Mailman 3 March 2004 - SciPy-Dev

Another issue with scipy_distutils and FORTRAN files
by Berthold Höllmann March 31, 2004

March 31, 2004

Hello, Our FORTRAN code often uses "include" statements. The FORTRAN compiler we use (DF 6.1, ifc 7.1, WorkShop 6 update 2 Fortran) recognize the -I flag for pointing to an include directory. I seems scipy_distutils have lost the ability to regognize the "include_dirs" argument to "Extensions". The compiler does not find the include files anymore. Kind regards Berthold Höllmann -- Germanischer Lloyd AG CAE Development Vorsetzen 35 20459 Hamburg Phone: +49(0)40 36149-7374 Fax: +49(0)40 36149-7320 e-mail: hoel(a)gl-group.com Internet: http://www.gl-group.com This e-mail contains confidential information for the exclusive attention of the intended addressee. Any access of third parties to this e-mail is unauthorised. Any use of this e-mail by unintended recipients such as copying, distribution, disclosure etc. is prohibited and may be unlawful. When addressed to our clients the content of this e-mail is subject to the General Terms and Conditions of GL's Group of Companies applicable at the date of this e-mail. GL's Group of Companies does not warrant and/or guarantee that this message at the moment of receipt is authentic, correct and its communication free of errors, interruption etc.

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scipy_distutils under cygwin using DF
by Berthold Höllmann March 31, 2004

March 31, 2004

Hello, I try to compile some python extension libraries under WinXP/cygwin. The fortran codes need DF, no chance for g77. But I get: >make test PYTHONPATH="w:\\hoel\\work\\GLPy\\lib;w:\\hoel\\work\\GLPy\\build\\lib.win32-2.3;" python setup.py config_fc --fcompiler=compaqv build_src build_clib build_ext ... customize CompaqVisualFCompiler customize CompaqVisualFCompiler using build_clib splitcmdline('DF /what') ******************************************************************************** scipy_distutils.compaqfcompiler.CompaqVisualFCompiler version_cmd = ['DF', '/what'] compiler_fix = ['DF', '/fixed', '/nologo', '/MD', '/WX', '/iface=(cref,nomixed_str_len_arg)', '/n ames:lowercase', '/assume:underscore', '/Ox', '/fast', '/optimize:5', '/unroll:0', '/math_library:fa st', '/threads'] ranlib = None archiver = ['C:\\Programme\\Microsoft Visual Studio\\VC98\\BIN\\lib.exe', '/OUT:'] compiler_f77 = ['DF', '/f77rtl', '/fixed', '/nologo', '/MD', '/WX', '/iface=(cref,nomixed_str_len _arg)', '/names:lowercase', '/assume:underscore', '/Ox', '/fast', '/optimize:5', '/unroll:0', '/math _library:fast', '/threads'] linker_so = ['DF'] compiler_f90 = ['DF', '/nologo', '/MD', '/WX', '/iface=(cref,nomixed_str_len_arg)', '/names:lower case', '/assume:underscore', '/Ox', '/fast', '/optimize:5', '/unroll:0', '/math_library:fast', '/thr eads'] version = None libraries = [] library_dirs = [] object_switch = '/object:' compile_switch = '/compile_only ' include_dirs = [] ******************************************************************************** building 'fortmisc' library compling Fortran sources DF(f77) options: '/f77rtl /fixed /nologo /MD /WX /iface=(cref,nomixed_str_len_arg) /names:lowercase/assume:underscore /Ox /fast /optimize:5 /unroll:0 /math_library:fast /threads' DF(f90) options: '/nologo /MD /WX /iface=(cref,nomixed_str_len_arg) /names:lowercase /assume:underscore /Ox /fast /optimize:5 /unroll:0 /math_library:fast /threads' DF(fix) options: '/fixed /nologo /MD /WX /iface=(cref,nomixed_str_len_arg) /names:lowercase /assume:underscore /Ox /fast /optimize:5 /unroll:0 /math_library:fast /threads' compile options: '-Ilib\numfort -c' DF:f77: lib\numfort\NB.F DF /f77rtl /fixed /nologo /MD /WX /iface=(cref,nomixed_str_len_arg) /names:lowercase /assume:underscore /Ox /fast /optimize:5 /unroll:0 /math_library:fast /threads -Ilib\numfort -c "/compile_only " lib\numfort\NB.F /object:build\temp.win32-2.3\lib\numfort\NB.o Microsoft: error: Unknown switch: '/compile_only ' error: Command "DF /f77rtl /fixed /nologo /MD /WX /iface=(cref,nomixed_str_len_arg) /names:lowercase /assume:underscore /Ox /fast /optimize:5 /unroll:0 /math_library:fast /threads -Ilib\numfort -c "/compile_only " lib\numfort\NB.F /object:build\temp.win32-2.3\lib\numfort\NB.o" failed with exit status 1 make: *** [build] Error 1 changing "compile_switch" in fcompiler.py from '/compile_only ' to '/compile_only' solves this problem, but now I get: DF:f77: lib\numfort\NB.F DF /f77rtl /fixed /nologo /MD /WX /iface=(cref,nomixed_str_len_arg) /names:lowercase /assume:undersc ore /Ox /fast /optimize:5 /unroll:0 /math_library:fast /threads -Ilib\numfort -c /compile_only lib\n umfort\NB.F /object:build\temp.win32-2.3\lib\numfort\NB.o Visual lib\numfort\NB.F f90: Severe: No such file or directory ... file is 'Visual' error: Command "DF /f77rtl /fixed /nologo /MD /WX /iface=(cref,nomixed_str_len_arg) /names:lowercase /assume:underscore /Ox /fast /optimize:5 /unroll:0 /math_library:fast /threads -Ilib\numfort -c /co mpile_only lib\numfort\NB.F /object:build\temp.win32-2.3\lib\numfort\NB.o" failed with exit status 1 make: *** [build] Error 1 I have no idea where the "Visual" is coming from. Is there anyone who can help me? Kind regards Berthold Höllmann -- Germanischer Lloyd AG CAE Development Vorsetzen 35 20459 Hamburg Phone: +49(0)40 36149-7374 Fax: +49(0)40 36149-7320 e-mail: hoel(a)gl-group.com Internet: http://www.gl-group.com This e-mail contains confidential information for the exclusive attention of the intended addressee. Any access of third parties to this e-mail is unauthorised. Any use of this e-mail by unintended recipients such as copying, distribution, disclosure etc. is prohibited and may be unlawful. When addressed to our clients the content of this e-mail is subject to the General Terms and Conditions of GL's Group of Companies applicable at the date of this e-mail. GL's Group of Companies does not warrant and/or guarantee that this message at the moment of receipt is authentic, correct and its communication free of errors, interruption etc.

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scipy distutils from CVS does not build code for fortran libraries
by Berthold Höllmann March 26, 2004

March 26, 2004

Hello, I tried to compile a project of ours under solaris5. I gave PYTHONPATH="/home/hoel/work/GLPy/lib:/home/hoel/work/GLPy/build/lib.solaris-2.8-sun4u-2.2:" python setup_Engmodel.py config_fc --fcompiler=sun build_src build_clib build_ext ... customize SunFCompiler customize SunFCompiler using build_clib ******************************************************************************** scipy_distutils.sunfcompiler.SunFCompiler archiver = ['ar', '-cr'] version_cmd = ['f90', '-V'] compiler_f77 = ['f90', '-f77', '-ftrap=%none', '-xcode=pic32'] linker_so = ['f90', '-Bdynamic', '-G'] compiler_fix = ['f90', '-fixed', '-xcode=pic32'] ranlib = ['ranlib'] compiler_f90 = ['f90', '-xcode=pic32'] version = None libraries = ['fsu', 'sunmath', 'mvec', 'f77compat'] library_dirs = [] object_switch = '-o ' compile_switch = '-c' include_dirs = [] ******************************************************************************** building 'engforcegen' library compling Fortran sources creating build.Engmodel/temp.solaris-2.8-sun4u-2.2 creating build.Engmodel/temp.solaris-2.8-sun4u-2.2/lib creating build.Engmodel/temp.solaris-2.8-sun4u-2.2/lib/engforcegen f90:f77: lib/engforcegen/engforcelib.f f90:f77: lib/engforcegen/totalforces.f f90:f77: lib/engforcegen/foucoefftable.f f90:f77: lib/engforcegen/esrheader.f f90:f77: lib/engforcegen/pphase.f f90:f77: lib/engforcegen/excnodes.f f90:f77: lib/engforcegen/fourier.f f90:f77: lib/engforcegen/cylphase.f f90:f77: lib/engforcegen/esrdata.f f90:f77: lib/engforcegen/normangle.f f90:f77: lib/engforcegen/cylforces.f ar: adding 11 object files to build.Engmodel/temp.solaris-2.8-sun4u-2.2/libengforcegen.a error: Command "ar -cr build.Engmodel/temp.solaris-2.8-sun4u-2.2/libengforcegen.a build.Engmodel/temp.solaris-2.8-sun4u-2.2/lib/engforcegen/engforcelib.o build.Engmodel/temp.solaris-2.8-sun4u-2.2/lib/engforcegen/cylforces.o build.Engmodel/temp.solaris-2.8-sun4u-2.2/lib/engforcegen/cylphase.o build.Engmodel/temp.solaris-2.8-sun4u-2.2/lib/engforcegen/esrdata.o build.Engmodel/temp.solaris-2.8-sun4u-2.2/lib/engforcegen/esrheader.o build.Engmodel/temp.solaris-2.8-sun4u-2.2/lib/engforcegen/excnodes.o build.Engmodel/temp.solaris-2.8-sun4u-2.2/lib/engforcegen/foucoefftable.o build.Engmodel/temp.solaris-2.8-sun4u-2.2/lib/engforcegen/fourier.o build.Engmodel/temp.solaris-2.8-sun4u-2.2/lib/engforcegen/pphase.o build.Engmodel/temp.solaris-2.8-sun4u-2.2/lib/engforcegen/totalforces.o build.Engmodel/temp.solaris-2.8-sun4u-2.2/lib/engforcegen/normangle.o" failed with exit status 1 all the ".o" files are missing. Just another problem with "exec_command"? Kind regards Berthold Höllmann -- Germanischer Lloyd AG CAE Development Vorsetzen 35 20459 Hamburg Phone: +49(0)40 36149-7374 Fax: +49(0)40 36149-7320 e-mail: hoel(a)gl-group.com Internet: http://www.gl-group.com This e-mail contains confidential information for the exclusive attention of the intended addressee. Any access of third parties to this e-mail is unauthorised. Any use of this e-mail by unintended recipients such as copying, distribution, disclosure etc. is prohibited and may be unlawful. When addressed to our clients the content of this e-mail is subject to the General Terms and Conditions of GL's Group of Companies applicable at the date of this e-mail. GL's Group of Companies does not warrant and/or guarantee that this message at the moment of receipt is authentic, correct and its communication free of errors, interruption etc.

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Log problem in exec_command.py
by Berthold Höllmann March 26, 2004

March 26, 2004

Hello, In an attempt to debug my Solaris compile problem I added from scipy_distutils.log import set_verbosity set_verbosity(2) to my setup.py file. Now I get ... File "/usr/local/gltools/python/Python-2.2.1/sol2/lib/python2.2/site-packages/scipy_distutils/exec_command.py", line 186, in exec_command ','.join(['%s=%r'%kv for kv in env.items()]))) File "<string>", line 23, in debug File "<string>", line 16, in _log TypeError: not enough arguments for format string The problem is one of the arguments to the sun FORTRAN compiler. log gets exec_command(['f90', '-f77', '-ftrap=%none', '-xcode=pic32', '-c', 'lib/engforcegen/engforcelib.f', '-o', 'build.Engmodel/temp.solaris-2.8-sun4u-2.2/lib/engforcegen/engforcelib.o'],) The problem seems to be in the '-ftrap=%none'. log() does string replacement. My solution is to change lines 186/7 to log.debug(('exec_command(%r,%s)' % (command,\ ','.join(['%s=%r'%kv for kv in env.items()]))).replace("%", "%%")) and lines 386/7 to log.debug(('Running %s(%s,%r,%r,os.environ)' \ % (spawn_command.__name__,os.P_WAIT,argv[0],argv)).replace("%", "%%")) Kind regards Berthold Höllmann -- Germanischer Lloyd AG CAE Development Vorsetzen 35 20459 Hamburg Phone: +49(0)40 36149-7374 Fax: +49(0)40 36149-7320 e-mail: hoel(a)gl-group.com Internet: http://www.gl-group.com This e-mail contains confidential information for the exclusive attention of the intended addressee. Any access of third parties to this e-mail is unauthorised. Any use of this e-mail by unintended recipients such as copying, distribution, disclosure etc. is prohibited and may be unlawful. When addressed to our clients the content of this e-mail is subject to the General Terms and Conditions of GL's Group of Companies applicable at the date of this e-mail. GL's Group of Companies does not warrant and/or guarantee that this message at the moment of receipt is authentic, correct and its communication free of errors, interruption etc.

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Further extensions for "fcompiler.py"?
by Berthold Höllmann March 23, 2004

March 23, 2004

Hello, Some of my Fortran source files for an extension module library require pre processing. Ifc for Linux uses fpp for files with the extension ".F" or ".F90" instead of ".f" and ".f90". Therefore I would like to find the list "src_extensions" extended by these extensions. Kind regards Berthold Höllmann -- Germanischer Lloyd AG CAE Development Vorsetzen 35 20459 Hamburg Phone: +49(0)40 36149-7374 Fax: +49(0)40 36149-7320 e-mail: hoel(a)gl-group.com Internet: http://www.gl-group.com This e-mail contains confidential information for the exclusive attention of the intended addressee. Any access of third parties to this e-mail is unauthorised. Any use of this e-mail by unintended recipients such as copying, distribution, disclosure etc. is prohibited and may be unlawful. When addressed to our clients the content of this e-mail is subject to the General Terms and Conditions of GL's Group of Companies applicable at the date of this e-mail. GL's Group of Companies does not warrant and/or guarantee that this message at the moment of receipt is authentic, correct and its communication free of errors, interruption etc.

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bug in scipy distutils / Scipy_core-0.2.2_alpha_104.1640
by Berthold Höllmann March 22, 2004

March 22, 2004

Hello, I installed Scipy_core-0.2.2_alpha_104.1640. Now trying to build a swig package I get: File "/usr/local/gltools/python/Python-2.3/linux/lib/python2.3/site-packages/scipy_distutils/command/build_src.py", line 311, in swig_sources assert name==ext_name[1:],'mismatch of extension names: '\ AssertionError: mismatch of extension names: lib/Metis/metis.i provides 'Metis_Wrapper' but expected 'etis_Wrapper' on the lines: // File : metis.i %module Metis_Wrapper changing line 311 of build_src.py to assert name==ext_name,'mismatch of extension names: '\ works for me Kind regards Berthold Höllmann -- Germanischer Lloyd AG CAE Development Vorsetzen 35 20459 Hamburg Phone: +49(0)40 36149-7374 Fax: +49(0)40 36149-7320 e-mail: hoel(a)gl-group.com Internet: http://www.gl-group.com This e-mail contains confidential information for the exclusive attention of the intended addressee. Any access of third parties to this e-mail is unauthorised. Any use of this e-mail by unintended recipients such as copying, distribution, disclosure etc. is prohibited and may be unlawful. When addressed to our clients the content of this e-mail is subject to the General Terms and Conditions of GL's Group of Companies applicable at the date of this e-mail. GL's Group of Companies does not warrant and/or guarantee that this message at the moment of receipt is authentic, correct and its communication free of errors, interruption etc.

1 0

scipy.xplt keywords / ghelp
by Arnd Baecker March 19, 2004

March 19, 2004

Hi, this is a follow-up to the discussion on ghelp and the keywors for the xplt commands. - In order to have the keyword help available in a doc-string I have added these for the course at the end of info_xplt.py If you want to include this in the general distribution I can send you the corresponding text (which was taken from http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/python/pygist_html/node57… and formatted properly. - Side remark: ghelp has not been added back into scipy.xplt. Personally I think this good, because there are already to many different help commands. - the help to scipy.xplt starts with """All Gist functions are also available as xplt.<command> xplt.ghelp('plsys')""" I think the "xplt.ghelp('plsys')" is left over and should be removed. Best, Arnd

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help and delayed import (once more)
by Arnd Baecker March 19, 2004

March 19, 2004

Hi, I hope I am not annoying you with this, but there is one open issue with the delayed importer: Starting in a fresh python session >>> help("scipy.linalg") gives Help on instance of _ModuleLoader in scipy: scipy.linalg = <module 'scipy.linalg' from '/opt/python/lib/pyt...e-packages/scipy/linalg/__init__.pyc' [imported]> Whereas >>> import scipy >>> help("scipy.linalg") is okay. Though in most cases the user will already have done an import of scipy or one of its modules, the above behaviour might be confusing. (Is it also problematic for doc-string extracting tools ?) There is one more thing I would like to say: _Many_ thanks to you, Pearu and Travis, for all your help and fixes! Best Arnd

1 0

system_info.py, blas_opt_info broken ?
by Arnd Baecker March 17, 2004

March 17, 2004

Hi, I just downloaded the CVS version and doing cd scipy_core/scipy_distutils python system_info.py gives blas_opt_info: Traceback (most recent call last): File "system_info.py", line 1263, in ? show_all() File "system_info.py", line 1260, in show_all r = c.get_info() File "/tmp/baecker/CompileDir/scipy/scipy_core/scipy_distutils/system_info.py", line 283, in get_info self.calc_info() File "/tmp/baecker/CompileDir/scipy/scipy_core/scipy_distutils/system_info.py", line 934, in calc_info atlas_version = get_atlas_version(**version_info) File "/tmp/baecker/CompileDir/scipy/scipy_core/scipy_distutils/system_info.py", line 775, in get_atlas_version from core import Extension, setup File "/tmp/baecker/CompileDir/scipy/scipy_core/scipy_distutils/core.py", line 5, in ? from scipy_distutils.dist import Distribution ImportError: No module named scipy_distutils.dist The same happens for lapack_opt_info. One more: can one safely ignore ====================================================================== FAIL: check_real (scipy_base.type_check.test_type_check.test_imag) ---------------------------------------------------------------------- Traceback (most recent call last): File "/opt/python/lib/python2.3/site-packages/scipy_base/tests/test_type_check.py", line 31, in check_real assert_array_equal(0,imag(y)) File "/opt/python/lib/python2.3/site-packages/scipy_test/testing.py", line 641, in assert_array_equal assert len(shape(x))==len(shape(y)) and \ AssertionError: Arrays are not equal (shapes (), (10,) mismatch): ? Many thanks, Arnd

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problem building scipy on win32
by Alexandre Gillet March 17, 2004

March 17, 2004

> > >n Wed, 10 Mar 2004, Alexandre Gillet wrote: > >>/ Hi, >/>/ I am trying to build SciPy-0.2.0_alpha_200.4161. >/>/ I did follow the note from Pearu Peterson >/>/ (http://cens.ioc.ee/~pearu/scipy/BUILD_WIN32.html <http://cens.ioc.ee/%7Epearu/scipy/BUILD_WIN32.html>) >/>/ I am not using the cvs version, but I did use the cvs version of >/>/ scipy_core for installing it. >/>/ Then I cd in SciPy-0.2.0_alpha_200.4161 and type msys.py python setup.py >/>/ build. >/>/ >/>/ I am now getting the following error: >/>/ >/>/ /building 'scipy_base.fastumath' extension >/>/ Traceback (most recent call last): >/>/ File "setup.py", line 111, in ? >/>/ setup_package() >/>/ File "setup.py", line 101, in setup_package >/>/ url = "http://www.scipy.org", <http://www.scipy.org%22,> >/>/ File "scipy_core\scipy_distutils\core.py", line 42, in setup >/>/ return old_setup(**new_attr) >/>/ File "c:\Python23\lib\distutils\core.py", line 149, in setup >/>/ dist.run_commands() >/>/ File "c:\Python23\lib\distutils\dist.py", line 907, in run_commands >/>/ self.run_command(cmd) >/>/ File "c:\Python23\lib\distutils\dist.py", line 927, in run_command >/>/ cmd_obj.run() >/>/ File "c:\Python23\lib\distutils\command\build.py", line 107, in run >/>/ self.run_command(cmd_name) >/>/ File "c:\Python23\lib\distutils\cmd.py", line 333, in run_command >/>/ self.distribution.run_command(command) >/>/ File "c:\Python23\lib\distutils\dist.py", line 927, in run_command >/>/ cmd_obj.run() >/>/ File "c:\Python23\lib\distutils\command\build_ext.py", line 269, in run >/>/ self.build_extensions() >/>/ File "c:\Python23\lib\distutils\command\build_ext.py", line 395, in >/>/ build_extensions >/>/ self.build_extension(ext) >/>/ File "scipy_core\scipy_distutils\command\build_ext.py", line 116, in >/>/ build_extension >/>/ res = old_build_ext.build_extension(self,ext) >/>/ File "c:\Python23\lib\distutils\command\build_ext.py", line 492, in >/>/ build_extension >/>/ target_lang=language) >/>/ File "c:\Python23\lib\distutils\ccompiler.py", line 843, in >/>/ link_shared_object >/>/ extra_preargs, extra_postargs, build_temp, target_lang) >/>/ TypeError: link() takes exactly 13 arguments (14 given) >/ >That error is due to the bug in Python 2.3 distutils. scipy_distutils >implements a workaround to this issue but the workaround is effective only >when setup scripts use scipy_distutils, the setup scripts in >SciPy-0.2.0_alpha_200.4161 apparently do not do that. > >>/ Any Idea. >/>/ I need to use that version of Scipy as the GA module seems not to work >/>/ on later version, that version was installed on Linux and works fine for us. >/ >It might be easier to fix whatever issues you have with the recent GA >module rather than trying to get SciPy-0.2.0_alpha_200.4161 working. What >problems exactly do you experience with the GA module? > >Pearu > Thanks for the answer, I am only trying to install Scipy and I am not using the GA module,I will ask the person in my lab who used the GA to provide me with the exact problem. And I will get back to you as soon as I have the information. Alex -- o Alexandre Gillet email: gillet(a)scripps.edu / The Scripps Research Institute, o Dept. Molecular Biology, MB-5, \ 10550 North Torrey Pines Road, o La Jolla, CA 92037-1000, USA. / tel: (858) 784-2053 o fax: (858) 784-2860

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