compilation - 编译并行netCDF时出错

Question

我正在尝试使用HDF5的并行构建来编译和安装netCDF。

首先，我安装了最新的zlib，然后安装了串行HDF5和并行HDF5，以便

/scratch/mycomputername/packages/...包含HDF5和zlib lib，包括bin文件夹。

/scratch/mycomputername/packages_parallel ...包含并行HDF5和zlib lib，include和bin文件夹。

*** ZLIB安装:

./configure --prefix=/scratch/mycomputername/packages
make
make test
make install prefix=/scratch/mycomputername/packages

和

./configure --prefix=/scratch/mycomputername/packages_parallel
make
make test
make install prefix=/scratch/mycomputername/packages_parallel

*** HDF5安装:

./configure --prefix=/scratch/mycomputername/packages --enable-fortran --with-zlib=/scratch/mycomputername/packages/include,/scratch/mycomputername/packages/lib
make
make check
make install prefix=/scratch/dione/packages

和

./configure --prefix=/scratch/mycomputername/packages_parallel --enable-parallel --enable-fortran --with-zlib=/scratch/mycomputername/packages_parallel/include,/scratch/mycomputername/packages_parallel/lib
make
make check
make install prefix=/scratch/mycomputername/packages_parallel

***然后，安装我使用的串行netCDF

./configure --prefix=/scratch/mycomputername/packages CPPFLAGS=-I/scratch/mycomputername/packages/include LDFLAGS=-L/scratch/computername/packages/lib
make
make check
make install prefix=/scratch/mycomputername/packages

这个工作成功了。

***但是，当我尝试对并行netCDF执行相同操作时，我遇到了错误。
我用了

./configure --prefix=/scratch/mycomputername/packages_parallel CPPFLAGS=-I/scratch/mycomputername/packages_parallel/include LDFLAGS=-L/scratch/mycomputername/packages_parallel/lib

我得到错误:
checking hdf5.h usability ... no
checking hdf5.h presence ... no
checking for hdf5.h ... no
configure: error: Compiling a test with HDF5 failed. Either hdf5.h cannot be found, or config.log should be checked for other reason

我也试过
./configure --prefix=/scratch/computername/packages_parallel --with-hdf5=/scratch/mycomputername/packages_parallel/ --with-zlib=/scratch/mycomputername/packages_parallel/lib
但我收到上面引用的错误消息。

有谁知道为什么并行版本可能找不到HDF5库？

Answer 1

确保对于您编译和安装的每个软件包，将必要的路径添加到.profile或.bashrc文件中。例如，您需要在ZLIB安装后添加它(假设安装目录为/usr/local):

if [ -z "${ZLIBDIR}" ]
then
ZLIBDIR="/usr/local"; export ZLIBDIR
else
ZLIBDIR="/usr/local:${ZLIBDIR}"; export ZLIBDIR
fi

对于HDF5，我始终使用以下命令:

export HDF5_LIB_DIR="/usr/local/lib"
if [ -z "${LD_LIBRARY_PATH}" ]
then
LD_LIBRARY_PATH="/usr/local/lib"; export LD_LIBRARY_PATH
else
LD_LIBRARY_PATH="/usr/local/lib:${LD_LIBRARY_PATH}"; export LD_LIBRARY_PATH
fi
if [ -z "${LIBDIR}" ]
then
LIBDIR="/usr/local/lib"; export LIBDIR
else
LIBDIR="/usr/local/lib:${LIBDIR}"; export LIBDIR
fi
export INCLUDE=/usr/local/lib:$Include
export PATH=/usr/local/bin:$PATH
export HDF5_LIB_DIR=/usr/local/lib
export HDF5DIR=/usr/local
export HDF5_DIR=/usr/local
export CPPFLAGS="-I$HDF5_DIR/include -I/usr/local/include"
export LDFLAGS="-L$HDF5_DIR/lib -L/usr/local/lib"

最后，在安装NetCDF之后，我使用:

export NETCDFHOME=/usr/local
export NETCDF_PREFIX=/usr/local
export NETCDF_LIB=/usr/local/lib
export NETCDF4_ROOT=/usr/local
export NETCDF4_DIR=/usr/local
export NETCDF_INC=/usr/local/include
export PATH=/usr/local/bin:$PATH

希望这可以帮助。干杯，特隆