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TOPIC: Compiling API v8p0r2 and Python 3

Compiling API v8p0r2 and Python 3 5 years 4 months ago #34042

The output is:

ldd _api.cpython-35m-x86_64-linux-gnu.so 
	linux-vdso.so.1 =>  (0x00007ffcbb3fd000)
	libapi.so => /home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib/libapi.so (0x00007fd9192e4000)
	libtelemac3d.so => /home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib/libtelemac3d.so (0x00007fd918fbf000)
	libtelemac2d.so => /home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib/libtelemac2d.so (0x00007fd918aa9000)
	libsisyphe.so => /home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib/libsisyphe.so (0x00007fd9187e9000)
	libnestor.so => /home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib/libnestor.so (0x00007fd9185bf000)
	libtomawac.so => /home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib/libtomawac.so (0x00007fd9182f2000)
	libartemis.so => /home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib/libartemis.so (0x00007fd917912000)
	libkhione.so => /home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib/libkhione.so (0x00007fd917683000)
	libwaqtel.so => /home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib/libwaqtel.so (0x00007fd91743f000)
	libgretel.so => /home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib/libgretel.so (0x00007fd917238000)
	libpartel.so => /home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib/libpartel.so (0x00007fd917017000)
	libbief.so => /home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib/libbief.so (0x00007fd916c0b000)
	libparallel.so => /home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib/libparallel.so (0x00007fd916a02000)
	libhermes.so => /home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib/libhermes.so (0x00007fd9163f5000)
	libdamocles.so => /home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib/libdamocles.so (0x00007fd9161e0000)
	libspecial.so => /home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib/libspecial.so (0x00007fd915fd7000)
	libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007fd915cac000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fd9158e2000)
	libmpi_mpifh.so.12 => /usr/lib/libmpi_mpifh.so.12 (0x00007fd915689000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fd915380000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fd915163000)
	libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fd914f4d000)
	libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007fd914d0e000)
	/lib64/ld-linux-x86-64.so.2 (0x00007fd9197bc000)
	libmpi.so.12 => /usr/lib/libmpi.so.12 (0x00007fd914a38000)
	libopen-pal.so.13 => /usr/lib/libopen-pal.so.13 (0x00007fd91479b000)
	libibverbs.so.1 => /usr/lib/libibverbs.so.1 (0x00007fd91458c000)
	libopen-rte.so.12 => /usr/lib/libopen-rte.so.12 (0x00007fd914312000)
	libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fd91410e000)
	librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fd913f06000)
	libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007fd913d03000)
	libhwloc.so.5 => /usr/lib/x86_64-linux-gnu/libhwloc.so.5 (0x00007fd913ac9000)
	libnuma.so.1 => /usr/lib/x86_64-linux-gnu/libnuma.so.1 (0x00007fd9138be000)
	libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 (0x00007fd9136b4000)
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Compiling API v8p0r2 and Python 3 5 years 4 months ago #34046

  • yugi
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Ok i see the issue I missed something in the error message.

The issue is with metis the path to the metis lib might be incorrect check your metishome and check that it is in the ld_library_path variable
There are 10 types of people in the world: those who understand binary, and those who don't.
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Compiling API v8p0r2 and Python 3 5 years 4 months ago #34052

My LD_LIBRARY_PATH variable contains:
$LD_LIBRARY_PATH
/home/ws/telemac-mascaret/v8p0r2/optionals/metis-5.1.0/build/lib:/home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib:/home/ws/telemac-mascaret/v8p0r2/optionals/metis-5.1.0/build/lib:/home/ws/telemac-mascaret/v8p0r2/builds/ubuntumpi/wrap_api/lib:

This seems okay to me. I tried it also with the python 2.7 version of the API, same error. I again attached my configfile and my source file. It is clearer than the bash script :whistle:
Attachments:
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Compiling API v8p0r2 and Python 3 5 years 4 months ago #34055

  • yugi
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Can you post what the command below returns:
ls /home/ws/telemac-mascaret/v8p0r2/optionals/metis-5.1.0/build/lib

Also Can you edit the script compile_telemac.py
search for compile_api around line 130 replace silent=True by silent=False
Rerun compilation (not need to add --clean) and post the result here.
There are 10 types of people in the world: those who understand binary, and those who don't.
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Compiling API v8p0r2 and Python 3 5 years 4 months ago #34059

The output is:
\'+1j*(            \'run_allocation                  \'+1j*(            \'run_init                        \'+1j*(            \'run_timestep                    \'+1j*(            \'run_finalize                    \' /)". Ignoring: invalid syntax (<string>, line 1)\nanalyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'32\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.'
    ~> First part of f2py for api passed
b'Unknown vendor: "gfortran"\nanalyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'32\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.analyzevars: charselector={\'len\': \'40\'} unhandled.analyzevars: charselector={\'len\': \'200\'} unhandled.getstrlength:intent(hide): expected a string with defined length but got: {\'typespec\': \'character\', \'attrspec\': [], \'intent\': [\'out\'], \'charselector\': {\'*\': \'(*)\'}}\ngetstrlength:intent(hide): expected a string with defined length but got: {\'typespec\': \'character\', \'attrspec\': [], \'intent\': [\'out\'], \'charselector\': {\'*\': \'(*)\'}}\ngetstrlength:intent(hide): expected a string with defined length but got: {\'typespec\': \'character\', \'attrspec\': [], \'intent\': [\'out\'], \'charselector\': {\'*\': \'(*)\'}}\nIn file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1777:0,\n                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,\n                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,\n                 from /tmp/tmpysugz3ud/src.linux-x86_64-3.5/fortranobject.h:13,\n                 from /tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c:19:\n/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]\n #warning "Using deprecated NumPy API, disable it by " \\\n  ^\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c: In function \xe2\x80\x98f2py_setup_api_handle_var_t3d\xe2\x80\x99:\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c:11584:46: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]\n   f2py_api_handle_var_t3d_def[i_f2py++].func = vname_t3d;\n                                              ^\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c:11585:46: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]\n   f2py_api_handle_var_t3d_def[i_f2py++].func = vinfo_t3d;\n                                              ^\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c: In function \xe2\x80\x98f2py_setup_api_handle_var_t2d\xe2\x80\x99:\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c:11614:46: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]\n   f2py_api_handle_var_t2d_def[i_f2py++].func = vname_t2d;\n                                              ^\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c:11617:46: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]\n   f2py_api_handle_var_t2d_def[i_f2py++].func = vinfo_t2d;\n                                              ^\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c: In function \xe2\x80\x98f2py_setup_api_handle_var_sis\xe2\x80\x99:\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c:11642:46: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]\n   f2py_api_handle_var_sis_def[i_f2py++].func = vname_sis;\n                                              ^\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c:11643:46: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]\n   f2py_api_handle_var_sis_def[i_f2py++].func = vinfo_sis;\n                                              ^\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c: In function \xe2\x80\x98f2py_setup_api_handle_var_art\xe2\x80\x99:\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c:11675:46: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]\n   f2py_api_handle_var_art_def[i_f2py++].func = vname_art;\n                                              ^\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c:11676:46: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]\n   f2py_api_handle_var_art_def[i_f2py++].func = vinfo_art;\n                                              ^\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c: In function \xe2\x80\x98f2py_setup_api_handle_var_wac\xe2\x80\x99:\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c:11700:46: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]\n   f2py_api_handle_var_wac_def[i_f2py++].func = vname_wac;\n                                              ^\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c:11705:46: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]\n   f2py_api_handle_var_wac_def[i_f2py++].func = vinfo_wac;\n                                              ^\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c: At top level:\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_apimodule.c:186:12: warning: \xe2\x80\x98f2py_size\xe2\x80\x99 defined but not used [-Wunused-function]\n static int f2py_size(PyArrayObject* var, ...)\n            ^\nIn file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1777:0,\n                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,\n                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,\n                 from /tmp/tmpysugz3ud/src.linux-x86_64-3.5/fortranobject.h:13,\n                 from /tmp/tmpysugz3ud/src.linux-x86_64-3.5/fortranobject.c:2:\n/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]\n #warning "Using deprecated NumPy API, disable it by " \\\n  ^\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_api-f2pywrappers2.f90:71:10:\n\n       use api_handle_var_t3d, only : vname_t3d\n          1\nWarning: Unused module variable \xe2\x80\x98vinfo_t3d\xe2\x80\x99 which has been explicitly imported at (1) [-Wunused-variable]\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_api-f2pywrappers2.f90:71:10:\n\n       use api_handle_var_t3d, only : vname_t3d\n          1\nWarning: Unused module variable \xe2\x80\x98vname_t3d\xe2\x80\x99 which has been explicitly imported at (1) [-Wunused-variable]\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_api-f2pywrappers2.f90:153:10:\n\n       use api_handle_var_t2d, only : t2d_var_len\n          1\nWarning: Unused module variable \xe2\x80\x98vinfo_t2d\xe2\x80\x99 which has been explicitly imported at (1) [-Wunused-variable]\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_api-f2pywrappers2.f90:153:10:\n\n       use api_handle_var_t2d, only : t2d_var_len\n          1\nWarning: Unused module variable \xe2\x80\x98vname_t2d\xe2\x80\x99 which has been explicitly imported at (1) [-Wunused-variable]\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_api-f2pywrappers2.f90:235:10:\n\n       use api_handle_var_sis, only : vname_sis\n          1\nWarning: Unused module variable \xe2\x80\x98vinfo_sis\xe2\x80\x99 which has been explicitly imported at (1) [-Wunused-variable]\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_api-f2pywrappers2.f90:235:10:\n\n       use api_handle_var_sis, only : vname_sis\n          1\nWarning: Unused module variable \xe2\x80\x98vname_sis\xe2\x80\x99 which has been explicitly imported at (1) [-Wunused-variable]\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_api-f2pywrappers2.f90:317:10:\n\n       use api_handle_var_art, only : art_var_len\n          1\nWarning: Unused module variable \xe2\x80\x98vinfo_art\xe2\x80\x99 which has been explicitly imported at (1) [-Wunused-variable]\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_api-f2pywrappers2.f90:317:10:\n\n       use api_handle_var_art, only : art_var_len\n          1\nWarning: Unused module variable \xe2\x80\x98vname_art\xe2\x80\x99 which has been explicitly imported at (1) [-Wunused-variable]\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_api-f2pywrappers2.f90:399:10:\n\n       use api_handle_var_wac, only : vname_wac\n          1\nWarning: Unused module variable \xe2\x80\x98vinfo_wac\xe2\x80\x99 which has been explicitly imported at (1) [-Wunused-variable]\n/tmp/tmpysugz3ud/src.linux-x86_64-3.5/_api-f2pywrappers2.f90:399:10:\n\n       use api_handle_var_wac, only : vname_wac\n          1\nWarning: Unused module variable \xe2\x80\x98vname_wac\xe2\x80\x99 which has been explicitly imported at (1) [-Wunused-variable]\n'
    ~> Second part of f2py of api passed
    ~> Compiling hermes api
b"analyzevars: charselector={'len': '16'} unhandled.analyzevars: charselector={'len': '16'} unhandled.analyzevars: charselector={'len': '32'} unhandled."
    ~> First part of f2py for hermes passed
b'Unknown vendor: "gfortran"\nIn file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1777:0,\n                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,\n                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,\n                 from /tmp/tmprb4_ma61/src.linux-x86_64-3.5/fortranobject.h:13,\n                 from /tmp/tmprb4_ma61/src.linux-x86_64-3.5/fortranobject.c:2:\n/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]\n #warning "Using deprecated NumPy API, disable it by " \\\n  ^\nIn file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1777:0,\n                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18,\n                 from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4,\n                 from /tmp/tmprb4_ma61/src.linux-x86_64-3.5/fortranobject.h:13,\n                 from /tmp/tmprb4_ma61/src.linux-x86_64-3.5/_hermesmodule.c:19:\n/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]\n #warning "Using deprecated NumPy API, disable it by " \\\n  ^\n/tmp/tmprb4_ma61/src.linux-x86_64-3.5/_hermesmodule.c:150:12: warning: \xe2\x80\x98f2py_size\xe2\x80\x99 defined but not used [-Wunused-function]\n static int f2py_size(PyArrayObject* var, ...)\n            ^\nanalyzevars: charselector={\'len\': \'32\'} unhandled.'
    ~> Second part of f2py of hermes passed

I added the response also in the attached file. ;)
Attachments:
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Compiling API v8p0r2 and Python 3 5 years 4 months ago #34062

  • yugi
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Well it looks ok.
And the ls ?
There are 10 types of people in the world: those who understand binary, and those who don't.
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Compiling API v8p0r2 and Python 3 5 years 2 months ago #34573

  • murphybeck
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More on..compiling and linking in Pyhon
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