３次元磁気流体シミュレーションと並列計算　〜　Athena++チュートリアル4

# JupyterLabが使えるDockerイメージ作成用のDockefileを元にして、
# athena++開発・実行で使えるDockerコンテナを作成する。

# ubuntu 22.04の最新版をベースとする。
FROM ubuntu:jammy-20240111

# Set bash as the default shell
ENV SHELL=/bin/bash

# Build with some basic utilities
RUN apt update && apt install -y \
    build-essential \
    python3-pip apt-utils vim \
    git git-lfs \
    curl unzip wget gnuplot \
    openmpi-bin libopenmpi-dev \
    openssh-client openssh-server \
    libhdf5-dev libhdf5-openmpi-dev

# alias python='python3'
RUN ln -s /usr/bin/python3 /usr/bin/python

# install python package to need
RUN pip install -U pip setuptools \
	&& pip install numpy scipy h5py mpmath

# The following stuff is derived for horovod in docker.
# Allow OpenSSH to talk to containers without asking for confirmation
RUN mkdir -p /var/run/sshd
RUN cat /etc/ssh/ssh_config | grep -v StrictHostKeyChecking > /etc/ssh/ssh_config.new && \
    echo "    StrictHostKeyChecking no" >> /etc/ssh/ssh_config.new && \
    mv /etc/ssh/ssh_config.new /etc/ssh/ssh_config

# --allow-run-as-root
ENV OMPI_ALLOW_RUN_AS_ROOT=1
ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1

# Set hdf5 path
ENV CPATH="/usr/include/hdf5/openmpi/"

# Create a working directory
WORKDIR /workdir

# command prompt
CMD ["/bin/bash"]

# python configure.py --prob blast -b --flux hlld -mpi -hdf5
  Your Athena++ distribution has now been configured with the following options: 
  Problem generator:            blast
  Coordinate system:            cartesian
  Equation of state:            adiabatic
  Riemann solver:               hlld
  Magnetic fields:              ON
  Number of scalars:            0
  Number of chemical species:   0
  Special relativity:           OFF
  General relativity:           OFF
  Radiative Transfer:           OFF
  Implicit Radiation:           OFF
  Cosmic Ray Transport:         OFF
  Frame transformations:        OFF
  Self-Gravity:                 OFF
  Super-Time-Stepping:          OFF
  Chemistry:                    OFF
  KIDA rates:                   OFF
  ChemRadiation:                OFF
  chem_ode_solver:              OFF
  Debug flags:                  OFF
  Code coverage flags:          OFF
  Linker flags:                   -lhdf5
  Floating-point precision:     double
  Number of ghost cells:        2
  MPI parallelism:              ON
  OpenMP parallelism:           OFF
  FFT:                          OFF
  HDF5 output:                  ON
  HDF5 precision:               single
  Compiler:                     g++
  Compilation command:          mpicxx  -O3 -std=c++11

# make clean
rm -rf obj/*
rm -rf bin/athena
rm -rf *.gcov

# make
mpicxx  -O3 -std=c++11 -c src/globals.cpp -o obj/globals.o
mpicxx  -O3 -std=c++11 -c src/main.cpp -o obj/main.o
In file included from src/main.cpp:46:
src/outputs/outputs.hpp:22:10: fatal error: hdf5.h: No such file or directory
   22 | #include <hdf5.h>
      |          ^~~~~~~~
compilation terminated.
make: *** [Makefile:119: obj/main.o] Error 1

# make
mpicxx  -O3 -std=c++11 -c src/globals.cpp -o obj/globals.o
・・・
・・・
mpicxx  -O3 -std=c++11 -c src/inputs/hdf5_reader.cpp -o obj/hdf5_reader.o
src/inputs/hdf5_reader.cpp: In function 'void HDF5ReadRealArray(const char*, const char*, int, const int*, const int*, int, const int*, const int*, AthenaArray<double>&, bool, bool)':
src/inputs/hdf5_reader.cpp:94:7: error: 'H5Pset_fapl_mpio' was not declared in this scope; did you mean 'H5Pset_fapl_stdio'?
   94 |       H5Pset_fapl_mpio(property_list_file, MPI_COMM_WORLD, MPI_INFO_NULL);
      |       ^~~~~~~~~~~~~~~~
      |       H5Pset_fapl_stdio
src/inputs/hdf5_reader.cpp:109:7: error: 'H5Pset_dxpl_mpio' was not declared in this scope; did you mean 'H5Pset_fapl_stdio'?
  109 |       H5Pset_dxpl_mpio(property_list_transfer, H5FD_MPIO_COLLECTIVE);
      |       ^~~~~~~~~~~~~~~~
      |       H5Pset_fapl_stdio
make: *** [Makefile:119: obj/hdf5_reader.o] Error 1

/usr/bin/ld: cannot find -lhdf5: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [Makefile:114: bin/athena] Error 1

# pwd
/workdir/kenji/t4
# ls -l
-rwxr-xr-x 1 root root  3613256 Mar  2 04:11 athena
-rw-r--r-- 1 root root     2193 Mar  2 08:12 athinput.blast

10c10
< file_type  = hdf5       # HDF5 data dump
---
> file_type  = vtk        # VTK data dump
13d12
< ghost_zones = true      # enables ghost zone output
24c23
< nx1        = 128         # Number of zones in X1-direction
---
> nx1        = 64         # Number of zones in X1-direction
30c29
< nx2        = 128         # Number of zones in X2-direction
---
> nx2        = 64         # Number of zones in X2-direction
36c35
< nx3        = 128         # Number of zones in X3-direction
---
> nx3        = 64         # Number of zones in X3-direction
42,47c41
< #num_threads = 1         # Number of OpenMP threads per process
< 
< <meshblock>
< nx1        = 32         # Number of zones per MeshBlock in X1-direction
< nx2        = 32         # Number of zones per MeshBlock in X2-direction
< nx3        = 32         # Number of zones per MeshBlock in X3-direction
---
> num_threads = 1         # Number of OpenMP threads per process

# cat mpi_run
mpirun -np $1 --hostfile myhosts \
-mca plm_rsh_args "-p 12345" \
-mca btl_tcp_if_exclude lo,docker0 \
-oversubscribe $(pwd)/athena \
-i $2 > log

# cat myhosts
europe slots=4
jupiter slots=4
ganymede slots=6

# mpi_run 2 athinput.blast
# mpi_run 4 athinput.blast
# mpi_run 8 athinput.blast