INFO: No output directory specified (--dir) INFO: Using directory: "NECSA_MIXRAD_Nikon_Tomo_20250514_061009" INFO: Regenerating c-file: NECSA_MIXRAD_Nikon_Tomo.c WARNING: Full-path code-generator "/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/bin/mcxtrace-antlr -I${MCXTRACE}" not found!! WARNING: Attempting replacement by "mcxtrace-antlr -I${MCXTRACE}" DEBUG: CMD: mcxtrace-antlr -I${MCXTRACE} -t -o ./NECSA_MIXRAD_Nikon_Tomo.c NECSA_MIXRAD_Nikon_Tomo.instr 2025-05-14 06:10:40.407 | DEBUG | mccode_antlr.translators.c:sort_include_hierarchy:41 - sort includes :Source_lab(0):read_table-lib :Fluorescence(0):read_table-lib 2025-05-14 06:10:40.408 | DEBUG | mccode_antlr.translators.c:sort_include_hierarchy:66 - sorted to read_table-lib 2025-05-14 06:10:40.408 | DEBUG | mccode_antlr.translators.c:sort_include_hierarchy:66 - sorted to read_table-lib line 2:2 extraneous input '%' expecting {, '__extension__', '__m128', '__m128d', '__m128i', '__typeof__', '__inline__', '__stdcall', '__declspec', '__cdecl', '__clrcall', '__fastcall', '__thiscall', '__vectorcall', '__attribute__', 'auto', 'char', 'const', 'double', 'enum', 'extern', 'float', 'inline', 'int', 'long', 'register', 'restrict', 'short', 'signed', 'static', 'struct', 'typedef', 'union', 'unsigned', 'void', 'volatile', '_Alignas', '_Atomic', '_Bool', '_Complex', '_Noreturn', '_Static_assert', '_Thread_local', '(', '*', '^', ';', Identifier} 2025-05-14 06:10:40.869 | ERROR | mccode_antlr.translators.c_listener:syntaxError:35 - Syntax error in parsing 2,2 2025-05-14 06:10:40.869 | ERROR | mccode_antlr.translators.c_listener:syntaxError:41 - ~~^ extraneous input '%' expecting {, '__extension__', '__m128', '__m128d', '__m128i', '__typeof__', '__inline__', '__stdcall', '__declspec', '__cdecl', '__clrcall', '__fastcall', '__thiscall', '__vectorcall', '__attribute__', 'auto', 'char', 'const', 'double', 'enum', 'extern', 'float', 'inline', 'int', 'long', 'register', 'restrict', 'short', 'signed', 'static', 'struct', 'typedef', 'union', 'unsigned', 'void', 'volatile', '_Alignas', '_Atomic', '_Bool', '_Complex', '_Noreturn', '_Static_assert', '_Thread_local', '(', '*', '^', ';', Identifier} 2025-05-14 06:10:40.870 | INFO | mccode_antlr.translators.c_listener:syntaxError:43 - 2025-05-14 06:10:40.870 | INFO | mccode_antlr.translators.c_listener:syntaxError:43 - #ifndef FLUORESCENCE_DECL line 2:11 no viable alternative at input 'include "interoff-lib"' 2025-05-14 06:10:40.914 | ERROR | mccode_antlr.translators.c_listener:syntaxError:35 - Syntax error in parsing 2,11 2025-05-14 06:10:40.914 | ERROR | mccode_antlr.translators.c_listener:syntaxError:41 - ~~~~~~~~~~~^ no viable alternative at input 'include "interoff-lib"' 2025-05-14 06:10:40.914 | INFO | mccode_antlr.translators.c_listener:syntaxError:43 - 2025-05-14 06:10:40.914 | INFO | mccode_antlr.translators.c_listener:syntaxError:43 - #ifndef FLUORESCENCE_DECL 2025-05-14 06:10:41.426 | INFO | mccode_antlr.translators.c_listener:visitDeclarator:341 - Could not convert an integer from ('XRAYLIB_LINES_MAX+1',) due to invalid literal for int() with base 10: 'XRAYLIB_LINES_MAX+1' The instrument has 7 parameters ----------------------------------------------------------- Generating single GPU kernel or single CPU section layout: ----------------------------------------------------------- Generating GPU/CPU -DFUNNEL layout: -> GPU kernel from component origin -> GPU kernel from component anode -> GPU kernel from component source_energy_monitor -> GPU kernel from component Sample_holder -> GPU kernel from component Sample_input Component Sample is NOACC, CPUONLY=True ->FUNNEL mode enabled, SPLIT within buffer. ----------------------------------------------------------- CFLAGS= -lxrl -DUSE_OFF -DFUNNEL DEBUG: CMD: mcxtrace-antlr -I${MCXTRACE} finished INFO: Recompiling: ./NECSA_MIXRAD_Nikon_Tomo.out DEBUG: CMD: mpicc -o ./NECSA_MIXRAD_Nikon_Tomo.out ./NECSA_MIXRAD_Nikon_Tomo.c -lm -DUSE_MPI -lmpi -fno-PIC -fPIE -flto -O3 -mtune=native -march=native -fno-math-errno -ftree-vectorize -g -DNDEBUG -D_POSIX_SOURCE -std=c99 -lm -lxrl -DUSE_OFF -DFUNNEL ./NECSA_MIXRAD_Nikon_Tomo.c:7215:3: error: expected identifier or '(' before '%' token 7215 | %include "interoff-lib" // for OFF/PLY geometry | ^ In file included from /home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/miniconda3/include/xraylib/xraylib.h:56, from ./NECSA_MIXRAD_Nikon_Tomo.c:7229: /home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/miniconda3/include/xraylib/xraylib-error.h:29:3: warning: data definition has no type or storage class 29 | } xrl_error_code; | ^~~~~~~~~~~~~~ /home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/miniconda3/include/xraylib/xraylib-error.h:29:3: warning: type defaults to 'int' in declaration of 'xrl_error_code' [-Wimplicit-int] /home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/miniconda3/include/xraylib/xraylib-error.h:44:3: error: expected specifier-qualifier-list before 'xrl_error_code' 44 | xrl_error_code code; | ^~~~~~~~~~~~~~ /home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/miniconda3/include/xraylib/xraylib-error.h:55:47: error: expected declaration specifiers or '...' before 'xrl_error_code' 55 | int xrl_error_matches(const xrl_error *error, xrl_error_code code); | ^~~~~~~~~~~~~~ ./NECSA_MIXRAD_Nikon_Tomo.c:7672:3: error: unknown type name 'off_struct' 7672 | off_struct offdata; | ^~~~~~~~~~ ./NECSA_MIXRAD_Nikon_Tomo.c: In function 'class_Fluorescence_initialize': ./NECSA_MIXRAD_Nikon_Tomo.c:10041:9: warning: implicit declaration of function 'off_init' [-Wimplicit-function-declaration] 10041 | if (off_init(geometry, xwidth, yheight, zdepth, 0, &offdata)) { | ^~~~~~~~ ./NECSA_MIXRAD_Nikon_Tomo.c:10089:41: error: 'xrl_error' {aka 'struct _xrl_error'} has no member named 'message' 10089 | NAME_CURRENT_COMP, material, error->message)); | ^~ ./NECSA_MIXRAD_Nikon_Tomo.c:647:10: note: in definition of macro 'exit' 647 | exit(code); \ | ^~~~ ./NECSA_MIXRAD_Nikon_Tomo.c:10114:79: error: 'xrl_error' {aka 'struct _xrl_error'} has no member named 'message' 10114 | exit(fprintf(stderr, "ERROR: %s: Z=%i %s\n", NAME_CURRENT_COMP, Z, error->message)); | ^~ ./NECSA_MIXRAD_Nikon_Tomo.c:647:10: note: in definition of macro 'exit' 647 | exit(code); \ | ^~~~ ./NECSA_MIXRAD_Nikon_Tomo.c: In function 'class_Fluorescence_trace': ./NECSA_MIXRAD_Nikon_Tomo.c:10875:19: warning: implicit declaration of function 'off_x_intersect'; did you mean 'box_intersect'? [-Wimplicit-function-declaration] 10875 | intersect=off_x_intersect(&l0, &l3, NULL, NULL, x, y, z, kx,ky,kz, thread_offdata ); | ^~~~~~~~~~~~~~~ | box_intersect ./NECSA_MIXRAD_Nikon_Tomo.c: In function 'class_Fluorescence_display': ./NECSA_MIXRAD_Nikon_Tomo.c:12471:7: warning: implicit declaration of function 'off_display'; did you mean 'display'? [-Wimplicit-function-declaration] 12471 | off_display(offdata); | ^~~~~~~~~~~ | display INFO: call to mpicc failed with Command 'mpicc -o ./NECSA_MIXRAD_Nikon_Tomo.out ./NECSA_MIXRAD_Nikon_Tomo.c -lm -DUSE_MPI -lmpi -fno-PIC -fPIE -flto -O3 -mtune=native -march=native -fno-math-errno -ftree-vectorize -g -DNDEBUG -D_POSIX_SOURCE -std=c99 -lm -lxrl -DUSE_OFF -DFUNNEL' returned non-zero exit status 1. Traceback (most recent call last): File "/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/mxrun.py", line 616, in main() File "/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/mxrun.py", line 524, in main mcstas.prepare(options) File "/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/mccode.py", line 311, in prepare Process(lexer.quote(options.cc)).run(args) File "/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/mccode.py", line 77, in run raise err File "/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/mccode.py", line 73, in run proc = run(command, shell=True, check=True, text=True, capture_output=pipe) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/miniconda3/lib/python3.12/subprocess.py", line 571, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command 'mpicc -o ./NECSA_MIXRAD_Nikon_Tomo.out ./NECSA_MIXRAD_Nikon_Tomo.c -lm -DUSE_MPI -lmpi -fno-PIC -fPIE -flto -O3 -mtune=native -march=native -fno-math-errno -ftree-vectorize -g -DNDEBUG -D_POSIX_SOURCE -std=c99 -lm -lxrl -DUSE_OFF -DFUNNEL' returned non-zero exit status 1.