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Created by: jychoi-hpc

Describe the bug I am working on Pixie3D to write restart files with appending mode without any success. I wrote a test case to reproduce the error.

In the test code, I am trying to write a file with appending mode but getting an error. When writing with adios2_mode_write, it works. But, a file with adios2_mode_append is corrupted and cannot do bpls (no error during the runtime though).

To Reproduce Here is my test code (writer.F90)

program writer
    use mpi
    use adios2

    implicit none

    integer(kind=8), dimension(1) :: shape_dims, start_dims, count_dims
    real, dimension(:), allocatable :: myArray
    integer :: inx, irank, isize, ierr, i, var1_type
    type(adios2_adios) :: adios
    type(adios2_io) :: io
    type(adios2_variable) :: var, var1
    type(adios2_attribute) :: attr
    type(adios2_engine) :: engine
    character(len=:), allocatable :: var1_name
    integer :: comm
    integer :: istatus

    real*8 :: totalpe;
    CHARACTER(len=32) :: arg
    integer :: mode
    logical :: do_read = .false.
    logical :: do_append = .false.

    do i = 1, iargc()
        call getarg(i, arg)
        if (trim(arg)=='-read') do_read = .true.
        if (trim(arg)=='-append') do_append = .true.
    end do

    ! Launch MPI
    comm = MPI_COMM_WORLD
    call MPI_Init(ierr)
    call MPI_Comm_rank(comm, irank, ierr)
    call MPI_Comm_size(comm, isize, ierr)

    ! Application variables
    inx = 10
    allocate( myArray(inx) )

    do i=1,inx
        myArray(i) = i-1
    end do

    ! Variable dimensions
    shape_dims(1) = isize * inx
    start_dims(1) = irank * inx
    count_dims(1) = inx

    if (do_append) then
        print *, 'Mode: append'
        mode = adios2_mode_append
    else
        print *, 'Mode: write'
        mode = adios2_mode_write
    endif

    ! Create adios handler passing the communicator, debug mode and error flag
    call adios2_init(adios, comm, adios2_debug_mode_on, ierr)

    ! Declare an IO process configuration inside adios
    call adios2_declare_io(io, adios, "group1", ierr)

    ! Defines a variable to be written in bp format
    ! call adios2_define_variable(var, io, 'totalpe', adios2_type_dp, ierr)
    call adios2_define_variable(var1, io, "totalpe", adios2_type_dp, 1, &
                                (/ 1_8 /), (/ 0_8 /), (/ 1_8 /), &
                                adios2_constant_dims, ierr)
    call adios2_define_variable(var1, io, "arr1", adios2_type_real, 1, &
                                shape_dims, start_dims, count_dims, &
                                adios2_constant_dims, ierr)
    call adios2_define_attribute(attr, io, "attr", "this is attr", ierr)

    ! Open myVector_f.bp in write mode, this launches an engine
    call adios2_open(engine, io, "out.bp", mode, comm, ierr)
    print *, 'adios2_open:ierr', ierr
    do i=1,4
        call adios2_begin_step(engine, adios2_step_mode_append, ierr)
        print *, 'adios2_begin_step:ierr', ierr

        ! Put myArray contents to bp buffer, based on var1 metadata
        call adios2_put(engine, 'totalpe', 777D0, ierr)
        call adios2_put(engine, var1, myArray, adios2_mode_sync, ierr)

        ! Closes engine and deallocates it, becomes unreachable
        call adios2_end_step(engine, ierr)
        print *, 'adios2_end_step:ierr', ierr
    enddo
    call adios2_close(engine, ierr)
    print *, 'adios2_close:ierr', ierr

    ! Deallocates adios and calls its destructor
    call adios2_finalize(adios, ierr)

    if( allocated(myArray) ) deallocate(myArray)
    if( allocated(var1_name) ) deallocate(var1_name)

    call MPI_Finalize(ierr)

end program writer

Makefile

FC=mpif90

ADIOS2_DIR=/opt/adios2
ADIOS2_INC=$(shell $(ADIOS2_DIR)/bin/adios2-config --fortran-flags)
ADIOS2_LIB=$(shell $(ADIOS2_DIR)/bin/adios2-config --fortran-libs)

BINS=writer
all: $(BINS)

writer: writer.F90
	$(FC) -g -ffree-line-length-0 $(ADIOS2_INC) -o $@ $? $(ADIOS2_LIB)

clean:
	rm -rf $(BINS) *.o *.dSYM

I am running in the following step. First, I create out.bp with adios2_mode_write mode

$ ./writer
$ bpls -lva out.bp
File info:
  of variables:  2
  of attributes: 1
  statistics:    Min / Max 

  float    arr1     4*{10} = 0 / 9
  string   attr     attr   = "this is attr"
  double   totalpe  4*{1} = 777 / 777

it works fine

Then, I am trying to do with adios2_mode_append:

$ ./writer -append
$ bpls -lva out.bp
$ bpls -lva out.bp/
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
  #000: H5F.c line 509 in H5Fopen(): unable to open file
    major: File accessibilty
    minor: Unable to open file
  #001: H5Fint.c line 1400 in H5F__open(): unable to open file
    major: File accessibilty
    minor: Unable to open file
  #002: H5Fint.c line 1700 in H5F_open(): unable to read superblock
    major: File accessibilty
    minor: Read failed

It should be BP4 file, not HDF5. It looks like the file corrupted.

Any help and advice will be appreciated.

Thanks.