Siesta Install

March 20, 2023

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the best way to install siesta (I think)

We have prepared recipes to install Siesta with it. Setup is simple. You need at least to install the miniconda framework (provide more details) and then do: conda install -c conda-forge siesta to install a serial Siesta executable (current version is 4.1.5).

To install a parallel version, you need to use, depending on your choice of parallel environment: conda install -c conda-forge "siesta=*=*openmpi*" conda install -c conda-forge "siesta=*=*mpich*"

from Building Siesta with conda — Siesta Documentation (siesta-project.org)

install netCDF4

Try conda install -c conda-forge netcdf4 first. If there is a conflict that requires siesta to be downgraded, try the following:

Use pip debug --verbose to check for compatible tags.
Download the appropriate whl files from the cftime website and the netCDF4 website.
Install the two files using pip install <file_name>.whl (numpy and wheel should be installed beforehand, which can be done directly with conda and should not result in errors).

Main reference to Centos6.6系统里安装SIESTA 4 | 知乎。
Related software and libraries are installed under ~/software if not otherwise specified.

system and environment

Linux version 5.15.90.1-microsoft-standard-WSL2 (oe-user@oe-host) (x86_64-msft-linux-gcc (GCC) 9.3.0, GNU ld (GNU Binutils) 2.34.0.20200220) #1 SMP Fri Jan 27 02:56:13 UTC 2023

Ubuntu 20.04.4 LTS

GCC already installed

openmpi

# download and unzip
wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.4.tar.gz
tar -xzvf openmpi-3.1.4.tar.gz
cd openmpi-3.1.4
# config and install
mkdir ~/software/openmpi/3.1.4
./configure --prefix=~/software/openmpi/3.1.4
make
make install
# profile
vi ~/.zshrc.local ## i use zsh; for bash it's ~/.bashrc or ~/.bashrc.local
## add following commands
OPENMPI=~/software/openmpi/3.1.4
export LD_LIBRARY_PATH=$OPENMPI/lib:$LD_LIBRARY_PATH
export PATH=$OPENMPI/bin:$PATH
export INCLUDE=$OPENMPI/include:$INCLUDE
export CPATH=$OPENMPI/include:$CPATH
export MANPATH=$OPENMPI/share/man:$MANPATH
## exit vim
source ~/.zshrc # or source ~/.bashrc
# test
ompi_info | grep Ident # version
cd ~/software/openmpi/3.1.4/examples
make
./hello_c

mpiblacs

# download and unzip
wget http://www.netlib.org/blacs/mpiblacs.tgz
tar -zxvf mpiblacs.tgz
cd BLACS
# config and make
cp BMAKES/Bmake.MPI-LINUX ./Bmake.inc
vi Bmake.inc
## modify some lines as
INTFACE  = -DAdd_
MPIdir = ~/software/openmpi/3.1.4
MPILIBdir = $(MPIdir)/lib # !! delet the last / !!
MPILIB = $(MPILIBdir)/libmpi.so # some people think it should be libmpi.a but i only find libmpi.so under the lib and it works
F77 = mpif90
## exit vim
make
# test
make mpi tester
make mpi what=clean
# ------
# NOTE:
# 1. you will find blacs_MPI-LINUX-0.a under BLACS/LIB if success
# 2. if it prints Error and exits during making, check the file path. You can temporarily move the folder BLACS to a suitable place and move back after making.
# ------

lapack

# download and unzip
wget http://www.netlib.org/lapack/lapack-3.6.1.tgz
tar -zxvf lapack-3.6.1.tgz
cd lapack-3.6.1
# config and make
cp make.inc.example make.inc
vi make.inc
## modify two lines (annotating and un-annotating) as
# TIMER = INT_ETIME # !! annotating !!
TIMER = NONE # !! un-annotating !!
## exit vim
vi Makefile
## modify two lines as
# lib: lapacklib tmglib # !! annotating !!
lib: blaslib lapacklib tmglib # !! un-annotating and delete variants !!
## exit vim
make
# ------
# NOTE:
# 1. you will get liblapack.a, librefblas.a, libtmglib.a if success
# 2. if it prints Error about znep.out ans exits during making, try run `ulimit -s unlimited` in command line.
# ------
## the following commands may need sudo
cp ./liblapack.a /usr/lib
cp ./liblapack.a /usr/local/lib
cp ./librefblas.a /usr/lib/libblas.a # !! rename !!
cp ./librefblas.a /usr/local/lib/libblas.a # !! rename !!
cp ./libtmglib.a /usr/lib
cp ./libtmglib.a /usr/local/lib

scalapack

# download and unzip
wget http://www.netlib.org/scalapack/scalapack.tgz
tar -zxvf scalapack.tgz
cd scalapack-2.2.0
# config and make
cp SLmake.inc.example SLmake.inc
make
make exe
# ------
# you will get libscalapack.a if success
# ------

siesta

# download and unzip
wget https://launchpad.net/siesta/4.0/4.0.2/+download/siesta-4.0.2.tar.gz
tar -zxvf siesta-4.0.2.tar.gz
cd siesta-4.0.2
# config and make
cd ./Obj
../Src/obj_setup.sh
../Src/configure \
	--enable-mpi FC=~/software/openmpi/3.1.4/bin/mpif90 \
	--with-blacs=~/software/BLACS/LIB/blacs_MPI-LINUX-0.a \
	--with-scalapack=~/software/scalapack-2.2.0/libscalapack.a
make
# ------
# you will get a file named siesta if success
# you can copy it every where you want in the system or build softlink
# ------
# test
cd ./Tests
vi test.mk
## modify SIESTA, for example
SIESTA= mpirun -np 16 --oversubscribe ~/software/Obj/siesta
## exit vim
make