Mtanaka77 / AlmaLinux-by-MD-and-Siesta

AlmaLinux on classic MD and ab-initio Siesta4

AlmaLinux on Water-Ice MD and Ab-initio Siesta Codes

We have tested the linux operating system, AlmaLinux-9. It runs well in normal operations except for some errors as shown below.

For the successor of CentOS 7 that is terminated in May 2024, we download the AlmaLinux on the laptop PC. The OS is AlmaLinux-9.4-x86_64-dvd.iso of 10 GB memory [1]. The actual installation time is about 15 minutes which is rebooted for new Linux windows.

At the first time, we open the gcc-gfotran (Fortran) by typing # gfortran -V, which is necessary on AlmaLinux-9. We also type # pip3 -V to open the python3-pip software. The MPI of mpich-4 is downloaded from the source site and installed, and the classic water and ice MD [2] and the ab-initio Siesta-4.1 code [3] are tested for AlmaLinux.

Classic MD

At the first test, the three-dimensional ice and water molecules @p3mtip5p03a.f03 is compiled with a parameter file parm_tip5p_D07a.h, and structure files 1cx666a.exyz and 1cx666a.q [2]. The mpich-4 and fftw-3 packages must be installed before the compilation. The exec run for 6 cpu at least with a start file TIP507_config.start0 is executed by # mpiexec -n 6 a.out &, which runs all right.

The initial state of the water and ice molecules is constructed in quaternions [4]. The pips package is installed at usual linux systems including CentOS 7. Also, the Windows 11 system at GitBash is fine using the C/C++ packages of Vidual Studio Community, and then the related pip3 packages. However, the AlmaLinux-9 shows strange errors at one of the packages of pairlist before we should install # pip3 install genice.

Ab-initio Siesta

Next at the second test, we download the Siesta-4.1b code [3] and unpack by:
% tar -zxvf siesta-4.1b.tar.gz. Before working on the Siesta code, it is necessary to install the OpenBLAS and Scalapack packages. For OpenBLAS, it is straight forward after a while. However, for Scalapack, the installation went wrong although we typed # make -i, since VirtualBox settings of AlmaLinux-9 showed unnecessary errors without success. So for the rescue, the import of ./lib/libscalapack.a is borrowed from the fading CentOS 7.

The arch.make file for the MPI case mpifort is the following (the upper half of the arch.make):
.SUFFIXES:
.SUFFIXES: .f .F .o .c .a .f90 .F90
SIESTA_ARCH = gfortran-MPI

CC = mpicc
FPP = $(FC) -E -P -x c
FC = mpifort

MPI_INTERFACE = libmpi_f90.a
MPI_INCLUDE = .

FFLAGS = -O2 -fPIC -ftree-vectorize -march=native -fallow-argument-mismatch
#FFLAGS = -O2 -fexpensive-optimizations -ftree-vectorize -fprefetch-loop-arrays -march=native -fPIC -fopenmp
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
LIBS += -L/opt/scalapack/lib -lscalapack

The Siesta-4.1b is installed by "make -i" because the error stop is avoided. The test is shown in the Siesta-4.1bTest.pdf [5].

References

1. AlmaLinux OS, https://almalinux.org/.

2. 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/ (May 2023).

3. J. M. Soler et al., J. Phys. Cond. Matt. 14, 2745 (2002).

4. M. Matsumoto, https://github.com/vitroid/GenIce.

5. This homepage PDF file of MD_Siesta-4_Tests.pdf.