netcdf4-python build


From: Jeff Whitaker <jeffrey.s.whitaker@…259…>
To: Michael Rawlins <rawlins02@…9…>
Sent: Wednesday, September 19, 2012 4:57 PM
Subject: Re: [Matplotlib-users] netcdf4-python build


From:
Johann Rohwer <jr@…841…>
To:
matplotlib-users@lists.sourceforge.net
Sent:
Wednesday, September 19, 2012 3:22 PM
Subject:
Re: [Matplotlib-users] netcdf4-python build

        > Just installed h5utils from package manager. Getting

same errors. In

        > package manager I'm searching on hdf5.  If there's a

package there I’m

        > missing, then it certainly is not obvious.



        Try



        libhdf5-serial

        libhdf5-serial-dev

        Johann







        After installing those two packages I was able build with

setup.py in netCDF4-1.0/

        Last few lines of the build:



        creating build/scripts.linux-i686-2.7

        copying and adjusting utils/nc3tonc4 ->

build/scripts.linux-i686-2.7

        copying and adjusting utils/nc4tonc3 ->

build/scripts.linux-i686-2.7

        changing mode of build/scripts.linux-i686-2.7/nc3tonc4 from

644 to 755

        changing mode of build/scripts.linux-i686-2.7/nc4tonc3 from

644 to 755

        Here is my initialization:



        from mpl_toolkits.basemap import Basemap, shiftgrid, cm

        from netCDF4 import Dataset as NetCDFFile



        Here is result of execution of script:



        Traceback (most recent call last):

          File "[map_PrcpBias_Northeast.py](http://map_prcpbias_northeast.py/)            ", line 21, in
            from netCDF4 import Dataset as NetCDFFile
Michael:  Please include the full traceback - what you posted

doesn’t really tell us anything.

How is full traceback obtained?

        I understand using the python-netcdf package is an option.

Installed that but am getting an eror saying missing
libhdf5_hl.so.6 when trying:

Do you have libhdf5_hl.so anywhere on your system after installing

the libhdf5-serial package? According to this

http://packages.ubuntu.com/lucid/i386/libhdf5-serial-1.8.4/filelist



it should be installed in /usr/lib.

Yes it is in /usr/lib.

Also, if I read this



http://packages.ubuntu.com/natty/libnetcdf6



correctly, just installing the libnetcdf6 and libnetcdf-dev packages

should be all you need to do - they depend on libhdf5-serial.

-Jeff

Both packages are installed.

MR

        from [Scientific.IO](http://scientific.io.net/).NetCDF import NetCDFFile



        MR

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        threats.

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···
  On 9/19/12 2:43 PM, Michael Rawlins > wrote:
        On 19/09/2012 21:14, Michael Rawlins wrote:

Michael: I just meant for you to paste the full output, not just
the first three lines.
Since you apparently have all the libs installed, I don’t understand
what’s going on. Please try deleting the netcdf4-python build
directory, and then run ‘python setup.py build’ again, capturing the
output in a file. Send me that file off-list and I’ll see if I can
suggest something.
-Jeff

···

On 9/19/12 3:29 PM, Michael Rawlins
wrote:


From:
Jeff Whitaker Michael Rawlins Wednesday, September 19, 2012 4:57 PM
Re: [Matplotlib-users] netcdf4-python build

                  On 9/19/12

2:43 PM, Michael Rawlins wrote:


From:
Johann Rohwer <jr@…841…>
To:
matplotlib-users@lists.sourceforge.net

                            **Sent:**
                            Wednesday, September 19, 2012 3:22 PM
                            **Subject:**
                            Re: [Matplotlib-users] netcdf4-python

build

                        On 19/09/2012 21:14, Michael Rawlins wrote:



                        > Just installed h5utils from package

manager. Getting same errors. In

                        > package manager I'm searching on hdf5. 

If there’s a package there I’m

                        > missing, then it certainly is not

obvious.

                        Try



                        libhdf5-serial

                        libhdf5-serial-dev

                        Johann







                        After installing those two packages I was

able build with setup.py
in netCDF4-1.0/

                        Last few lines of the build:



                        creating build/scripts.linux-i686-2.7

                        copying and adjusting utils/nc3tonc4 ->

build/scripts.linux-i686-2.7

                        copying and adjusting utils/nc4tonc3 ->

build/scripts.linux-i686-2.7

                        changing mode of

build/scripts.linux-i686-2.7/nc3tonc4 from
644 to 755

                        changing mode of

build/scripts.linux-i686-2.7/nc4tonc3 from
644 to 755

                        Here is my initialization:



                        from mpl_toolkits.basemap import Basemap,

shiftgrid, cm

                        from netCDF4 import Dataset as NetCDFFile



                        Here is result of execution of script:



                        Traceback (most recent call last):

                          File "[map_PrcpBias_Northeast.py](http://map_prcpbias_northeast.py/)                            ",

line 21, in

                            from netCDF4 import Dataset as

NetCDFFile

                Michael:  Please include the full traceback - what

you posted doesn’t really tell us anything.

                How is full traceback obtained?
                        I understand using the python-netcdf package

is an option. Installed that but am getting
an eror saying missing libhdf5_hl.so.6 when
trying:

                Do you have libhdf5_hl.so anywhere on your system

after installing the libhdf5-serial package?
According to this

                it should be installed in /usr/lib.

Yes it is in /usr/lib.
Also, if I read this
correctly, just installing the libnetcdf6 and
libnetcdf-dev packages should be all you need to do

  • they depend on libhdf5-serial.
    -Jeff
    Both packages are installed.
    MR

<jeffrey.s.whitaker@…259…>
To:<rawlins02@…9…>
Sent:
Subject:
http://packages.ubuntu.com/lucid/i386/libhdf5-serial-1.8.4/filelist

http://packages.ubuntu.com/natty/libnetcdf6

                        from [Scientific.IO](http://scientific.io.net/)                            .NetCDF

import NetCDFFile

                        MR

                        Live Security Virtual Conference

                        Exclusive live event will cover all the ways

today’s security and

                        threat landscape has changed and how IT

managers can respond. Discussions

                        will include endpoint security, mobile

security and the latest in malware

                        threats.

Matplotlib-users mailing list

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. [http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/](http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/)
_______________________________________________
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
[https://lists.sourceforge.net/lists/listinfo/matplotlib-users](https://lists.sourceforge.net/lists/listinfo/matplotlib-users)

http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/

Matplotlib-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-users

-- Jeffrey S. Whitaker Phone : (303)497-6313
Meteorologist FAX : (303)497-6449
NOAA/OAR/PSD R/PSD1 Email : Jeffrey.S.Whitaker@...259...
325 Broadway Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web :

http://tinyurl.com/5telg


From: Jeff Whitaker <jeffrey.s.whitaker@…259…>
To: Michael Rawlins <rawlins02@…9…>
Cc: "matplotlib-users@lists.sourceforge.net"
matplotlib-users@lists.sourceforge.net
Sent: Wednesday, September 19, 2012 5:57 PM
Subject: Re: [Matplotlib-users] netcdf4-python build

How is full traceback obtained?

Michael:  I just meant for you to paste the full output, not just

the first three lines.

That’s all that appears at standard output and I do not know how to generate/find anything else.

Since you apparently have all the libs installed, I don't understand

what’s going on. Please try deleting the netcdf4-python build
directory, and then run ‘python setup.py build’ again, capturing the
output in a file. Send me that file off-list and I’ll see if I can
suggest something.

-Jeff

Out of build, after removing build/ directory:

HDF5_DIR environment variable not set, checking some standard locations …
checking /home/rawlins …
checking /usr/local …
HDF5 found in /usr/local

NETCDF4_DIR environment variable not set, checking standard locations…
checking /home/rawlins …
checking /usr/local …
netCDF4 found in /usr/local
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler opti
ons
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler opt
ions
running build_src
build_src
building py_modules sources
building extension “netCDF4” sources
build_src: building npy-pkg config files
running build_py
creating build
creating build/lib.linux-i686-2.7
copying netcdftime.py -> build/lib.linux-i686-2.7
copying netCDF4_utils.py ->
build/lib.linux-i686-2.7
copying ordereddict.py -> build/lib.linux-i686-2.7
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
building ‘netCDF4’ extension
compiling C sources
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wst
rict-prototypes -fPIC

creating build/temp.linux-i686-2.7
compile options: ‘-I/usr/local/include -I/usr/local/include -I/usr/lib/python2.7
/dist-packages/numpy/core/include -I/usr/include/python2.7 -c’
gcc: netCDF4.c
netCDF4.c: In function ‘__pyx_f_7netCDF4__find_cmptype’:
netCDF4.c:46724:13: warning: ‘__pyx_v_xtype’ may be used uninitialized in this f
unction [-Wuninitialized]
netCDF4.c:37881:11: note: ‘__pyx_v_xtype’ was declared here
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -
Wl,-z,relro build/temp.linux-i686-2.7/netCDF4.o -L/usr/local/lib -L/usr/local/li
b
-Wl,-R/usr/local/lib -Wl,-R/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lz -o bui
ld/lib.linux-i686-2.7/netCDF4.so
running scons
running build_scripts
creating build/scripts.linux-i686-2.7
copying and adjusting utils/nc3tonc4 -> build/scripts.linux-i686-2.7
copying and adjusting utils/nc4tonc3 -> build/scripts.linux-i686-2.7
changing mode of build/scripts.linux-i686-2.7/nc3tonc4 from 644 to 755
changing mode of build/scripts.linux-i686-2.7/nc4tonc3 from 644 to 755

···
  On 9/19/12 3:29 PM, Michael Rawlins > wrote: