INFO: No output directory specified (--dir) INFO: Using directory: "NECSA_MIXRAD_Nikon_Tomo_20250426_060725" 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 2025-04-26 06:07:55.566 | DEBUG | mccode_antlr.translators.c:sort_include_hierarchy:41 - sort includes :Source_lab(0):read_table-lib :Fluorescence(0):read_table-lib 2025-04-26 06:07:55.566 | DEBUG | mccode_antlr.translators.c:sort_include_hierarchy:66 - sorted to read_table-lib 2025-04-26 06:07:55.566 | 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} 2025-04-26 06:07:56.026 | ERROR | mccode_antlr.translators.c_listener:syntaxError:35 - Syntax error in parsing 2,2 2025-04-26 06:07:56.026 | 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} 2025-04-26 06:07:56.026 | INFO | mccode_antlr.translators.c_listener:syntaxError:43 - 2025-04-26 06:07:56.026 | INFO | mccode_antlr.translators.c_listener:syntaxError:43 - #ifndef FLUORESCENCE_DECL line 2:11 no viable alternative at input 'include "interoff-lib"' 2025-04-26 06:07:56.068 | ERROR | mccode_antlr.translators.c_listener:syntaxError:35 - Syntax error in parsing 2,11 2025-04-26 06:07:56.069 | ERROR | mccode_antlr.translators.c_listener:syntaxError:41 - ~~~~~~~~~~~^ no viable alternative at input 'include "interoff-lib"' 2025-04-26 06:07:56.069 | INFO | mccode_antlr.translators.c_listener:syntaxError:43 - 2025-04-26 06:07:56.069 | INFO | mccode_antlr.translators.c_listener:syntaxError:43 - #ifndef FLUORESCENCE_DECL 2025-04-26 06:07:56.508 | 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:5619:6: error: conflicting types for 'mt_srandom'; have 'void(uint32_t)' {aka 'void(unsigned int)'} 5619 | void mt_srandom(uint32_t seed) { | ^~~~~~~~~~ ./NECSA_MIXRAD_Nikon_Tomo.c:887:6: note: previous declaration of 'mt_srandom' with type 'void(long unsigned int)' 887 | void mt_srandom (unsigned long x); | ^~~~~~~~~~ ./NECSA_MIXRAD_Nikon_Tomo.c:5657:10: error: conflicting types for 'mt_random'; have 'uint32_t(void)' {aka 'unsigned int(void)'} 5657 | uint32_t mt_random(void) { | ^~~~~~~~~ ./NECSA_MIXRAD_Nikon_Tomo.c:886:15: note: previous declaration of 'mt_random' with type 'long unsigned int(void)' 886 | unsigned long mt_random(void); | ^~~~~~~~~ ./NECSA_MIXRAD_Nikon_Tomo.c:7199:3: error: expected identifier or '(' before '%' token 7199 | %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:7212: /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: In function 'fluo_get_material': ./NECSA_MIXRAD_Nikon_Tomo.c:7344:18: warning: implicit declaration of function 'Open_File' [-Wimplicit-function-declaration] 7344 | FILE *file = Open_File(filename, "r", NULL); | ^~~~~~~~~ ./NECSA_MIXRAD_Nikon_Tomo.c:7344:18: warning: initialization of 'FILE *' from 'int' makes pointer from integer without a cast [-Wint-conversion] ./NECSA_MIXRAD_Nikon_Tomo.c: At top level: ./NECSA_MIXRAD_Nikon_Tomo.c:7640:3: error: unknown type name 'off_struct' 7640 | off_struct offdata; | ^~~~~~~~~~ ./NECSA_MIXRAD_Nikon_Tomo.c:7865:9: error: conflicting types for 'Open_File'; have 'FILE *(char *, const char *, char *)' 7865 | FILE *Open_File(char *File, const char *Mode, char *Path) | ^~~~~~~~~ ./NECSA_MIXRAD_Nikon_Tomo.c:7344:18: note: previous implicit declaration of 'Open_File' with type 'int()' 7344 | FILE *file = Open_File(filename, "r", NULL); | ^~~~~~~~~ ./NECSA_MIXRAD_Nikon_Tomo.c: In function 'class_Fluorescence_initialize': ./NECSA_MIXRAD_Nikon_Tomo.c:10010:9: warning: implicit declaration of function 'off_init' [-Wimplicit-function-declaration] 10010 | if (off_init(geometry, xwidth, yheight, zdepth, 0, &offdata)) { | ^~~~~~~~ ./NECSA_MIXRAD_Nikon_Tomo.c:10055:41: error: 'xrl_error' {aka 'struct _xrl_error'} has no member named 'message' 10055 | NAME_CURRENT_COMP, material, error->message)); | ^~ ./NECSA_MIXRAD_Nikon_Tomo.c:622:10: note: in definition of macro 'exit' 622 | exit(code); \ | ^~~~ ./NECSA_MIXRAD_Nikon_Tomo.c:10080:79: error: 'xrl_error' {aka 'struct _xrl_error'} has no member named 'message' 10080 | exit(fprintf(stderr, "ERROR: %s: Z=%i %s\n", NAME_CURRENT_COMP, Z, error->message)); | ^~ ./NECSA_MIXRAD_Nikon_Tomo.c:622:10: note: in definition of macro 'exit' 622 | exit(code); \ | ^~~~ ./NECSA_MIXRAD_Nikon_Tomo.c: In function 'class_Fluorescence_trace': ./NECSA_MIXRAD_Nikon_Tomo.c:10846:19: warning: implicit declaration of function 'off_x_intersect'; did you mean 'box_intersect'? [-Wimplicit-function-declaration] 10846 | intersect=off_x_intersect(&l0, &l3, NULL, NULL, x, y, z, kx,ky,kz, thread_offdata ); | ^~~~~~~~~~~~~~~ | box_intersect 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.