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. 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