INFO: No output directory specified (--dir)
INFO: Using directory: "Test_SAXS_20250426_065329"
INFO: Regenerating c-file: Test_SAXS.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 ./Test_SAXS.c Test_SAXS.instr
2025-04-26 06:54:45.479 | DEBUG    | mccode_antlr.translators.c:sort_include_hierarchy:41 - sort includes :Source_flat(0):read_table-lib
2025-04-26 06:54:45.479 | DEBUG    | mccode_antlr.translators.c:sort_include_hierarchy:66 - sorted to read_table-lib
line 2:2 extraneous input '%' expecting {<EOF>, '__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 06:54:46.731 | ERROR    | mccode_antlr.translators.c_listener:syntaxError:35 - Syntax error in parsing 2,2
2025-04-26 06:54:46.732 | ERROR    | mccode_antlr.translators.c_listener:syntaxError:41 - ~~^ extraneous input '%' expecting {<EOF>, '__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 06:54:46.732 | INFO     | mccode_antlr.translators.c_listener:syntaxError:43 -   
2025-04-26 06:54:46.732 | INFO     | mccode_antlr.translators.c_listener:syntaxError:43 - 	#include <gsl/gsl_sf_legendre.h>
line 2:11 no viable alternative at input 'include "read_table-lib"'
2025-04-26 06:54:46.770 | ERROR    | mccode_antlr.translators.c_listener:syntaxError:35 - Syntax error in parsing 2,11
2025-04-26 06:54:46.770 | ERROR    | mccode_antlr.translators.c_listener:syntaxError:41 - ~~~~~~~~~~~^ no viable alternative at input 'include "read_table-lib"'
2025-04-26 06:54:46.770 | INFO     | mccode_antlr.translators.c_listener:syntaxError:43 -   
2025-04-26 06:54:46.770 | INFO     | mccode_antlr.translators.c_listener:syntaxError:43 - 	#include <gsl/gsl_sf_legendre.h>
line 2:2 extraneous input '%' expecting {<EOF>, '__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 06:54:47.700 | ERROR    | mccode_antlr.translators.c_listener:syntaxError:35 - Syntax error in parsing 2,2
2025-04-26 06:54:47.701 | ERROR    | mccode_antlr.translators.c_listener:syntaxError:41 - ~~^ extraneous input '%' expecting {<EOF>, '__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 06:54:47.701 | INFO     | mccode_antlr.translators.c_listener:syntaxError:43 -   
2025-04-26 06:54:47.701 | INFO     | mccode_antlr.translators.c_listener:syntaxError:43 - 	#include <gsl/gsl_sf_legendre.h>
line 2:11 no viable alternative at input 'include "read_table-lib"'
2025-04-26 06:54:47.723 | ERROR    | mccode_antlr.translators.c_listener:syntaxError:35 - Syntax error in parsing 2,11
2025-04-26 06:54:47.723 | ERROR    | mccode_antlr.translators.c_listener:syntaxError:41 - ~~~~~~~~~~~^ no viable alternative at input 'include "read_table-lib"'
2025-04-26 06:54:47.723 | INFO     | mccode_antlr.translators.c_listener:syntaxError:43 -   
2025-04-26 06:54:47.723 | INFO     | mccode_antlr.translators.c_listener:syntaxError:43 - 	#include <gsl/gsl_sf_legendre.h>
The instrument has 9 parameters

-----------------------------------------------------------

Generating single GPU kernel or single CPU section layout:

-----------------------------------------------------------

Generating GPU/CPU -DFUNNEL layout:
-> GPU kernel from component Origin
-> GPU kernel from component Source
-> GPU kernel from component FirstPinhole
-> GPU kernel from component SecondPinhole
-> GPU kernel from component Sample0
-> GPU kernel from component Sample1
Component Sample2 is NOACC, CPUONLY=True
->FUNNEL mode enabled, SPLIT within buffer.
Component Sample3 is NOACC, CPUONLY=True
->FUNNEL mode enabled, SPLIT within buffer.
-> CPU section from component Sample3
Component Sample5 is NOACC, CPUONLY=True
->FUNNEL mode enabled, SPLIT within buffer.
Component Sample6 is NOACC, CPUONLY=True
->FUNNEL mode enabled, SPLIT within buffer.
-> CPU section from component Sample6
Component Sample7 is NOACC, CPUONLY=True
->FUNNEL mode enabled, SPLIT within buffer.
-> CPU section from component Sample7
Component Sample9 is NOACC, CPUONLY=True
->FUNNEL mode enabled, SPLIT within buffer.
-> CPU section from component Sample9
Component Sample10 is NOACC, CPUONLY=True
->FUNNEL mode enabled, SPLIT within buffer.
-> CPU section from component Sample10
Component Sample11 is NOACC, CPUONLY=True
->FUNNEL mode enabled, SPLIT within buffer.
-> CPU section from component Sample11
-> GPU kernel from component PSDMonitor
-> GPU kernel from component QMonitor

-----------------------------------------------------------
CFLAGS=  -lgsl -lgslcblas  -DFUNNEL
DEBUG: CMD: mcxtrace-antlr -I${MCXTRACE} finished
INFO: Recompiling: ./Test_SAXS.out
DEBUG: CMD: mpicc -o ./Test_SAXS.out ./Test_SAXS.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 -lgsl -lgslcblas -DFUNNEL
./Test_SAXS.c:5619:6: error: conflicting types for 'mt_srandom'; have 'void(uint32_t)' {aka 'void(unsigned int)'}
 5619 | void mt_srandom(uint32_t seed) {
      |      ^~~~~~~~~~
./Test_SAXS.c:887:6: note: previous declaration of 'mt_srandom' with type 'void(long unsigned int)'
  887 | void mt_srandom (unsigned long x);
      |      ^~~~~~~~~~
./Test_SAXS.c:5657:10: error: conflicting types for 'mt_random'; have 'uint32_t(void)' {aka 'unsigned int(void)'}
 5657 | uint32_t mt_random(void) {
      |          ^~~~~~~~~
./Test_SAXS.c:886:15: note: previous declaration of 'mt_random' with type 'long unsigned int(void)'
  886 | unsigned long mt_random(void);
      |               ^~~~~~~~~
./Test_SAXS.c:7491:3: error: expected identifier or '(' before '%' token
 7491 |   %include "read_table-lib"; // for Open_File
      |   ^
./Test_SAXS.c: In function 'CountResidues':
./Test_SAXS.c:7582:27: warning: implicit declaration of function 'Open_File' [-Wimplicit-function-declaration]
 7582 |                 PDBFile = Open_File(PDBFilepath, "r",NULL);
      |                           ^~~~~~~~~
./Test_SAXS.c:7582:25: warning: assignment to 'FILE *' from 'int' makes pointer from integer without a cast [-Wint-conversion]
 7582 |                 PDBFile = Open_File(PDBFilepath, "r",NULL);
      |                         ^
./Test_SAXS.c: In function 'ReadAminoPDB':
./Test_SAXS.c:7652:55: warning: assignment to 'FILE *' from 'int' makes pointer from integer without a cast [-Wint-conversion]
 7652 |                 if (NumberOfResidues <= 0 || (PDBFile = Open_File(PDBFilename, "r",NULL)) == 0) {
      |                                                       ^
./Test_SAXS.c: At top level:
./Test_SAXS.c:8036:3: error: expected identifier or '(' before '%' token
 8036 |   %include "read_table-lib"; // for Open_File
      |   ^
./Test_SAXS.c:9260:9: error: conflicting types for 'Open_File'; have 'FILE *(char *, const char *, char *)'
 9260 |   FILE *Open_File(char *File, const char *Mode, char *Path)
      |         ^~~~~~~~~
./Test_SAXS.c:7582:27: note: previous implicit declaration of 'Open_File' with type 'int()'
 7582 |                 PDBFile = Open_File(PDBFilepath, "r",NULL);
      |                           ^~~~~~~~~
INFO: call to mpicc failed with Command 'mpicc -o ./Test_SAXS.out ./Test_SAXS.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 -lgsl -lgslcblas -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 <module>
    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 ./Test_SAXS.out ./Test_SAXS.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 -lgsl -lgslcblas -DFUNNEL' returned non-zero exit status 1.