AlmaLinux v.s. Debian OS's on MD and Siesta

....For the termination of CentOS 7, we have tested the AlmaLinux and
Debian OS's. For these operating systems, we want to choose the OS that is
superior with the desktop or laptop PC for computer physicists.

　The installation of AlmaLinux uses AlmaLinux-9.4-x86_64-dvd.iso of
10 GB memory size [1]. The installation is finished in 15 minutes and
is rebooted for a new Linux PC. We open the gfortran package by typing
$ gfortran -V ("$" is the sign to type gfortran as an example), which is
necessary on AlmaLinux-9. We also type $ pip -V, to open PIP

....For Debian OS, the first installation time requires only 4 GB packages,
for internet access or a CD disk. The Debian OS can be updated as
one-by-one basis, as much as gfortran, make, pip, mpich... at one's choice.
The MPI package of mpich4 is downloaded and installed in 30 minutes.
Also, Openblas and Scalapack have to be installed, which may require some
technique.
....After these preparation, we will test water-and-ice MD [2] and ab-initio
molecular dynamics Siesta-4.1 [3].

PDF: Simulations of Molecular Dynamics in AlmaLinux and Debian


* Classical MD
....As the first test, the three-dimensional water molecules @p3mtip5p03a.f03
is compiled [2] with a parameter file param_tip5p-D07a.h and structure files
1cx666a.exyz and 1cx666a.q. Quaternions xxx.q are used for our accuracy.
The mpich-4 and fftw-3 must be installed before the compilation of the water
case. The exec run for 6 cpu (at least) with a starting file TIP07_config-start0
is executed, $ mpiexec -n 6 a.out &.
....The AlmaLinux-9 and Debian-12 have been tested successfully with the mpich-4
software.

....The initial state of the water molecules and methane hydrate as the second test
is constructed with quaternions [4]. The pips package is installed and is fine at usual
Linux systems including Debian OS. Similarly, the pip3 package for water is installed
as $ pip3 install genice, with a complete success.
....For AlmaLinux, the Windows 11 is installed using the C/C++ packages of
Vidual Studio Community, and then the pip3 package. However, the AlmaLinux
fails in .py errors of "pairlist" before installing the genice package.

* Ab-initio Siesta code
....As the final third test, we have downloaded the Siesta-4.1b [3]
and unpacked it: $ tar -zxvf siesta-4.1b.tar.gz. The make and make install steps
are made where the root password is required in the last step. Similarly, the MPI
or/and OMP packages are installed.

....Before working on the Siesta code, it is necessary to install OpenBLAS
and Scalapack packages. For OpenBLAS, it is straight forward after a while.
However for the Scalapack v.2 package, the installation method fails in the
previous Scalapack v.1. Here, the BLACS, PBLAS,... subdirectories are made
with $ make. But, a keyword "-fallow-argument-mismatch" is given prior to
$*.f of Makefile in the SRC subdirectory, and should do $ make -B -k -r.

....The Siesta-4.1b has been compiled by $ make, without errors while
"-fallow-argument-mismatch" is needed at the FFLGS argument of "arch.make".

....The arch.make file for the MPI and OMP cases is the following (the top half
part of arch.make is listed):

.SUFFIXES:
.SUFFIXES: .f .F .o .c .a .f90 .F90
SIESTA_ARCH = fortran-MPI-OMP
CC = mpicc -O2
FPP = $(FC) -E -P -x c
FC = mpifort

MPI_INTERFACE = libmpi_f90.a
MPI_INCLUDE = .

# in gfortran
FFLAGS = -O2 -fPIE -ftree-vectorize -fprefetch-loop-arrays -march=native \
-fallow-argument-mismatch -fopenmp
FC_SERIAL = gfortran
# in Intel 64-bit
# FFLAGS = -O2 -fPIC -qopenmp
# FC_SERIAL = ifort

AR = ar
RANLIB = ranlib
SYS = nag
SP_KIND = 4
DP_KIND = 8
KINDS = $(SP_KIND) $(DP_KIND)

FPPFLAGS = -DMPI
LDFLAGS =
INCFLAGS =
INSDIR = /opt

COMP_LIBS = 　 # libsiestaLAPACK.a libsiestaBLAS.a
# in gfortran
LDFLAGS += -L$(INSDIR)/openblas/lib -Wl,-rpath=$(INSDIR)/openblas/lib
LIBS = -lgomp -L/opt/openblas/lib -lopenblas /opt/scalapack/lib/libscalapack.a
# in Intel 64-bit
# LIBS = -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 \
# -lmkl_core -lmkl_blacs_intelmpi_lp64 -mkl -qopenmp -lpthread -lm -ldl

The test of the Siesta-4.1b code has been shown in the Siesta-4.1bTest.pdf in https://github.com/Mtanaka77/ [5]. No errors are found for AlmaLinux and Debian-12 OS's.

....In conclusion, the Debian-12 OS should be installed for stable performance,
with good "--help" commands in this operating system.

References
1. AlmaLinux OS, https://almalinux.org/.
2. Debian OS, https://www.debian.org/.
3. M. Tanaka, and M. Sato, J. Chem. Physics, 126, 034509 (2007);
　M. Tanaka, Microwave heating of water and ice by TIP5P code, 　
　https://github.com/Mtanaka77/Water_and_methene_hydrate_by_
　TIP5P_code (May 2023).
4. J. M. Soler et al., J. Phys. Cond. Matt. 14, 2745 (2002).
5. M. Matsumoto, https://github.com/vitroid/GenIce/.
6. This PDF file, https://github.com/Mtanaka77/AlmaLinux9_
　Debian-12.pdf/.
　
Go to the homepage