Overview
(few words about the application)
Building and Running example
1. where to get the code, and input example
building example
running example
…
Tasks
what to do
Submissions
(what is needed to submit)CONQUEST is a DFT code designed for large-scale calculations, with excellent parallelisation. It gives an exact diagonalisation approach for systems from 1 to 10,000+ atoms, and brings the possibility of linear scaling calculations on over 1,000,000 atoms. In this task, you will be using the linear scaling approach, which can show perfect weak scaling of thousands of cores.
Note: The page may be changed until the competition stats, maybe sure to follow up until the opening ceremony.
Conquest presentation to the teams:
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Presentation file:
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Building and Running example
Download v1.2 from https://github.com/OrderN/CONQUEST-release.git.
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wget https://github.com/OrderN/CONQUEST-release/releases/download/v1.2/CONQUEST-release-1.2.tar.gz |
Download libxc 6.2.2 from https://www.tddft.org/programs/libxc/download/.
Prerequisites
FFTW/MKL package
SCALAPACK
Build libxc:
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# Load intel compilers and mpi modules
cd libxc-6.2.2
./configure --prefix=<path> CC=mpicc FC=mpif90
make
make install |
Build Conquest:
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# Load intel compilers and mpi modules
cd CONQUEST-release/src
# Edit system.make for XC lib and include paths, and FFT & blas libraries.
# Add correct flag (-qopenmp for Intel) for OpenMP to compile and link arguments
# Set MULT_KERN to ompGemm
make |
Sample build script for libxc and Conquest on PSC:
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#!/bin/bash
BASE=$PWD
source /jet/packages/oneapi/v2023.2.0/compiler/2023.2.1/env/vars.sh
rm -rf libxc-6.2.2
tar xfp libxc-6.2.2.tar.gz
cd libxc-6.2.2
MPI=impi-2021.10.0
MPI=hpcx-2.18
if [[ "$MPI" =~ ^impi ]]; then
source /jet/packages/oneapi/v2023.2.0//mpi/2021.10.0/env/vars.sh
export MPIFC=mpiifort
export CC=mpiicc
export FC=$MPIFC
elif [[ "$MPI" =~ ^hpcx ]]; then
module use $HOME/tools/$MPI/modulefiles
module load hpcx
export OMPI_CC=icc
export OMPI_CXX=icpc
export OMPI_FC=ifort
export OMPI_F90=ifort
export MPIFC=mpif90
export CC=mpicc
export FC=mpif90
fi
rm -rf $BASE/libxc-6.2.2-$MPI
./configure --prefix=$BASE/libxc-6.2.2-$MPI
make -j 16 install |
Modify src/system.make under Conquest source directory,
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#
# Set compilers
FC=$(MPIFC)
F77=$(FC)
# Linking flags
LINKFLAGS= -L/usr/local/lib
ARFLAGS=
# Compilation flags
# NB for gcc10 you need to add -fallow-argument-mismatch
COMPFLAGS= -O3 $(XC_COMPFLAGS)
COMPFLAGS_F77= $(COMPFLAGS)
# Set BLAS and LAPACK libraries
# MacOS X
# BLAS= -lvecLibFort
# Intel MKL use the Intel tool
# Generic
# BLAS= -llapack -lblas
# Full library call; remove scalapack if using dummy diag module
LIBS= -qmkl=sequential -lmkl_scalapack_lp64 -lmkl_blacs_$(WHICHMPI)_lp64 $(XC_LIB)
# LIBS= $(FFT_LIB) $(XC_LIB) -lscalapack $(BLAS)
# LibXC compatibility (LibXC below) or Conquest XC library
# Conquest XC library
#XC_LIBRARY = CQ
#XC_LIB =
#XC_COMPFLAGS =
# LibXC compatibility
# Choose LibXC version: v4 (deprecated) or v5/6 (v5 and v6 have the same interface)
# XC_LIBRARY = LibXC_v4
XC_DIR = <path>/libxc-6.2.2-$(MPI)
XC_LIBRARY = LibXC_v5
XC_LIB = -L$(XC_DIR)/lib -lxcf90 -lxc
XC_COMPFLAGS = -I$(XC_DIR)/include
# Set FFT library
FFT_LIB=-lfftw3
FFT_OBJ=fft_fftw3.o
# Matrix multiplication kernel type
MULT_KERN = default
# Use dummy DiagModule or not
DIAG_DUMMY = |
Build Conquest:
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#!/bin/bash
BASE=$PWD
source /jet/packages/oneapi/v2023.2.0/compiler/2023.2.1/env/vars.sh
MPI=impi-2021.10.0
MPI=hpcx-2.18
if [[ "$MPI" =~ ^impi ]]; then
source /jet/packages/oneapi/v2023.2.0//mpi/2021.10.0/env/vars.sh
export MPIFC=mpiifort
export CC=mpiicc
export FC=$MPIFC
export WHICHMPI=intelmpi
elif [[ "$MPI" =~ ^hpcx ]]; then
module use $HOME/tools/$MPI/modulefiles
module load hpcx
export OMPI_CC=icc
export OMPI_CXX=icpc
export OMPI_FC=ifort
export OMPI_F90=ifort
export MPIFC=mpif90
export CC=mpicc
export FC=mpif90
export WHICHMPI=openmpi
fi
cd src
export MPI
make clean
make
cd $BASE/bin
mv Conquest Conquest-$MPI |
Running Conquest:
You will need to set the number of threads per process for OpenMP as well as the number of MPI processes.
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export OMP_NUM_THREADS=XX
mpirun -np YY path/to/Conquest |
Application metric is wall-time “Total run time”.
Tasks & Submissions
Input:
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The virtual task involves performing linear scaling calculations on samples of bulk silicon with different numbers of atoms. Conquest weak scaling is seen when the number of atoms per MPI process is kept fixed, and the number of processes is scaled with the system size (number of atoms). You have been provided with three inputs, with 512 atoms (si_444.xtl), 1728 atoms (si_666.xtl) and 4096 atoms (si_888.xtl). The minimum number of atoms per MPI process is 8; the maximum will be dictated by memory limitations. The simplest way to examine weak scaling is to keep the product of MPI processes and OpenMP threads per process constant, and vary system size. You might also explore the effect of under-populating nodes where that is possible.
The smaller inputs are only for practice, not for submissions. The only input for submission is si_888.xtl.
Find the best balance between OpenMP threads and MPI processes, show your work in the team’s interview presentation. Investigate the weak scaling (with the other inputs) as the MPI/OpenMP balance is changed. present your work in the interview.
Run CONQUEST on 4 nodes and submit the results to the team’s folder (any number of PPN you choose).
Run IPM profile or any other MPI profile on 4 nodes, and find the 3 most used MPI calls, show your work in the team interview presentation.
Try run the application on 1,2,4 nodes (for the si_888.xtl input) and present strong scaling graph in the teams interview presentation.