Question

我注意到，在以下程序中，创建的netcdf文件已损坏，即执行ncdump -h out.nc会产生错误。

#include <netcdf>

/**
 * This file produces a corrupted nc output file.
 * Compile with `g++ -std=c++11 -o test test.cpp -lnetcdf -lnetcdf_c++4 
 */

// this is the first non-working 
// chunk size. It does work with 1048576
// 1048576 is representable by exactly 20 bits.
#define CHUNK_SIZE 1048577

using namespace std;
using namespace netCDF;
using namespace netCDF::exceptions;

int main() 
{
    typedef std::vector<size_t> vs;
    typedef std::vector<netCDF::NcDim> vd;

    try
    {
        NcFile outFile = NcFile("out.nc", NcFile::replace);

        // create the dimensions complying to the AMBER specs
        NcDim frameDim   = outFile.addDim("frame");
        NcDim atomDim    = outFile.addDim("atom");
        NcDim spatialDim = outFile.addDim("spatial", 3);
        NcDim radiusDim  = outFile.addDim("radius",1);

        // create the variables
        NcVar coords = outFile.addVar("coordinates", ncFloat, vd({frameDim, atomDim, spatialDim}));
        NcVar radii  = outFile.addVar("radius", ncFloat, vd({frameDim, atomDim}));

        // set up chunking
        vs chunk_coords({1, CHUNK_SIZE, 3});
        vs chunk_radii({1, CHUNK_SIZE, 1});
        coords.setChunking(NcVar::nc_CHUNKED, chunk_coords);
        radii.setChunking(NcVar::nc_CHUNKED, chunk_radii);

        // set up compression
        coords.setCompression(false, true, 1);
        radii.setCompression(false, true, 1);

        return 0;

    }
    catch(NcException& e)
    {
        return -1;
    }
}

{...}} {...}}成为有效且有效的out.nc文件。

... CHUNK_SIZE小于1048577
... CHUNKING已停用
...未使用的“半径”维度的命名方式不同或根本不添加

注意，最大工作数netcdf，CHUNK_SIZE是可用20位表示的最大整数。

导致这种行为的原因是什么？通过重命名1048576维度很容易解决，但我仍然很好奇为什么这与HDF5 / netcdf的分块有任何关联。

与块大小或维度命名相关的损坏的netcdf输出文件

0 个答案: