I am doing a make test after compiling nco 4.4.2 and I see that there are several failures (see table below). Is this normal? Some of the outputs contain segmentation faults.
ncrenam test 22: Variables: Absolute rename '/g1/v1' to '/g1/new_v1' (input absolute name)..........Segmentation fault
Test Results Seconds to complete
-------------------------- ----------------------------------------
Test Success Failure Total WallClock Real User System Diff
ncap2: 10 1 11 6.83 0.00 0.00 0.00 0.00
NB:MD5: test passes MD5 checksum on file(s) May be more than one intermediate file.
SVx: test passes single terminal value check SVn=numeric, SVa=alphabetic
OK - data NOT sent, thanks for using NCO anyway - bye!
Thanks for your help,
Oriol
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As the tests themselves say, about 8 ncrename tests will fail unless
netCDF 4.3.1 or later is installed. Do not worry about the failures unless you need that functionality.
cz
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I now have a problem compiling with netcdf 4.3.1.1.
As I have GSL on standard distribution and I have to versions of netcdf, on on the standard path and the other on /opt/, due to the following line
src/nco++/Makefile.in: $(CXXFLAGS) $(ncap2_LDFLAGS) $(LDFLAGS) -o $@
nco tries to link with netcdf distribution version.
Due to this it ends failing with the following error as OS version is 4.1.3 and doeesn't have those functions.
/tmp/NCO/4.4.2/ictce-6.1.5/nco-4.4.2/src/nco/.libs/libnco.so: undefined reference to nc_inq_format_extended'
/tmp/NCO/4.4.2/ictce-6.1.5/nco-4.4.2/src/nco/.libs/libnco.so: undefined reference tonc_rename_grp'
Should $(ncap2_LDFLAGS) and $(LDFLAGS) bew changed?
Thanks,
Oriol
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi,
I am doing a make test after compiling nco 4.4.2 and I see that there are several failures (see table below). Is this normal? Some of the outputs contain segmentation faults.
ncrenam test 22: Variables: Absolute rename '/g1/v1' to '/g1/new_v1' (input absolute name)..........Segmentation fault
Linux amdahl 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux; gcc (Debian 4.7.2-5) 4.7.2;
ncatted: 5 6 11 1.01 0.00 0.00 0.00 0.00
ncbo: 16 8 24 7.73 0.00 0.00 0.00 0.00
ncflint: 7 1 8 4.78 0.00 0.00 0.00 0.00
nces: 14 5 19 1.02 0.00 0.00 0.00 0.00
ncecat: 4 8 12 3.34 0.00 0.00 0.00 0.00
ncks: 31 59 90 6.67 0.00 0.00 0.00 0.00
ncpdq: 36 12 48 3.46 0.00 0.00 0.00 0.00
ncra: 22 9 31 3.57 0.00 0.00 0.00 0.00
ncrcat: 20 10 30 41.75 10.00 0.00 0.00 10.00
ncrename: 0 22 22 1.38 0.00 0.00 0.00 0.00
ncwa: 2 55 57 4.95 0.00 0.00 0.00 0.00
NB:MD5: test passes MD5 checksum on file(s) May be more than one intermediate file.
SVx: test passes single terminal value check SVn=numeric, SVa=alphabetic
OK - data NOT sent, thanks for using NCO anyway - bye!
Thanks for your help,
Oriol
The regression tests require that these environment variables be defined
NCKS_BIN - location of ncks
DATA - any path with write access
MY_BIN_DIR - the 'bin' subfolder of the NCO installation
examples
NCKS_BIN=/home/pvicente/nco_install/bin/ncks
DATA=~/data_nco
MY_BIN_DIR=~/nco_install/bin
Can you try to define these and post results here?
Pedro
As the tests themselves say, about 8 ncrename tests will fail unless
netCDF 4.3.1 or later is installed. Do not worry about the failures unless you need that functionality.
cz
I now have a problem compiling with netcdf 4.3.1.1.
As I have GSL on standard distribution and I have to versions of netcdf, on on the standard path and the other on /opt/, due to the following line
src/nco++/Makefile.in: $(CXXFLAGS) $(ncap2_LDFLAGS) $(LDFLAGS) -o $@
nco tries to link with netcdf distribution version.
Due to this it ends failing with the following error as OS version is 4.1.3 and doeesn't have those functions.
/tmp/NCO/4.4.2/ictce-6.1.5/nco-4.4.2/src/nco/.libs/libnco.so: undefined reference to
nc_inq_format_extended' /tmp/NCO/4.4.2/ictce-6.1.5/nco-4.4.2/src/nco/.libs/libnco.so: undefined reference to
nc_rename_grp'Should $(ncap2_LDFLAGS) and $(LDFLAGS) bew changed?
Thanks,
Oriol
Please be sure '/opt/whatever/' precedes the standard path ('/usr/'?) in all your environments variables, especially LD_LIBRARY_PATH.
cz
Dear Charlie,
LD_LIBRARY_PATH is ok. Would you mind to have a look to src/nco++/Makefile.in line 171 and tell me if any other variable might be the problem, please?
Cheers,
Oriol
You are probably mixing netCDF headers and library versions.
Be sure CPPFLAGS points to the headers for the library version in LDFLAGS.
cz
Sorry, yesterday I meant exchange the two variables. I have tested the change and it works for me.
I think this is related with a previous post: https://sourceforge.net/p/nco/discussion/9829/thread/162f24bc/