[ncl-talk] ESMF, was: WRAPIT

Wed Jul 29 12:18:36 MDT 2020

Harry, I see that you are using Macports.  They updated ESMF from version
7.* to 8_0_1 about four days ago.  I wonder whether you picked up that
update, and whether that needs some adjustment inside NCL.

On Wed, Jul 29, 2020 at 11:05 AM Ian Harris (ENV - Staff) via ncl-talk <
ncl-talk at mailman.ucar.edu> wrote:

> Hi,
>
>
>
> I’m still at it. I had to abandon the efforts to write NetCDF in Fortran
> via WRAPIT – in the end it just refused to compile, even when I hard-coded
> the Includes into the WRAPIT script.
>
>
>
> [as a complete aside: Mac users! Do not, I repeat, do NOT upgrade your
> system to 10.14 or higher. The system security is full-on paranoia, and
> editing files in (eg) /usr or /opt requires a lot of tomfoolery. I know I
> mentioned it last time but it’s worth mentioning again.]
>
>
>
> So I’ve split the task into two scripts, working on two sections of the
> year range I need, and with handovers of key settings and data in files.
>
>
>
> New problem! The ESMF gridding isn’t working any more:
>
>
>
> Fortran runtime error: shape and target do not conform
>
> fatal:The result of the conditional expression yields a missing value. NCL
> can not determine branch, see ismissing function
>
> fatal:["Execute.c":8637]:Execute: Error occurred at or near line 2977 in
> file $NCARG_ROOT/lib/ncarg/nclscripts/esmf/ESMF_regridding.ncl
>
>
>
> fatal:["Execute.c":8637]:Execute: Error occurred at or near line 4052 in
> file $NCARG_ROOT/lib/ncarg/nclscripts/esmf/ESMF_regridding.ncl
>
>
>
> fatal:["Execute.c":8637]:Execute: Error occurred at or near line 484 in
> file verifyforcev3.2a.ncl
>
>
>
> The relevant lines in my script are:
>
>
>
> Opt = True
>
> Opt at DstGridLat = dlats;
>
> Opt at DstGridLon = dlons;
>
> Opt at SrcRegional = True;
>
> Opt at DstRegional = True;
>
> Opt at SrcGridLat = crulats;
>
> Opt at SrcGridLon = crulons;
>
> Opt at InterpMethod = "neareststod"; we just want to replicate CRU TS into
> the higher-resolution grid
>
> Opt at WgtFileName = "weights_cruts_subset_neareststod.nc";
>
> crutmp125 = ESMF_regrid(crutmp,Opt); copy CRUTMP into the high-resolution
> grid
>
>
>
> That last line is, of course, #484.
>
>
>
> None of the gridding code has changed, and I can’t work out what the error
> messages are trying to tell me. Previous versions of the script, ie, ones
> that haven’t been fiddled with in the latest shenanigans, give the same
> error. This leads me to suspect the new install of NCL.
>
>
>
> Finally, because I know I’ll be asked for it, here’s the regridding with
> Debug = True:
>
>
>
> (0)  get_src_grid_info: source lat dims = (76)
>
> (0)  get_src_grid_info: source lon dims = (140)
>
> (0)  get_src_grid_info: source grid type is 'rectilinear'
>
> (0)  curvilinear_to_SCRIP: calculating grid corners...
>
> (0)  curvilinear_to_SCRIP: no lat values are at the poles, so
>
> (0)        calculating grid corners using
>
> (0)        calc_SCRIP_corners_noboundaries...
>
> (0)  calc_SCRIP_corners_noboundaries
>
> (0)      min/max original lat: 35.25/72.75
>
> (0)      min/max original lon: -24.75/44.75
>
> (0)  calc_SCRIP_corners_noboundaries
>
> (0)      min/max Extlat2d: 34.75/73.25
>
> (0)      min/max Extlon2d: -25.25/45.25
>
> (0)  calc_SCRIP_corners_noboundaries
>
> (0)      min/max ExtGridCenter_lat: 35/73
>
> (0)      min/max ExtGridCenter_lon: -25/45
>
> (0)  get_dst_grid_info: destination lat dims = (304)
>
> (0)  get_dst_grid_info: destination lon dims = (560)
>
> (0)  curvilinear_to_SCRIP: calculating grid corners...
>
> (0)  curvilinear_to_SCRIP: no lat values are at the poles, so
>
> (0)        calculating grid corners using
>
> (0)        calc_SCRIP_corners_noboundaries...
>
> (0)  calc_SCRIP_corners_noboundaries
>
> (0)      min/max original lat: 35.0625/72.9375
>
> (0)      min/max original lon: -24.9375/44.9375
>
> (0)  calc_SCRIP_corners_noboundaries
>
> (0)      min/max Extlat2d: 34.9375/73.0625
>
> (0)      min/max Extlon2d: -25.0625/45.0625
>
> (0)  calc_SCRIP_corners_noboundaries
>
> (0)      min/max ExtGridCenter_lat: 35/73
>
> (0)      min/max ExtGridCenter_lon: -25/45
>
> (0)  ESMF_regrid_gen_weights: number of processors used: 1
>
> (0)  --------------------------------------------------
>
> (0)  ESMF_regrid_gen_weights: the following command is about to be
> executed on the system:
>
> (0)  'ESMF_RegridWeightGen --ignore_degenerate  --source
> source_grid_file.nc --destination destination_grid_file.nc --weight
> weights_cruts_subset_neareststod.nc --method neareststod --src_regional
> --dst_regional -i'
>
> (0)  --------------------------------------------------
>
> Fortran runtime error: shape and target do not conform
>
> (0)  ESMF_regrid_gen_weights: output from 'ESMF_RegridWeightGen':
>
> (0)      missing
>
> (0)  --------------------------------------------------
>
> fatal:The result of the conditional expression yields a missing value. NCL
> can not determine branch, see ismissing function
>
> fatal:["Execute.c":8637]:Execute: Error occurred at or near line 2977 in
> file $NCARG_ROOT/lib/ncarg/nclscripts/esmf/ESMF_regridding.ncl
>
>
>
> fatal:["Execute.c":8637]:Execute: Error occurred at or near line 4052 in
> file $NCARG_ROOT/lib/ncarg/nclscripts/esmf/ESMF_regridding.ncl
>
>
>
> fatal:["Execute.c":8637]:Execute: Error occurred at or near line 485 in
> file verifyforcev3.2a.ncl
>
>
>
> Cheers for any insights,
>
>
>
> Harry
>
>
>
> *From: *ncl-talk <ncl-talk-bounces at mailman.ucar.edu> on behalf of "Ian
> Harris (ENV - Staff) via ncl-talk" <ncl-talk at mailman.ucar.edu>
> *Reply to: *"Ian Harris (ENV - Staff)" <I.Harris at uea.ac.uk>
> *Date: *Sunday, 19 July 2020 at 01:05
> *To: *"ncl-talk at mailman.ucar.edu" <ncl-talk at mailman.ucar.edu>
> *Subject: *Re: [ncl-talk] Using NetCDF with WRAPIT
>
>
>
> Okay, I’ve moved things on.
>
>
>
> 1. I located and edited the WRAPIT script. This has a ’set compiler
> options’ section, and within that a 'Darwin' subsection. Here I was able to
> add the minimum includes and libraries for NetCDF to be incorporated. Easy.
> This meant I didn’t need to spend two days upgrading everything, which is a
> shame, because of point 2.
>
>
>
> 2. Because I upgraded the Mac to 10.14 ('Mojave'), a security feature
> called FDA (Full Disk Access) prevents me from running WRAPIT! It’s very
> restrictive if you want to do things outside of the approved areas (ie,
> buying Apple Music, joining Apple TV, etc). You can add apps to FDA in the
> system Prefs, but not scripts. I tried writing a dummy Fortran proglet to
> run the script, but I don’t get any outputs, so that’s not working.
>
>
>
> It doesn’t get easier!
>
>
>
> Harry
>
>
>
> *From: *ncl-talk <ncl-talk-bounces at mailman.ucar.edu> on behalf of "Ian
> Harris (ENV - Staff) via ncl-talk" <ncl-talk at mailman.ucar.edu>
> *Reply-To: *Ian Harris <i.harris at uea.ac.uk>
> *Date: *Friday, 17 July 2020 at 23:57
> *To: *ncl-talk <ncl-talk at mailman.ucar.edu>
> *Subject: *Re: [ncl-talk] Using NetCDF with WRAPIT
>
>
>
> Hi Rick,
>
>
>
> Nice suggestion, sadly no difference.
>
>
>
> One of the reasons I went for a manual ncl install (“You have chosen Slow
> and Painful”) was in case I could mod WRAPIT to recognise Includes (or even
> just hard code NetCDF into it). I haven’t attempted that *yet*..
>
>
>
> Cheers
>
>
>
> Harry
>
>
>
>
>
> *From: *Rick Brownrigg <brownrig at ucar.edu>
> *Date: *Friday, 17 July 2020 at 18:41
> *To: *Ian Harris <i.harris at uea.ac.uk>
> *Cc: *ncl-talk <ncl-talk at mailman.ucar.edu>
> *Subject: *Re: [ncl-talk] Using NetCDF with WRAPIT
>
>
>
> Hi Harry,
>
>
>
> I don't know for certain. It really looks like the compiler is not finding
> the netcdf header, and needs the equivalent of a -I/usr/local/include
> option. As you point out, WRAPIT doesn't accept that (seems like an
> oversight to me).
>
>
>
> I presume you are using gfortran?  It manual states: "The gfortran
> compiler currently does not make use of any environment variables to
> control its operation above and beyond those that affect the operation of
> gcc"
>
>
>
> With that, you might try setting CPATH:
>
>
>
> export CPATH=/usr/local/include
>
>
>
> Other than that, you might try running WRAPIT with the -d switch. This
> will show the build commands and not delete temporary outputs. From there
> you might be able to manually fix-up and run the appropriate build commands.
>
>
>
> Wish I had a better answer...
>
> Rick
>
>
>
>
>
> On Fri, Jul 17, 2020 at 10:32 AM Ian Harris (ENV - Staff) via ncl-talk <
> ncl-talk at mailman.ucar.edu> wrote:
>
> Hi Rick,
>
>
>
> WRAPIT Version: 120209
>
> A syntax error occurred while parsing: include
>
> COMPILING /Users/ianharris/Programs/Fortran/forverify3.for
>
> /Users/ianharris/Programs/Fortran/forverify3.for:443: Error: Can't open
> included file 'netcdf.inc'
>
> LINKING
>
> gcc: error: forverify3.o: No such file or directory
>
> rm: forverify3.o: No such file or directory
>
> END WRAPIT
>
>
>
> This is the gfortran equivalent that works:
>
>
>
> % gfortran -m64 -I/usr/local/include/ -L/usr/local/lib -lnetcdf
> /usr/local/lib/libnetcdff.a ~/Programs/Fortran/forverify3.for
>
> also, new tree from macports:
>
> % gfortran -m64 -I/opt/local/include/ -L/opt/local/lib -lnetcdf
> /opt/local/lib/libnetcdff.a ~/Programs/Fortran/forverify3.for
>
>
>
> Now WRAPIT doesn't like Includes, and you have to put spaces after the -L
> and -l linkages, but:
>
>
>
> % WRAPIT -m64 -L /opt/local/lib -l netcdf /opt/local/lib/libnetcdff.a
> ~/Programs/Fortran/forverify3.for
>
>
>
> WRAPIT Version: 120209
>
> A syntax error occurred while parsing: include
>
> COMPILING /Users/ianharris/Programs/Fortran/forverify3.for
>
> /Users/ianharris/Programs/Fortran/forverify3.for:442: Error: Can't open
> included file 'netcdf.inc'
>
> LINKING
>
> gcc: error: forverify3.o: No such file or directory
>
> rm: forverify3.o: No such file or directory
>
> END WRAPIT
>
>
>
> Cheers
>
>
>
> Harry
> ------------------------------
>
> *From:* Rick Brownrigg <brownrig at ucar.edu>
> *Sent:* 17 July 2020 17:15
> *To:* Ian Harris (ENV - Staff) <I.Harris at uea.ac.uk>
> *Cc:* Dennis Shea via ncl-talk <ncl-talk at mailman.ucar.edu>
> *Subject:* Re: [ncl-talk] Using NetCDF with WRAPIT
>
>
>
> Hi,
>
>
>
> What do you mean by "cannot get WRAPIT to recognise the "include
> 'netcdf.inc'""?  Are you getting a compiler error, or an error from WRAPIT
> itself, or?  I see you have -L directives pointing to where the netcdf
> library resides; do you need a similar -I directive to point to where the
> header is?
>
>
>
> Rick
>
>
>
> On Fri, Jul 17, 2020 at 10:03 AM Ian Harris (ENV - Staff) via ncl-talk <
> ncl-talk at mailman.ucar.edu> wrote:
>
> Hi,
>
>
>
> I need to write NetCDF files with a Fortran subroutine, because there
> seems to be a memory leak in addfile(). I know that was supposed to be
> fixed years back, but I have memory usage graphs that indicate otherwise.
> And yes, I have comprehensive deletion strategies.
>
>
>
> I've tried a lot of things, including reinstalling ncl, (oh, yes..),
> NetCDF, etc, etc, but I cannot get WRAPIT to recognise the "include
> 'netcdf.inc'" line in the subroutine. Has anyone managed this? How did you
> link to the libraries?
>
>
>
> Here are a couple examples that don't work:
>
>
>
> WRAPIT  -L/usr/local/lib -l netcdf -L /usr/local
> /usr/local/lib/libnetcdff.a /usr/local/lib/libnetcdf.a
> ~/Programs/Fortran/forverify3.for
>
> WRAPIT -L /opt/local/lib -l netcdf -L /opt/local -l libnetcdff.a
> ~/Programs/Fortran/forverify3.for
>
>
>
> ..I just chose two from dozens.
>
>
>
> Is it actually *possible* to have a NetCDF-aware Fortran subroutine under
> WRAPIT?
>
>
>
> Cheers
>
>
>
> Harry
>
>
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