Build NCO with dap from netcdf

Developers
2010-07-25
2013-10-17
  • Igor Monteiro

    Igor Monteiro - 2010-07-25

    I'm trying to build nco with enable dap from netcdf in a computer with ubuntu 10.4 and in spite of my netcdf (4.1.1) has dap when I try to configure nco I received the message that dap is disable. For example,

    ./configure -enable-dap-netcdf -enable-ncap2 -enable-udunits -with-zlib=/opt/zlib/zlib-1.2.5/gfortran -with-hdf5=/opt/hdf5/hdf5-1.8.5/gfortran -prefix=/opt/nco/nco-4.0.2/gfortran

    Testing for DAP-netCDF support (is DAP in libnetcdf.a?)…
    checking for nc__opendap in -lnetcdf… no
    configure: WARNING: DAP-netCDF support through libnetCDF disabled (missing DAP library)

    if check my netcdf instalation with nc-config I get

    /opt/netcdf4/netcdf-4.1.1/gfortran/bin/nc-config -all

    This netCDF 4.1.1 has been built with the following features:

      -cc        -> cc
      -cflags    ->  -I/opt/netcdf4/netcdf-4.1.1/gfortran/include
      -libs      -> -L/opt/netcdf4/netcdf-4.1.1/gfortran/lib -lnetcdf

      -cxx       -> c++
      -has-c++   -> yes

      -fc        -> gfortran
      -fflags    -> -g -O2 -I/opt/netcdf4/netcdf-4.1.1/gfortran/include
      -flibs     -> -L/opt/netcdf4/netcdf-4.1.1/gfortran/lib -lnetcdff -lnetcdf
      -has-f77   -> yes
      -has-f90   -> yes

      -has-dap   -> yes
      -has-nc2   -> yes
      -has-nc4   -> yes
      -has-hdf5  -> yes
      -has-hdf4  -> no
      -has-szlib -> no

      -prefix    -> /opt/netcdf4/netcdf-4.1.1/gfortran
      -includedir-> /opt/netcdf4/netcdf-4.1.1/gfortran/include
      -version   -> netCDF 4.1.1

    Have you same idea why this is happen?

    Thank you

     
  • Charlie Zender

    Charlie Zender - 2010-07-26

    hello,

    not sure why this happens.
    please run the following command on your libnetcdf.a and post the results:

    zender@givre:/usr/local/lib$ nm -a libnetcdf.a | grep nc__opendap
    0000000000000000 T nc__opendap

     
  • Igor Monteiro

    Igor Monteiro - 2010-07-27

    Hi,

    igor@singularity:/opt/netcdf4/netcdf-4.1.1/gfortran/lib$ nm -a libnetcdf.a | grep nc__opendap
    0000000000000000 T nc__opendap

    tks,

    Igor

     
  • Charlie Zender

    Charlie Zender - 2010-07-27

    my guess is that configure is using a different libnetcdf.a than you think.
    try configuring NCO with, e.g.,

    export NETCDF4_ROOT='/opt/netcdf4/netcdf-4.1.1/gfortran'
    export NETCDF_INC='opt/netcdf4/netcdf-4.1.1/gfortran/include'
    export NETCDF_LIB='opt/netcdf4/netcdf-4.1.1/gfortran/lib'
    ./configure …

     
  • Igor Monteiro

    Igor Monteiro - 2010-07-27

    Hi Zender,

    I set it:

    export NETCDF4_ROOT='/opt/netcdf4/netcdf-4.1.1/gfortran'
    export NETCDF_LIB='/opt/netcdf4/netcdf-4.1.1/gfortran/lib'
    export NETCDF_INC='/opt/netcdf4/netcdf-4.1.1/gfortran/include'

    and run

    ./configure -enable-dap-netcdf -enable-netcdf4 -enable-ncap2 -enable-udunits -with-zlib=/opt/zlib/zlib-1.2.5/gfortran -with-hdf5=/opt/hdf5/hdf5-1.8.5/gfortran -prefix=/opt/nco/nco-4.0.2/gfortran

    the response was

    Beginning generic tests for DAP support
    DEBUG: enable_dap_netcdf = yes and enable_dap_opendap = yes
    WARNING: Requested both DAP-netCDF and DAP-OPeNDAP support--overriding OPeNDAP
    Will attempt to build NCO with DAP support from netCDF4, not from OPeNDAP
    Testing for DAP-netCDF support (is DAP in libnetcdf.a?)…
    checking for nc__opendap in -lnetcdf… no
    configure: WARNING: DAP-netCDF support through libnetCDF disabled (missing DAP library)
    checking netcdf.h usability… yes
    checking netcdf.h presence… yes
    checking for netcdf.h… yes
    #################################
    #  Test for netCDF4 support     #
    #################################
    DEBUG: After netCDF4 section LIBS =
    DEBUG: After netCDF4 section header_defines_nc_chunked =
    configure: Checking default compiler flags
    checking for nc_open in -lnetcdf… yes
    configure: Good news: Simple program compiles and links to libnetcdf.a with default compiler flags
    DEBUG: After netCDF3 section LIBS = -lnetcdf

    in the final has

    Configuration Parameters:
    AR_FLAGS…………. cru
    CC………………. gcc -std=gnu99
    CFLAGS…………… -g -O2 -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE
    CPP……………… gcc -E
    CPPFLAGS…………. -I/opt/netcdf4/netcdf-4.1.1/gfortran/include 
    CXX……………… g++
    CXXFLAGS…………. -g -O2
    ENABLE_DAP_NETCDF…. no
    ENABLE_DAP_OPENDAP… no
    ENABLE_DAP……….. no
    ENABLE_GSL……….. no
    ENABLE_MPI………..
    ENABLE_NETCDF4……. no
    ENABLE_UDUNITS……. no
    ENABLE_UDUNITS2…… yes
    GSL_ROOT………….
    HAVE_NETCDF4_H…….
    HOST……………..
    host…………….. x86_64-unknown-linux-gnu
    HOSTNAME…………. singularity
    LDFLAGS………….. -L/opt/netcdf4/netcdf-4.1.1/gfortran/lib 
    LIBS…………….. -ludunits2 -lm -lnetcdf  -ludunits2
    NETCDF4_ROOT……… /opt/netcdf4/netcdf-4.1.1/gfortran

    Are there something wrong?

    Igor

     
  • Charlie Zender

    Charlie Zender - 2010-07-28

    igor,

    i can confirm that i got the same behavior as you when trying to build with netcdf4.
    i have re-jiggered the configure scripts to work better with netCDF4, ncap2, UDUnits2, and DAP.
    all of this is now committed to the main trunk.
    if you are comfortable with CVS, then i suggest you try checking out the latest version
    and configuring it. or just copy the latest configure file over that fro your 4.0.2 distribution
    and try that. let us know how it works. See new example configure at

    http://nco.sf.net#bld_cnf

    cz

     
  • ocehugo

    ocehugo - 2010-07-28

    i can confirm that to…so i try to use the new CVS and nothing happens, same error, cant find the dap on the netcdf.

    I see another bug to, if u have enable-udunits2 the ./configure cant find the udunits.xml because the path is wrong in the configure

    my udunits.xml stay on ~/netcdf-4.1.1/share/udunits, and in configure the path=netcdf-4.1.1/share/
    Line 18925  and others

    tks

     
  • ocehugo

    ocehugo - 2010-07-28

    Hi again,

    hey zender , i think there still a bug in the configure, my knowledge in configure is very basic but i think that we have a typo in the line 16872  about the HAVE_NETCDF_H . ( x""yes maybe needs to be x"yes" ) .

     
  • ocehugo

    ocehugo - 2010-07-28

    wtf, missclick on relpy and cant edit the message.

    So after change the typos of udunits and the HAVE_NETCDF_H i try configure but the error still persists.

    So i change the variable ac_cv_lib_netcdf_nc__opendap to yes in the if line 16685 , and the configure "finds" the libnetcdf. But when i make the code, an error apears in the g++ section:

    " Invoke.cc:15:25 error: antlr/AST.hpp: No Such file or directory.  " And so on with a lot of no such files….

    So i check the antlr package, and was already installed. but i search a litle bit more and install the libantlr-dev. And the make pass throught the error above.So maybe an verification of this package might be useful in the configure!

    So, all compile and i do a make test and receive this:

    1 Test Passed…blablabla

    ../src/nco/ncap2 does not exist.

    But after a make install i can see ncap2. So i copy the ncap2 to this location and run again the make test, but i receive a lot of FAILED itens .

    I hope this route can help u zender ;)

    tks

     
  • Charlie Zender

    Charlie Zender - 2010-07-28

    sorry the configure is not working on your ubuntu system.
    it works on mine, but we probably installed netcdf4, etc in different locations.
    you might do better to try the bld/Makefile method instead of configure, e.g.,

    cd ${HOME}/nco/bld;make OMP=Y OPTS=D NETCDF4=Y UDUNITS2=Y allinone

    cz

     
  • ocehugo

    ocehugo - 2010-07-29

    Hello again,
    sorry about the confusing post, i was doing the test in other computer without internet access so the outputs was supressed.

    Now below is what i have done to make the package working , but with some tests FAILED ( in the end of message):

    Compile hdf5. Compile netcdf4 with dap and netcdf4 support.

    So my "nc-config -all" :

    This netCDF 4.1.1 has been built with the following features: 
      --cc        -> gcc
      --cflags    ->  -I/home/hugo/apps/netcdf-4.1.1/include
      --libs      -> -L/home/hugo/apps/netcdf-4.1.1/lib -lnetcdf
      --cxx       -> c++
      --has-c++   -> yes
      --fc        -> gfortran
      --fflags    -> -g -O2 -I/home/hugo/apps/netcdf-4.1.1/include
      --flibs     -> -L/home/hugo/apps/netcdf-4.1.1/lib -lnetcdff -lnetcdf
      --has-f77   -> yes
      --has-f90   -> yes
      --has-dap   -> yes
      --has-nc2   -> yes
      --has-nc4   -> yes
      --has-hdf5  -> yes
      --has-hdf4  -> no
      --has-szlib -> no
      --prefix    -> /home/hugo/apps/netcdf-4.1.1
      --includedir-> /home/hugo/apps/netcdf-4.1.1/include
      --version   -> netCDF 4.1.1
    

    With everything in this netcdf working out of the box ( ncdump for opendap servers ok, ncgen ok, all make tests from netcdf runs as expected)

    install the antlr and lib-devs associated .

    So i Download the lastest source for NCO ( i forget the last cvs because that configure doesnt work for me either)

    After that i try to run the configure:

    hugo@hostname: ~/pathUDUNITS2_PATH=/home/hugo/apps/netcdf-4.1.1 PATH=$PATH:/home/hugo/apps/netcdf-4.1.1/bin CXXFLAGS="-fPIC -O2" NETCDF_INC=/home/hugo/apps/netcdf-4.1.1/include NETCDF_LIB=/home/hugo/apps/netcdf-4.1.1/lib NETCDF4_ROOT=/home/hugo/apps/netcdf-4.1.1 HDF5_LIB_DIR=/home/hugo/apps/hdf5-1.8.5/lib ./configure --prefix=/home/hugo/apps/nco-4.0.2 --enable-dap-netcdf --enable-netcdf4 --enable-netcdf-4 --enable-ncap2 --enable-nco-cplusplus --enable-gsl --enable-udunits2 --disable-udunits
    [code]
    The important output:
    [code]Configuration Parameters:
    AR_FLAGS............. cru
    CC................... gcc -std=gnu99
    CFLAGS............... -fPIC -O2 -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE
    CPP.................. gcc -E
    CPPFLAGS............. -I/usr/include -I/home/hugo/apps/netcdf-4.1.1/include -I/home/hugo/apps/netcdf-4.1.1/include   -I/home/hugo/apps/netcdf-4.1.1/include
    CXX.................. g++
    CXXFLAGS............. -fPIC -O2
    ENABLE_DAP_NETCDF.... no
    ENABLE_DAP_OPENDAP... no
    ENABLE_DAP........... no
    ENABLE_GSL........... yes
    ENABLE_MPI........... 
    ENABLE_NETCDF4....... yes
    ENABLE_UDUNITS....... no
    ENABLE_UDUNITS2...... yes
    GSL_ROOT............. /usr
    HAVE_NETCDF4_H....... 
    HOST................. 
    host................. x86_64-unknown-linux-gnu
    HOSTNAME............. galleon
    LDFLAGS.............. -L/home/hugo/apps/netcdf-4.1.1/lib -L/home/hugo/apps/hdf5-1.8.5/lib -L/home/hugo/apps/netcdf-4.1.1/lib    -L/home/hugo/apps/netcdf-4.1.1/lib
    LIBS................. -ludunits2 -lgsl -L/usr/lib -lgsl -lgslcblas -lm -lm -lnetcdf -lhdf5_hl -lhdf5 -lz  -ludunits2
    NETCDF4_ROOT......... /home/hugo/apps/netcdf-4.1.1 
    [code]
    So i change the configure script to believe that my ncopendap exist:
    Change the line 16685: [code] ac_cv_lib_netcdf_nc__opendap=no" [code]
    to yes.
    I note that the udunits2.xml was not found so i change the configure line 18923 ( because i use the netcdf_inc):
    [code] nco_udunits_xml="${NETCDF_INC}/../share/udunits2.xml"[code]
    to my path ( just add a udunits/ after the share/)
    run the configure again and get this:
    [code]
    Configuration Parameters:
    AR_FLAGS............. cru
    CC................... gcc -std=gnu99
    CFLAGS............... -fPIC -O2 -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE
    CPP.................. gcc -E
    CPPFLAGS............. -I/usr/include -I/home/hugo/apps/netcdf-4.1.1/include -I/home/hugo/apps/netcdf-4.1.1/include   -I/home/hugo/apps/netcdf-4.1.1/include
    CXX.................. g++
    CXXFLAGS............. -fPIC -O2
    ENABLE_DAP_NETCDF.... yes
    ENABLE_DAP_OPENDAP... no
    ENABLE_DAP........... yes
    ENABLE_GSL........... yes
    ENABLE_MPI........... 
    ENABLE_NETCDF4....... yes
    ENABLE_UDUNITS....... no
    ENABLE_UDUNITS2...... yes
    GSL_ROOT............. /usr
    HAVE_NETCDF4_H....... 
    HOST................. 
    host................. x86_64-unknown-linux-gnu
    HOSTNAME............. galleon
    LDFLAGS.............. -L/home/hugo/apps/netcdf-4.1.1/lib -L/home/hugo/apps/hdf5-1.8.5/lib -L/home/hugo/apps/netcdf-4.1.1/lib    -L/home/hugo/apps/netcdf-4.1.1/lib
    LIBS................. -ludunits2 -lgsl -L/usr/lib -lgsl -lgslcblas -lm -lm -lnetcdf -lhdf5_hl -lhdf5 -lz -lnetcdf  -ludunits2
    NETCDF4_ROOT......... /home/hugo/apps/netcdf-4.1.1
    [code]
    After a make & make install i sucefully compile everything without an error. So First i check some operators in ncks ( like ncks -H url, ncrcat with 3 files, and others things i need to do, and everything seems to work fine).
    But i use nco with a lot of files and with operations like mean,std, interpolations and so on. So i like to check out the tests that came with NCO.
    Before the results, i think that this make test r still beta right? Because in some place they want to ftp to a link that i dont have a password, so i think its some private test from the developers ( in the running case, some inputs like login and password r asked, but this kind of thing its uncommon rigth!?)
    So here the fulloutput, after i copy the ncap2 binary from my install dir  to the ../src/nco/ncap2 because of the missing file error , and after some ftp logins that asking for passwords: 
    [code]
    make check
    make[1]: Entering directory `/home/hugo/data/downloads/test/nco-4.0.2'
    Making check in data
    make[2]: Entering directory `/home/hugo/data/downloads/test/nco-4.0.2/data'
    make[2]: Nothing to be done for `check'.
    make[2]: Leaving directory `/home/hugo/data/downloads/test/nco-4.0.2/data'
    Making check in src
    make[2]: Entering directory `/home/hugo/data/downloads/test/nco-4.0.2/src'
    Making check in nco
    make[3]: Entering directory `/home/hugo/data/downloads/test/nco-4.0.2/src/nco'
    make  check-TESTS
    make[4]: Entering directory `/home/hugo/data/downloads/test/nco-4.0.2/src/nco'
    ==================
    All 0 tests passed
    ==================
    make[4]: Leaving directory `/home/hugo/data/downloads/test/nco-4.0.2/src/nco'
    make[3]: Leaving directory `/home/hugo/data/downloads/test/nco-4.0.2/src/nco'
    Making check in nco_c++
    make[3]: Entering directory `/home/hugo/data/downloads/test/nco-4.0.2/src/nco_c++'
    make  tst
    make[4]: Entering directory `/home/hugo/data/downloads/test/nco-4.0.2/src/nco_c++'
    make[4]: `tst' is up to date.
    make[4]: Leaving directory `/home/hugo/data/downloads/test/nco-4.0.2/src/nco_c++'
    make  check-TESTS
    make[4]: Entering directory `/home/hugo/data/downloads/test/nco-4.0.2/src/nco_c++'
    libnco_c++ version  1.3 last modified 2010/01/05 20:02:18 built Jul 29 2010 on myhostname by hugo
    Number of wavelengths in in.nc is 2
    Value of wvl[0] in in.nc is 5e-07
    INFO External netCDF type of prc_cmp variables will be NC_FLOAT
    Currently there are 3 dimensions defined
    Defined sz with long_name = Size at bin center and units = meter
    Defined sz_ldb with long_name = Size at bin center and units = meter
    Defined sz_nbr with long_name = Number of sizes and units = number
    Defined wvl with long_name = Wavelength at band center and units = meter
    Defined wvl_valarray with long_name = valarray and units = meter
    tst: nco_inq_varid() for variable "quark" with rcd_opt = -49 yields rcd = -49
    tst: nco_inq_varndims() for variable "quark" with rcd_opt = -49 yields rcd = -49
    Wrote results to out.nc
    ncks: ncks -C -H -F -m -u -d wvl,0.5e-6 -v wvl out.nc
    PASS: tst
    =============
    1 test passed
    =============
    make[4]: Leaving directory `/home/hugo/data/downloads/test/nco-4.0.2/src/nco_c++'
    make[3]: Leaving directory `/home/hugo/data/downloads/test/nco-4.0.2/src/nco_c++'
    Making check in nco++
    make[3]: Entering directory `/home/hugo/data/downloads/test/nco-4.0.2/src/nco++'
    make[3]: Nothing to be done for `check'.
    make[3]: Leaving directory `/home/hugo/data/downloads/test/nco-4.0.2/src/nco++'
    make[3]: Entering directory `/home/hugo/data/downloads/test/nco-4.0.2/src'
    make[3]: Nothing to be done for `check-am'.
    make[3]: Leaving directory `/home/hugo/data/downloads/test/nco-4.0.2/src'
    make[2]: Leaving directory `/home/hugo/data/downloads/test/nco-4.0.2/src'
    Making check in man
    make[2]: Entering directory `/home/hugo/data/downloads/test/nco-4.0.2/man'
    make[2]: Nothing to be done for `check'.
    make[2]: Leaving directory `/home/hugo/data/downloads/test/nco-4.0.2/man'
    Making check in doc
    make[2]: Entering directory `/home/hugo/data/downloads/test/nco-4.0.2/doc'
    make[2]: Nothing to be done for `check'.
    make[2]: Leaving directory `/home/hugo/data/downloads/test/nco-4.0.2/doc'
    make[2]: Entering directory `/home/hugo/data/downloads/test/nco-4.0.2'
    make[2]: Leaving directory `/home/hugo/data/downloads/test/nco-4.0.2'
    make[1]: Leaving directory `/home/hugo/data/downloads/test/nco-4.0.2'
    cd bm && env MY_BIN_DIR=../src/nco DATA=/tmp ./nco_bm.pl --regress
    INFO: Testing for required modules
        Time::HiRes ... found.
        IO::Socket  ... found.
    INFO: Using your environment variable DATA 
           [/tmp]
         as the root DATA directory for this series of tests.
    ncap2   test 01: running ncap2.in script in nco_bm.pl (failure expe... SVn ok
    ncap2   test 02: Testing float modulo float........................... SVa ok
    ncap2   test 03: Testing foo=log(e_flt)^1 (fails on AIX TODO ncap57... SVn ok
    ncap2   test 04: Testing foo=log(e_dbl)^1............................. SVn ok
    ncap2   test 05: Testing foo=4*atan(1)................................ SVn ok
    ncap2   test 06: Testing foo=erf(1) (fails on AIX TODO ncap57)........ SVn prov. ok
    ncap2   test 07: Testing foo=gamma(0.5) (fails on AIX TODO ncap57).... SVn prov. ok
    ncap2   test 08: Testing foo=sin(pi/2)................................ SVn ok
    ncap2   test 09: Testing foo=cos(pi).................................. SVn ok
    ncap2   test 10: Casting variable with same name as dimension (fail... SVn ok
    ncap2   test 11: Casting variable with a single dim of sz=1 .......... SVn ok
    ncatted test 01: Modify all existing units attributes to meter seco... SVa ok
    ncatted test 02: Change _FillValue attribute from 1.0e36 to 0.0....... SVn ok
    ncatted test 03: Create new _FillValue attribute ..................... SVn ok
    ncatted test 04: Pad header with 1000B extra for future metadata (f... SVn ok
    ncatted test 05: Check ncatted variable wildcarding -(Failure expec... SVn ok
    ncbo    test 01: Difference a packed variable and be sure everythin... SVn ok
    ncbo    test 02: Whole file difference with broadcasting (OK to fai... SVn ok
    ncbo    test 03: difference scalar missing value...................... SVn ok
    ncbo    test 04: difference with missing value attribute.............. SVn ok
    ncbo    test 05: difference without missing value attribute........... SVn ok
    ncbo    test 06: _FillValues differ between files..................... SVa ok
    ncbo    test 07: _FillValue in one variable (not both variables)...... SVn ok
    ncbo    test 08: ncdiff symbolically linked to ncbo................... SVn ok
    ncbo    test 09: difference with missing value attribute.............. SVn ok
    ncbo    test 10: Difference without missing value attribute........... SVn ok
    ncbo    test 11: Difference which tests broadcasting and changing v... SVn ok
    ncbo    test 12: Difference which tests 3D broadcasting............... SVn ok
    ncbo    test 13: Addition + 3D broadcasting+ MSA...................... SVn ok
    ncea    test 01: ensemble mean of int across two files................ SVn ok
    ncea    test 02: ensemble mean with missing values across two files... SVn ok
    ncea    test 03: ensemble min of float across two files............... SVn ok
    ncea    test 04: scale factor + add_offset packing/unpacking.......... SVn ok
    ncea    test 05: ensemble mean of integer with integer missing valu... SVa ok
    ncea    test 06: ensemble mean of 3D variable across two files with... SVn ok
    ncea    test 07: Check op with OpenMP................................. SVa ok
    ncecat  test 01: concatenate two files containing only scalar varia... SVa ok
    ncecat  test 02: concatenate two 3D vars with multihyperslabbing...... SVn ok
    ncflint test 01: identity weighting................................... SVn ok
    ncflint test 02: identity interpolation............................... SVn ok
    ncflint test 03: switch order of occurrence to test for commutivity... SVn ok
    ncks    test 01: Create T42 variable named one, uniformly 1.0 over ... SVn ok
    ncks    test 02: extract filename string.............................. SVa ok
    ncks    test 03: extract a dimension.................................. SVa ok
    ncks    test 04: extract a variable with limits....................... SVn ok
    ncks    test 05: extract variable of type NC_INT...................... SVn ok
    ncks    test 06: Multi-slab lat and lon with srd...................... SVa ok
    ncks    test 07: Multi-slab with redundant hyperslabs................. SVa ok
    ncks    test 08: Multi-slab with coordinates.......................... SVa ok
    ncks    test 09: Double-wrapped hyperslab............................. SVa ok
    ncks    test 10: dimension slice using UDUnits library (fails witho... SVn ok
    ncks    test 11: dim slice using UDUnits library and cal 365_days (... SVa ok
    ncks    test 12: dim slice using UDUnits library and cal 360_days (... SVa ok
    ncks    test 13: dimension slice using UDUnit conversion (fails wit... SVn prov. ok
    ncks    test 14: variable wildcards A (fails without regex library)... SVn ok
    ncks    test 15: variable wildcards B (fails without regex library)... SVn ok
    ncks    test 16: Offset past end of file (OK. TODO nco693. ncks beh... SVa ok
    ncks    test 17: Print byte value..................................... SVn ok
    ncks    test 18: CF convention coordinates attribute.................. SVn ok
    ncks    test 19: Check creation/copying of global _FillValue.......... SVn ok
    ncpdq   test 01: reverse coordinate................................... SVn ok
    ncpdq   test 02: reverse three dimensional variable................... SVn ok
    ncpdq   test 03: re-order three dimensional variable.................. SVn ok
    ncpdq   test 04: re-order 3D variable with multihyperslabbing......... SVn ok
    ncpdq   test 05: re-order 3D variable with MSA+ reversal of time di... SVn ok
    ncpdq   test 06: re-order 3D variable with MSA and --msa_usr_rdr fl... SVa ok
    ncpdq   test 07: Pack and then unpack scalar (uses only add_offset)... SVn ok
    ncpdq   test 08: unpack 1D variable with MSA (failure expected with... SVn ok
    ncpdq   test 09: Pack 3D double variable with MSA (failure expected... SVn ok
    ncrcat  test 01: Concatenate float with double missing values acros... SVn ok
    ncrcat  test 02: Concatenate float variable with multi-hyperlsbs ac... SVn ok
    ncrcat  test 03: Concatenate int variable with multi-hyperlsbs acro... SVn ok
    ncrcat  test 04: Concatenate float 4D variable with multi-hyperlsbs... SVn ok
    ncrcat  test 05: Concatenate 1D variable with stride across two fil... SVa ok
    ncrcat  test 06: Concatenate 1D variable with stride across three f... SVa ok
    ncrcat  test 07: Concatentate 1D variable with stride across files ... SVa ok
    ncrcat  test 08: Concatenate 1D variable across two files no limits... SVa ok
    ncrcat  test 09: Concatenate 1D variable across three files double ... SVa ok
    ncrcat  test 10: Concatenate 1D variable across three files double ... SVa ok
    ncrcat  test 11: Concatenate 1D variable across three files time st... SVa ok
    ncrcat  test 12: Conc 1D var over 3 files with  Large stride Requir... SVa ok
    ncrcat  test 13: Conc 1D var over 3 files coo-rd limits+stride  Req... SVa ok
    ncrcat  test 14: Conc 1D var over three files date-stamp limits+str... SVa ok
    ncrcat  test 15: Conc 1D var over 3 files date-stamp limits+stride ... SVa ok
    ncrcat  test 16: Conc 1D variable over 3 files dmn limits+stride  R... SVa ok
    ncrcat  test 17: Conc 1D var over 4 files - different rec sizes  Re... SVa ok
    ncrcat  test 18: Conc 1D var over 4 files - with srd=4  different r... SVa ok
    ncrcat  test 19: Conc 1D var over 4 files - with srd=3 str/end time... SVa ok
    ncra    test 01: record sdn of float with double missing values acr... SVn ok
    ncra    test 02: record mean of int across two files.................. SVn ok
    ncra    test 03: record mean of float with double missing values...... SVn ok
    ncra    test 04: record mean of float with integer missing values..... SVn ok
    ncra    test 05: record mean of integer with integer missing values... SVn ok
    ncra    test 06: record mean of integer with integer missing values... SVn ok
    ncra    test 07: record mean of integer with float missing values..... SVn ok
    ncra    test 08: record mean of integer with float missing values a... SVn ok
    ncra    test 09: record mean of packed double with double missing v... SVn ok
    ncra    test 10: record mean of packed double to test precision....... SVn ok
    ncra    test 11: record mean of packed float to test precision........ SVn ok
    ncra    test 12: pass through non-record (i.e., non-processed) pack... SVn ok
    ncra    test 13: record mean of float with double missing values ac... SVn ok
    ncra    test 14: record min of float with double missing values acr... SVn ok
    ncra    test 15: record max of float with double missing values acr... SVn ok
    ncra    test 16: record ttl of float with double missing values acr... SVn ok
    ncra    test 17: record rms of float with double missing values acr... SVn ok
    ncra    test 18: Return mean time coordinate (when computing totals... SVn ok
    ncra    test 19: Return total record (when computing totals) across... SVn ok
    ncra    test 20: Return record average of cell-based geodesic data.... SVa ok
    ncra    test 21: Check op with OpenMP................................. SVa ok
    ncwa    test 01: Creating %tempf_03% again (FAILURE netcdf4 ncrenam... SVn ok
    ncwa    test 02: normalize by denominator upper hemisphere (FAILURE... SVn ok
    ncwa    test 03: minimize coordinate variable......................... SVn ok
    ncwa    test 04: pass through non-averaged (i.e., non-processed) pa... SVn ok
    ncwa    test 05: do not normalize by denominator (FAILURE netcdf4 n... SVn ok
    ncwa    test 06: average with missing value attribute................. SVn ok
    ncwa    test 07: average without missing value attribute.............. SVn ok
    ncwa    test 08: average masked coordinate............................ SVn ok
    ncwa    test 09: average masked variable.............................. SVn ok
    ncwa    test 10: average masked, weighted coordinate.................. SVn ok
    ncwa    test 11: average masked, weighted variable.................... SVn ok
    ncwa    test 12: weight conforms to variable first time............... SVn ok
    ncwa    test 13: average all missing values with weights.............. SVn ok
    ncwa    test 14: average some missing values with unity weights....... SVn ok
    ncwa    test 15: average masked variable with some missing values..... SVn ok
    ncwa    test 16: min switch on type double, some missing values....... SVn ok
    ncwa    test 17: Dimension reduction with min switch and missing va... SVn ok
    ncwa    test 18: Dimension reduction with min switch.................. SVn ok
    ncwa    test 19: Dimension reduction on type int with min switch an... SVn ok
    ncwa    test 20: Dimension reduction on type int variable............. SVn ok
    ncwa    test 21: Dimension reduction on type short variable with mi... SVn ok
    ncwa    test 22: Dimension reduction on type short variable........... SVn ok
    ncwa    test 23: Dimension reduction with min flag on type float va... SVn ok
    ncwa    test 24: Max flag on type float variable...................... SVn ok
    ncwa    test 25: Dimension reduction on type double variable with m... SVn ok
    ncwa    test 26: Dimension reduction on type double variable.......... SVn ok
    ncwa    test 27: Dimension reduction on type int variable with min ... SVn ok
    ncwa    test 28: Dimension reduction on type int variable............. SVn ok
    ncwa    test 29: Dimension reduction on type short variable with ma... SVn ok
    ncwa    test 30: Dimension reduction on type short, max switch vari... SVn ok
    ncwa    test 31: rms with weights..................................... SVn ok
    ncwa    test 32: weights would cause SIGFPE without dbl_prc patch..... SVn ok
    ncwa    test 33: avg would overflow without dbl_prc patch............. SVn ok
    ncwa    test 34: test wrapped ttl with dbl_prc patch (harmless fail... FAILED!
       ERR: FAILURE in ncwa failure: test wrapped ttl with dbl_prc patch (harmless failure expected/OK on all chips since wrap behavior is not IEEE-specified)
       ERR::EXPLAIN: Result: [-31536] != Expected: [-32768]
    ncwa    test 35: min with weights..................................... SVn ok
    ncwa    test 36: max with weights..................................... SVn ok
    ncwa    test 37: Return mean time coordinate (when computing totals... SVn ok
    ncwa    test 38: Return total record (when computing totals).......... SVn ok
    net     test 01: Anonymous FTP protocol (requires anonymous FTP acc... !!FAILED
      $cmd_rsl_is_num = 0 and $xpc_is_num = 1
       ERR: FAILURE in net failure: Anonymous FTP protocol (requires anonymous FTP access to dust.ess.uci.edu)
       ERR::EXPLAIN: Result: [Not connected.] != Expected: [1.000000e+00]
    net     test 02: Secure FTP (SFTP) protocol (requires SFTP access t... FAILED!
       ERR: FAILURE in net failure: Secure FTP (SFTP) protocol (requires SFTP access to dust.ess.uci.edu)
       ERR::EXPLAIN: Result: [] != Expected: [1.000000e+00]
    net     test 03: SSH protocol (requires authorized SSH/scp access t... FAILED!
       ERR: FAILURE in net failure: SSH protocol (requires authorized SSH/scp access to dust.ess.uci.edu)
       ERR::EXPLAIN: Result: [] != Expected: [1]
    net     test 04: OPeNDAP protocol (requires OPeNDAP/DODS-enabled NC... SVn ok
    WARN: Skipping net tests of mss: and password protected FTP protocol retrieval---user not zender
    WARN: Skipping net test wget: protocol retrieval---not implemented yet
    Linux myhostname 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 08:03:28 UTC 2010 x86_64 GNU/Linux; gcc (Ubuntu 4.4.3-4ubuntu5) 4.4.3; 
                        Test Results                Seconds to complete
                 --------------------------   ----------------------------------------
          Test   Success    Failure   Total   WallClock    Real   User  System    Diff
         ncap2:       11                 11       0.47     0.00   0.00    0.00    0.00
       ncatted:        5                  5       0.33     0.00   0.00    0.00    0.00
          ncbo:       13                 13       1.16     0.00   0.00    0.00    0.00
       ncflint:        3                  3       0.38     0.00   0.00    0.00    0.00
          ncea:        7                  7       1.12     0.00   0.00    0.00    0.00
        ncecat:        2                  2       0.27     0.00   0.00    0.00    0.00
          ncks:       19                 19       1.17     0.00   0.00    0.00    0.00
         ncpdq:        9                  9       0.55     0.00   0.00    0.00    0.00
          ncra:       21                 21       1.58     0.00   0.00    0.00    0.00
        ncrcat:       19                 19       3.13     0.00   0.00    0.00    0.00
          ncwa:       37          1      38       2.50     0.00   0.00    0.00    0.00
           net:        1          3       4       0.02     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
    The log-formatted result from this regression test is:
    Linux myhostname 2.6.32-23-generic #37-Ubuntu SMP Fri Jun 11 08:03:28 UTC 2010 x86_64 GNU/Linux using: gcc (Ubuntu 4.4.3-4ubuntu5) 4.4.3|NCO ver: /||ncap2  11  11   0.47   0.00   0.00   0.00   0.00:ncatted   5   5   0.33   0.00   0.00   0.00   0.00:ncbo  13  13   1.16   0.00   0.00   0.00   0.00:ncflint   3   3   0.38   0.00   0.00   0.00   0.00:ncea   7   7   1.12   0.00   0.00   0.00   0.00:ncecat   2   2   0.27   0.00   0.00   0.00   0.00:ncks  19  19   1.17   0.00   0.00   0.00   0.00:ncpdq   9   9   0.55   0.00   0.00   0.00   0.00:ncra  21  21   1.58   0.00   0.00   0.00   0.00:ncrcat  19  19   3.13   0.00   0.00   0.00   0.00:ncwa  37  38   2.50   0.00   0.00   0.00   0.00:net   1   4   0.02   0.00   0.00   0.00   0.00:
    
        --== REQUEST for TEST RESULTS ==--
            
            The NCO team would REALLY appreciate it if you would allow us to have
            the above results of this regression testIf you type 'yes' in
            response to this question, the results of this regression test will
            be sent verbatim as above, anonymously, to the NCO dev team via UDP on
            port 29659If your institution has a firewall that prohibits this,
            it will simply fail silentlyWe want this info so we can fix failures,
            improve efficiency, mitigate global warming, and bring about world peace. If
            you DO NOT want to participate in this, type in anything OTHER than
       [y, Y, yes or YES].  <Enter> will also decline sending the data.
       Do you allow the above regression data to be sent back to the NCO dev team?
       [default is No, y, Y, yes, YES to send it]
    Answer: 
    OK - data NOT sent, thanks for using NCO anyway - bye!
    [code]
    After that, can i use all operators from NCO. The last message i wrote, i see a lot of failures in some tests , because i used the newest CVS code . So because of that i try with the standard source code (4.0.2 ).
    So i might this can help others users that still have problems with that, until the fix of configure.
    Good luck and sorry about the long post!
    
     
  • Charlie Zender

    Charlie Zender - 2010-07-29

    thank you for your report.
    it seems like the configure support for dap and udunits is the primary obstacle for you.
    it is beyond my autotools abilities to fix this stuff without breaking it more.
    croos your fingers that we get funding or volunteers who can help…

     
  • Charlie Zender

    Charlie Zender - 2010-07-29

    fyi, i think netcdf installs udunits2 in /usr/local/share/udunits/udunits2.xml
    for some reason, perhaps because i was an early udunits2 beta tester, i thought
    it would be in /usr/local/share/udunits2.xml. i seem to have it in both locations,
    but i suspect yours is the correct location.
    so i have updated configure to look in  /usr/local/share/udunits as you suggest.
    thx,
    cz

     
  • ocehugo

    ocehugo - 2010-07-30

    Hi zender, thanks for ur help! Dont give up hehe, nco is very nice and i use a lot of features!

    Recently i was installing ncview 2.0 beta. On the configure they have a script to check for netcdf based on the nc-config application. i think that if u try to do something with the nc-config binary in the netcdf to check for opendap t will be more easy to check it on the configure.

    This can be a fast fix, u can put in the end of the "IF tree " of the configure ( if everything go's wrong, u try this…or whatever;
    and of course that needs some more checks in the configure)

    Something like that:

    -enable-nc-config-path=$PATH_TO_NCCONFIG

    HEY_I_HAVE_DAP=`./nc-config --all | grep dap | cut -d ">" -f 2 | cut -d " " -f 2` 
    if [ "HEY_I_HAVE_DAP == "yes" ]; then blablabla ;fi
    [code]
    Where, blablabla is the configure checks and so on.
    hehe
    Thankz!
    
     
  • Igor Monteiro

    Igor Monteiro - 2010-07-30

    Hi Zender,

    I did the same things that ocehugo said and now it works. Thank you for your help.

    Igor

     
  • Igor Monteiro

    Igor Monteiro - 2011-02-18

    Hi Zender,

    Finally I think can suggest an algorithm to install nco with dap from netcdf4 on a ubuntu 10.10 system.
    First you have to install netcdf-4.1.1 with dap. You can check this using ../netcdf-4.1.1/bin/nc-config -has-dap

    Then you have to install the libraries from the ubuntu repository:

        antlr, libantlr-dev
        libxml2-dev
        bison, flex
        gsl-bin, libgsl0-dev
        udunits-bin, libudunits2-0, libudunits2-dev

    After you have to set some environmental variables:

        export NETCDF4_ROOT=/opt/teste/netcdf4/
        export NETCDF_INC=/opt/teste/netcdf4/include
        export NETCDF_LIB='/opt/teste/netcdf4/lib'
        export LIBS=-L/opt/teste/netcdf4/lib -lnetcdf -L/opt/teste/hdf5/lib -lhdf5_hl -lhdf5  -L/opt/teste/zlib/lib -lz -lm  -lcurl -Wl,-Bsymbolic-functions

    Then,

        ./configure -prefix=/opt/nco-4.0.6/gfortran/ -enable-dap-netcdf -enable-netcdf4 -enable-netcdf-4

    Finally,

    make
    make install

    It works well for me.

    Is important to note that make check isn't work.

    Thanks in advance,

    Igor Monteiro

     
  • Charlie Zender

    Charlie Zender - 2011-02-22

    OK, thanks. netCDF DAP works fine on my Ubuntu system with the current ./configure.
    Modifying the configure scripts so it works on other Ubuntu systems is the baffling part :)
    I need a volunteer who is not afraid to rewrite ./configure from scratch…

     

Log in to post a comment.

Get latest updates about Open Source Projects, Conferences and News.

Sign up for the SourceForge newsletter:





No, thanks