Linux 下基于R语言打开hdf5(.h5)文件异常的处理方法

Linux 平台使用无法通过R语言的 rhdf5::H5Fopen和 hdf5r::H5File$new打开H5格式文件，抛出异常“HDF5. File accessibility. Unable to open file.” 参考 https://github.com/GreenleafLab/ArchR/issues/248?spm=a2c6h.13046898.0.0.5ae16ffa2qPYS6 完成Debug 过程记录：

1、异常 INFO

• 1.rhdf5::H5Fopen 函数异常 error：

  data.h5 <- H5Fopen(name = "exp_matrix.hdf5")
  Error in H5Fopen(name = "exp_matrix.hdf5",  : 
  HDF5. File accessibility. Unable to open file.
  

• 2.hdf5r::H5File$new 函数异常 error：

  hdf5r::H5File$new("exp_matrix.hdf5", mode="r")
  Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : 
  HDF5-API Errors:
    error #000: H5F.c in H5Fopen(): line 620: unable to open file
        class: HDF5
        major: File accessibility
        minor: Unable to open file
  
    error #001: H5VLcallback.c in H5VL_file_open(): line 3501: failed to iterate over available VOL connector plugins
        class: HDF5
        major: Virtual Object Layer
        minor: Iteration failed
  
    error #002: H5PLpath.c in H5PL__path_table_iterate(): line 578: can't iterate over plugins in plugin path '(null)'
        class: HDF5
        major: Plugin for dynamically loaded library
        minor: Iteration failed
  
    error #003: H5PLpath.c in H5PL__path_table_iterate_process_path(): line 620: can't open directory: ~/local/Minconda/envs/scRNA/lib/hdf5/plugin
        class: HDF5
        major: Plugin for dynamically loaded library
        minor: Can't open directory or file
  
    error #004: H5VLcallback.c in H5VL__file_open(): line 3351: open faile
  

2、处理策略

引发该异常的原因是系统默认打开了使用HDF5库时启用文件锁定。解决方案：编辑Linux 用户的配置文件(.bashrc)添加以下两句环境变量：

export HDF5_USE_FILE_LOCKING="FALSE"
export RHDF5_USE_FILE_LOCKING="FALSE"

然后执行source ~/.bashrc,就可以解决Linux环境下无法读取h5文件的错误了。

Reference

Error in H5Fopen(file): Unable to open HDF5 file when using subsetArchRProject to create new arrow files · Issue #248 · GreenleafLab/ArchR (github.com)