LIB

The possibility of using external libraries (that are loaded at runtime) has been available in C/C++ for a long time, but in Fortran became only available as of Fortran2003.

In the case of XDS, frame-reading and computation can be separated starting with version November-2016. The LIB= keyword allows users/companies to develop their own specialized frame-reading libraries, and relieves the XDS maintainers from implementing even more file formats. The feature was developed in order to be able to natively (i.e. without temporary intermediates) read the HDF5 files written for data from the Eiger detector.

In the following, small examples are given for

• how a program ("host") may use an existing external library, e.g. the dectris-neggia library (source; pre-compiled)
• how an external library ("client") may be implemented that XDS can use

The glue code between host and client is based on http://cims.nyu.edu/~donev/Fortran/DLL/DLL.Forum.txt . There should be no need to change this, unless the interface design changes.

The interface was designed by Markus Mathes (Dectris), Vittorio Boccone (Dectris) and Kay Diederichs. It is supposed to be generic, i.e. useful beyond XDS. In particular, the 4096 bytes of the info_array can be utilized to obtain and use header information (e.g. wavelength, distance, axes specifications and other metadata).

The interface has several implementations.

Host code example

! Example test program for existing external library
! This should be saved in a file called test_generic_host.f90
! Kay Diederichs 4/2017
!
! compile with 
! ifort -qopenmp generic_data_plugin.f90 test_generic_host.f90 -o test_generic_host
! or
! gfortran -O -fopenmp generic_data_plugin.f90 test_generic_host.f90 -ldl -o test_generic_host
! run with 
! ./test_generic_host < test.in
! To test the dectris-neggia library, one could use this test.in:
!/usr/local/lib64/dectris-neggia.so
!/scratch/data/Eiger_16M_Nov2015/2015_11_10/insu6_1_??????.h5
!1 900
!
! The OMP_NUM_THREADS environment variable may be used for benchmarks!


PROGRAM test_generic_host
    USE generic_data_plugin, ONLY: library, firstqm, lastqm, nx, ny, is_open, &
        generic_open, generic_get_header, generic_get_data, generic_close
    IMPLICIT            NONE
    INTEGER            :: ier,nxny,ilow,ihigh,nbyte,info_array(1024),  &
                          number_of_frames,len,numfrm
    INTEGER, ALLOCATABLE :: iframe(:)
    REAL               :: qx,qy,avgcounts
    CHARACTER(len=:), ALLOCATABLE :: master_file
    CHARACTER(len=512) :: ACTNAM

! what should be done?
    WRITE(*,*)'enter parameter of LIB= keyword:'
    READ(*,'(a)') actnam
    library=TRIM(actnam)
    WRITE(*,*)'enter parameter of NAME_TEMPLATE_OF_DATA_FRAMES= keyword:'
    READ(*,'(a)') actnam
    WRITE(*,*)'enter parameters of the DATA_RANGE= keyword:'
    READ(*,*) ilow,ihigh
    
! set some more module variables
    firstqm=INDEX(actnam,'?')   ! qm means question mark
    lastqm =INDEX(actnam,'?',BACK=.TRUE.)
    len    =LEN_TRIM(actnam)
    IF (actnam(len-2:len)=='.h5')THEN
      master_file=actnam(:len-9)//'master.h5'
      PRINT*,'master_file=',TRIM(master_file)
    ELSE
       master_file=TRIM(actnam)
    ENDIF
    info_array(1) = 1         ! 1=XDS  (generic_open may check this)
    info_array(2) = 123456789 ! better: e.g. 20160510; generic_open may check this

! initialize
    CALL generic_open(library, master_file,info_array, ier)
    IF (ier<0) THEN
      WRITE(*,*)'error from generic_open, ier=',ier       
      STOP
    END IF
    is_open=.TRUE.

! get header and report
    CALL generic_get_header(nx,ny,nbyte,qx,qy,number_of_frames,info_array,ier)
    IF (ier<0) THEN
      WRITE(*,*)'error from generic_get_header, ier=',ier       
      STOP
    END IF
    WRITE(*,'(a,3i6,2f10.6,i6)')'nx,ny,nbyte,qx,qy,number_of_frames=', &
                                 nx,ny,nbyte,qx,qy,number_of_frames
    WRITE(*,'(a,4i4,i12)')'INFO(1:5)=vendor/major version/minor version/patch/timestamp=', &
         info_array(1:5)
    IF (info_array(1)==0) THEN
       WRITE(*,*) 'generic_getfrm: data are not vendor-specific',info_array(1) ! 1=Dectris
    ELSE IF (info_array(1)==1) THEN
      WRITE(*,*) 'generic_getfrm: data are from Dectris'
    END IF
    nxny=nx*ny
    avgcounts=0.
    
! read the data (possibly in parallel)
!$omp parallel default(shared) private(numfrm,iframe,info_array,ier)
    ALLOCATE(iframe(nxny))
!$omp do reduction(+:avgcounts)
    DO numfrm=ilow,ihigh
      CALL generic_get_data(numfrm, nx, ny, iframe, info_array, ier)
      IF (ier<0) THEN
        WRITE(*,*)'error from generic_get_data, numfrm, ier=',numfrm,ier       
        STOP
      END IF
      avgcounts=avgcounts + SUM(iframe)/REAL(nxny) ! do something with data
    END DO
!$omp end parallel
    WRITE(*,*)'average counts:',avgcounts/(ihigh-ilow+1)
    
! close
    CALL generic_close(ier)
    IF (ier<0) THEN
      WRITE(*,*)'error from generic_close, ier=',ier       
      STOP
    END IF
    
END PROGRAM test_generic_host

Client code example

The following code should be saved as file test_generic_client.f90 :

! This reads single data files which have a header of 7680 bytes
! Kay Diederichs 4/2017
! Kay Diederichs 7/2021 add code for the case that fn_template has no '?', and simplify&comment gfortran command.
!
! compile with
! ifort -fpic -shared -static-intel -qopenmp -qopenmp-link=static -traceback -sox test_generic_client.f90 -o libtest_generic_client.so
! (this includes all required compiler libraries into the libtest_generic_client.so library)
! or
! gfortran -fpic test_generic_client.f90 -shared -o libtest_generic_client.so
! (this does not include the compiler's libgfortran.so and libquadmath.so into the library; don't know how to achieve this so
! gfortran is only useful if it is anyway installed on the machine)
! The resulting file can be used with a LIB=./libtest_generic_client.so line in XDS.INP, and enables
! reading of data files with a 7680 bytes header plus 1024*1024 pixels of integer data, without any record structure.

MODULE plugin_test_mod
       CHARACTER :: fn_template*132='',cformat*6='(i4.4)'
       INTEGER   :: lenfn,firstqm,lastqm
END MODULE

SUBROUTINE plugin_open(filename, info_array, error_flag) bind(C)
       USE ISO_C_BINDING
       USE plugin_test_mod
       integer(c_int)                  :: error_flag
       character(kind=c_char)          :: filename(*)
       integer(c_int), dimension(1024) :: info_array
       INTEGER i
       
       DO i=1,LEN(fn_template)
         IF (filename(i)==C_NULL_CHAR) EXIT
         fn_template(i:i)=filename(i)
       END DO
       WRITE(*,*)'libtest_generic_client v1.0; Kay Diederichs 20.4.17'
       WRITE(*,*)'plugin_open: fn_template=',TRIM(fn_template)
       lenfn=LEN_TRIM(fn_template)
       info_array=0
       error_flag=0
       firstqm=INDEX(fn_template,'?')
       lastqm =INDEX(fn_template,'?',BACK=.TRUE.)
       IF (firstqm==0) THEN
         firstqm=lenfn-7
         lastqm =lenfn-4
       END IF
       WRITE(cformat(3:5),'(i1,a1,i1)')lastqm-firstqm+1,'.',lastqm-firstqm+1
END SUBROUTINE plugin_open
!
subroutine plugin_get_header(nx, ny, nbyte, qx, qy, number_of_frames, info_array, error_flag) bind(C)
       USE ISO_C_BINDING
       integer(c_int)                  :: nx, ny, nbyte, number_of_frames       
       real(c_float)                   :: qx, qy
       integer(c_int)                  :: error_flag
       integer(c_int), dimension(1024) :: info_array
       
!       WRITE(*,*)'plugin_get_header was called'
       nx=1024
       ny=1024
       nbyte=4
       qx=0.172
       qy=0.172
       number_of_frames=9999
       info_array=0
       info_array(1)=0
       error_flag=0
END SUBROUTINE plugin_get_header
!
SUBROUTINE plugin_get_data(frame_number, nx, ny, data_array, info_array, error_flag)  BIND(C,NAME="plugin_get_data")
    USE ISO_C_BINDING
    USE plugin_test_mod
    integer(c_int)                    :: nx, ny, frame_number
    integer(c_int)                    :: error_flag
    integer(c_int), dimension(1024)   :: info_array
    integer(c_int), dimension (nx*ny) :: data_array
! local variables
    INTEGER k,i,dummy
    CHARACTER :: fn*132
    fn=fn_template
    IF (frame_number>0) WRITE(fn(firstqm:lastqm),cformat) frame_number
! -qopenmp compile option needs to be used otherwise race in writing fn
    OPEN(newunit=k,file=fn,action='READ',ACCESS='STREAM',form='unformatted')
    WRITE(*,*)'plugin_get_data was called; frame_number,k=',frame_number,k
    READ(k)(dummy,i=1,1920) ! read 15*512=7680 header bytes 
    READ(k) data_array
    CLOSE(k)
    error_flag=0
END SUBROUTINE plugin_get_data
!
SUBROUTINE plugin_close(error_flag) BIND(C,NAME="plugin_close")
    USE ISO_C_BINDING
    integer(c_int)                     :: error_flag
!    WRITE(*,*)'plugin_close was called'
    error_flag=0
END SUBROUTINE plugin_close

Glue code

The following code should be saved as generic_data_plugin.f90 .

!
! This is free and unencumbered software released into the public domain.!
! Anyone is free to copy, modify, publish, use, compile, sell, or distribute this software, 
! either in source code form or as a compiled binary, for any purpose, commercial or non-commercial,
! and by any means.
!
! In jurisdictions that recognize copyright laws, the author or authors of this software dedicate 
! any and all copyright interest in the software to the public domain. We make this dedication for
! the benefit of the public at large and to the detriment of our heirs and successors. We intend
! this dedication to be an overt act of relinquishment in perpetuity of all present and future 
! rights to this software under copyright law.
!
! THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT
! NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
! IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
! ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR 
! THE USE OR OTHER DEALINGS IN THE SOFTWARE.
!
! For more information, please refer to <http://unlicense.org/>
!
!
! vittorio.boccone@dectris.com
! Dectris Ltd., Taefernweg 1, 5405 Baden-Daettwil, Switzerland.
!
! (proof_of_concept)
!
! Interoperability with C in Fortran 2003
!
! Wrap up module to abstract the interface from 
! http://cims.nyu.edu/~donev/Fortran/DLL/DLL.Forum.txt
!
module iso_c_utilities
   use iso_c_binding ! intrinsic module

   character(c_char), dimension(1), save, target, private :: dummy_string="?"
   
contains   
   
   function c_f_string(cptr) result(fptr)
      ! convert a null-terminated c string into a fortran character array pointer
      type(c_ptr), intent(in) :: cptr ! the c address
      character(kind=c_char), dimension(:), pointer :: fptr
      
      interface ! strlen is a standard C function from <string.h>
         integer(int64) function strlen(string) result(len) bind(C,name="strlen")
            use iso_fortran_env, only : int64 
            use iso_c_binding
            type(c_ptr), value :: string ! a C pointer
         end function
      end interface   
      
      if(c_associated(cptr)) then
         call c_f_pointer(fptr=fptr, cptr=cptr, shape=[strlen(cptr)])
      else
         ! to avoid segfaults, associate fptr with a dummy target:
         fptr=>dummy_string
      end if
            
   end function

end module iso_c_utilities

!
! Interoperability with C in Fortran 2003
!
! Wrap up module to abstract the interface from 
! http://cims.nyu.edu/~donev/Fortran/DLL/DLL.Forum.txt
!
module dlfcn
   use iso_c_binding
   use iso_c_utilities
   implicit none
   private

   public :: dlopen, dlsym, dlclose, dlerror ! dl api
   
   ! valid modes for mode in dlopen:
   integer(c_int), parameter, public :: rtld_lazy=1, rtld_now=2, rtld_global=256, rtld_local=0
      ! obtained from the output of the previously listed c program 
         
   interface ! all we need is interfaces for the prototypes in <dlfcn.h>
      function dlopen(file,mode) result(handle) bind(C,name="dlopen")
         ! void *dlopen(const char *file, int mode);
         use iso_c_binding
         character(c_char), dimension(*), intent(in) :: file
            ! c strings should be declared as character arrays
         integer(c_int), value :: mode
         type(c_ptr) :: handle
      end function
      function dlsym(handle,name) result(funptr) bind(C,name="dlsym")
         ! void *dlsym(void *handle, const char *name);
         use iso_c_binding
         type(c_ptr), value :: handle
         character(c_char), dimension(*), intent(in) :: name
         type(c_funptr) :: funptr ! a function pointer
      end function
      function dlclose(handle) result(status) bind(C,name="dlclose")
         ! int dlclose(void *handle);
         use iso_c_binding
         type(c_ptr), value :: handle
         integer(c_int) :: status
      end function
      function dlerror() result(error) bind(C,name="dlerror")
         ! char *dlerror(void);
         use iso_c_binding
         type(c_ptr) :: error
      end function         
   end interface
      
 end module dlfcn

!
! Generic handle for share-object like structures
!
! Wrap up module to abstract the interface from 
! http://cims.nyu.edu/~donev/Fortran/DLL/DLL.Forum.txt
!
module generic_data_plugin
  use iso_c_binding
  implicit none

  character(kind=c_char,len=1024) :: dll_filename
  character(kind=c_char,len=1024) :: image_data_filename
  integer(c_int)                  :: status
  type(c_ptr)                     :: handle=c_null_ptr
  INTEGER :: nx,ny,firstqm=0,lastqm=0   ! global variables that do not change    
! firstqm, lastq     mark ? characters in NAME_TEMPLATE that get replaced by an image number
  CHARACTER(len=:), allocatable :: library ! global variable that does not change 
  LOGICAL :: is_open=.FALSE.           ! set .TRUE. if library successfully opened

  !public                          :: generic_open !, generic_header, generic_data, generic_clone

  !
  ! Abstract interfaces for C mapped functions
  !
  !
  ! get_header -> dll_get_header 
  abstract interface

     subroutine plugin_open(filename, info_array, error_flag) bind(C)
       use iso_c_binding
       integer(c_int)                  :: error_flag
       character(kind=c_char)          :: filename(*)
       integer(c_int), dimension(1024) :: info_array


     end subroutine plugin_open

     subroutine plugin_close(error_flag) bind(C)
       use iso_c_binding
       integer (c_int)          :: error_flag

     end subroutine plugin_close

     subroutine plugin_get_header(nx, ny, nbyte, qx, qy, number_of_frames, info_array, error_flag) bind(C)
       use iso_c_binding
       integer(c_int)                  :: nx, ny, nbyte, number_of_frames       
       real(c_float)                   :: qx, qy
       integer(c_int)                  :: error_flag
       integer(c_int), dimension(1024) :: info_array
     end subroutine plugin_get_header

     subroutine plugin_get_data(frame_number, nx, ny, data_array, info_array, error_flag) bind(C)
       use iso_c_binding
       integer(c_int)                   :: nx, ny, frame_number
       integer(c_int)                   :: error_flag
       integer(c_int), dimension(nx:ny) :: data_array
       integer(c_int), dimension(1024)  :: info_array
     end subroutine plugin_get_data
  end interface

  ! dynamically-linked procedures
  procedure(plugin_open),  pointer :: dll_plugin_open
  procedure(plugin_get_header), pointer :: dll_plugin_get_header 
  procedure(plugin_get_data),   pointer :: dll_plugin_get_data   
  procedure(plugin_close), pointer :: dll_plugin_close
   



contains


  ! 
  ! Open the shared-object 
  subroutine generic_open(library, template_name, info_array, error_flag)    ! Requirements:
    !  'LIBRARY'                      input  (including path, otherwise using LD_LIBRARY_PATH)
    !  'TEMPLATE_NAME'                input  (the resource in image data masterfile)
    !  'INFO' (integer array)         input  Array of (1024) integers:
    !                                          INFO(1)    = Consumer ID (1:XDS)
    !                                          INFO(2)    = Version Number of the Consumer software
    !                                          INFO(3:8)  = Unused
    !                                          INFO(9:40) = 1024bit signature of the consumer software
    !                                          INFO(>41)  = Unused
    !  'INFO' (integer array)         output Array of (1024) integers:
    !                                          INFO(1)    = Vendor ID (1:Dectris)
    !                                          INFO(2)    = Major Version number of the library
    !                                          INFO(3)    = Minor Version number of the library
    !                                          INFO(4)    = Parch Version number of the library
    !                                          INFO(5)    = Linux timestamp of library creation
    !                                          INFO(6:8)  = Unused
    !                                          INFO(9:40) = 1024bit signature of the library
    !                                          INFO(>41)  = Unused
    !  'ERROR_FLAG'                   output Return values
    !                                         0 Success
    !                                        -1 Handle already exists
    !                                        -2 Cannot open Library
    !                                        -3 Function not found in library
    !                                        -4 Master file cannot be opened (coming from C function)
    !                                        -10 Consumer identity not supported (coming from C function)
    !                                        -11 Consumer identity could not be verified (coming from C function)
    !                                        -12 Consumer software version not supported (coming from C function)

    use iso_c_binding
    use iso_c_utilities
    use dlfcn
    implicit none    

    character(len=:), allocatable      :: library, template_name
    integer(c_int)                     :: error_flag
    integer(c_int), dimension(1024)    :: info_array
    type(c_funptr)                     :: fun_plugin_open_ptr   = c_null_funptr
    type(c_funptr)                     :: fun_plugin_close_ptr  = c_null_funptr
    type(c_funptr)                     :: fun_plugin_get_header_ptr  = c_null_funptr
    type(c_funptr)                     :: fun_plugin_get_data_ptr    = c_null_funptr
    integer(c_int)                     :: external_error_flag
    logical                            :: loading_error_flag     = .false.

    error_flag=0

    write(6,*) "[generic_data_plugin] - INFO - generic_open"
    write(6,*) "      + library          = <", library,      ">"
    write(6,*) "      + template_name    = <", template_name, ">"

    if ( c_associated(handle) ) then
       write(6,*) "[generic_data_plugin] - ERROR - 'handle' not null"
       error_flag = -1
       return
    endif

    dll_filename=library
    error_flag = 0 
    write(6,*)  "      + dll_filename     = <", trim(dll_filename)//C_NULL_CHAR, ">"
 
    image_data_filename=trim(template_name)//C_NULL_CHAR
    error_flag = 0 
    write(6,*)  "      + image_data_filename   = <", trim(image_data_filename)//C_NULL_CHAR, ">"

    !
    ! Open the DL:
    ! The use of IOR is not really proper...wait till Fortran 2008  
    handle=dlopen(trim(dll_filename)//C_NULL_CHAR, IOR(RTLD_NOW, RTLD_GLOBAL))

    !
    ! Check if can use handle
    if(.not.c_associated(handle)) then
       write(6,*) "[generic_data_plugin] - ERROR - Cannot open Handle: ", c_f_string(dlerror())
       error_flag = -2
       return
    end if
    

    !
    ! Find the subroutines in the DL:
    fun_plugin_get_data_ptr   = DLSym(handle,"plugin_get_data")
    if(.not.c_associated(fun_plugin_get_data_ptr))  then
       write(6,*) "[generic_data_plugin] - ERROR in DLSym(handle,'plugin_get_data'): ", c_f_string(dlerror())
       loading_error_flag = .true.
    else
       call c_f_procpointer(cptr=fun_plugin_get_data_ptr,   fptr=dll_plugin_get_data)
    endif
    !
    fun_plugin_get_header_ptr = DLSym(handle,"plugin_get_header")
    if(.not.c_associated(fun_plugin_get_header_ptr))  then
       write(6,*) "[generic_data_plugin] - ERROR in DLSym(handle,'plugin_get_header'): ",c_f_string(dlerror())
       loading_error_flag = .true.
    else
       call c_f_procpointer(cptr=fun_plugin_get_header_ptr, fptr=dll_plugin_get_header)
    endif
    !
    fun_plugin_open_ptr   = DLSym(handle,"plugin_open")
    if(.not.c_associated(fun_plugin_open_ptr))  then
       write(6,*) "[generic_data_plugin] - ERROR in DLSym(handle,'plugin_open'): ", c_f_string(dlerror())
       loading_error_flag = .true.
    else
       call c_f_procpointer(cptr=fun_plugin_open_ptr,   fptr=dll_plugin_open)
    endif
    
    fun_plugin_close_ptr = DLSym(handle,"plugin_close")
    if(.not.c_associated(fun_plugin_close_ptr)) then
       write(6,*) "[generic_data_plugin] - ERROR in DLSym(handle,'plugin_close'): ", c_f_string(dlerror())
       loading_error_flag = .true.
    else
       call c_f_procpointer(cptr=fun_plugin_close_ptr, fptr=dll_plugin_close)
    endif


    if (loading_error_flag) then
       write(6,*) "[generic_data_plugin] - ERROR - Cannot map function(s) from the dll"
       error_flag = -3
    else   
       call dll_plugin_open(image_data_filename, info_array, external_error_flag)
       error_flag = external_error_flag
    endif
    IF (error_flag == 0) is_open=.TRUE.
    return

  end subroutine generic_open

  !
  ! Get the header
  subroutine generic_get_header(nx, ny, nbyte, qx, qy, number_of_frames, info_array, error_flag)
    ! Requirements:
    !  'NX' (integer)                  output  Number of pixels along X 
    !  'NY' (integer)                  output  Number of pixels along Y
    !  'NBYTE' (integer)               output  Number of bytes in the image... X*Y*DEPTH
    !  'QX' (4*REAL)                   output  Pixel size
    !  'QY' (4*REAL)                   output  Pixel size
    !  'NUMBER_OF_FRAMES' (integer)    output  Number of frames for the full datase. So far unused
    !  'INFO' (integer array)           input  Array of (1024) integers:
    !                                          INFO(>1)     = Unused
    !  'INFO' (integer array)          output  Array of (1024) integers:
    !                                           INFO(1)       = Vendor ID (1:Dectris)
    !                                           INFO(2)       = Major Version number of the library
    !                                           INFO(3)       = Minor Version number of the library
    !                                           INFO(4)       = Patch Version number of the library
    !                                           INFO(5)       = Linux timestamp of library creation
    !                                           INFO(6:64)    = Reserved
    !                                           INFO(65:1024) = Dataset parameters
    !  'ERROR_FLAG'                    output  Return values
    !                                            0      Success
    !                                           -1      Cannot open library
    !                                           -2      Cannot read header (will come from C function)
    !                                           -4      Cannot read dataset informations (will come from C function)
    !                                           -10     Error in the determination of the Dataset parameters (will come from C function)
    !
    use iso_c_binding
    use iso_c_utilities
    use dlfcn
    implicit none    
    
    integer(c_int)                   :: nx, ny, nbyte, number_of_frames
    real(c_float)                    :: qx, qy
    integer(c_int)                   :: error_flag
    integer(c_int)                   :: external_error_flag
    integer(c_int), dimension(1024)  :: info_array
    error_flag=0

    write(6,*) "[generic_data_plugin] - INFO - generic_get_header"
    
    ! Check if can use handle
    if(.not.c_associated(handle)) then
       write(6,*) "[generic_data_plugin] - ERROR - Cannot open Handle"
       write(6,*) "                        ", c_f_string(dlerror())
       error_flag = -1
       return
    end if
 
    ! finally, invoke the dynamically-linked subroutine:
    call dll_plugin_get_header(nx, ny, nbyte, qx, qy, number_of_frames, info_array, external_error_flag)
    return 
  end subroutine generic_get_header


  ! 
  ! Dynamically map function and execute it 
  subroutine generic_get_data(frame_number, nx, ny, data_array, info_array, error_flag)
    ! Requirements:
    !  'FRAME_NUMBER' (integer)        input  Number of frames for the full datase. So far unused
    !  'NX' (integer)                  input  Number of pixels along X 
    !  'NY' (integer)                  input  Number of pixels along Y
    !  'DATA_ARRAY' (integer array)   output  1D array containing pixel data with lenght = NX*NY
    !  'INFO' (integer array)         output Array of (1024) integers:
    !                                          INFO(1)     = Vendor ID (1:Dectris)
    !                                          INFO(2)     = Major Version number of the library
    !                                          INFO(3)     = Minor Version number of the library
    !                                          INFO(4)     = Parch Version number of the library
    !                                          INFO(5)     = Linux timestamp of library creation
    !                                          INFO(6:8)   = Unused
    !                                          INFO(9:40)  = 1024bit verification key
    !                                          INFO(41:44) = Image MD5 Checksum 
    !                                          INFO()  = Unused
    !  'ERROR_FLAG' (integer)         output  Provides error state condition
    !                                           0 Success
    !                                          -1 Cannot open library 
    !                                          -2 Cannot open frame (will come from C function)
    !                                          -3 Datatype not supported (will come from C function)
    !                                          -4 Cannot read dataset informations (will come from C function)
    !                                         -10 MD5 Checksum Error 
    !                                         -11 Verification key error
    !  
    use iso_c_binding
    use iso_c_utilities
    use dlfcn
    implicit none    

    integer(c_int)                    :: nx, ny, frame_number
    integer(c_int)                    :: error_flag
    integer(c_int), dimension(1024)   :: info_array
    integer(c_int), dimension (nx*ny) :: data_array


    error_flag=0
    call dll_plugin_get_data(frame_number, nx, ny, data_array, info_array, error_flag)
   
  end subroutine generic_get_data

  ! Close the shared-object 
  ! 
  subroutine generic_close(error_flag)
    ! Requirements:
    !      'ERROR_FLAG' (integer)     output  Return values:
    !                                           0 Success
    !                                          -1 Error closing Masterfile
    !                                          -2 Error closing Shared-object

    use iso_c_binding
    use iso_c_utilities
    use dlfcn
    implicit none    

    integer(c_int) :: error_flag
    integer(c_int) :: external_error_flag

    IF (.NOT.is_open) RETURN
    ! Check if can use handle
    if(.not.c_associated(handle)) then
       write(6,*) "[generic_data_plugin] - ERROR - Cannot open Handle"
       write(6,*) "                        ", c_f_string(dlerror())
       error_flag = -1
       return
    end if

    write(6,*) "[generic_data_plugin] - INFO - 'call generic_close()'"
    
    call dll_plugin_close(external_error_flag)
    error_flag = external_error_flag

    ! now close the dl:
    status=0   ! inserted Feb 3, 2021 KD
!    status=dlclose(handle)  ! commented out Feb 3, 2021 KD
    if(status/=0) then
       write(6,*) "[generic_data_plugin] - ERROR - Cannot open Handle"
       write(6,*) "                        ", c_f_string(dlerror())
       error_flag = -2
    else
       error_flag = 0
    end if

    return 
  end subroutine generic_close

end module generic_data_plugin

Problems

Programs using dlclose (which is what the glue code does) may display

Program received signal SIGSEGV, Segmentation fault.

at termination. Using gdb, this reveals

#0  0x00000000410c08b0 in ?? ()
#1  0x00000000406acbc2 in __nptl_deallocate_tsd () from /lib64/libpthread.so.0
#2  0x00000000406acdd3 in start_thread () from /lib64/libpthread.so.0
#3  0x00000000409b873d in clone () from /lib64/libc.so.6

Google returns https://github.com/apple/cups/issues/4410 and https://bugzilla.redhat.com/show_bug.cgi?id=1065695 when searching for similar problems. Overall, this appears to be harmless and in fact I don't know how to change the code to make the segfault disappear - I'd appreciate a patch! Feb 3, 2021: commented out the line 'status=dlclose(handle)' and replaced it with 'status=0'. According to Sebastian Thorarensen this has no negative consequences on XDS, and solves the segfault problem.

Existing implementations

1. Dectris Neggia-plugin to read HDF5 written by Dectris-supplied software of Eiger detectors
2. Diamond's Durin-plugin to read HDF5 written by Eiger detectors at Diamond (and presumably elsewhere); latest binaries for MacOS and Linux (RHEL6) as well as example XDS.INP and source at https://github.com/DiamondLightSource/durin/releases/latest . A binary for M1 Mac is available - see Installation
3. EMBL-Hamburg's zcbf-plugin to read gzip-compressed CBF files without intermediate file . A binary for M1 Mac is available - see Installation.

Plugins for Linux and Intel-Mac can also be obtained through GPhL's autoPROC.

See also Installation.

See also

1. https://rosettacode.org/wiki/Call_a_function_in_a_shared_library#GNU_Fortran_on_Linux