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make test

2014-03-04
2014-03-07
  • Oriol Mula-Valls

    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;

                    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
    

    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

     
  • Pedro Vicente

    Pedro Vicente - 2014-03-04

    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

     
  • Charlie Zender

    Charlie Zender - 2014-03-04

    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

     
  • Oriol Mula-Valls

    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

     
  • Charlie Zender

    Charlie Zender - 2014-03-06

    Please be sure '/opt/whatever/' precedes the standard path ('/usr/'?) in all your environments variables, especially LD_LIBRARY_PATH.
    cz

     
  • Oriol Mula-Valls

    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

     
  • Charlie Zender

    Charlie Zender - 2014-03-06

    You are probably mixing netCDF headers and library versions.
    Be sure CPPFLAGS points to the headers for the library version in LDFLAGS.
    cz

     

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