I know there is/was a bug that affected OS X when trying to write a dataset larger than 2^31 bytes. It is solved in the current development branch. I am not sure if this effects Linux x64 though. but it sure looks like the stack traces I was getting.
Try checking out the development code from: The code can be checked out from: http://svn.hdfgroup.uiuc.edu/hdf5/branches/hdf5_1_8_10 and see if the problem still persists. ___________________________________________________________ Mike Jackson Principal Software Engineer BlueQuartz Software Dayton, Ohio [email protected] www.bluequartz.net -- Mike Jackson <www.bluequartz.net> On Jan 24, 2013, at 4:01 PM, Robert McLay wrote: > I am unable to write a 2GB dataset from a single task. I have the same > problem with 1.8.8, 1.8.9, and 1.8.10. I have attached a FORTRAN 90 program > that shows the problem. I also have a C program that shows the same problem > so I do not think this is a problem of FORTRAN to C convertion. The program > is a parallel f90 program run as a single task. > > Here is the error report: > > $ ./example > HDF5-DIAG: Error detected in HDF5 (1.8.10) MPI-process 0: > #000: H5Dio.c line 266 in H5Dwrite(): can't write data > major: Dataset > minor: Write failed > #001: H5Dio.c line 673 in H5D__write(): can't write data > major: Dataset > minor: Write failed > #002: H5Dmpio.c line 544 in H5D__contig_collective_write(): couldn't finish > shared collective MPI-IO > major: Low-level I/O > minor: Write failed > #003: H5Dmpio.c line 1523 in H5D__inter_collective_io(): couldn't finish > collective MPI-IO > major: Low-level I/O > minor: Can't get value > #004: H5Dmpio.c line 1567 in H5D__final_collective_io(): optimized write > failed > major: Dataset > minor: Write failed > #005: H5Dmpio.c line 312 in H5D__mpio_select_write(): can't finish > collective parallel write > major: Low-level I/O > minor: Write failed > #006: H5Fio.c line 158 in H5F_block_write(): write through metadata > accumulator failed > major: Low-level I/O > minor: Write failed > #007: H5Faccum.c line 816 in H5F_accum_write(): file write failed > major: Low-level I/O > minor: Write failed > #008: H5FDint.c line 185 in H5FD_write(): driver write request failed > major: Virtual File Layer > minor: Write failed > #009: H5FDmpio.c line 1842 in H5FD_mpio_write(): MPI_File_write_at_all > failed > major: Internal error (too specific to document in detail) > minor: Some MPI function failed > #010: H5FDmpio.c line 1842 in H5FD_mpio_write(): Invalid argument, error > stack: > MPI_FILE_WRITE_AT_ALL(84): Invalid count argument > major: Internal error (too specific to document in detail) > minor: MPI Error String > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line Source > > libpthread.so.0 00000031C4D0C4F0 Unknown Unknown Unknown > libc.so.6 00000031C3E721E3 Unknown Unknown Unknown > example 000000000071C646 Unknown Unknown Unknown > libmpich.so.3 00002B0682CBF48C Unknown Unknown Unknown > libmpich.so.3 00002B0682E6AE91 Unknown Unknown Unknown > libmpich.so.3 00002B0682E6BDB2 Unknown Unknown Unknown > example 00000000004AE9EC Unknown Unknown Unknown > example 00000000004A9014 Unknown Unknown Unknown > example 0000000000497040 Unknown Unknown Unknown > example 00000000004990A2 Unknown Unknown Unknown > example 0000000000693991 Unknown Unknown Unknown > example 00000000004597A9 Unknown Unknown Unknown > example 000000000045C144 Unknown Unknown Unknown > example 000000000043B6B4 Unknown Unknown Unknown > > Attached is the configuration data > > Attached is a program which produces the error report. I compiled this > fortran 90 program with: > > h5pfc -g -O0 -o example example.f90 > > Internal to the program is a variable "LocalSz" which is 646. 8*(646^3) is > bigger than 2*1024^3. The program works if LocalSz is 645. > > Thanks for looking at this. > > > > -- > Robert McLay, Ph.D. > TACC > Manager, HPC Software Tools > (512) 232-8104 > > <h5.config.txt><example.f90>_______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
