netcdf4-python build

Ubuntu 12.04

hdf5-tools installed from package manager

netcdf-bin and python-netcdf installed from package manager

I downloaded netCDF4-1.0fix1.tar.gz from http://code.google.com/p/netcdf4-python/downloads/list

python
setup.py build

/usr/bin/ld: cannot find -lhdf5_hl
/usr/bin/ld: cannot find -lhdf5
collect2: ld returned 1 exit status
/usr/bin/ld: cannot find -lhdf5_hl
/usr/bin/ld: cannot find -lhdf5
collect2: ld returned 1 exit status
error: Command “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/lib -Wl,-R/usr/local/lib -Wl,-R/usr/local/lib -lnetcdf -lhdf5_hl
-lhdf5 -lz -o build/lib.linux-i686-2.7/netCDF4.so” failed with exit status 1

Michael: You’re missing the hdf5 library. You should be able to
install that (along with the netcdf version 4 library) using the
Ubuntu package manager. I don’t know what the relevant package names
are.
See the docs at netcdf4-python.googlecode.com for installation
instructions (including how to install the dependencies). You can also file a help request there and I’ll see it (since this
is not really a basemap issue).
-Jeff

···

On 9/19/12 11:30 AM, Michael Rawlins
wrote:

Ubuntu 12.04

      hdf5-tools installed from

package manager

      netcdf-bin and python-netcdf

installed from package manager

I downloaded netCDF4-1.0fix1.tar.gz
from

python setup.py build

      /usr/bin/ld: cannot find

-lhdf5_hl

      /usr/bin/ld: cannot find -lhdf5

      collect2: ld returned 1 exit status

      /usr/bin/ld: cannot find -lhdf5_hl

      /usr/bin/ld: cannot find -lhdf5

      collect2: ld returned 1 exit status

      error: Command "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/lib -Wl,-R/usr/local/lib -Wl,-R/usr/local/lib
-lnetcdf -lhdf5_hl -lhdf5 -lz -o
build/lib.linux-i686-2.7/netCDF4.so" failed with exit status 1

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

http://code.google.com/p/netcdf4-python/downloads/listJeffrey.S.Whitaker@…259…http://tinyurl.com/5telg

···

From: Jeff Whitaker <jeffrey.s.whitaker@…259…>
To: Michael Rawlins <rawlins02@…9…>; Matplotlib Users <matplotlib-users@…2982…e.net>
Sent: Wednesday, September 19, 2012 2:35 PM
Subject: Re: [Matplotlib-users] netcdf4-python build

  On 9/19/12 11:30 AM, Michael Rawlins wrote:

Ubuntu 12.04

      hdf5-tools installed from

package manager

      netcdf-bin and python-netcdf

installed from package manager

I downloaded netCDF4-1.0fix1.tar.gz
from http://code.google.com/p/netcdf4-python/downloads/list

python setup.py build

      /usr/bin/ld: cannot find

-lhdf5_hl

      /usr/bin/ld: cannot find -lhdf5

      collect2: ld returned 1 exit status

      /usr/bin/ld: cannot find -lhdf5_hl

      /usr/bin/ld: cannot find -lhdf5

      collect2: ld returned 1 exit status

      error: Command "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/lib -Wl,-R/usr/local/lib -Wl,-R/usr/local/lib
-lnetcdf -lhdf5_hl -lhdf5 -lz -o
build/lib.linux-i686-2.7/netCDF4.so" failed with exit status 1

Michael:  You're missing the hdf5 library.  You should be able to

install that (along with the netcdf version 4 library) using the
Ubuntu package manager. I don’t know what the relevant package names
are.

See the docs at [netcdf4-python.googlecode.com](http://netcdf4-python.googlecode.com/) for installation

instructions (including how to install the dependencies).

You can also file a help request there and I'll see it (since this

is not really a basemap issue).

-Jeff

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.

Mike

-- 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

Try

libhdf5-serial
libhdf5-serial-dev
Johann

···

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.

···

From: Johann Rohwer <jr@…841…>
To: matplotlib-users@…504…et
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”, line 21, in
from netCDF4 import Dataset as NetCDFFile

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:

from Scientific.IO.NetCDF import NetCDFFile

MR


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