Re: Changing netCDF dimensions

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On 02/04/2013 12:56 PM, Durga Kafle wrote:
> 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
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> checking for strchr... yes
> checking for strerror... yes
> checking for strpbrk... yes
> checking for strrchr... yes
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> checking for strtol... yes
> checking for ANSI C header files... (cached) yes
> checking getopt.h usability... yes
> checking getopt.h presence... yes
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> checking limits.h usability... yes
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> 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 <mailto: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
> <mailto: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 <http://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 <mailto: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
> <mailto: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 <mailto:ktravis@fas.harvard.edu>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> ncl-talk mailing list
> >>>> List instructions, subscriber options, unsubscribe:
> >>>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
> >>>>
> >>>
> >>
> >
>
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Received on Mon Feb 4 13:10:13 2013