官方文档：https://h5bench.readthedocs.io/en/latest/buildinstructions.html
¶ 编译安装 HDFS
截至发文，这里最新版本只有1.12.1：https://www.hdfgroup.org/downloads/hdf5/
要下载1.13，需要到这里下载：https://portal.hdfgroup.org/display/support/Downloads
要按照这里面的提示安装启用了parallel的HDF5：release_docs/INSTALL_parallel
如果没有启用parallel的话，之后编译h5bench的时候会报MPI_COMM_WORLD undeclared的错误。
其他选项是根据vol-async的文档加上的。
./configure --prefix=$(pwd)/install --enable-parallel --enable-threadsafe --enable-unsupported
make -j$(nproc)
make install
echo "export HDF5_HOME=$(pwd)/install" >> ~/.bashrc
source ~/.bashrc¶ 编译安装 argobots
https://github.com/pmodels/argobots
./configure --prefix=$(pwd)/install
make -j$(nproc)
make install¶ 编译安装 VOL (Virtual Object Layer)
所有可用的VOL: https://portal.hdfgroup.org/display/support/Registered+VOL+Connectors
这里用vol-async: https://github.com/hpc-io/vol-async
cd src
cp Makefile.summit Makefile然后把Makefile里的HDF5_DIR和ABT_DIR分别改成HDFS和argobots的安装目录。
然后就可以编译了：
make -j$(nproc)注意，vol-async v1.1与 HDF5 v1.12.1不兼容。
¶ 编译 h5bench
https://github.com/hpc-io/h5bench
sudo apt install libpnetcdf-dev不知道为啥，就算没有-DH5BENCH_ALL=ON，也要依赖AMReX和openPMD。
mkdir build
cd build
cmake .. -DH5BENCH_ALL=ON
make -j$(nproc)
echo "export PATH=$(pwd):\$PATH" >> ~/.bashrc
source ~/.bashrc如果提示mpi.h找不到的话，就把mpi的include路径放到CPATH环境变量中。
不需要跑sudo make install。而且跑了之后，安装在系统目录下的h5bench的权限位是700，所以普通用户没法执行。
注意，一定要把build目录加入到PATH里，不然后面跑实验的时候会报这个错：
execvp error on file h5bench_write (No such file or directory)¶ 运行 h5bench
官方文档
https://h5bench.readthedocs.io/en/latest/running.html
https://h5bench.readthedocs.io/en/latest/vpic.html
配置文件的一些坑：
不能有多余的逗号，不然log里会报错：CRITICAL - Unable to find and parse the input configuration file。
benchmarks下面的每个benchmark里的configuration都要加上"MODE": "SYNC"或者"MODE": "ASYNC"，并且把"ASYNC_MODE": "NON",去掉。不然会报这个错：h5bench - ERROR - Unable to run the benchmark: 'MODE'。
mpi的configuration要去掉--oversubscribe。
我的配置文件：
{
"mpi": {
"command": "mpirun",
"ranks": "4",
"configuration": "-np 8"
},
"vol": {
"library": "/home/searchstar/git/others/vol-async/src:/home/searchstar/Downloads/argobots-1.1/install/lib:/home/searchstar/Downloads/hdf5-1.13.1/install/lib:",
"path": "/home/searchstar/git/others/vol-async/src",
"connector": "async under_vol=0;under_info={}"
},
"file-system": {
"lustre": {
"stripe-size": "1M",
"stripe-count": "4"
}
},
"directory": "test-dir",
"benchmarks": [
{
"benchmark": "write",
"file": "test.h5",
"configuration": {
"MEM_PATTERN": "CONTIG",
"FILE_PATTERN": "CONTIG",
"NUM_PARTICLES": "16 M",
"TIMESTEPS": "5",
"DELAYED_CLOSE_TIMESTEPS": "2",
"COLLECTIVE_DATA": "NO",
"COLLECTIVE_METADATA": "NO",
"EMULATED_COMPUTE_TIME_PER_TIMESTEP": "1 s",
"NUM_DIMS": "1",
"DIM_1": "10000",
"DIM_2": "1",
"DIM_3": "1",
"CSV_FILE": "output.csv",
"MODE": "SYNC"
}
}
]
}其中DIM_1乘上1300差不多就是生成的文件的字节数了。
我保存为了write.json。然后运行测试：
./h5bench write.json