Writing File Fails on Windows 10 with Intel Fortran 17 with HDF5 1.8.15

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Writing File Fails on Windows 10 with Intel Fortran 17 with HDF5 1.8.15

Michael Jackson
I have been trying to figure out an error that we are getting using the
HDF5 library for a fairly simple program. The original error started out
in our project but we have been able to narrow it down to this sample.
Here is the setup:

Windows 10 x64, Intel Fortran v17.20160721, Visual Studio 2013 SP5,
CMake 3.5.1 and NMake files

We have built HDF5 1.8.15 with STATIC libraries, High Level, CPP and
FORTRAN interfaces.

Both our code and HDF5 were built as Debug in one folder and Release in
another. Neither version will execute correctly.

We then try to use CMake (not sure if this matters at all) to compile
and run a simple program using pure HDF5 calls (versus some higher level
functions that we had written earlier). When we execute the program we
get the following runtime error:

forrtl: severe (170): Program Exception - stack overflow
and then a stack trace but the stack does not show anything except a
bunch of "unknown" files and line numbers.

The code will be included below. The same code also had issues on OS X
when we linked against an intermediate dynamic library but we fixed that
issue. This makes me think that maybe we are mixing libraries maybe?
Debug and Release?

Has anyone else had issues with the Intel Fortran compiler on Windows
and HDF5? We can not use GFORTRAN because there isn't a new enough
version available for Windows (we need GFortran 5.2 or newer).
--
Michael A. Jackson              400 S. Pioneer Blvd
Owner, President                Springboro, Ohio 45066
BlueQuartz Software, LLC        EMail: [hidden email]

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Re: Writing File Fails on Windows 10 with Intel Fortran 17 with HDF5 1.8.15

Michael Jackson
Code is at the bottom:
--
Mike Jackson:

Michael Jackson wrote:

> I have been trying to figure out an error that we are getting using the
> HDF5 library for a fairly simple program. The original error started out
> in our project but we have been able to narrow it down to this sample.
> Here is the setup:
>
> Windows 10 x64, Intel Fortran v17.20160721, Visual Studio 2013 SP5,
> CMake 3.5.1 and NMake files
>
> We have built HDF5 1.8.15 with STATIC libraries, High Level, CPP and
> FORTRAN interfaces.
>
> Both our code and HDF5 were built as Debug in one folder and Release in
> another. Neither version will execute correctly.
>
> We then try to use CMake (not sure if this matters at all) to compile
> and run a simple program using pure HDF5 calls (versus some higher level
> functions that we had written earlier). When we execute the program we
> get the following runtime error:
>
> forrtl: severe (170): Program Exception - stack overflow
> and then a stack trace but the stack does not show anything except a
> bunch of "unknown" files and line numbers.
>
> The code will be included below. The same code also had issues on OS X
> when we linked against an intermediate dynamic library but we fixed that
> issue. This makes me think that maybe we are mixing libraries maybe?
> Debug and Release?
>
> Has anyone else had issues with the Intel Fortran compiler on Windows
> and HDF5? We can not use GFORTRAN because there isn't a new enough
> version available for Windows (we need GFortran 5.2 or newer).

--
Michael A. Jackson                     400 S. Pioneer Blvd

!*****************************************************************************************
program jsontest

!! this is a test program for HDF5 commands without any reference to
EMsoftLib.

use ISO_C_BINDING
use hdf5

IMPLICIT NONE

character(len=1),target   :: chararr2(256,256)
integer*4,target          :: iarr(256,256,256)

integer*4                 :: i1, i2, i3, dim0, dim1, dim3, hdferr, rnk
integer(HID_T)            :: file_id, group_id
integer(HID_T)                         :: space, dset
integer(HSIZE_T), DIMENSION(1:2)       :: dims
integer(HSIZE_T), DIMENSION(1:3)       :: dims3
character(len=8)          :: dataset1

TYPE(C_PTR), dimension(1:256,1:256), TARGET          :: wdata
TYPE(C_PTR), dimension(1:256,1:256,1:256), TARGET    :: wdata3
TYPE(C_PTR)                            :: f_ptr

character(len=132)        :: outname, groupname, nmlname, dataset

!==================================
! Initialize FORTRAN interface.
write(*,"('opening HDF-fortran interface ')")
call h5open_f(hdferr)
!==================================

!==================================
! Create a new file using the default properties.
outname ='Test.h5'
write(*,"('creating file ',$)")
call h5fcreate_f(trim(outname), H5F_ACC_TRUNC_F, file_id, hdferr)
write(*,*) trim(outname), file_id
if (hdferr.ne.0) then
   write(*,*) 'HDF_createFile: error creating file; error code = ',hdferr
   STOP
end if
!==================================

!==================================
! create the TestData group
groupname ='TestData'
write(*,"('creating group ',$)")
call H5Gcreate_f(file_id, groupname, group_id, hdferr)
write(*,*) trim(groupname), group_id
!==================================

!==================================
! generate a 3D integer array and write it to the file
do i1=1,256
  do i2=1,256
   do i3=1,256
    iarr(i1,i2,i3) = i1+i2+i3
   end do
  end do
end do

dataset = 'intarr3D'
dim0 = 256

dims3(1:3) = (/ dim0, dim0, dim0 /)
wdata3 = C_LOC(iarr(1,1,1))

! Create dataspace.
rnk = 3
write (*,*) '  intarr3: h5screate_simple_f'
call h5screate_simple_f(rnk, dims3, space, hdferr)
!
! Create the dataset and write the data to it
write (*,*) '  intarr3: h5screate_f ',H5T_STD_I32LE, H5T_NATIVE_INTEGER
dataset1 = 'intarr3D'
call h5dcreate_f(group_id, dataset1, H5T_STD_I32LE, space, dset, hdferr)
if (hdferr.ne.0) then
   write(*,*) 'h5dcreate_f: error creating int3D dataset; error code =
',hdferr
   STOP
end if

write (*,*) '  intarr3: h5dwrite_f'
call h5dwrite_f(dset, H5T_STD_I32LE, iarr, dims3, hdferr )
if (hdferr.ne.0) then
   write(*,*) 'h5dwrite_f: error writing int3D dataset; error code =
',hdferr
   STOP
end if
!
! Close and release resources.
!
call h5dclose_f(dset , hdferr)
call h5sclose_f(space, hdferr)
!==================================


!==================================
! generate a 2D char array and write it to the file
do i1=1,256
  do i2=1,256
   chararr2(i1,i2) = char(mod(i1+i2-2,256))
  end do
end do

dataset = 'chararray2D'
dim0 = 256

wdata = C_LOC(chararr2(1,1))
dims(1:2) = (/ dim0, dim0 /)

! Create dataspace.
rnk = 2
write (*,*) '  chararr2: h5screate_simple_f'
call h5screate_simple_f(rnk, dims, space, hdferr)
!
! Create the dataset and write the c_char data to it.
write (*,*) '  chararr2: h5dcreate_f '
call h5dcreate_f(group_id, trim(dataset), H5T_STD_U8LE, space, dset, hdferr)
if (hdferr.ne.0) then
   write(*,*) 'h5dcreate_f: error creating char2D dataset; error code =
',hdferr
   STOP
end if

write (*,*) '  chararr2: h5dwrite_f'
call h5dwrite_f(dset, H5T_STD_U8LE, chararr2, dims, hdferr )
if (hdferr.ne.0) then
   write(*,*) 'h5dwrite_f: error writing char2D dataset; error code =
',hdferr
   STOP
end if
!
! Close and release resources.
!
call h5dclose_f(dset , hdferr)
call h5sclose_f(space, hdferr)
!==================================



!==================================
! close group and file
call h5gclose_f(group_id, hdferr)
call h5fclose_f(file_id, hdferr)

! and close the fortran hdf interface
call h5close_f(hdferr)

end program jsontest
!*****************************************************************************************

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Re: Writing File Fails on Windows 10 with Intel Fortran 17 with HDF5 1.8.15

Scot Breitenfeld
In reply to this post by Michael Jackson
How far in the program does it get before it segfaults? Can you post the output from the program?

I tried a sample program on Windows 10, Intel 17, and HDF5 1.8.17, but I’m having issues with the HDF5 Fortran parameters not getting set when building the program inside Visual Studio. Can you verify the HDF5 parameters, such as H5T_NATIVE_INTEGER, are getting set.

I tried replacing one of the fortran examples in the source with your code and then compiled it with cmake. The program did not segfault and completed as expected.

Thanks,
Scot

> On Oct 26, 2016, at 1:05 PM, Michael Jackson <[hidden email]> wrote:
>
> I have been trying to figure out an error that we are getting using the HDF5 library for a fairly simple program. The original error started out in our project but we have been able to narrow it down to this sample. Here is the setup:
>
> Windows 10 x64, Intel Fortran v17.20160721, Visual Studio 2013 SP5, CMake 3.5.1 and NMake files
>
> We have built HDF5 1.8.15 with STATIC libraries, High Level, CPP and FORTRAN interfaces.
>
> Both our code and HDF5 were built as Debug in one folder and Release in another. Neither version will execute correctly.
>
> We then try to use CMake (not sure if this matters at all) to compile and run a simple program using pure HDF5 calls (versus some higher level functions that we had written earlier). When we execute the program we get the following runtime error:
>
> forrtl: severe (170): Program Exception - stack overflow
> and then a stack trace but the stack does not show anything except a bunch of "unknown" files and line numbers.
>
> The code will be included below. The same code also had issues on OS X when we linked against an intermediate dynamic library but we fixed that issue. This makes me think that maybe we are mixing libraries maybe? Debug and Release?
>
> Has anyone else had issues with the Intel Fortran compiler on Windows and HDF5? We can not use GFORTRAN because there isn't a new enough version available for Windows (we need GFortran 5.2 or newer).
> --
> Michael A. Jackson              400 S. Pioneer Blvd
> Owner, President                Springboro, Ohio 45066
> BlueQuartz Software, LLC        EMail: [hidden email]
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> [hidden email]
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
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