Re: Changing netCDF dimensions

Hi

I am new to NCL and NCO. I installed NCL and trying to install NCO and get
running but I got error message as below. Can anyone please help me on this
how I can install NCO properly and get it running? the error message I got
is given below,

vortex1:nco durgakafle$ ./configure
--prefix=/Volumes/users/durgakafle/nco_install
checking build system type... x86_64-apple-darwin12.2.0
checking host system type... x86_64-apple-darwin12.2.0
checking target system type... x86_64-apple-darwin12.2.0
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... autobld/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking how to run the C preprocessor... gcc -E
checking how to run the C++ preprocessor... g++ -E
checking for gcc option to accept ISO C99... -std=gnu99
checking for gcc -std=gnu99 option to accept ISO Standard C... (cached)
-std=gnu99
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... -ll
checking whether yytext is a pointer... yes
checking for bison... bison -y
checking whether ln -s works... yes
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc -std=gnu99...
/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld
checking if the linker
(/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
checking the name lister (/usr/bin/nm) interface... BSD nm
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-apple-darwin12.2.0 file names to
x86_64-apple-darwin12.2.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin12.2.0 file names to toolchain
format... func_convert_file_noop
checking for /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld
option to reload object files... -r
checking for objdump... no
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm output from gcc -std=gnu99 object...
ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no
checking for gcc -std=gnu99 option to produce PIC... -fno-common -DPIC
checking if gcc -std=gnu99 PIC flag -fno-common -DPIC works... yes
checking if gcc -std=gnu99 static flag -static works... no
checking if gcc -std=gnu99 supports -c -o file.o... yes
checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes
checking whether the gcc -std=gnu99 linker
(/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld) supports
shared libraries... yes
checking dynamic linker characteristics... darwin12.2.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++...
/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld
checking if the linker
(/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld) is GNU ld... no
checking whether the g++ linker
(/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld) supports
shared libraries... yes
checking for g++ option to produce PIC... -fno-common -DPIC
checking if g++ PIC flag -fno-common -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker
(/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld) supports
shared libraries... yes
checking dynamic linker characteristics... darwin12.2.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether to enable maintainer-specific portions of Makefiles... no
checking for working memcmp... yes
checking whether lstat correctly handles trailing slash... no
checking whether stat accepts an empty string... no
checking for working strtod... yes
checking for canonicalize_file_name... no
checking for floor... yes
checking for gethostname... yes
checking for getpagesize... yes
checking for getrusage... yes
checking for memchr... yes
checking for memmove... yes
checking for memset... yes
checking for mkstemp... yes
checking for pow... yes
checking for readlink... yes
checking for realpath... yes
checking for regcomp... yes
checking for setlocale... yes
checking for sqrt... yes
checking for strchr... yes
checking for strerror... yes
checking for strpbrk... yes
checking for strrchr... yes
checking for strstr... yes
checking for strtol... yes
checking for ANSI C header files... (cached) yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking libintl.h usability... no
checking libintl.h presence... no
checking for libintl.h... no
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking cstdlib usability... yes
checking cstdlib presence... yes
checking for cstdlib... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for pid_t... yes
checking for size_t... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for uid_t in sys/types.h... yes
checking for ptrdiff_t... yes
checking size of int*... 8
checking whether C++ compiler implements namespaces... yes
checking whether C++ compiler has working valarray<T>... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking netcdf.h usability... no
checking netcdf.h presence... no
checking for netcdf.h... no
configure: error: in `/Users/durgakafle/nco':
configure: error: cannot find netCDF header
See `config.log' for more details

Thanks

Duirga

On Mon, Feb 4, 2013 at 11:46 AM, Travis, Katherine
<ktravis@fas.harvard.edu>wrote:

> Dennis,
> I have attempted to put both files on the ftp site, with no luck. I get
> the following error:
>
> ftp> put
> /Users/ktravis/Desktop/NEI06_ModelReady/emis_mole_all_20061231_12US1_cmaq_c
> b05_soa_E21_2007ed_06.nc
> local:
> /Users/ktravis/Desktop/NEI06_ModelReady/emis_mole_all_20061231_12US1_cmaq_c
> b05_soa_E21_2007ed_06.nc remote:
> /Users/ktravis/Desktop/NEI06_ModelReady/emis_mole_all_20061231_12US1_cmaq_c
> b05_soa_E21_2007ed_06.nc
>
> 229 Entering Extended Passive Mode (|||49152|).
> 553 Could not create file.
>
> ftp> put /Users/ktravis/Desktop/NEIData/gridFile.csv
> local: /Users/ktravis/Desktop/NEIData/gridFile.csv remote:
> /Users/ktravis/Desktop/NEIData/gridFile.csv
>
> 229 Entering Extended Passive Mode (|||49174|).
> 553 Could not create file.
>
>
> I think my last answer was cut off:
> [3] I am just starting to learn NCL and NCO, so I am not yet familiar.
> I have been working in R until this point.
>
>
> I just downloaded NCO and am working on trying it out.
> Thank you!
> ~Katie
>
> On 2/4/13 12:59 PM, "Dennis Shea" <shea@ucar.edu> wrote:
>
> >Hi Katherine.
> >
> >Rather unusual looking dump .... This looks like
> >fortran array ordering (ie, column major). I say this cuz
> >the TSTEP is the rightmost dimension which is the slowest
> >varying in fortran *and* it is unlimited. The netCDF
> >software requires that the unlimited dimension be the
> >slowest varying.
> >
> >Also, you did not answer ... Are you familiar with the
> >netCDF operators and have available: ncks
> >
> >If you are not and you are going to deal with netCDF on a regular
> >basis, I suggest you (or a system person) download and install
> >these tools. They are not associated with NCL but in data processing
> >you will likely have to use multiple tools.
> >
> >---
> >You can sent the two files to
> >
> >ftp ftp.cgd.ucar.edu
> >anonymous
> >email
> >cd incoming
> >put emis_mole_all_20061231_12US1_cmaq_cb05_soa_E21_2007ed_06.nc
> >put ... the 2nd file with coordinate info ...
> >quit
> >
> >after you have successfuly completed the transfer,
> >send me or, better', ncl-talk@ucar.edu [don't cc me]
> >that you have completed the transfer.
> >---
> >
> >We are asking that people respond only to ncl-talk (no personal cc).
> >We all see the responses but we want to separate NCL
> >related correspondence form other email. Many of us that
> >respond on ncl-talk are not paid by the NCL project, we do it
> >cuz we want to help people.
> >
> >Regards
> >D
> >
> >On 02/04/2013 10:37 AM, Travis, Katherine wrote:
> >> Dennis,
> >> Thanks! I deleted most of the variables since there are 56, but here is
> >> everything else that comes out.
> >> [1]
> >> 1] "File emis_mole_all_20061231_12US1_cmaq_cb05_soa_E21_2007ed_06.nc
> >> (NC_FORMAT_CLASSIC):"
> >> [1] ""
> >> [1] " 56 variables:"
> >> [1] " int TFLAG[DATE-TIME,VAR,TSTEP] "
> >> [1] " units: <YYYYDDD,HHMMSS>"
> >> [1] " long_name: TFLAG "
> >> [1] " var_desc: Timestep-valid flags: (1) YYYYDDD or (2)
> >> HHMMSS "
> >> [1] " float ACROLEIN[COL,ROW,LAY,TSTEP] "
> >> [1] " long_name: ACROLEIN "
> >> [1] " units: moles/s "
> >> [1] " var_desc: Model species ACROLEIN
> >> "
> >> [1] " float ALD2[COL,ROW,LAY,TSTEP] "
> >> [1] " long_name: ALD2 "
> >> [1] " units: moles/s "
> >> [1] " var_desc: Model species ALD2
> >> "
> >> [1] ""
> >> [1] " 6 dimensions:"
> >> [1] " TSTEP Size:25 *** is unlimited ***"
> >> [1] " DATE-TIME Size:2"
> >> [1] " LAY Size:1"
> >> [1] " VAR Size:55"
> >> [1] " ROW Size:299"
> >> [1] " COL Size:459"
> >> [1] ""
> >> [1] " 33 global attributes:"
> >> [1] " IOAPI_VERSION: $Id: @(#) ioapi library version 3.0 $
> >> "
> >> [1] " EXEC_ID: ????????????????
> >> "
> >> [1] " FTYPE: 1"
> >> [1] " CDATE: 2012314"
> >> [1] " CTIME: 32930"
> >> [1] " WDATE: 2012314"
> >> [1] " WTIME: 32930"
> >> [1] " SDATE: 2006365"
> >> [1] " STIME: 0"
> >> [1] " TSTEP: 10000"
> >> [1] " NTHIK: 1"
> >> [1] " NCOLS: 459"
> >> [1] " NROWS: 299"
> >> [1] " NLAYS: 1"
> >> [1] " NVARS: 55"
> >> [1] " GDTYP: 2"
> >> [1] " P_ALP: 33"
> >> [1] " P_BET: 45"
> >> [1] " P_GAM: -97"
> >> [1] " XCENT: -97"
> >> [1] " YCENT: 40"
> >> [1] " XORIG: -2556000"
> >> [1] " YORIG: -1728000"
> >> [1] " XCELL: 12000"
> >> [1] " YCELL: 12000"
> >> [1] " VGTYP: -1"
> >> [1] " VGTOP: 0"
> >> [1] " VGLVLS: 0" " VGLVLS: 0"
> >> [1] " GDNAM: 12US1_459X299 "
> >> [1] " UPNAM: MRGGRID "
> >> [1] " VAR-LIST: ACROLEIN ALD2 ALD2_PRIMARY
> >> ALDX BENZENE BUTADIENE13 CH4 CL2
> >> CO ETH ETHA ETOH
> >>FORM
> >> FORM_PRIMARY HCL HFLUX HONO
> >> IOLE ISOP MEOH NH3 NH3_FERT
> >> NO NO2 NVOL OLE
> >>PAL
> >> PAR PCA PCL PEC
> >> PFE PH2O PK PMC PMFINE
> >> PMG PMN PMOTHR PNA
> >>PNCOM
> >> PNH4 PNO3 POC PSI
> >> PSO4 PTI SO2 SULF TERP
> >> TOL UNK UNR VOC_INV
> >>XYL
> >> "
> >> [1] " FILEDESC: Area source emissions data
> >> /FROM/ OPENMRGOUT
> >> /VERSION/ $
> >>
> >> /BASE YEAR/ 2008
> >> /NUMBER OF FILES/ 1
> >> /FILE POSITION/
> >>1
> >> /NUMBER OF
> >> VARIABLES/ 20
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> "
> >> [1] " HISTORY: "
> >>
> >>
> >> [2] This is just a .csv file with
> >> Lat (dimension 459*299), lon (dimension 459*299)
> >>
> >> [3] I am just starting to learn NCL and NCO, so I am not yet familiar.
> >> I have been working in R until this point.
> >>
> >> ~Katie
> >>
> >> On 2/4/13 12:29 PM, "Dennis Shea" <shea@ucar.edu> wrote:
> >>
> >>> A bit more information would be helpful.
> >>>
> >>> [1] What does
> >>>
> >>> %> ncl_filedump .... (or: ncdump -h ...)
> >>>
> >>> show for the the original file?
> >>>
> >>> [2] The same for the 2nd file containing the lat/lon coordinates
> >>>
> >>> [3] Are you familiar and have available the netCDF Operators?
> >>> eg: the 'ncks' operator
> >>>
> >>> Cheers
> >>>
> >>>
> >>> On 02/04/2013 10:24 AM, Travis, Katherine wrote:
> >>>> Hi,
> >>>> I have species data (NO, NO2 etc) with dimensions 459x299x25 for
> >>>> lat/lon/time. However the lat and lon dimensions are 1-459 and 1-299
> >>>> rather than actual lat/lon values. I have a lat and lon coordinate
> >>>>for
> >>>> each datapoint, and I want to append the netcdf file with this
> >>>> information so that the actual grid points are associated with the
> >>>>data.
> >>>> Is there a simple way to do this?
> >>>> Thanks,
> >>>> --
> >>>> Katherine R. Travis
> >>>> PhD Student
> >>>> Harvard University
> >>>> SEAS
> >>>> ktravis@fas.harvard.edu
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> ncl-talk mailing list
> >>>> List instructions, subscriber options, unsubscribe:
> >>>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
> >>>>
> >>>
> >>
> >
>
> _______________________________________________
> ncl-talk mailing list
> List instructions, subscriber options, unsubscribe:
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>

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Received on Mon Feb 4 12:56:13 2013