Pragma error while running test cases

Errors
1

I’m trying to run the viscous shock tube test case and the double Mach reflection case.

I’m getting the following error, please help me resolve this

:~/PyFR-Test-Cases/2d-viscous-shock-tube$ pyfr import viscous-shock-tube.msh viscous-shock-tube.pyfrm
:~/PyFR-Test-Cases/2d-viscous-shock-tube$ ls
viscous-shock-tube.ini  viscous-shock-tube.msh  viscous-shock-tube.msh.xz  viscous-shock-tube.pyfrm
:~/PyFR-Test-Cases/2d-viscous-shock-tube$ pyfr run -b openmp viscous-shock-tube.pyfrm viscous-shock-tube.ini
Traceback (most recent call last):
  File "/usr/local/bin/pyfr", line 33, in <module>
    sys.exit(load_entry_point('pyfr==1.15.0', 'console_scripts', 'pyfr')())
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/__main__.py", line 125, in main
    args.process(args)
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/__main__.py", line 272, in process_run
    _process_common(
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/__main__.py", line 257, in _process_common
    solver = get_solver(backend, rallocs, mesh, soln, cfg)
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/solvers/__init__.py", line 14, in get_solver
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/integrators/__init__.py", line 34, in get_integrator
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/integrators/std/controllers.py", line 11, in __init__
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/integrators/std/base.py", line 26, in __init__
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/solvers/base/system.py", line 67, in commit
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/solvers/base/system.py", line 213, in _gen_kernels
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/solvers/navstokes/inters.py", line 106, in <lambda>
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/backends/base/backend.py", line 174, in kernel
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/backends/base/kernels.py", line 157, in kernel_meth
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/backends/openmp/provider.py", line 73, in _build_kernel
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/util.py", line 39, in newmeth
    res = cache[key] = meth(self, *args, **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/backends/openmp/provider.py", line 65, in _build_library
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/backends/openmp/compiler.py", line 58, in build
  File "/usr/lib/python3/dist-packages/pytools/prefork.py", line 226, in call_capture_output
    return forker.call_capture_output(cmdline, cwd, error_on_nonzero)
  File "/usr/lib/python3/dist-packages/pytools/prefork.py", line 182, in call_capture_output
    return self._remote_invoke("call_capture_output", cmdline, cwd,
  File "/usr/lib/python3/dist-packages/pytools/prefork.py", line 164, in _remote_invoke
    raise result
pytools.prefork.ExecError: error invoking 'cc -shared -std=c99 -Ofast -march=native -fopenmp -fPIC -o libtmp.so tmp.c -lm': status 1 invoking 'cc -shared -std=c99 -Ofast -march=native -fopenmp -fPIC -o libtmp.so tmp.c -lm': tmp.c: In function ‘bccent’:
tmp.c:17:39: error: expected ‘read’, ‘write’, ‘update’, ‘capture’, ‘seq_cst’, ‘acq_rel’, ‘release’, ‘relaxed’ or ‘hint’ clause
   17 | #define atomic_min_fpdtype(addr, val) _Pragma("omp atomic compare") if ((val) < *(addr)) { *(addr) = (val); }
      |                                       ^~~~~~~
tmp.c:80:1: note: in expansion of macro ‘atomic_min_fpdtype’
   80 | atomic_min_fpdtype(&entmin_lhs_v[entmin_lhs_vix[BLK_IDX + X_IDX]], entmin_lhs);
      | ^~~~~~~~~~~~~~~~~~
tmp.c:17:39: error: expected end of line before ‘compare’
   17 | #define atomic_min_fpdtype(addr, val) _Pragma("omp atomic compare") if ((val) < *(addr)) { *(addr) = (val); }
      |                                       ^~~~~~~
tmp.c:80:1: note: in expansion of macro ‘atomic_min_fpdtype’
   80 | atomic_min_fpdtype(&entmin_lhs_v[entmin_lhs_vix[BLK_IDX + X_IDX]], entmin_lhs);
      | ^~~~~~~~~~~~~~~~~~
tmp.c:17:69: error: expected expression before ‘if’
   17 | #define atomic_min_fpdtype(addr, val) _Pragma("omp atomic compare") if ((val) < *(addr)) { *(addr) = (val); }
      |                                                                     ^~
tmp.c:80:1: note: in expansion of macro ‘atomic_min_fpdtype’
   80 | atomic_min_fpdtype(&entmin_lhs_v[entmin_lhs_vix[BLK_IDX + X_IDX]], entmin_lhs);
      | ^~~~~~~~~~~~~~~~~~
tmp.c:17:39: error: expected ‘read’, ‘write’, ‘update’, ‘capture’, ‘seq_cst’, ‘acq_rel’, ‘release’, ‘relaxed’ or ‘hint’ clause
   17 | #define atomic_min_fpdtype(addr, val) _Pragma("omp atomic compare") if ((val) < *(addr)) { *(addr) = (val); }
      |                                       ^~~~~~~
tmp.c:125:1: note: in expansion of macro ‘atomic_min_fpdtype’
  125 | atomic_min_fpdtype(&entmin_lhs_v[entmin_lhs_vix[BLK_IDX + X_IDX]], entmin_lhs);
      | ^~~~~~~~~~~~~~~~~~
tmp.c:17:39: error: expected end of line before ‘compare’
   17 | #define atomic_min_fpdtype(addr, val) _Pragma("omp atomic compare") if ((val) < *(addr)) { *(addr) = (val); }
      |                                       ^~~~~~~
tmp.c:125:1: note: in expansion of macro ‘atomic_min_fpdtype’
  125 | atomic_min_fpdtype(&entmin_lhs_v[entmin_lhs_vix[BLK_IDX + X_IDX]], entmin_lhs);
      | ^~~~~~~~~~~~~~~~~~
tmp.c:17:69: error: expected expression before ‘if’
   17 | #define atomic_min_fpdtype(addr, val) _Pragma("omp atomic compare") if ((val) < *(addr)) { *(addr) = (val); }
      |                                                                     ^~
tmp.c:125:1: note: in expansion of macro ‘atomic_min_fpdtype’
  125 | atomic_min_fpdtype(&entmin_lhs_v[entmin_lhs_vix[BLK_IDX + X_IDX]], entmin_lhs);
      | ^~~~~~~~~~~~~~~~~~
2

PyFR requires GCC >= 12.0 or another C compiler with OpenMP 5.1 support. Do you meet this?

3

Yeah Im running GCC 12.2, please help me resolve this

4

If you were running GCC 12 you would not be getting this error. Please check exactly what compiler PyFR is using.

Regards, Freddie.

5

Please help me to resolve this, I’m using GCC 12.2.0

I am not able to move forward in research work

:~/PyFR-Test-Cases/2d-viscous-shock-tube$ pyfr run -b openmp viscous-shock-tube.pyfrm viscous-shock-tube.ini
Traceback (most recent call last):
  File "/usr/local/bin/pyfr", line 33, in <module>
    sys.exit(load_entry_point('pyfr==1.15.0', 'console_scripts', 'pyfr')())
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/__main__.py", line 125, in main
    args.process(args)
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/__main__.py", line 272, in process_run
    _process_common(
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/__main__.py", line 257, in _process_common
    solver = get_solver(backend, rallocs, mesh, soln, cfg)
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/solvers/__init__.py", line 14, in get_solver
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/integrators/__init__.py", line 34, in get_integrator
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/integrators/std/controllers.py", line 11, in __init__
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/integrators/std/base.py", line 26, in __init__
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/solvers/base/system.py", line 67, in commit
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/solvers/base/system.py", line 213, in _gen_kernels
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/solvers/navstokes/inters.py", line 106, in <lambda>
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/backends/base/backend.py", line 174, in kernel
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/backends/base/kernels.py", line 157, in kernel_meth
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/backends/openmp/provider.py", line 73, in _build_kernel
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/util.py", line 39, in newmeth
    res = cache[key] = meth(self, *args, **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/backends/openmp/provider.py", line 65, in _build_library
  File "/usr/local/lib/python3.10/dist-packages/pyfr-1.15.0-py3.10.egg/pyfr/backends/openmp/compiler.py", line 58, in build
  File "/usr/lib/python3/dist-packages/pytools/prefork.py", line 226, in call_capture_output
    return forker.call_capture_output(cmdline, cwd, error_on_nonzero)
  File "/usr/lib/python3/dist-packages/pytools/prefork.py", line 182, in call_capture_output
    return self._remote_invoke("call_capture_output", cmdline, cwd,
  File "/usr/lib/python3/dist-packages/pytools/prefork.py", line 164, in _remote_invoke
    raise result
pytools.prefork.ExecError: error invoking 'cc -shared -std=c99 -Ofast -march=native -fopenmp -fPIC -o libtmp.so tmp.c -lm': status 1 invoking 'cc -shared -std=c99 -Ofast -march=native -fopenmp -fPIC -o libtmp.so tmp.c -lm': tmp.c: In function ‘bccent’:
tmp.c:17:39: error: expected ‘read’, ‘write’, ‘update’, ‘capture’, ‘seq_cst’, ‘acq_rel’, ‘release’, ‘relaxed’ or ‘hint’ clause
   17 | #define atomic_min_fpdtype(addr, val) _Pragma("omp atomic compare") if ((val) < *(addr)) { *(addr) = (val); }
      |                                       ^~~~~~~
tmp.c:81:1: note: in expansion of macro ‘atomic_min_fpdtype’
   81 | atomic_min_fpdtype(&entmin_lhs_v[entmin_lhs_vix[BLK_IDX + X_IDX]], entmin_lhs);
      | ^~~~~~~~~~~~~~~~~~
tmp.c:17:39: error: expected end of line before ‘compare’
   17 | #define atomic_min_fpdtype(addr, val) _Pragma("omp atomic compare") if ((val) < *(addr)) { *(addr) = (val); }
      |                                       ^~~~~~~
tmp.c:81:1: note: in expansion of macro ‘atomic_min_fpdtype’
   81 | atomic_min_fpdtype(&entmin_lhs_v[entmin_lhs_vix[BLK_IDX + X_IDX]], entmin_lhs);
      | ^~~~~~~~~~~~~~~~~~
tmp.c:17:69: error: expected expression before ‘if’
   17 | #define atomic_min_fpdtype(addr, val) _Pragma("omp atomic compare") if ((val) < *(addr)) { *(addr) = (val); }
      |                                                                     ^~
tmp.c:81:1: note: in expansion of macro ‘atomic_min_fpdtype’
   81 | atomic_min_fpdtype(&entmin_lhs_v[entmin_lhs_vix[BLK_IDX + X_IDX]], entmin_lhs);
      | ^~~~~~~~~~~~~~~~~~
tmp.c:17:39: error: expected ‘read’, ‘write’, ‘update’, ‘capture’, ‘seq_cst’, ‘acq_rel’, ‘release’, ‘relaxed’ or ‘hint’ clause
   17 | #define atomic_min_fpdtype(addr, val) _Pragma("omp atomic compare") if ((val) < *(addr)) { *(addr) = (val); }
      |                                       ^~~~~~~
tmp.c:127:1: note: in expansion of macro ‘atomic_min_fpdtype’
  127 | atomic_min_fpdtype(&entmin_lhs_v[entmin_lhs_vix[BLK_IDX + X_IDX]], entmin_lhs);
      | ^~~~~~~~~~~~~~~~~~
tmp.c:17:39: error: expected end of line before ‘compare’
   17 | #define atomic_min_fpdtype(addr, val) _Pragma("omp atomic compare") if ((val) < *(addr)) { *(addr) = (val); }
      |                                       ^~~~~~~
tmp.c:127:1: note: in expansion of macro ‘atomic_min_fpdtype’
  127 | atomic_min_fpdtype(&entmin_lhs_v[entmin_lhs_vix[BLK_IDX + X_IDX]], entmin_lhs);
      | ^~~~~~~~~~~~~~~~~~
tmp.c:17:69: error: expected expression before ‘if’
   17 | #define atomic_min_fpdtype(addr, val) _Pragma("omp atomic compare") if ((val) < *(addr)) { *(addr) = (val); }
      |                                                                     ^~
tmp.c:127:1: note: in expansion of macro ‘atomic_min_fpdtype’
  127 | atomic_min_fpdtype(&entmin_lhs_v[entmin_lhs_vix[BLK_IDX + X_IDX]], entmin_lhs);
      | ^~~~~~~~~~~~~~~~~~

:~/PyFR-Test-Cases/2d-viscous-shock-tube$ which gcc
/usr/local/bin/gcc
:~/PyFR-Test-Cases/2d-viscous-shock-tube$ gcc --version
gcc (GCC) 12.2.0
Copyright (C) 2022 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
111
6

What does cc --version give, as this is the compiler PyFR will try and use by default.

Regards, Freddie.

7

~/PyFR-Test-Cases/2d-viscous-shock-tube$ cc --version
cc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.

8

As I noted above, you are using an old version of GCC.

Regards, Freddie.

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