AlmaLinux v.s. Debian OS's on Water MD
and Siesta-4
....For the successor of terminated CentOS 7, we have tested the AlmaLinux
and Debian OS's. We download them on the laptop PC. The installation
is made in AlmaLinux-9.4-x86_64-dvd.iso of 10 GB memory [1].
This is finished in 15 minutes which is rebooted for new Linux windows.
At first, we open the gfortran package by typing $ gfortran -V, which is
necessary on AlmaLinux-9. We also type $ pip -V to open PIP
....For Debian the first installation is only 4 GB, which can be updated by
one-by-one basis as much as gfortran, make, pip, mpich... at your choice.
The MPI of mpich4 is downloaded and installed for the tested case of
water-and-ice MD [2] and ab-initio molecular dynamics Siesta-4.1 program
[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 are used for accuracy. The mpich-4
and fftw-3 must be installed before the compilation of water. The exec run for
6 cpu (at least) with a starting parameter file TIP07_config-start0 is
executed,
$ mpiexec -n 6 a.out &, which runs all right.
....The Debian-12 has been tested with mpich4 software successfully.
....The initial state of the water molecules and methane hydrate as the second
test is constructed in quaternions [4]. The pips package is installed and
is fine
at usual linux systems including Debian. The pip3 package is installed and
$ pip3 install genice, is installed with 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
has failed in .py errors of one of the packages - pairlist.
* Ab-initio Siesta code
....As the third test, we download the Siesta-4.1b code [3] to unpack it:
$ tar -zxvf siesta-4.1b.tar.gz. The make and make install steps are made
where.
the root user is required in the last step. It runs in the MPI or OMP cases.
....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 package, the installation went wrong. Instead,
the insert -falloe-argument-mismatch must be given in SRC directory of
Makefile of Scalapack. 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 case is the following (the top half part of
arch.make is listed):
.SUFFIXES:
.SUFFIXES: .f .F .o .c .a .f90 .F90
SIESTA_ARCH = gfortran-MPI-OMP
CC = mpicc
FPP = $(FC) -E -P -x c
FC = mpifort
MPI_INTERFACE = libmpi_f90.a
MPI_INCLUDE = .
FFLAGS = -O2 -fPIE -ftree-vectorize -fprefetch-loop-arrays -march=native
\
-fallow-argument-mismatch -fopenmp
# the OMP case, gcc, gfortran and FFLAGS, and Scalapack are empty
FC_SERIAL = gfortran
AR = ar
RANLIB = ranlib
SYS = nag
SP_KIND = 4
DP_KIND = 8
KINDS = $(SP_KIND) $(DP_KIND)
FPPFLAGS = -DMPI
LDFLAGS =
INCFLAGS =
INSDIR = /opt
COMP_LIBS = # libsiestaLAPACK.a libsiestaBLAS.a
LDFLAGS += -L$(INSDIR)/openblas/lib -Wl,-rpath=$(INSDIR)/openblas/lib
LIBS = -lgomp -L/opt/openblas/lib -lopenblas /opt/scalapack/lib/libscalapack.a
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 occur for Debian-12 OS.
....So in conclusion, the Debian-12 OS should be installed for stable
performance.
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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