Inc_cylinder_2d testcase fails

General
1

On FreeBSD 11.2 (with the clang compiler) this command fails:

$ pyfr run -b openmp -p inc_cylinder_2d.pyfrm inc_cylinder_2d.ini

Traceback (most recent call last):
File "/usr/local/lib/python3.6/site-packages/pyfr/util.py", line 33, in __call__
res = cache[key]
KeyError: (<function OpenMPKernelProvider._build_kernel at 0x80d54d158>, b'\x80\x03X\t\x00\x00\x00gimmik_mmq\x00X\xaf\x07\x00\x00\nvoid\ngimmik_mm(int ncol,\n const double* restrict b, int ldb,\n double* restrict c, int ldc)\n{\n double dotp;\n\n #pragma omp parallel for simd private(dotp)\n for (int i = 0; i < ncol; i++)\n {\n dotp = 1.478830557701236*b[i + 0*ldb] + -0.6666666666666666*b[i + 3*ldb] + 0.1878361089654305*b[i + 6*ldb];\n c[i + 0*ldc] = dotp;\n dotp = 1.478830557701236*b[i + 1*ldb] + -0.6666666666666666*b[i + 4*ldb] + 0.1878361089654305*b[i + 7*ldb];\n c[i + 1*ldc] = dotp;\n dotp = 1.478830557701236*b[i + 2*ldb] + -0.6666666666666666*b[i + 5*ldb] + 0.1878361089654305*b[i + 8*ldb];\n c[i + 2*ldc] = dotp;\n dotp = 0.1878361089654305*b[i + 0*ldb] + -0.6666666666666666*b[i + 1*ldb] + 1.478830557701236*b[i + 2*ldb];\n c[i + 3*ldc] = dotp;\n dotp = 0.1878361089654305*b[i + 3*ldb] + -0.6666666666666666*b[i + 4*ldb] + 1.478830557701236*b[i + 5*ldb];\n c[i + 4*ldc] = dotp;\n dotp = 0.1878361089654305*b[i + 6*ldb] + -0.6666666666666666*b[i + 7*ldb] + 1.478830557701236*b[i + 8*ldb];\n c[i + 5*ldc] = dotp;\n dotp = 0.1878361089654305*b[i + 0*ldb] + -0.6666666666666666*b[i + 3*ldb] + 1.478830557701236*b[i + 6*ldb];\n c[i + 6*ldc] = dotp;\n dotp = 0.1878361089654305*b[i + 1*ldb] + -0.6666666666666666*b[i + 4*ldb] + 1.478830557701236*b[i + 7*ldb];\n c[i + 7*ldc] = dotp;\n dotp = 0.1878361089654305*b[i + 2*ldb] + -0.6666666666666666*b[i + 5*ldb] + 1.478830557701236*b[i + 8*ldb];\n c[i + 8*ldc] = dotp;\n dotp = 1.478830557701236*b[i + 0*ldb] + -0.6666666666666666*b[i + 1*ldb] + 0.1878361089654305*b[i + 2*ldb];\n c[i + 9*ldc] = dotp;\n dotp = 1.478830557701236*b[i + 3*ldb] + -0.6666666666666666*b[i + 4*ldb] + 0.1878361089654305*b[i + 5*ldb];\n c[i + 10*ldc] = dotp;\n dotp = 1.478830557701236*b[i + 6*ldb] + -0.6666666666666666*b[i + 7*ldb] + 0.1878361089654305*b[i + 8*ldb];\n c[i + 11*ldc] = dotp;\n }\n}\nq\x01]q\x02(cnumpy\nint32\nq\x03cnumpy\nint64\nq\x04h\x03h\x04h\x03e\x87q\x05.', b'\x80\x03}q\x00.')

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/usr/local/bin/pyfr", line 11, in <module>
load_entry_point('pyfr==1.7.6', 'console_scripts', 'pyfr')()
File "/usr/local/lib/python3.6/site-packages/pyfr/__main__.py", line 110, in main`
args.process(args)
File "/usr/local/lib/python3.6/site-packages/pyfr/__main__.py", line 235, in process_run`
args, NativeReader(args.mesh), None, Inifile.load(args.cfg)
File "/usr/local/lib/python3.6/site-packages/pyfr/__main__.py", line 216, in _process_common
solver = get_solver(backend, rallocs, mesh, soln, cfg)
File "/usr/local/lib/python3.6/site-packages/pyfr/solvers/__init__.py", line 16, in get_solver
return get_integrator(backend, systemcls, rallocs, mesh, initsoln, cfg)
File "/usr/local/lib/python3.6/site-packages/pyfr/integrators/__init__.py", line 46, in get_integrator
return integrator(backend, systemcls, rallocs, mesh, initsoln, cfg)
File "/usr/local/lib/python3.6/site-packages/pyfr/integrators/dual/multip.py", line 54, in __init__
super().__init__(backend, systemcls, rallocs, mesh, initsoln, cfg)
File "/usr/local/lib/python3.6/site-packages/pyfr/integrators/dual/controllers.py", line 48, in __init__
super().__init__(*args, **kwargs)
File "/usr/local/lib/python3.6/site-packages/pyfr/integrators/dual/controllers.py", line 15, in __init__
super().__init__(*args, **kwargs)
File "/usr/local/lib/python3.6/site-packages/pyfr/integrators/dual/steppers.py", line 8, in __init__
super().__init__(*args, **kwargs)
File "/usr/local/lib/python3.6/site-packages/pyfr/integrators/dual/base.py", line 10, in __init__
super().__init__(*args, **kwargs)
File "/usr/local/lib/python3.6/site-packages/pyfr/integrators/base.py", line 58, in __init__
self._init_system(systemcls, backend, rallocs, mesh, initsoln)
File "/usr/local/lib/python3.6/site-packages/pyfr/integrators/dual/multip.py", line 208, in _init_system
*args, nreg=self.nreg + (2 if l != self._order else 0), cfg=cfg
File "/usr/local/lib/python3.6/site-packages/pyfr/solvers/base/system.py", line 65, in __init__
self._gen_kernels(eles, int_inters, mpi_inters, bc_inters)
File "/usr/local/lib/python3.6/site-packages/pyfr/solvers/base/system.py", line 174, in _gen_kernels
kernels[pn, kn].append(kgetter())
File "/usr/local/lib/python3.6/site-packages/pyfr/solvers/baseadvec/elements.py", line 57, in <lambda>
out=self._scal_fpts
File "/usr/local/lib/python3.6/site-packages/pyfr/backends/base/backend.py", line 166, in kernel
return kern(*args, **kwargs)
File "/usr/local/lib/python3.6/site-packages/pyfr/backends/openmp/gimmik.py", line 34, in mul
[np.int32] + [np.intp, np.int32]*2)
File "/usr/local/lib/python3.6/site-packages/pyfr/util.py", line 35, in __call__
res = cache[key] = self.func(*args, **kwargs)
File "/usr/local/lib/python3.6/site-packages/pyfr/backends/openmp/provider.py", line 13, in _build_kernel
mod = SourceModule(src, self.backend.cfg)
File "/usr/local/lib/python3.6/site-packages/pyfr/backends/openmp/compiler.py", line 59, in __init__
call_capture_output(self.cc_cmd(cname, lname), cwd=tmpdir)
File "/usr/local/lib/python3.6/site-packages/pytools/prefork.py", line 223, in call_capture_output
return forker.call_capture_output(cmdline, cwd, error_on_nonzero)
File "/usr/local/lib/python3.6/site-packages/pytools/prefork.py", line 180, in call_capture_output
error_on_nonzero)
File "/usr/local/lib/python3.6/site-packages/pytools/prefork.py", line 162, 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': b'warning: loop not vectorized: failed explicitly specified loop vectorization [-Wpass-failed=loop-vectorize]\n1 warning generated.\n/usr/bin/ld: cannot find -lomp\ncc: error: linker command failed with exit code 1 (use -v to see invocation)\n'
2

Hi Yuri,

As the name suggests the OpenMP backend requires a compiler which
supports OpenMP. From the linker error above it appears as if libomp is
missing on your system (although this is an implementation detail). You
may need to either install an additional support library or a different
compiler version.

Regards, Freddie.

3

Hi Freddie,

I do have libomp installed: /usr/local/lib/libomp.so.0
It looks like -L/usr/local/lib isn’t passed to the linker.
LDFLAGS should be preserved from the time when the project was built, and passed to the linker every time thereafter.

Yuri

4

Hi Yuri,

I do have libomp installed: /usr/local/lib/libomp.so.0
It looks like -L/usr/local/lib isn't passed to the linker.
LDFLAGS should be preserved from the time when the project was built,
and passed to the linker every time thereafter.

PyFR is not 'built' per se. All C code is generated, compiled, and
linked, at run time. Indeed, many users of PyFR just run it directly
from a clone of the git repository without every going through setup.py.

If your compiler requires additional flags you have a few options. One
is to simply export the relevant environmental variables before running
PyFR. Alternatively, in your .ini file you may set

[backend-openmp]
cflags = -L/usr/local/lib

as appropriate. (It says cflags however everything is done in one shot
and so linker flags are fine here, too.)

Regards, Freddie.

5

I patched the FreeBSD port with -I/-L flags.
Thanks!