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

Synopsis
....We have tested the AlmaLinux OS with the standard Debian OS.
For these operating systems, we will be choosing the Debian OS
that can be superior in the desktop and laptop PC for computer physicists.

Main part
　The installation of AlmaLinux uses AlmaLinux-9.6 of 11 GB memory size [1].
The installation is finished in 15 minutes and is rebooted for a new Linux PC.
We open the pip and gfortran packages by typing $ gfortran -V as example
("$" is the type sign), which is necessary on AlmaLinux-9.

....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 gcc, gfortran, pip, ... at one's choice.
The MPI package of mpich4 or openmpi is downloaded and installed in
30 minutes. Also, Openblas and Scalapack have to be installed.
....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 Genice is
installed as $ pip3 install genice, with a complete success.
....For AlmaLinux, the "pip3 install genice" software seems to be successful, but
the AlmaLinux 9.6 becomes errors in "genice CS1...".

* Ab-initio Siesta code
....As the final third test, we have downloaded the Siesta-4.1b [3]
and unpacked it: $ tar xf siesta-4.1b.tar.gz (does not require xfvz any more).
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 may need
keywords "-fallow-argument-mismatch" in $*.f for Fortran and also
"-Wno-imolicit-function-declaration for GCC in the SLmake.inc and
do $ make of the scalapack top directory.

....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 -lopenblasomp /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-13 OS's.

....In conclusion, the Debian-13 OS is 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/.
　
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