Undefined symbol, nc_inq_var_fletcher32 whem importing netCDF4 #60
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From deatho...@googlemail.com on July 20, 2010 10:34:36 Sorry, forgot to mention it's on an i686 running fedora 11 |
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From bast...@gmail.com on July 20, 2010 12:14:15 What did you compile with? |
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From whitaker.jeffrey@gmail.com on July 20, 2010 12:56:44 A missing symbol error like this usually means you linked a netcdf library that does not have netcdf-4 support. Since you indicated that you used --enable-netcdf-4 when building netcdf, it may be that there is another older version of the netcdf library on your system that the python build is picking up. Try "ldd /usr/lib/python2.6/site-packages/netCDF4.so" to see what netcdf library was actually linked. Another possibility is that the HDF5 headers and libs were not found by the netcdf-4 configure step, so it was built without netcdf-4 support. I would need to see the output of configure to know whether that is the case. -Jeff |
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From deatho...@googlemail.com on July 21, 2010 02:42:08 Thanks very much for your replies. It was compiled with gcc and gfortran. The netCDF4.so file links against otus% ldd /usr/lib/python2.6/site-packages/netCDF4.so Which of those should I then be checking? In the netcdf configure log, it refers to HDF5 a few times; configure:3042: checking whether HDF5 should do data conversions I'm afraid I don;t understand what those last two lines mean. Does a "#" mean that it's not false, or that it is false? Thanks again |
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From whitaker.jeffrey@gmail.com on July 21, 2010 05:16:02 Looks like netcdf was compiled statically, so ldd doesn't show you the path. Try running "nm -p /usr/local/lib/libnetcdf.a | grep nc_inq_var_fletcher32". That will tell you if the symbol is in there. If it isn't, try re-running the configure step for the netcdf lib, saving it to a file. Then post the file as an attachment. Also post the output of "python setup.py build". Note that netcdf 4.1.1 is required - you appear to be using 4.0.1 -Jeff |
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From deatho...@googlemail.com on July 21, 2010 05:21:37 Thanks again The search gave; otus% nm -p /usr/local/lib/libnetcdf.a | grep nc_inq_var_fletcher32 which I suppose means it's in there. The configure file used for this compilation is attached. Thanks very much again Attachment: config.log |
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From deatho...@googlemail.com on July 21, 2010 05:23:59 The output of python setup.py build [root@otus netCDF4-0.9.1]# python setup.py build HDF5_DIR environment variable not set, checking some standard locations .., NETCDF4_DIR environment variable not set, checking some standard locations .., Thanks |
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From whitaker.jeffrey@gmail.com on July 21, 2010 06:04:14 You have to remove the build directory before running setup.py, otherwise it doesn't recompile. |
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From deatho...@googlemail.com on July 21, 2010 06:07:17 Thanks. Just compiling version 4.1.1 of netcdf now, I'll have a go at that. |
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From whitaker.jeffrey@gmail.com on July 21, 2010 06:09:52 I was asking for you to save the output of running the configure script, not the config.log file, for example ./configure <configure options 1> configure.log 2> configure.log or with csh ./configure &! configure.log Since the missing symbol appears to be in the library, I suspect you are actually linking another version of the library on your system somewhere when you run setup.py. -Jeff |
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From deatho...@googlemail.com on July 21, 2010 06:13:12 Ah, sorry. I'll have another go as soon as the compilation's finished. |
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From whitaker.jeffrey@gmail.com on July 21, 2010 06:57:20 OK, but from your config.log I doubt that your build is the problem. You do need to use 4.1.1 though, not 4.0.1. While you are rebuilding, please use --enable-shared, that way ldd will reveal if you have linked the correct library. Do you by any chance have a libnetcdf.a in /usr/lib? |
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From deatho...@googlemail.com on July 21, 2010 08:30:22 Thanks very much for your help, I've compiled the netcdf-4.1.1 library and that seems to work. I can now import the netCDF4 module in to python. I have a libnetcdf.a in /usr/local/lib Steve |
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From whitaker.jeffrey@gmail.com on July 21, 2010 08:37:43 Great - let me know if you have any other issues. -Jeff Status: Invalid |
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From jakobru...@gmail.com on December 11, 2010 12:22:53 I have the same problem, but unresolved... I built netcdf-4.1.1 with Then (atfer removing build) ran: HDF5_DIR environment variable not set, checking some standard locations .., NETCDF4_DIR environment variable not set, checking some standard locations .., creating build/temp.linux-i686-2.6 But when testing I get: $ python run_all.py Any solution? Thanks, |
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From whitaker.jeffrey@gmail.com on December 11, 2010 13:16:46 Jakub: You need to build netcdf with --enable-netcdf-4 --enable-shared (and --enable-dap if you want opendap support). |
From deatho...@googlemail.com on July 20, 2010 11:32:34
Hi, I'm trying to import the netCDF4 module into a python script.
So far I have;
compiled the HDF5 library (v1.8.5).
configure --enable-hl --with-zlib=/usr/local
make check install
compiled the netCDF4 library linked against the HDF5 library (v4.0.1).
configure --enable-netcdf-4 --with-hdf5=/usr/local --with-zlib=/usr/local --prefix=/usr/local
make check install
then run the python netCDF4 installer.
python setup.py install
This all seems to work without an error message.
When I try importing the netCDF4 module;
Does anyone know what I'm doing wrong (I'm new to python).
Thanks
Original issue: http://code.google.com/p/netcdf4-python/issues/detail?id=60
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