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The possibility of using external libraries (that are loaded at runtime) has been available in C/C++ | 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. | In the case of XDS, frame-reading and computation can be separated starting with version November-2016. The [https://xds.mr.mpg.de/html_doc/xds_parameters.html#LIB= 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 | In the following, small examples are given for | ||
* how a program ("'''host'''") may use an existing external library, e.g. the dectris-neggia library ([https://github.com/dectris/neggia source]; [https://www.dectris.com/ | * how a program ("'''host'''") may use an existing external library, e.g. the dectris-neggia library ([https://github.com/dectris/neggia source]; [https://www.dectris.com/company/news/newsroom/news-details/process-eiger-data-with-xds-fast pre-compiled]) | ||
* how an external library ("'''client'''") may be implemented that XDS can use | * how an external library ("'''client'''") may be implemented that XDS can use | ||
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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 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 [[LIB#Existing_implementations|implementations]]. | |||
== Host code example == | == Host code example == | ||
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! ifort -qopenmp generic_data_plugin.f90 test_generic_host.f90 -o test_generic_host | ! ifort -qopenmp generic_data_plugin.f90 test_generic_host.f90 -o test_generic_host | ||
! or | ! or | ||
! gfortran -O -fopenmp | ! gfortran -O -fopenmp generic_data_plugin.f90 test_generic_host.f90 -ldl -o test_generic_host | ||
! run with | ! run with | ||
! ./test_generic_host < test.in | ! ./test_generic_host < test.in | ||
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! set some more module variables | ! set some more module variables | ||
firstqm=INDEX(actnam,'?') | firstqm=INDEX(actnam,'?') ! qm means question mark | ||
lastqm =INDEX(actnam,'?',BACK=.TRUE.) | lastqm =INDEX(actnam,'?',BACK=.TRUE.) | ||
len =LEN_TRIM(actnam) | len =LEN_TRIM(actnam) | ||
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! This reads single data files which have a header of 7680 bytes | ! This reads single data files which have a header of 7680 bytes | ||
! Kay Diederichs 4/2017 | ! 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 | ! compile with | ||
! ifort -fpic -shared -static-intel -qopenmp -traceback -sox test_generic_client.f90 -o libtest_generic_client.so | ! 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 | ! or | ||
! gfortran | ! 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 | ! 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. | ! reading of data files with a 7680 bytes header plus 1024*1024 pixels of integer data, without any record structure. | ||
MODULE plugin_test_mod | MODULE plugin_test_mod | ||
CHARACTER :: fn_template*132='' | CHARACTER :: fn_template*132='',cformat*6='(i4.4)' | ||
INTEGER :: lenfn,firstqm,lastqm | INTEGER :: lenfn,firstqm,lastqm | ||
END MODULE | END MODULE | ||
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firstqm=INDEX(fn_template,'?') | firstqm=INDEX(fn_template,'?') | ||
lastqm =INDEX(fn_template,'?',BACK=.TRUE.) | 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 | END SUBROUTINE plugin_open | ||
! | ! | ||
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! local variables | ! local variables | ||
INTEGER k,i,dummy | INTEGER k,i,dummy | ||
CHARACTER :: fn*132 | CHARACTER :: fn*132 | ||
fn=fn_template | fn=fn_template | ||
IF (frame_number>0) WRITE(fn(firstqm:lastqm),cformat) frame_number | IF (frame_number>0) WRITE(fn(firstqm:lastqm),cformat) frame_number | ||
! -qopenmp compile option needs to be used otherwise race in writing fn | ! -qopenmp compile option needs to be used otherwise race in writing fn | ||
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! THE USE OR OTHER DEALINGS IN THE SOFTWARE. | ! THE USE OR OTHER DEALINGS IN THE SOFTWARE. | ||
! | ! | ||
! | ! For more information, please refer to <http://unlicense.org/> | ||
! | ! | ||
! | ! | ||
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interface ! strlen is a standard C function from <string.h> | interface ! strlen is a standard C function from <string.h> | ||
function strlen(string) result(len) bind(C,name="strlen") | integer(int64) function strlen(string) result(len) bind(C,name="strlen") | ||
use iso_fortran_env, only : int64 | |||
use iso_c_binding | use iso_c_binding | ||
type(c_ptr), value :: string ! a C pointer | type(c_ptr), value :: string ! a C pointer | ||
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! now close the dl: | ! now close the dl: | ||
status=dlclose(handle) | status=0 ! inserted Feb 3, 2021 KD | ||
! status=dlclose(handle) ! commented out Feb 3, 2021 KD | |||
if(status/=0) then | if(status/=0) then | ||
write(6,*) "[generic_data_plugin] - ERROR - Cannot open Handle" | write(6,*) "[generic_data_plugin] - ERROR - Cannot open Handle" | ||
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#3 0x00000000409b873d in clone () from /lib64/libc.so.6 | #3 0x00000000409b873d in clone () from /lib64/libc.so.6 | ||
</pre> | </pre> | ||
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! | 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 == | |||
# [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 (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]] | |||
# [https://git.embl.de/nikolova/xds-zcbf/ 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 [https://www.globalphasing.com/autoproc/ GPhL's autoPROC]. | |||
See also [[Installation]]. | |||
== See also == | |||
# https://rosettacode.org/wiki/Call_a_function_in_a_shared_library#GNU_Fortran_on_Linux | |||