Dear Freddle,
I updated the gcc to 4.9 version while it shows me another error,
dellblack@ubuntu1204:~/Downloads/PyFR-1.6.0/examples_copy/couette_flow_2d$
pyfr run -b openmp -p couette_flow_2d.pyfrm couette_flow_2d.ini
Traceback (most recent call last):
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/util.py",
line 33, in __call__
KeyError: (<function OpenMPKernelProvider._build_kernel at 0x7f97006d9730>,
b'\x80\x03X\t\x00\x00\x00gimmik_mmq\x00X\xc7\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
= 1.4788305577012362*b[i + 0*ldb] + -0.6666666666666666*b[i + 3*ldb] +
0.18783610896543051*b[i + 6*ldb];\n c[i + 0*ldc] = dotp;\n
dotp = 1.4788305577012362*b[i + 1*ldb] + -0.6666666666666666*b[i + 4*ldb] +
0.18783610896543051*b[i + 7*ldb];\n c[i + 1*ldc] = dotp;\n
dotp = 1.4788305577012362*b[i + 2*ldb] + -0.6666666666666666*b[i + 5*ldb] +
0.18783610896543051*b[i + 8*ldb];\n c[i + 2*ldc] = dotp;\n
dotp = 0.18783610896543051*b[i + 0*ldb] + -0.6666666666666666*b[i + 1*ldb]
+ 1.4788305577012362*b[i + 2*ldb];\n c[i + 3*ldc] = dotp;\n
dotp = 0.18783610896543051*b[i + 3*ldb] + -0.6666666666666666*b[i + 4*ldb]
+ 1.4788305577012362*b[i + 5*ldb];\n c[i + 4*ldc] = dotp;\n
dotp = 0.18783610896543051*b[i + 6*ldb] + -0.6666666666666666*b[i + 7*ldb]
+ 1.4788305577012362*b[i + 8*ldb];\n c[i + 5*ldc] = dotp;\n
dotp = 0.18783610896543051*b[i + 0*ldb] + -0.6666666666666666*b[i + 3*ldb]
+ 1.4788305577012362*b[i + 6*ldb];\n c[i + 6*ldc] = dotp;\n
dotp = 0.18783610896543051*b[i + 1*ldb] + -0.6666666666666666*b[i + 4*ldb]
+ 1.4788305577012362*b[i + 7*ldb];\n c[i + 7*ldc] = dotp;\n
dotp = 0.18783610896543051*b[i + 2*ldb] + -0.6666666666666666*b[i + 5*ldb]
+ 1.4788305577012362*b[i + 8*ldb];\n c[i + 8*ldc] = dotp;\n
dotp = 1.4788305577012362*b[i + 0*ldb] + -0.6666666666666666*b[i + 1*ldb] +
0.18783610896543051*b[i + 2*ldb];\n c[i + 9*ldc] = dotp;\n
dotp = 1.4788305577012362*b[i + 3*ldb] + -0.6666666666666666*b[i + 4*ldb] +
0.18783610896543051*b[i + 5*ldb];\n c[i + 10*ldc] = dotp;\n
dotp = 1.4788305577012362*b[i + 6*ldb] + -0.6666666666666666*b[i + 7*ldb] +
0.18783610896543051*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 "/home/dellblack/anaconda3/bin/pyfr", line 11, in <module>
load_entry_point('pyfr==1.6.0', 'console_scripts', 'pyfr')()
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/__main__.py",
line 110, in main
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/__main__.py",
line 235, in process_run
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/__main__.py",
line 216, in _process_common
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/solvers/__init__.py",
line 16, in get_solver
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/integrators/__init__.py",
line 43, in get_integrator
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/integrators/std/controllers.py",
line 14, in __init__
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/integrators/std/steppers.py",
line 8, in __init__
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/integrators/std/base.py",
line 12, in __init__
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/integrators/base.py",
line 59, in __init__
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/solvers/base/system.py",
line 65, in __init__
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/solvers/base/system.py",
line 174, in _gen_kernels
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/solvers/baseadvec/elements.py",
line 57, in <lambda>
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/backends/base/backend.py",
line 166, in kernel
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/backends/openmp/gimmik.py",
line 34, in mul
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/util.py",
line 35, in __call__
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/backends/openmp/provider.py",
line 13, in _build_kernel
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/backends/openmp/compiler.py",
line 64, in __init__
File
"/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/backends/openmp/compiler.py",
line 127, in _cache_set_and_loadlib
File "/home/dellblack/anaconda3/lib/python3.6/ctypes/__init__.py", line
344, in __init__
self._handle = _dlopen(self._name, mode)
OSError: /home/dellblack/anaconda3/bin/../lib/libgomp.so.1: version
`GOMP_4.0' not found (required by
/home/dellblack/.cache/pyfr/libc109c2a0864201c2d29f1b5cc6ee57133e70c853d42a55bfa4013aab42133b7a.so)
It seems that libgomp.so.1 is not not found. And I find in this link
https://groups.google.com/forum/#!topic/pyfrmailinglist/UMbx-7M3JT4, I add
this *cflags**=-Wl,-rpath /usr/**lib64 in configuration line. *And
fortunately it works. But it runs very slowly.
*And I do not quite follow what you mean *Cheers
*,*Henry
Hi Henry,
>
> The issue appears to be that your version of GCC is too old to compile
> the kernels which are generated by PyFR. As per the user guide PyFR
> requires GCC 4.9 or newer (alternatively, a recent version of the Intel
> compiler may also be used).
>
> Regards, Freddie.
>
> On 24/05/2017 07:36, Henry LOO wrote:
> > Dear all,
> >
> > I am new to PyFR and have installed it these days. I d like to run the
> > first tutorial with -b openmp but I received the following error. I am
> > quite confused about it. By the way, I installed openblas in anaconda
> > and the python version is 3.6 as well as the ubuntu version is 12.04.5
> > LTS. Could anyone help me out?
> >
> > Thank you all in advance!
> >
> > %%
> >
> >
> dellblack@ubuntu1204:~/Downloads/PyFR-1.6.0/examples_copy/couette_flow_2d$
> pyfr run -b openmp couette_flow_2d.pyfrm couette_flow_2d.ini
> > Traceback (most recent call last):
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/util.py",
>
>
> > line 33, in __call__
> > KeyError: (<function OpenMPKernelProvider._build_kernel at
> > 0x7fd9b99da6a8>,
> >
> b'\x80\x03X\t\x00\x00\x00gimmik_mmq\x00X\xc7\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 = 1.4788305577012362*b[i + 0*ldb] +
> > -0.6666666666666666*b[i + 3*ldb] + 0.18783610896543051*b[i +
> > 6*ldb];\n c[i + 0*ldc] = dotp;\n dotp =
> > 1.4788305577012362*b[i + 1*ldb] + -0.6666666666666666*b[i + 4*ldb] +
> > 0.18783610896543051*b[i + 7*ldb];\n c[i + 1*ldc] = dotp;\n
>
> > dotp = 1.4788305577012362*b[i + 2*ldb] + -0.6666666666666666*b[i +
> > 5*ldb] + 0.18783610896543051*b[i + 8*ldb];\n c[i + 2*ldc] =
> > dotp;\n dotp = 0.18783610896543051*b[i + 0*ldb] +
> > -0.6666666666666666*b[i + 1*ldb] + 1.4788305577012362*b[i +
> > 2*ldb];\n c[i + 3*ldc] = dotp;\n dotp =
> > 0.18783610896543051*b[i + 3*ldb] + -0.6666666666666666*b[i + 4*ldb] +
> > 1.4788305577012362*b[i + 5*ldb];\n c[i + 4*ldc] = dotp;\n
> > dotp = 0.18783610896543051*b[i + 6*ldb] + -0.6666666666666666*b[i +
> > 7*ldb] + 1.4788305577012362*b[i + 8*ldb];\n c[i + 5*ldc] =
> > dotp;\n dotp = 0.18783610896543051*b[i + 0*ldb] +
> > -0.6666666666666666*b[i + 3*ldb] + 1.4788305577012362*b[i +
> > 6*ldb];\n c[i + 6*ldc] = dotp;\n dotp =
> > 0.18783610896543051*b[i + 1*ldb] + -0.6666666666666666*b[i + 4*ldb] +
> > 1.4788305577012362*b[i + 7*ldb];\n c[i + 7*ldc] = dotp;\n
> > dotp = 0.18783610896543051*b[i + 2*ldb] + -0.6666666666666666*b[i +
> > 5*ldb] + 1.4788305577012362*b[i + 8*ldb];\n c[i + 8*ldc] =
> > dotp;\n dotp = 1.4788305577012362*b[i + 0*ldb] +
> > -0.6666666666666666*b[i + 1*ldb] + 0.18783610896543051*b[i +
> > 2*ldb];\n c[i + 9*ldc] = dotp;\n dotp =
> > 1.4788305577012362*b[i + 3*ldb] + -0.6666666666666666*b[i + 4*ldb] +
> > 0.18783610896543051*b[i + 5*ldb];\n c[i + 10*ldc] =
> > dotp;\n dotp = 1.4788305577012362*b[i + 6*ldb] +
> > -0.6666666666666666*b[i + 7*ldb] + 0.18783610896543051*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 "/home/dellblack/anaconda3/bin/pyfr", line 11, in <module>
> > load_entry_point('pyfr==1.6.0', 'console_scripts', 'pyfr')()
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/__main__.py",
>
>
> > line 110, in main
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/__main__.py",
>
>
> > line 235, in process_run
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/__main__.py",
>
>
> > line 216, in _process_common
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/solvers/__init__.py",
>
>
> > line 16, in get_solver
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/integrators/__init__.py",
>
>
> > line 43, in get_integrator
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/integrators/std/controllers.py",
>
>
> > line 14, in __init__
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/integrators/std/steppers.py",
>
>
> > line 8, in __init__
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/integrators/std/base.py",
>
>
> > line 12, in __init__
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/integrators/base.py",
>
>
> > line 59, in __init__
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/solvers/base/system.py",
>
>
> > line 65, in __init__
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/solvers/base/system.py",
>
>
> > line 174, in _gen_kernels
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/solvers/baseadvec/elements.py",
>
>
> > line 57, in <lambda>
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/backends/base/backend.py",
>
>
> > line 166, in kernel
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/backends/openmp/gimmik.py",
>
>
> > line 34, in mul
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/util.py",
>
>
> > line 35, in __call__
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/backends/openmp/provider.py",
>
>
> > line 13, in _build_kernel
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pyfr-1.6.0-py3.6.egg/pyfr/backends/openmp/compiler.py",
>
>
> > line 58, in __init__
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pytools-2016.2.6-py3.6.egg/pytools/prefork.py",
>
>
> > line 223, in call_capture_output
> > return forker.call_capture_output(cmdline, cwd, error_on_nonzero)
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pytools-2016.2.6-py3.6.egg/pytools/prefork.py",
>
>
> > line 180, in call_capture_output
> > error_on_nonzero)
> > File
> >
> "/home/dellblack/anaconda3/lib/python3.6/site-packages/pytools-2016.2.6-py3.6.egg/pytools/prefork.py",
>
>
> > line 162, in _remote_invoke
> > raise result
> > pytools.prefork.ExecError: error invoking 'gcc -shared -std=c99 -Ofast
> > -march=native -fopenmp -fPIC -o libtmp.so tmp.c -lm': status 1 invoking
> > 'gcc -shared -std=c99 -Ofast -march=native -fopenmp -fPIC -o libtmp.so
> > tmp.c -lm': b'tmp.c: In function
> > \xe2\x80\x98gimmik_mm\xe2\x80\x99:\ntmp.c:9:30: error: expected
> > \xe2\x80\x98#pragma omp\xe2\x80\x99 clause before
> > \xe2\x80\x98simd\xe2\x80\x99\n'
> >
> > --
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