loading system configuration loading override configuration from /home/nexmap/pkwi/mxtest/mctest/../mccodelib/mcxtrace-test/McXtrace_CPU_MPICC_KISS/mccode_config.json INFO: No output directory specified (--dir) INFO: Using directory: "Test_SAXS_20230901_052942" INFO: Regenerating c-file: Test_SAXS.c DEBUG: CMD: mcxtrace -t -o ./Test_SAXS.c /home/nexmap/pkwi/xTESTS/2023-09-01/McXtrace_CPU_MPICC_KISS_5e7/Test_SAXS/Test_SAXS.instr Info: 'SAXSSpheres' is a contributed component. Info: 'SAXSShells' is a contributed component. Info: 'SAXSCylinders' is a contributed component. Info: 'SAXSEllipticCylinders' is a contributed component. Info: 'SAXSLiposomes' is a contributed component. Info: 'SAXSNanodiscs' is a contributed component. Info: 'SAXSNanodiscsWithTags' is a contributed component. Info: 'SAXSPDB' is a contributed component. Info: 'SAXSPDBFast' is a contributed component. Info: 'SAXSNanodiscsFast' is a contributed component. Info: 'SAXSNanodiscsWithTagsFast' is a contributed component. Info: 'SAXSQMonitor' is a contributed component. CFLAGS= -I@MCCODE_LIB@/miniconda3/include -Wl,-rpath,@MCCODE_LIB@/miniconda3/lib -L@MCCODE_LIB@/miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I@MCCODE_LIB@/miniconda3/include -Wl,-rpath,@MCCODE_LIB@/miniconda3/lib -L@MCCODE_LIB@/miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I@MCCODE_LIB@/miniconda3/include -Wl,-rpath,@MCCODE_LIB@/miniconda3/lib -L@MCCODE_LIB@/miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I@MCCODE_LIB@/miniconda3/include -Wl,-rpath,@MCCODE_LIB@/miniconda3/lib -L@MCCODE_LIB@/miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I@MCCODE_LIB@/miniconda3/include -Wl,-rpath,@MCCODE_LIB@/miniconda3/lib -L@MCCODE_LIB@/miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I@MCCODE_LIB@/miniconda3/include -Wl,-rpath,@MCCODE_LIB@/miniconda3/lib -L@MCCODE_LIB@/miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I@MCCODE_LIB@/miniconda3/include -Wl,-rpath,@MCCODE_LIB@/miniconda3/lib -L@MCCODE_LIB@/miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I@MCCODE_LIB@/miniconda3/include -Wl,-rpath,@MCCODE_LIB@/miniconda3/lib -L@MCCODE_LIB@/miniconda3/lib -lgsl -pj ----------------------------------------------------------- Generating single GPU kernel or single CPU section layout: ----------------------------------------------------------- Generating GPU/CPU -DFUNNEL layout: Component Sample2 is NOACC, CPUONLY=1 -> FUNNEL mode enabled, SPLIT within buffer. -> CPU section from component Sample2 Component Sample3 is NOACC, CPUONLY=1 -> FUNNEL mode enabled, SPLIT within buffer. -> GPU kernel from component Sample4 Component Sample5 is NOACC, CPUONLY=1 -> FUNNEL mode enabled, SPLIT within buffer. -> CPU section from component Sample5 Component Sample6 is NOACC, CPUONLY=1 -> FUNNEL mode enabled, SPLIT within buffer. Component Sample7 is NOACC, CPUONLY=1 -> FUNNEL mode enabled, SPLIT within buffer. Component Sample9 is NOACC, CPUONLY=1 -> FUNNEL mode enabled, SPLIT within buffer. Component Sample10 is NOACC, CPUONLY=1 -> FUNNEL mode enabled, SPLIT within buffer. Component Sample11 is NOACC, CPUONLY=1 -> FUNNEL mode enabled, SPLIT within buffer. -> GPU kernel from component Beamstop ----------------------------------------------------------- DEBUG: CMD: mcxtrace finished INFO: Recompiling: ./Test_SAXS.out DEBUG: CMD: mpicc -o ./Test_SAXS.out ./Test_SAXS.c -lm -DUSE_MPI -lmpi -g -lm -O2 -DUSE_MPI -lmpi -std=c99 -D_POSIX_SOURCE -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUN` j /bin/sh: -c: line 0: unexpected EOF while looking for matching ``' /bin/sh: -c: line 1: syntax error: unexpected end of file INFO: call to mpicc failed with Command 'mpicc -o ./Test_SAXS.out ./Test_SAXS.c -lm -DUSE_MPI -lmpi -g -lm -O2 -DUSE_MPI -lmpi -std=c99 -D_POSIX_SOURCE -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUN` j' returned non-zero exit status 1. Traceback (most recent call last): File "/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/bin/../tools/Python/mxrun/mxrun.py", line 541, in main() File "/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/bin/../tools/Python/mxrun/mxrun.py", line 455, in main mcstas.prepare(options) File "/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/mccode.py", line 213, in prepare Process(options.cc).run(args) File "/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/mccode.py", line 70, in run raise err File "/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/mccode.py", line 66, 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/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command 'mpicc -o ./Test_SAXS.out ./Test_SAXS.c -lm -DUSE_MPI -lmpi -g -lm -O2 -DUSE_MPI -lmpi -std=c99 -D_POSIX_SOURCE -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUNNEL -I/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/include -Wl,-rpath,/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -L/home/nexmap/pkwi/McXtrace/mcxtrace/3.x-dev/tools/Python/mxrun/../mccodelib/../../../miniconda3/lib -lgsl -lgslcblas -DFUN` j' returned non-zero exit status 1.