[Met_help] error messages while compiling MET

Fri Aug 28 08:58:02 MDT 2009

Marlous,

That's odd.  I took a look at the polyline file you sent, and found that
there's a trailing invisible character at the end of each line of the
file.  If you look at the file using the "vi" editor, the trailing
characters show up as "^M".  Whatever text editor you were using probably
inserted that.

Gen-Poly-Mask doesn't do anything fancy.  It just grabs the polyline name
from the first line and creates a NetCDF variable using that name.  But
the NetCDF library doesn't like that trailing character.

Once I removed it, the tool worked fine.  I've attached a version of your
polyline file with that character removed.

Sorry for the trouble.

Thanks,
John

> Hi John,
>
>
>
> In the attachment you find a small text file with the little_r format. A
> table with more information is inserted below.
>
>
>
> Furthermore I've got a question about running Gen-Poly-Mask with some
> own WRF-output data (grb format).
>
>
>
> I ran the following command and gain the following error:
>
>
>
> mm5 at aurora:~/MET/METv2.0$ bin/gen_poly_mask
> data/test_grib/WRF_2009082706_06.grb data/poly/BENELUX.poly
> out/gen_poly_mask/test/BENELUX_GRB_poly.nc
>
> Input Data File:        data/test_grib/WRF_2009082706_06.grb
>
> Input Poly File:        data/poly/BENELUX.poly
>
> Parsed Grid:            LatLon (214 x 241)
>
>  containing 4 points    BENELUX
>
> NetCDF: Name contains illegal characters
>
>
>
> The poly file I used (for Belgium, the Netherlands and Luxembourg) is in
> the other attachment (BENELUX.poly). Do you have any suggestions what
> went wrong?
>
>
>
> Cheers and thanks again for your help,
>
> Marlous
>
>
>
> Little_r format
>
>
>
> HEADER
>
>
>
>
>
>
>
>
>
> Variable
>
> Fortran I/O format
>
>
>
> Description
>
> 1
>
> latitude
>
> F20.5
>
> 70.93333
>
> station latitude (north positive)
>
> 2
>
> longitude
>
> F20.5
>
> -8.66670
>
> station longitude (east positive)
>
> 3
>
> id
>
> A40
>
> 1001.00000
>
> ID of station
>
> 4
>
> name
>
> A40
>
> dart_name
>
> Name of station
>
> 5
>
> platform
>
> A40
>
> FM-35 TEMP
>
> Description of the measurement device
>
> 6
>
> source
>
> A40
>
> dart_src
>
> GTS, NCAR/ADP, BOGUS, etc.
>
> 7
>
> elevation
>
> F20.5
>
> 9.00000
>
> station elevation (m)
>
> 8
>
> num_vld_fld
>
> I10
>
> 1.00000
>
> Number of valid fields in the report
>
> 9
>
> num_error
>
> I10
>
> -888888.00000
>
> Number of errors encountered during the decoding of this observation
>
> 10
>
> num_warning
>
> I10
>
> -888888.00000
>
> Number of warnings encountered during decoding of this observation.
>
> 11
>
> seq_num
>
> I10
>
> -888888.00000
>
> Sequence number of this observation
>
> 12
>
> num_dups
>
> I10
>
> -888888.00000
>
> Number of duplicates found for this observation
>
> 13
>
> is_sound
>
> L10
>
> F
>
> T/F Multiple levels or a single level
>
> 14
>
> bogus
>
> L10
>
> F
>
> T/F bogus report or normal one
>
> 15
>
> discard
>
> L10
>
> F
>
> T/F Duplicate and discarded (or merged) report.
>
> 16
>
> sut
>
> I10
>
> -888888.00000
>
> Seconds since 0000 UTC 1 January 1970
>
> 17
>
> julian
>
> I10
>
> -888888.00000
>
> Day of the year
>
> 18
>
> date_char
>
> A20
>
> 200803090700
>
> YYYYMMDDHHmmss
>
> 19
>
> slp, qc
>
> F13.5, I7
>
> 97900.00000
>
> Sea-level pressure (Pa) and a QC flag
>
> 20
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 21
>
> ref_pres, qc
>
> F13.5, I7
>
> -888888.00000
>
> Reference pressure level (for thickness) (Pa) and a QC flag
>
> 22
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 23
>
> ground_t, qc
>
> F13.5, I7
>
> -888888.00000
>
> Ground Temperature (T) and QC flag
>
> 24
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 25
>
> sst, qc
>
> F13.5, I7
>
> -888888.00000
>
> Sea-Surface Temperature (K) and QC
>
> 26
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 27
>
> psfc, qc
>
> F13.5, I7
>
> 97790.95000
>
> Surface pressure (Pa) and QC
>
> 28
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 29
>
> precip, qc
>
> F13.5, I7
>
> -888888.00000
>
> Precipitation Accumulation and QC
>
> 30
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 31
>
> t_max, qc
>
> F13.5, I7
>
> -888888.00000
>
> Daily maximum T (K) and QC
>
> 32
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 33
>
> t_min, qc
>
> F13.5, I7
>
> -888888.00000
>
> Daily minimum T (K) and QC
>
> 34
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 35
>
> t_min_night, qc
>
> F13.5, I7
>
> -888888.00000
>
> Overnight minimum T (K) and QC
>
> 36
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 37
>
> p_tend03, qc
>
> F13.5, I7
>
> -888888.00000
>
> 3-hour pressure change (Pa) and QC
>
> 38
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 39
>
> p_tend24, qc
>
> F13.5, I7
>
> -888888.00000
>
> 24-hour pressure change (Pa) and QC
>
> 40
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 41
>
> cloud_cvr, qc
>
> F13.5, I7
>
> -888888.00000
>
> Total cloud cover (oktas) and QC
>
> 42
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 43
>
> ceiling, qc
>
> F13.5, I7
>
> -888888.00000
>
> Height (m) of cloud base and QC
>
> 44
>
> qc flag
>
>
>
> 0.00000
>
>
>
>
>
> RECORD
>
>
>
>
>
>
>
> 45
>
> pressure, qc
>
> F13.5, I7
>
> 97790.95000
>
> Pressure (Pa) of observation, and QC
>
> 46
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 47
>
> height, qc
>
> F13.5, I7
>
> 9.00000
>
> Height (m MSL) of observation, and QC
>
> 48
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 49
>
> temperature, qc
>
> F13.5, I7
>
> 275.56000
>
> Temperature (K) and QC
>
> 50
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 51
>
> dew_point, qc
>
> F13.5, I7
>
> 273.56000
>
> Dewpoint (K) and QC
>
> 52
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 53
>
> speed, qc
>
> F13.5, I7
>
> 16.98000
>
> Wind speed (m s -1 ) and QC
>
> 54
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 55
>
> direction, qc
>
> F13.5, I7
>
> 70.00000
>
> Wind direction (degrees) and QC
>
> 56
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 57
>
> u, qc
>
> F13.5, I7
>
> -15.95271
>
> u component of wind (m s -1 ), and QC
>
> 58
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 59
>
> v, qc
>
> F13.5, I7
>
> -5.80631
>
> v component of wind (m s -1 ), and QC
>
> 60
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 61
>
> rh, qc
>
> F13.5, I7
>
> 89.91344
>
> Relative Humidity (%) and QC
>
> 62
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 63
>
> thickness, qc
>
> F13.5, I7
>
> -888888.00000
>
> Thickness (m), and QC
>
> 64
>
> qc flag
>
>
>
> 0.00000
>
>
>
>
>
> END DATA RECORD
>
>
>
>
>
> 65
>
> pressure, qc
>
>
>
> -777777.00000
>
> Pressure (Pa) of observation, and QC
>
> 66
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 67
>
> height, qc
>
>
>
> -777777.00000
>
> Height (m MSL) of observation, and QC
>
> 68
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 69
>
> num_vld_fld
>
> I10
>
> 1.00000
>
> Number of valid fields in the report
>
> 70
>
> qc flag
>
>
>
> 0.00000
>
>
>
> 71
>
> ???
>
>
>
> -888888.00000
>
>
>
> 72
>
> ???
>
>
>
> 0.00000
>
>
>
> 73
>
> ???
>
>
>
> -888888.00000
>
>
>
> 74
>
> ???
>
>
>
> 0.00000
>
>
>
> 75
>
> ???
>
>
>
> -888888.00000
>
>
>
> 76
>
> ???
>
>
>
> 0.00000
>
>
>
> 77
>
> ???
>
>
>
> -888888.00000
>
>
>
> 78
>
> ???
>
>
>
> 0.00000
>
>
>
> 79
>
> ???
>
>
>
> -888888.00000
>
>
>
> 80
>
> ???
>
>
>
> 0.00000
>
>
>
> 81
>
> ???
>
>
>
> -888888.00000
>
>
>
> 82
>
> ???
>
>
>
> 0.00000
>
>
>
> 83
>
> ???
>
>
>
> -888888.00000
>
>
>
> 84
>
> ???
>
>
>
> 0.00000
>
>
>
>
>
> END REPORT RECORD
>
>
>
>
>
>
>
> 85
>
> num_vld_fld
>
> I10
>
> 1.00000
>
>
>
> 86
>
> ??
>
>
>
> 0.00000
>
>
>
> 87
>
> ??
>
>
>
> 0.00000
>
>
>
>
>
>
>
> -----Oorspronkelijk bericht-----
> Van: John Halley Gotway [mailto:johnhg at rap.ucar.edu]
> Verzonden: donderdag 27 augustus 2009 17:48
> Aan: Marlous Jonker
> CC: met_help at ucar.edu
> Onderwerp: RE: [Met_help] error messages while compiling MET
>
>
>
> Marlous,
>
>
>
> Great.  Thanks for letting us know.  Would you be able to send us some
>
> sample little_r files?  That'd help us evaluate how much work it'd take
> to
>
> read them.
>
>
>
> Thanks,
>
> John
>
>
>
>> Hi John,
>
>>
>
>> To process observations into WRF, we use the little_r format.
> Therefore,
>
>> we use a program that converts the company's lay-out to little_r, so I
>
>> think little_r would be most suitable for us.
>
>>
>
>> Cheers,
>
>> Marlous
>
>>
>
>> -----Oorspronkelijk bericht-----
>
>> Van: John Halley Gotway [mailto:johnhg at rap.ucar.edu]
>
>> Verzonden: woensdag 26 augustus 2009 17:11
>
>> Aan: Marlous Jonker
>
>> CC: met_help at ucar.edu
>
>> Onderwerp: RE: [Met_help] error messages while compiling MET
>
>>
>
>> Marlous,
>
>>
>
>> Actually no, they are not.  We've initially chosen a more simple ASCII
>
>> format where each line of data corresponds to a single observation
>
>> value.
>
>> This format is discussed in the ASCII2NC section of the MET User's
>
>> Guide.
>
>> Also, here's a link to a page in the MET Online Tutuorial that
> describes
>
>> it:
>
>>
> http://www.dtcenter.org/met/users/support/online_tutorial/METv2.0/ascii2
>
>> nc/index.php
>
>>
>
>> And also, you can find the sample data that's used in the MET test
>
>> scripts
>
>> in the file METv2.0/data/sample_obs/ascii/sample_ascii_obs.txt
>
>>
>
>> However, we anticipate that in the future we'll provide support in the
>
>> ASCII2NC tool for parsing additional ASCII observation formats, such
> as
>
>> "little_r".  This will be based on user feedback to determine what
>
>> formats
>
>> would be most useful.  But to date, we haven't received much feedback.
>
>> What ASCII observation format(s) would be most useful for you?
>
>>
>
>> Thanks,
>
>> John
>
>>
>
>>> Hi John,
>
>>>
>
>>> I've got a small question about the ASCII observation files that MET
>
>> is
>
>>> able to handle in the "ascii2nc" tool.
>
>>> Are they formatted in "little_r" format as used in WRF?
>
>>>
>
>>> Cheers!
>
>>> Marlous
>
>>>
>
>>> -----Oorspronkelijk bericht-----
>
>>> Van: John Halley Gotway [mailto:johnhg at rap.ucar.edu]
>
>>> Verzonden: woensdag 26 augustus 2009 15:43
>
>>> Aan: Marlous Jonker
>
>>> CC: met_help at ucar.edu
>
>>> Onderwerp: RE: [Met_help] error messages while compiling MET
>
>>>
>
>>> Great.  I'm glad that did the trick.  Just let us know if any
>
>> questions
>
>>> come up in your use of MET.
>
>>>
>
>>> Thanks,
>
>>> John
>
>>>
>
>>>> Hi John,
>
>>>>
>
>>>> This solved my problem: MET is now able to compile. Thanks a lot for
>
>>>> your very useful help!
>
>>>>
>
>>>> Cheers,
>
>>>> Marlous Jonker
>
>>>>
>
>>>> -----Oorspronkelijk bericht-----
>
>>>> Van: John Halley Gotway [mailto:johnhg at rap.ucar.edu]
>
>>>> Verzonden: dinsdag 25 augustus 2009 15:12
>
>>>> Aan: Marlous Jonker
>
>>>> CC: met_help at ucar.edu
>
>>>> Onderwerp: Re: [Met_help] error messages while compiling MET
>
>>>>
>
>>>> Marlous,
>
>>>>
>
>>>> I see that you're compiling MET using the Portland Group compilers
>
>> and
>
>>>> are linking to a NetCDF library built for use with WRF.  The error
>
>>>> messages you're seeing indicate that the NetCDF build to which
>
>>>> you're linking is not compatible with the PGI compilers you're using
>
>>> for
>
>>>> building MET.  The most likely explanation for this is that the
>
>> NetCDF
>
>>>> library may not have been built with the PGI compilers.
>
>>>>
>
>>>> I'd suggest building another version of the NetCDF library, making
>
>>> sure
>
>>>> the build it using the PGI compilers.  And then try rebuilding MET
>
>>> using
>
>>>> that updated NetCDF library.
>
>>>>
>
>>>> Here's how you'd build NetCDF using the PGI compilers.  From the
>
>>>> top-level NetCDF directory and using the C-shell:
>
>>>>
>
>>>> csh
>
>>>> setenv CC /usr/pgi/linux86/7.1-6/bin/pgcc
>
>>>> setenv CXX /usr/pgi/linux86/7.1-6/bin/pgCC
>
>>>> setenv FC ""
>
>>>> setenv F90 ""
>
>>>> ./configure --prefix=/path/where/you/want/netcdf/installed
>
>>>> make
>
>>>> make install
>
>>>>
>
>>>> I usually just "install" the NetCDF library in the same directory as
>
>>> the
>
>>>> source code.  But you're welcome to put it wherever you'd like.
>
>>>>
>
>>>> Hope that helps.  Good luck.
>
>>>>
>
>>>> John Halley Gotway
>
>>>> johnhg at ucar.edu
>
>>>>
>
>>>> Marlous Jonker wrote:
>
>>>>> Hello!
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> While compiling the MET software I encountered the error messages
>
>>>> below.
>
>>>>> The Makefile I used is in the attachment.
>
>>>>>
>
>>>>> I am pretty stuck on how to solve the error, so I hope you have
> some
>
>>>>> ideas to tackle the problem.
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> Kind regards,
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> Marlous Jonker
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> -------------------------------------------------------------------
>
>>>>>
>
>>>>>   Marlous Jonker
>
>>>>>
>
>>>>>   Meteorological Researcher
>
>>>>>
>
>>>>>   Meteo Consult BV, Wageningen, the Netherlands
>
>>>>>
>
>>>>>   Tel: +31 (0)317 399872
>
>>>>>
>
>>>>>   Email: M.Jonker at weer.nl
>
>>>>>
>
>>>>> -------------------------------------------------------------------
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> Error messages encountered:
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> *** Making pcp_combine application ***
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> /usr/pgi/linux86/7.1-6/bin/pgCC -o pcp_combine pcp_combine.cc \
>
>>>>>
>
>>>>>         -Bstatic -Msecond_underscore
>
>>>>> -DMET_BASE=\"/home/mm5/MET/METv2.0\" \
>
>>>>>
>
>>>>>         -I../../lib -I/home/mm5/WRF/netcdf/netcdf-4.0/include
>
>>>>> -I/home/mm5/MET/gsl/gsl-1.9/include \
>
>>>>>
>
>>>>>         -L../../lib -L/home/mm5/WRF/netcdf/netcdf-4.0/lib
>
>>>>> -L/home/mm5/MET/gsl/gsl-1.9/lib \
>
>>>>>
>
>>>>>         -lvx_met_util -lvx_analysis_util -lvx_wrfdata -lvx_met_util
>
>> \
>
>>>>>
>
>>>>>         -lvx_contable -lvx_grib_classes \
>
>>>>>
>
>>>>>         -lvx_econfig -lvx_gsl_prob -lgsl \
>
>>>>>
>
>>>>>         -lvx_plot_util  -lvx_render -lvx_pxm -lvx_color -lvx_ps
>
>>>> -lvx_afm
>
>>>>> \
>
>>>>>
>
>>>>>         -lvx_data_grids -lvx_gnomon -lvx_nav -lvx_cal -lvx_util
>
>>>>> -lvx_math -lm \
>
>>>>>
>
>>>>>         -lnetcdf_c++ -lnetcdf \
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> pcp_combine.cc:
>
>>>>>
>
>>>>> pcp_combine.o: In function `write_netcdf__FLT1iR10GribRecord':
>
>>>>>
>
>>>>> pcp_combine.cc:(.text+0x3421): undefined reference to
>
>>>> `NcFile::__ct(char
>
>>>>> const *, NcFile::FileMode, unsigned int *, unsigned int,
>
>>>>> NcFile::FileFormat)'
>
>>>>>
>
>>>>> pcp_combine.cc:(.text+0x3466): undefined reference to
>
>>>> `NcFile::is_valid(
>
>>>>> const(void))'
>
>>>>>
>
>>>>> pcp_combine.cc:(.text+0x34f4): undefined reference to
>
>>>>> `NcFile::close(void)'
>
>>>>>
>
>>>>> pcp_combine.cc:(.text+0x369a): undefined reference to
>
>>>>> `NcFile::add_att(char const *, char const *)'
>
>>>>>
>
>>>>> pcp_combine.cc:(.text+0x3927): undefined reference to
>
>>>>> `NcFile::add_att(char const *, char const *)'
>
>>>>>
>
>>>>> pcp_combine.cc:(.text+0x3b5b): undefined reference to
>
>>>>> `NcVar::add_att(char const *, int)'
>
>>>>>
>
>>>>> pcp_combine.cc:(.text+0x3ba7): undefined reference to
>
>>>>> `NcVar::add_att(char const *, char const *)'
>
>>>>>
>
>>>>> pcp_combine.cc:(.text+0x3bf3): undefined reference to
>
>>>>> `NcVar::add_att(char const *, char const *)'
>
>>>>>
>
>>>>> pcp_combine.cc:(.text+0x3c42): undefined reference to
>
>>>>> `NcVar::add_att(char const *, char const *)'
>
>>>>>
>
>>>>> pcp_combine.cc:(.text+0x3c66): undefined reference to
>
>>>>> `NcVar::add_att(char const *, float)'
>
>>>>>
>
>>>>> pcp_combine.cc:(.text+0x3d4e): undefined reference to
>
>>>>> `NcVar::add_att(char const *, char const *)'
>
>>>>>
>
>>>>> pcp_combine.cc:(.text+0x3d74): undefined reference to
>
>>>>> `NcVar::add_att(char const *, long)'
>
>>>>>
>
>>>>> pcp_combine.cc:(.text+0x3e46): undefined reference to
>
>>>>> `NcVar::add_att(char const *, char const *)'
>
>>>>>
>
>>>>> pcp_combine.cc:(.text+0x3e6c): undefined reference to
>
>>>>> `NcVar::add_att(char const *, long)'
>

>>>>>
>
>>>>> pcp_combine.cc:(.text+0x3eee): undefined reference to
>
>>>>> `NcVar::add_att(char const *, char const *)'
>
>>>>>
>
>>>>> pcp_combine.cc:(.text+0x3f11): undefined reference to
>
>>>>> `NcVar::add_att(char const *, int)'
>
>>>>>
>
>>>>> pcp_combine.cc:(.text+0x3f7f): undefined reference to
>
>>>> `NcVar::put(float
>
>>>>> const *, long, long, long, long, long)'
>
>>>>>
>
>>>>> pcp_combine.cc:(.text+0x3fef): undefined reference to
>
>>>>> `NcFile::close(void)'
>
>>>>>
>
>>>>> ../../lib/libvx_met_util.a(write_netcdf.o): In function
>
>>>>> `write_netcdf_proj(NcFile *, Grid const &)':
>
>>>>>
>
>>>>> write_netcdf.cc:(.text+0x71): undefined reference to
>
>>>>> `NcFile::add_att(char const *, char const *)'
>
>>>>>
>
>>>>> write_netcdf.cc:(.text+0xe6): undefined reference to
>
>>>>> `NcFile::add_att(char const *, char const *)'
>
>>>>>
>
>>>>> write_netcdf.cc:(.text+0x135): undefined reference to
>
>>>>> `NcFile::add_att(char const *, char const *)'
>
>>>>>
>
>>>>> write_netcdf.cc:(.text+0x17f): undefined reference to
>
>>>>> `NcFile::add_att(char const *, char const *)'
>
>>>>>
>
>>>>> write_netcdf.cc:(.text+0x1c9): undefined reference to
>
>>>>> `NcFile::add_att(char const *, char const *)'
>
>>>>>
>
>>>>>
>
>>>>
>
>>>
>
>>
> ../../lib/libvx_met_util.a(write_netcdf.o):write_netcdf.cc:(.text+0x20c)
>
>>>>> : more undefined references to `NcFile::add_att(char const *, char
>
>>>> const
>
>>>>> *)' follow
>
>>>>>
>
>>>>> make[3]: *** [pcp_combine] Error 2
>
>>>>>
>
>>>>> make[2]: *** [all] Error 2
>
>>>>>
>
>>>>> make[1]: *** [targets] Error 2
>
>>>>>
>
>>>>> make: *** [all] Error 2
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>
>
>>>
>
>>
> ------------------------------------------------------------------------
>
>>>>>
>
>>>>> _______________________________________________
>
>>>>> Met_help mailing list
>
>>>>> Met_help at mailman.ucar.edu
>
>>>>> http://mailman.ucar.edu/mailman/listinfo/met_help
>
>>>>
>
>>>
>
>>>
>
>>>
>
>>
>
>>
>
>>
>
>
>
>
>
>
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