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# [https://github.com/dectris/neggia Dectris Neggia-plugin] to read HDF5 written by Dectris-supplied software of Eiger detectors | # [https://github.com/dectris/neggia Dectris Neggia-plugin] to read HDF5 written by Dectris-supplied software of Eiger detectors | ||
# [https://github.com/DiamondLightSource/durin Diamond's Durin-plugin] to read HDF5 written by Eiger detectors at Diamond | # [https://github.com/DiamondLightSource/durin Diamond's Durin-plugin] to read HDF5 written by Eiger detectors at Diamond; latest binaries for MacOS and Linux (RHEL6) as well as example XDS.INP and source at https://github.com/DiamondLightSource/durin/releases/latest | ||
# [https://git.embl.de/nikolova/xds-zcbf/ EMBL-Hamburg's zcbf-plugin] to read gzip-compressed CBF files without intermediate file | # [https://git.embl.de/nikolova/xds-zcbf/ EMBL-Hamburg's zcbf-plugin] to read gzip-compressed CBF files without intermediate file | ||
Revision as of 10:30, 8 May 2019
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. This allows users/companies to develop their own specialized frame-reading libraries, and relieves the XDS maintainers from implementing even more file formats.
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 -ldl generic_data_plugin.f90 test_generic_host.f90 -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
! compile with
! ifort -fpic -shared -static-intel -qopenmp -traceback -sox test_generic_client.f90 -o libtest_generic_client.so
! or
! gfortran -c -fpic test_generic_client.f90 && ld -shared test_generic_client.o -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/ -lgfortran -o libtest_generic_client.so
! (attention: the above - from "gfortran" to "libtest_generic_client.so" - is one looong line)
! 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=''
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.)
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,cformat*6='(i4.4)'
fn=fn_template
WRITE(cformat(3:5),'(i1,a1,i1)')lastqm-firstqm+1,'.',lastqm-firstqm+1
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>
function strlen(string) result(len) bind(C,name="strlen")
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=dlclose(handle)
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!
Existing implementations
- Dectris Neggia-plugin to read HDF5 written by Dectris-supplied software of Eiger detectors
- Diamond's Durin-plugin to read HDF5 written by Eiger detectors at Diamond; latest binaries for MacOS and Linux (RHEL6) as well as example XDS.INP and source at https://github.com/DiamondLightSource/durin/releases/latest
- EMBL-Hamburg's zcbf-plugin to read gzip-compressed CBF files without intermediate file