -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lifcore -liomp5 -lpthread -lm -ldl
249c249
< $(FC) $(OBJS) $(LIB) -lm -nofor-main -o openmx
---
> $(CC) $(OBJS) $(LIB) -lm -o openmxTo build openmx using openmpi module on PSC.
If everything goes well, there will be an executable called openmx in the ../work directory. (See also Installation tips.)
You can build your openmpi with latest Intel compilers or use any other MPI.
You will also need (at the same level where your work and source3.962 directories are), the DFT_DATA19 directory that contains the database needed by OpenMX.
Tasks and Submissions
You can practice building and running with a tiny input, Methane, below.
Run the application on 4 CPU nodes with the NVC input and submit the results in the team’s folder. Try varying the number of OpenMP threads per MPI rank for your optimal run.
Run MPI Profiler to profile the application. Which three MPI calls are mostly used? Include your results in the team's interview ppt slides.
Visualize the results, create a short video that demonstrate the given input via OpenMXViewer (https://www.openmx-square.org/viewer/ just drag and drop). Include it in the team’s interview ppt slides. If you use have an X (Twitter) account, please tag the video/photo with your team name and the hashtags “#ISC25 #ISC25_SCC” prior to the team interview.