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From: Strong, S. B. <Sha...@jh...> - 2012-07-17 14:39:02
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Peter, Thanks so much for your fast reply. I actually went ahead and downloaded the 64-bit version of Python prior to your reply and everything built this time. Now I can test drive ccplot! Thanks again, Shay On 7/17/12 10:22 AM, "Peter Kuma" <pet...@us...> wrote: >On 07/17/2012 03:45 PM, Strong, Shadrian B. wrote: >> I am having a lot of Mac installation problems. I understand you >> recommend a linux machine, but I don't have one to work from. Are there >> any suggestions you might have with building on a Mac? I continue to get >> fatal errors when trying to build (see below) >> >> *bash-3.2$* python setup.py build >> >> running build >> running build_ext >> building 'cctk' extension >> gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv >> -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch >> x86_64 -pipe >> >>-I/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/pyt >>hon/numpy/core/include >> >>-I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python >>2.6 >> -c cctkmodule.c -o build/temp.macosx-10.6-universal-2.6/cctkmodule.o >> /usr/libexec/gcc/powerpc-apple-darwin10/4.2.1/as: assembler >> (/usr/bin/../libexec/gcc/darwin/ppc/as or >> /usr/bin/../local/libexec/gcc/darwin/ppc/as) for architecture ppc not >> installed >> Installed assemblers are: >> /usr/bin/../libexec/gcc/darwin/x86_64/as for architecture x86_64 >> /usr/bin/../libexec/gcc/darwin/i386/as for architecture i386 >> cctkmodule.c:467: fatal error: error writing to -: Broken pipe >> compilation terminated. >> lipo: can't open input file: >> /var/folders/5n/5nmXq6bHFwGnb61yF+TAkVwwcxU/-Tmp-//ccHNmoeO.out (No such >> file or directory) >> error: command 'gcc-4.2' failed with exit status 1 >> >> Thanks, >> Shay Strong >> >> *Dr. Shadrian B. Strong* >> The Johns Hopkins University Applied Physics Laboratory >> Space Department >> EO/IR Sensors and Atmospheric Modeling >> >> Office: (443)778-9998 >> Email: Sha...@jh... > >Dear Shay, > >I don't own a mac system, so I can't really test myself, but is seems to >me that this report relates to the same problem: > >http://stackoverflow.com/questions/6324912/issue-installing-python-module- >on-osx-10-6-and-with-gcc-4-0-and-4-2 > >Allegedly, it is an incompatibility between the version of Xcode and >Python. On the python release page for 2.7.3 there is a note: > >`Also, on Mac OS X 10.6, if you need to build C extension modules with >the 32-bit-only Python installed, you will need Apple Xcode 3, not 4. >The 64-bit/32-bit Python can use either Xcode 3 or Xcode 4.' > >Therefore, I'd suggest you install the 64-bit version of Python if you >haven't already. If you have, the problem might be somewhere else. >Please do let me know in that case. > >Also note that the version of python ccplot is compatible with is >restricted by pynio. Unless you are willing the compile the library from >source (rather complicated), the binaries are available only for python >up to 2.7.1 on the EOS, or 2.6.5 on ccplot.org, even though the version >for 2.7.1 might happen to work with the latest 2.7.3. > >Good luck! > >Regards, > >Peter |
|
From: Peter K. <pet...@us...> - 2012-07-17 14:22:44
|
On 07/17/2012 03:45 PM, Strong, Shadrian B. wrote: > I am having a lot of Mac installation problems. I understand you > recommend a linux machine, but I don't have one to work from. Are there > any suggestions you might have with building on a Mac? I continue to get > fatal errors when trying to build (see below) > > *bash-3.2$* python setup.py build > > running build > running build_ext > building 'cctk' extension > gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv > -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch > x86_64 -pipe > -I/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpy/core/include > -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 > -c cctkmodule.c -o build/temp.macosx-10.6-universal-2.6/cctkmodule.o > /usr/libexec/gcc/powerpc-apple-darwin10/4.2.1/as: assembler > (/usr/bin/../libexec/gcc/darwin/ppc/as or > /usr/bin/../local/libexec/gcc/darwin/ppc/as) for architecture ppc not > installed > Installed assemblers are: > /usr/bin/../libexec/gcc/darwin/x86_64/as for architecture x86_64 > /usr/bin/../libexec/gcc/darwin/i386/as for architecture i386 > cctkmodule.c:467: fatal error: error writing to -: Broken pipe > compilation terminated. > lipo: can't open input file: > /var/folders/5n/5nmXq6bHFwGnb61yF+TAkVwwcxU/-Tmp-//ccHNmoeO.out (No such > file or directory) > error: command 'gcc-4.2' failed with exit status 1 > > Thanks, > Shay Strong > > *Dr. Shadrian B. Strong* > The Johns Hopkins University Applied Physics Laboratory > Space Department > EO/IR Sensors and Atmospheric Modeling > > Office: (443)778-9998 > Email: Sha...@jh... Dear Shay, I don't own a mac system, so I can't really test myself, but is seems to me that this report relates to the same problem: http://stackoverflow.com/questions/6324912/issue-installing-python-module-on-osx-10-6-and-with-gcc-4-0-and-4-2 Allegedly, it is an incompatibility between the version of Xcode and Python. On the python release page for 2.7.3 there is a note: `Also, on Mac OS X 10.6, if you need to build C extension modules with the 32-bit-only Python installed, you will need Apple Xcode 3, not 4. The 64-bit/32-bit Python can use either Xcode 3 or Xcode 4.' Therefore, I'd suggest you install the 64-bit version of Python if you haven't already. If you have, the problem might be somewhere else. Please do let me know in that case. Also note that the version of python ccplot is compatible with is restricted by pynio. Unless you are willing the compile the library from source (rather complicated), the binaries are available only for python up to 2.7.1 on the EOS, or 2.6.5 on ccplot.org, even though the version for 2.7.1 might happen to work with the latest 2.7.3. Good luck! Regards, Peter |
|
From: Strong, S. B. <Sha...@jh...> - 2012-07-17 13:46:13
|
I am having a lot of Mac installation problems. I understand you recommend a linux machine, but I don't have one to work from. Are there any suggestions you might have with building on a Mac? I continue to get fatal errors when trying to build (see below) bash-3.2$ python setup.py build running build running build_ext building 'cctk' extension gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc -arch x86_64 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpy/core/include -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c cctkmodule.c -o build/temp.macosx-10.6-universal-2.6/cctkmodule.o /usr/libexec/gcc/powerpc-apple-darwin10/4.2.1/as: assembler (/usr/bin/../libexec/gcc/darwin/ppc/as or /usr/bin/../local/libexec/gcc/darwin/ppc/as) for architecture ppc not installed Installed assemblers are: /usr/bin/../libexec/gcc/darwin/x86_64/as for architecture x86_64 /usr/bin/../libexec/gcc/darwin/i386/as for architecture i386 cctkmodule.c:467: fatal error: error writing to -: Broken pipe compilation terminated. lipo: can't open input file: /var/folders/5n/5nmXq6bHFwGnb61yF+TAkVwwcxU/-Tmp-//ccHNmoeO.out (No such file or directory) error: command 'gcc-4.2' failed with exit status 1 Thanks, Shay Strong Dr. Shadrian B. Strong The Johns Hopkins University Applied Physics Laboratory Space Department EO/IR Sensors and Atmospheric Modeling Office: (443)778-9998 Email: Sha...@jh... |
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From: Devon <de...@aw...> - 2011-03-23 05:21:51
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<p>Bonjour,</p> <p>Je gère de nombreux sites opérant sur plusieurs marchés. Je serais heureux d'échanger avec votre site ccplot.org un ou plusieurs liens de qualité.</br> Le but étant d'optimiser les positions de nos sites respectifs dans les moteurs de recherche et donc d'augmenter le trafic. C'est gratuit et ca peut rapporter!</br> Contactez-moi pour explorer un éventuel partenariat.</p> <p>Cordialement,</br> Devon</p> |
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From: Peter K. <pet...@wa...> - 2010-08-31 13:11:39
|
Serge-Alexandre Demers Giroux wrote: > Hi everybody, just finish installing ccplot. I had some problems with > the installation of libfreetype6-dev and libcairo2-dev (dependant of > libfreetype6-dev). I'm on Ubuntu 10.04, and I had to update the apt-get > command with: > > $ sudo apt-get update > > After that I was able to install libfreetype6-dev and libcairo2-dev. > > I had some problems with the installation of PyNio... It wasn't working > with the precompiled binaries and the command line you give on the > website (even if I'm logged as super user ). > > When I was sure that I had the right PyNio precompiled binaries package, > I unzipped/untarred it and copied everything that was in the directory > /site-packages in /usr/lib/python2.6/dist-packages. And this is it! > > Thank you! > > Serge Hi Serge, Thank you for the information. I have updated the installation instructions accordingly. Peter |
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From: Serge-Alexandre D. G. <ser...@ho...> - 2010-08-24 17:56:12
|
Hi everybody, just finish installing ccplot. I had some problems with the installation of libfreetype6-dev and libcairo2-dev (dependant of libfreetype6-dev). I'm on Ubuntu 10.04, and I had to update the apt-get command with: $ sudo apt-get update After that I was able to install libfreetype6-dev and libcairo2-dev. I had some problems with the installation of PyNio... It wasn't working with the precompiled binaries and the command line you give on the website (even if I'm logged as super user ). When I was sure that I had the right PyNio precompiled binaries package, I unzipped/untarred it and copied everything that was in the directory /site-packages in /usr/lib/python2.6/dist-packages. And this is it! Thank you! Serge |
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From: Peter K. <pet...@wa...> - 2010-08-21 09:30:01
|
Serge-Alexandre Demers Giroux wrote: > Hi everybody, I tried installing PyNIO with the binary version and I > couldn't manage to get it done properly (all the previous steps (1-6) > were done)... You have the log file from an unsuccessfull try attached > to the mail. > > I'm on Ubuntu 10.04 LTS. > > Thanks a lot for the help!!! > > Serge Hi Serge, Sorry, this was a mistake in the installation instructions. This command should be run as root. On Ubuntu: sudo tar -C /usr/local -xzf PyNIO-1.3.0b5.linux-x86_64-py264-gcc432.tar.gz I guess this was the problem. Regards, Peter |
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From: Serge-Alexandre D. G. <ser...@ho...> - 2010-08-20 18:24:42
|
demers@demers:~/Downloads$ tar -C /usr/local -xzf PyNIO-1.3.0b5.linux-x86_64-py264-gcc432.tar.gz tar: ./lib/python2.6/site-packages/PyNIO/setup.pyc: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/xarray.pyc: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/pynio_version.py: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/coordsel.py: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/nio.so: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/xarray.py: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/setup.py: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/__init__.pyc: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/6/6.0.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/6: Cannot utime: Operation not permitted tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/1/1.0.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/1/1.2.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/1/1.4.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/1/1.3.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/1/1.1.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/1: Cannot utime: Operation not permitted tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/3/3.10.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/3/3.7.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/3/3.21.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/3/3.0.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/3/3.8.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/3/3.15.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/3/3.20.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/3/3.5.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/3/3.9.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/3/3.2.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/3/3.4.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/3/3.6.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/3/3.11.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/3/3.3.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/3/3.1.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/3: Cannot utime: Operation not permitted tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/4/4.9.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/4/4.2.0.18.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/4/4.205.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/4/4.213.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/4/4.1.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/4/4.2.10.0.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/4/4.8.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/4/4.2.10.3.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/4/4.2.0.4.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/4/4.2.10.1.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/4/4.2.1.1.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/4/4.204.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/4/4.2.0.16.table: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables/tigge/4/4.222.table: Cannot open: File exists 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./lib/python2.6/site-packages/PyNIO/ncarg/grib2_codetables: Cannot utime: Operation not permitted tar: ./lib/python2.6/site-packages/PyNIO/ncarg: Cannot utime: Operation not permitted tar: ./lib/python2.6/site-packages/PyNIO/_xarray.py: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/coordsel.pyc: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/Nio.pyc: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/Nio.py: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/_xarray.pyc: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/__init__.py: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO/pynio_version.pyc: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO: Cannot utime: Operation not permitted tar: ./lib/python2.6/site-packages/Nio.pth: Cannot open: File exists tar: ./lib/python2.6/site-packages/PyNIO-1.3.0b5-py2.6.egg-info: Cannot open: File exists tar: ./lib/python2.6/site-packages: Cannot utime: Operation not permitted tar: ./lib/python2.6: Cannot utime: Operation not permitted tar: ./lib: Cannot utime: Operation not permitted tar: .: Cannot utime: Operation not permitted tar: Exiting with failure status due to previous errors |
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From: Peter K. <pet...@wa...> - 2010-08-18 10:08:17
|
Hi Erik, Erik Bryer wrote: > Numpy had installed arrayobject.h here: > /usr/local/lib/python2.6/site-packages/numpy/core/include/numpy/. > However, cctkmodule.c looks for arrayobject.h with: > #include <numpy/arrayobject.h> > > I noticed PyNIO was detected ok, and I thought maybe because it had a > Nio.pth. So, I tried adding a .pth to add numpy to python's path. Python > reported the new path (import sys;sys.path), but "build" still did not > find arrayobject.h. I just changed the include statement to > #include > </usr/local/lib/python2.6/site-packages/numpy/core/include/numpy/arrayobject.h> > > and ccplot built ok. It seems to be running ok too. On CentOS numpy does not install its header files in the standard locations such as /usr/include or /usr/local/include as on e.g. Debian. > Out of curiosity: We have ccplot installed on our server; we noticed the > client's X-server needs to be running in order to run ccplot on the > server, and we wondered why this is. This is because matplotlib imports some Gtk-specific modules by default, which expect an X server to be available. > Thanks for the help, > > Erik I have fixed both of these issues in ccplot 1.43. Thank you reporting them. Peter |
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From: Peter K. <pet...@wa...> - 2010-08-12 22:57:07
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Erik Bryer wrote:
> Hi Peter,
>
> I cleared the cruft from all the software, and I compiled Python 2.6.2.
> I then re-extracted and recompiled the other software: numpy,
> matplotlib, and basemap. Things seemed to go well enough and any tests
> ran ok. However, when I installed PyNIO and typed '#
> /usr/local/bin/python -c "import Nio;"' the error was essentially
> identical. To debug, I typed '# /usr/local/bin/python -v -c "import
> Nio;"'. Here is the output just before the text of the error output I
> emailed you last time:
> [...]
> dlopen("/usr/local/lib/python2.6/lib-dynload/datetime.so", 2);
> import datetime # dynamically loaded from
> /usr/local/lib/python2.6/lib-dynload/datetime.so
> # /usr/local/lib/python2.6/site-packages/PyNIO/_xarray.pyc matches
> /usr/local/lib/python2.6/site-packages/PyNIO/_xarray.py
> import _xarray # precompiled from
> /usr/local/lib/python2.6/site-packages/PyNIO/_xarray.pyc
> Traceback (most recent call last):
> File "<string>", line 1, in <module>
> File "/usr/local/lib/python2.6/site-packages/PyNIO/Nio.py", line 145,
> in <module>
> _is_new_ma = get_integer_version(np.__version__) > 10004
> [...]
>
> I'm not sure what this tells us except it seems to be loading, then
> crashes.
>
> This is a non-sequiter, but could this be numpy related? I only ask
> because I saw during compile on numpy (using --fcompiler=gnu95) this
> remark:
> [...]
> FOUND:
> libraries = ['blas']
> library_dirs = ['/usr/lib64']
> language = f77
> [...]
> Yet the libraries seem dependent on gfortran, not f77 (an alias to g77).
> # ldd libblas.so.3.0.3
> libm.so.6 => /lib64/libm.so.6 (0x00002b12ae958000)
> libgfortran.so.1 => /usr/lib64/libgfortran.so.1
> (0x00002b12aebdb000)
> libc.so.6 => /lib64/libc.so.6 (0x00002b12aee72000)
> /lib64/ld-linux-x86-64.so.2 (0x0000003a3f800000)
>
> I've verified all my blas and lapack shared object files are dependent
> on libgfortran.
>
> By the way, I had installed lapack-devel and blas-devel rpms before
> recompiling numpy. (I'm not using Atlas. From what I read at the Atlas
> site, it provides a speedier blas/lapack.) Another oddity when compiling
> numpy is:
> [...]
> customize GnuFCompiler
> gnu: no Fortran 90 compiler found
> gnu: no Fortran 90 compiler found
> customize GnuFCompiler using config
> C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3
> -Wall -Wstrict-prototypes -fPIC
> [...]
> There are other warnings of various kinds while building numpy. But
> again, the test in the README.txt runs with 4 failures of 2962 tests and
> $?=0.
>
> Erik
Erik,
This is a bug in PyNIO. The error happens because PyNIO expects numpy
version to be in the format x.x.x, where x are numbers. I presume you
are using the 1.5.0b1 version of numpy.
Attached is a patch for Nio.py, which can be applied by:
$ cd /usr/local/lib/python2.6/site-packages/PyNIO/
$ patch < /path/to/pynio.diff
(replacing /path/to/pynio.diff with the actual path)
Peter
/If that does not help or if you have any more questions I will not be
able to respond until Tuesday, because I will be on holiday./
|
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From: Erik B. <eb...@fs...> - 2010-08-12 18:15:21
|
On Thu, 12 Aug 2010, Peter Kuma wrote:
> Hi Erik,
> The PyNIO binary should match exactly with the version of Python
> installed. The easiest way would be to install Python 2.6.2. Precompiled
> version of PyNIO for Python 2.7 is not yet available, and compiling it
> with all the third-party libraries it needs would take a long time.
> Regards,
> Peter Kuma
Hi Peter,
I cleared the cruft from all the software, and I compiled Python 2.6.2. I
then re-extracted and recompiled the other software: numpy, matplotlib,
and basemap. Things seemed to go well enough and any tests ran ok.
However, when I installed PyNIO and typed '# /usr/local/bin/python -c
"import Nio;"' the error was essentially identical. To debug, I typed '#
/usr/local/bin/python -v -c "import Nio;"'. Here is the output just
before the text of the error output I emailed you last time:
[...]
dlopen("/usr/local/lib/python2.6/lib-dynload/datetime.so", 2);
import datetime # dynamically loaded from
/usr/local/lib/python2.6/lib-dynload/datetime.so
# /usr/local/lib/python2.6/site-packages/PyNIO/_xarray.pyc matches
/usr/local/lib/python2.6/site-packages/PyNIO/_xarray.py
import _xarray # precompiled from
/usr/local/lib/python2.6/site-packages/PyNIO/_xarray.pyc
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/local/lib/python2.6/site-packages/PyNIO/Nio.py", line 145, in
<module>
_is_new_ma = get_integer_version(np.__version__) > 10004
[...]
I'm not sure what this tells us except it seems to be loading, then
crashes.
This is a non-sequiter, but could this be numpy related? I only ask
because I saw during compile on numpy (using --fcompiler=gnu95) this
remark:
[...]
FOUND:
libraries = ['blas']
library_dirs = ['/usr/lib64']
language = f77
[...]
Yet the libraries seem dependent on gfortran, not f77 (an alias to g77).
# ldd libblas.so.3.0.3
libm.so.6 => /lib64/libm.so.6 (0x00002b12ae958000)
libgfortran.so.1 => /usr/lib64/libgfortran.so.1
(0x00002b12aebdb000)
libc.so.6 => /lib64/libc.so.6 (0x00002b12aee72000)
/lib64/ld-linux-x86-64.so.2 (0x0000003a3f800000)
I've verified all my blas and lapack shared object files are dependent on
libgfortran.
By the way, I had installed lapack-devel and blas-devel rpms before
recompiling numpy. (I'm not using Atlas. From what I read at the Atlas
site, it provides a speedier blas/lapack.) Another oddity when
compiling numpy is:
[...]
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler using config
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3
-Wall -Wstrict-prototypes -fPIC
[...]
There are other warnings of various kinds while building numpy. But again,
the test in the README.txt runs with 4 failures of 2962 tests and
$?=0.
Erik
|
|
From: Peter K. <pet...@wa...> - 2010-08-12 09:01:59
|
Erik Bryer wrote: > Hi, > > I followed the install directions for ccplot with success up to testing > the install of PyNIO. My only deviation from the instructions was to > (accidentally) use a slightly newer version of Python, 2.7, rather than > the 2.6.2 that matches my gcc version.My setup: > > Quad-core Intel Xeon CPU E5345 @ 2.33GHz (only standard > packages from standard repositories except "sshfs" from dag). > > Python 2.4, the standard CentOS 5 version is in /usr/bin. Python 2.7 is > in /usr/local/bin. By default, PATH=/usr/local/bin:/usr/bin > > RPM installed software includes gcc version 4.1.2, libpng and freetype > (including their devel files). > > Installed in /usr/local are: Python 2.7, numpy (--fcompiler=gnu95 to > match lapack/blas), matplotlib, basemap, and GEOS. I was able to test > numpy with this command: > /usr/local/bin/python -c 'import numpy; numpy.test()' > Running unit tests for numpy > NumPy version 1.5.0b1 > NumPy is installed in /usr/local/lib/python2.7/site-packages/numpy > Python version 2.7 (r27:82500, Aug 11 2010, 13:21:14) [GCC 4.1.2 > 20080704 (Red Hat 4.1.2-48)] > nose version 0.11.4 > .......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K................................................................................................................................................................................................................................K............................................................................................K......................K............................................................................................................................................................................... .. > > ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ . > > ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................Warning: > divide by zero encountered in log > ....................................................................................................................................................................................................................................... > > ---------------------------------------------------------------------- > Ran 2962 tests in 10.621s > > OK (KNOWNFAIL=4) > [But the exit status of the test was zero.] > > With those prerequisites installed, I untarred > PyNIO-1.3.0b5.linux-x86_64-redhat-py262-gcc412.tar.gz to /usr/local, > which made a /usr/local/lib/python2.6/site-packages directory, so I > copied the files over to the /usr/local/lib/python2.7/site-packages/. I > next ran the test listed in ccplot's "INSTALL" file. It failed: > > /usr/local/bin/python -c "import Nio; print Nio.__version__" > Traceback (most recent call last): > File "<string>", line 1, in <module> > File "/usr/local/lib/python2.7/site-packages/PyNIO/Nio.py", line 145, > in <module> > _is_new_ma = get_integer_version(np.__version__) > 10004 > File "/usr/local/lib/python2.7/site-packages/PyNIO/Nio.py", line 138, > in get_integer_version > v = int(d[0]) * 10000 + int(d[1]) * 100 + int(d[2]) > ValueError: invalid literal for int() with base 10: '0b1' > > I tried changing the name of > /usr/local/lib/python2.7/site-packages/PyNIO-1.3.0b5-py2.6.egg-info to > PyNIO-1.3.0b5-py2.7.egg-info. > > I haven't been able to get it to budge further. I wonder if I ought to > pull 2.6.2 Python from the CVS tree. Do you have a suggestion? > > Regards, > > Erik Bryer > Krishnamurti Numerical Weather Prediction Lab > EOAS/Meteorology > Florida State University > Tallahassee, FL 32306-4520 > 850-644-9277 > eb...@fs... Hi Erik, The PyNIO binary should match exactly with the version of Python installed. The easiest way would be to install Python 2.6.2. Precompiled version of PyNIO for Python 2.7 is not yet available, and compiling it with all the third-party libraries it needs would take a long time. Regards, Peter Kuma |
|
From: Erik B. <eb...@fs...> - 2010-08-11 22:23:21
|
Hi,
I followed the install directions for ccplot with success up to testing
the install of PyNIO. My only deviation from the instructions was to
(accidentally) use a slightly newer version of Python, 2.7, rather than
the 2.6.2 that matches my gcc version. My setup:
Quad-core Intel Xeon CPU E5345 @ 2.33GHz CentOS 5 (only standard packages
from standard repositories except "sshfs" from dag).
Python 2.4, the standard CentOS 5 version is in /usr/bin. Python 2.7 is in
/usr/local/bin. By default, PATH=/usr/local/bin:/usr/bin
RPM installed software includes gcc version 4.1.2, libpng and
freetype (including their devel files).
Installed in /usr/local are: Python 2.7, numpy (--fcompiler=gnu95 to match
lapack/blas), matplotlib, basemap, and GEOS. I was able to test numpy with
this command:
/usr/local/bin/python -c 'import numpy; numpy.test()'
Running unit tests for numpy
NumPy version 1.5.0b1
NumPy is installed in /usr/local/lib/python2.7/site-packages/numpy
Python version 2.7 (r27:82500, Aug 11 2010, 13:21:14) [GCC 4.1.2 20080704
(Red Hat 4.1.2-48)]
nose version 0.11.4
.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K................................................................................................................................................................................................................................K............................................................................................K......................K.................................................................................................................................................................................
.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................Warning:
divide by zero encountered in log
.......................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 2962 tests in 10.621s
OK (KNOWNFAIL=4)
[But the exit status of the test was zero.]
With those prerequisites installed, I untarred
PyNIO-1.3.0b5.linux-x86_64-redhat-py262-gcc412.tar.gz to /usr/local, which
made a /usr/local/lib/python2.6/site-packages directory, so I copied the
files over to the /usr/local/lib/python2.7/site-packages/. I next ran the
test listed in ccplot's "INSTALL" file. It failed:
/usr/local/bin/python -c "import Nio; print Nio.__version__"
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/local/lib/python2.7/site-packages/PyNIO/Nio.py", line 145, in
<module>
_is_new_ma = get_integer_version(np.__version__) > 10004
File "/usr/local/lib/python2.7/site-packages/PyNIO/Nio.py", line 138, in
get_integer_version
v = int(d[0]) * 10000 + int(d[1]) * 100 + int(d[2])
ValueError: invalid literal for int() with base 10: '0b1'
I tried changing the name of
/usr/local/lib/python2.7/site-packages/PyNIO-1.3.0b5-py2.6.egg-info to
PyNIO-1.3.0b5-py2.7.egg-info.
I haven't been able to get it to budge further. I wonder if I ought to
pull 2.6.2 Python from the CVS tree. Do you have a suggestion?
Regards,
Erik Bryer
Krishnamurti Numerical Weather Prediction Lab
EOAS/Meteorology
Florida State University
Tallahassee, FL 32306-4520
850-644-9277
eb...@fs... |
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From: Peter K. <pet...@ce...> - 2010-05-14 18:27:32
|
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From: Peter K. <pet...@wa...> - 2010-05-14 17:20:47
|
Test 1. |
2 messages has been excluded from this view by a project administrator.
