[ncl-talk] Missing color fill when using gsn_csm_contour_map (ncl V 6.4.0)
Mary Haley
haley at ucar.edu
Fri Aug 24 08:26:51 MDT 2018
Adriana,
This is a mystery to all of us, but I noticed you are on an Ubuntu system
and somebody else had issues running NCL under Ubuntu that appeared to be
related to the cairo library being out of sync for what NCL expects.
How did you install NCL on your system? I noticed you are loading libraries
with "/usr/lib" paths, which looks to me like you used "apt-get". This
method of installing NCL could be the problem because it will use whatever
cairo library is on your system. If your system cairo is too old or too
new, then this can be an issue for color-filled plots.
If you did use apt-get, then please try installing NCL using conda instead,
as this will give you the correct version of cairo. You can see our conda
instructions here:
http://www.ncl.ucar.edu/Applications/system.shtml
However, before you do any of this, please follow Adam's suggestion of
running gsun01n. If that example doesn't produce any color plots, then try
the conda installation. In any case, post back to ncl-talk and let us know
how it goes.
Good luck, and sorry about all the problems.
--Mary
On Thu, Aug 23, 2018 at 7:32 AM, <adriana.bossolasco at cnrs-orleans.fr> wrote:
> Hi Dennis
>
> Yes I tryed your code with my file, but I still have the same "no color"
> graphic, I will attached again the png
>
> Also I executed the command in the linux command line (I copy again what I
> get):
>
> abossola at olivia:~$ ncl -V
> 6.4.0
> abossola at olivia:~$ gcc --version
> gcc (Ubuntu 7.3.0-16ubuntu3) 7.3.0
> Copyright (C) 2017 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions. There
> is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
> PURPOSE.
>
> abossola at olivia:~$ uname -a
> Linux olivia 4.15.0-32-generic #35-Ubuntu SMP Fri Aug 10 17:58:07
> UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
>
> Le 23/08/2018 15:21, Dennis Shea a écrit :
>
>> [1] Run the code I sent you. Use your file.
>>
>> [2] As noted by Guido, the commands are to be issued from the
>> unix/linux command line. NOT FROM WITHIN NCL.
>>
>>
>> %> ncl -V
>> %> uname -a
>> %> gcc --version
>>
>> On Thu, Aug 23, 2018 at 4:39 AM, <adriana.bossolasco at cnrs-orleans.fr>
>> wrote:
>>
>> Thanks for the correction
>>>
>>> Now I get
>>>
>>> abossola at olivia:~$ gcc --version
>>> gcc (Ubuntu 7.3.0-16ubuntu3) 7.3.0
>>> Copyright (C) 2017 Free Software Foundation, Inc.
>>> This is free software; see the source for copying conditions. There
>>> is NO
>>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
>>> PURPOSE.
>>>
>>> abossola at olivia:~$ uname -a
>>> Linux olivia 4.15.0-32-generic #35-Ubuntu SMP Fri Aug 10 17:58:07
>>> UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> I tryed the script that Denis send me and is the same I have the
>>> contour lines but not the color (see the attached graphic)
>>>
>>> Le 23/08/2018 12:09, Guido Cioni a écrit :
>>>
>>> Be careful!
>>>
>>> abossola at olivia:~/Adriana/CESM/MAM7/MAM7_tes4$ gcc--version
>>> gcc--version: command not found
>>>
>>> It should be gcc --version (NOTE THE SPACE!!) and not gcc--version
>>>
>>> You do the same error afterwards
>>>
>>> ncl 1> ncl-V
>>>
>>> instead than ncl -V, although also this command should be executed
>>> oustide of NCL (only in the bash). The commands uname -a and gcc
>>> --version as well need to be executed outside of NCL.
>>>
>>> I'd suggest you to have a general introduction on Linux and NCL
>>> before
>>> attempting to fix your plot.
>>>
>>> However, did you try the script that Dennis sent?
>>>
>>> On 23. Aug 2018, at 11:12, adriana.bossolasco at cnrs-orleans.fr
>>> wrote:
>>>
>>> Hi
>>>
>>> I try the commands and this is what I obtain:
>>>
>>> abossola at olivia:~/Adriana/CESM/MAM7/MAM7_tes4$ ncl -V
>>> 6.4.0
>>> abossola at olivia:~/Adriana/CESM/MAM7/MAM7_tes4$ uname -a
>>> Linux olivia 4.15.0-32-generic #35-Ubuntu SMP Fri Aug 10 17:58:07
>>> UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
>>> abossola at olivia:~/Adriana/CESM/MAM7/MAM7_tes4$ gcc--version
>>> gcc--version: command not found
>>>
>>> Other wise if I type this command in the ncl shell, then says:
>>>
>>> ncl 1> ncl-V
>>> fatal:syntax error: line 1 before or near -
>>> ncl-
>>>
>>> ncl 3> uname -a
>>> fatal:syntax error: line 3 before or near -
>>> uname -
>>> ------^
>>>
>>> fatal:error in statement
>>> ncl 4> gcc--version
>>> fatal:syntax error: line 4 before or near -
>>> gcc-
>>> ----^
>>>
>>> fatal:error in statement
>>>
>>> I know that it is very strange because in my old computer everything
>>> working, it could be due to the version of Linux?
>>>
>>> This is my version now:
>>> NAME="Ubuntu"
>>> VERSION="18.04.1 LTS (Bionic Beaver)"
>>> ID=ubuntu
>>> ID_LIKE=debian
>>> PRETTY_NAME="Ubuntu 18.04.1 LTS"
>>> VERSION_ID="18.04"
>>> HOME_URL="https://www.ubuntu.com/ [1]"
>>> SUPPORT_URL="https://help.ubuntu.com/ [2]"
>>> BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/ [3]"
>>>
>>>
>>> PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-
>> policies/privacy-policy
>>
>>> [4]"
>>>
>>> VERSION_CODENAME=bionic
>>> UBUNTU_CODENAME=bionic
>>>
>>> I really appreciate any help!
>>>
>>> Le 22/08/2018 17:58, Dennis Shea a écrit :
>>> Sorry. I accidentally hit "Send".
>>> Attached is the 2nd plot.
>>> On Wed, Aug 22, 2018 at 9:56 AM, Dennis Shea <shea at ucar.edu> wrote:
>>> Not sure why you are not getting color.
>>> If the following does not create color then please send the output
>>> from
>>> %> ncl -V
>>> %> uname -a
>>> %> gcc--version
>>> =========
>>> ;---read in zonal winds
>>> ;a = addfile("MAM_GEOS_1anee.cam.h0.2000-12-07-00000.nc [5]
>>> [1]","r")
>>> ;u = a->U(0,35,:,:)
>>> a = addfile("uwnd.2008.nc [6] [2]","r")
>>>
>>> u = a->uwnd(0,10,:,:)
>>> printVarSummary (u)
>>> ;print(u)
>>> wks = gsn_open_wks("png","adriana") ; send graphics to PNG file
>>> res = True
>>> res at gsnMaximize = True ; maximize in frame
>>> res at cnLinesOn = True
>>> res at cnFillOn = True
>>> res at cnFillPalette = "BlueYellowRed" ; change the color palette
>>> res at tiMainString = "Default"
>>> plot = gsn_csm_contour_map(wks,u,res)
>>> res at mpFillDrawOrder = "PostDraw" ; Make sure land fill is drawn
>>> ; on top of filled contours
>>> res at tiMainString = "add gray land fill after contouring"
>>> plot = gsn_csm_contour_map(wks,u,res)
>>> On Wed, Aug 22, 2018 at 2:22 AM,
>>> <adriana.bossolasco at cnrs-orleans.fr> wrote:
>>> Hi thank you very much for the answer
>>> I corrected U and print the variable for see if this have values
>>> now is U(0,34,:,:)
>>> Variable: u
>>> Type: float
>>> Total Size: 55296 bytes
>>> 13824 values
>>> Number of Dimensions: 2
>>> Dimensions and sizes: [lat | 96] x [lon | 144]
>>> Coordinates:
>>> lat: [ -90.. 90]
>>> lon: [ 0..357.5]
>>> Number Of Attributes: 6
>>> lev : 581.2501460313797
>>> time : 327
>>> mdims : 1
>>> units : m/s
>>> long_name : Zonal wind
>>> cell_methods : time: mean
>>> And also have values, I checked it with print(u)
>>> But still the graphic is empty (white, no contour fill)
>>> On the other hand I can not access to ftp.cgd.ucar.edu [7] [1] [3]
>>> for
>>>
>>> attach my file. Say:
>>> ERROR
>>> The requested URL could not be retrieved
>>> Any other idea how can I pass the file
>>> MAM_GEOS_1anee.cam.h0.2000-12-07-00000.nc [5] [1]
>>> Thank you very much
>>> Le 21/08/2018 20:36, Dennis Shea a écrit :
>>> [0]
>>> If you are just learning NCL, I suggest you look at the USER MANUAL
>>> at:
>>> HTTP://WWW.NCL.UCAR.EDU/DOCUMENT/MANUALS/ [8] [4] [6]
>>> [1]
>>> As noted by Toni,
>>> u = U(0,,:,:)
>>> is not correct. In fact, it should have generated a FATAL subscript
>>> syntax error.
>>> Note: although "fatal", NCL will continue. In fact, it will still
>>> try
>>> to create the plot. Since it did not have valid data, NCL generated
>>> a
>>> background and a default color lable bar. That is what you attached.
>>> [2]
>>> Your following resource setting needs some clarification:
>>> res at tiMainString = "NCL version 6.1.x will give you gray land"
>>> For historical reasons, NCL's default graphic mode is
>>> black-and-white
>>> (B/W). This is true of *all* NCL versions. Not just 6.1.x.
>>> When, 'gsn_csm_contour_map' is used, the default background is
>>> continental outlines with light gray used to fill land areas. See:
>>> HTTP://WWW.NCL.UCAR.EDU/APPLICATIONS/CYLINEQ.SHTML [9] [5] [7]
>>> Examples 1 and 2
>>> Color is turned on via:
>>> res at cnFillOn = True ; make color graphic
>>> When color is activated, (a) the background map including the light
>>> gray land fil is generated; then, (b) the color contour are drawn
>>> over
>>> that background. The light gray land fill is overwritten (no big
>>> deal). The following resource setting tells the
>>> 'gsn_csm_contour_map'
>>> do the colr contours and then force the gray land fill last. [There
>>> are some reasons for doing that.]
>>> res at mpFillDrawOrder = "PostDraw" ; Make sure land fill is drawn
>>> ; on top of filled contours
>>> [3]
>>> If you want you can ftp a sample file to:
>>> ftp ftp.cgd.ucar.edu [7] [1] [3] [8]
>>> anonymous
>>> your_email
>>> cd incoming
>>> put MAM_GEOS_1anee.cam.h0.2000-12-07-00000.nc [5] [1] [9]
>>> quit
>>> On Tue, Aug 21, 2018 at 9:45 AM, Toni Klemm <toni-klemm at tamu.edu>
>>> wrote:
>>> Hi Adriana,
>>> I noticed there are two commas in the command to extract the sind
>>> vectors: u = a->U(0,,:,:) Could that be the problem?
>>> Could you attach the netCDF file from the example that you’re
>>> using? (MAM_GEOS_1anee.cam.h0.2000-12-07-00000.nc [5] [1] [1])
>>> Toni
>>> Toni Klemm, Ph.D.
>>> Postdoctoral Research Associate
>>> Department of Ecosystem Science and Management
>>> College of Agriculture and Life Sciences
>>> Texas A&M University, College Station, TX
>>> Contributor to the Early Career Climate Forum [3]
>>> www.toni-klemm.de [10] [2] [6] [4] | @toniklemm [5]
>>>
>>> On Aug 21, 2018, at 10:01 AM, adriana.bossolasco at cnrs-orleans.fr
>>> wrote:
>>> Hi all
>>> I have a problem with ncl when I try to plot a contour graphic. I
>>> thought it was a mistake I was making, but then when I try with a
>>> example very simple still appears blank. And ncl does not tell me
>>> any error.
>>> Here is the script (have my file but is exactly the same that
>>> newcolor_1.ncl)
>>> ;************************************************
>>> ; zonal_2.ncl
>>> ;
>>> ; Concepts illustrated:
>>> ; - Drawing a zonal means plot
>>> ; - Using dim_avg_Wrap to calculate a zonal average
>>> ;************************************************
>>> ;load "/usr/lib/ncarg/nclscripts/csm/gsn_code.ncl"
>>> ;load "/usr/lib/ncarg/nclscripts/csm/gsn_csm.ncl"
>>> ;load "/usr/lib/ncarg/nclscripts/csm/contributed.ncl"
>>> ;************************************************
>>> begin
>>> ;************************************************
>>> ; variable and file handling
>>> ;************************************************
>>> ;---read in zonal winds
>>> a = addfile("MAM_GEOS_1anee.cam.h0.2000-12-07-00000.nc [5] [1]
>>>
>>> [1]","r")
>>> u = a->U(0,,:,:) ; July zonal
>>> winds
>>> wks = gsn_open_wks("png","newcolor") ; send graphics to PNG
>>> file
>>> res = True
>>> res at gsnMaximize = True ; maximize in frame
>>> res at cnLinesOn = False
>>> res at cnFillOn = True
>>> res at cnFillPalette = "BlueYellowRed" ; change the color
>>> palette
>>> res at mpFillDrawOrder = "PostDraw" ; Make sure land fill is drawn
>>> ; on top of filled contours
>>> res at tiMainString = "NCL version 6.1.x will give you gray land"
>>> plot = gsn_csm_contour_map(wks,u,res)
>>> end
>>> I obtained a map without color fill, I was looking in some
>>> previous talk but nothing works. Can Anyone help me on this?
>>> thanks
>>> I attached the maps
>>> Thank you
>>> --
>>> Adriana Bossolasco
>>> LPC2E UMR 7328 (CNRS, Université d'Orléans)
>>> 3A avenue de la Recherche Scientifique
>>> 45071 Orléans Cedex 2 - FRANCE
>>> Tel +33 (0)2 38 25 52 85
>>> e-mail:
>>>
>>>
>>> adriana.bossolasco at cnrs-orleans.fr<newcolor.png>____________
>> ___________________________________
>>
>>> ncl-talk mailing list
>>> ncl-talk at ucar.edu
>>> List instructions, subscriber options, unsubscribe:
>>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk [11] [7] [2]
>>> _______________________________________________
>>> ncl-talk mailing list
>>> ncl-talk at ucar.edu
>>> List instructions, subscriber options, unsubscribe:
>>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk [11] [7] [2]
>>> Links:
>>> ------
>>> [1] http://MAM_GEOS_1anee.cam.h0.2000-12-07-00000.nc [5] [3] [1]
>>>
>>> [2] http://mailman.ucar.edu/mailman/listinfo/ncl-talk [11] [7]
>>> [3] http://www.eccforum.org
>>> [4] http://www.toni-klemm.de
>>> [5] http://twitter.com/toniklemm
>>> [6] http://www.ncl.ucar.edu/Document/Manuals/ [12] [8]
>>> [7] http://www.ncl.ucar.edu/Applications/cylineq.shtml [13] [9]
>>> [8] http://ftp.cgd.ucar.edu
>>> [9] http://12-07-00000.nc
>>> --
>>> Adriana Bossolasco
>>> LPC2E UMR 7328 (CNRS, Université d'Orléans)
>>> 3A avenue de la Recherche Scientifique
>>> 45071 Orléans Cedex 2 - FRANCE
>>> Tel +33 (0)2 38 25 52 85
>>> e-mail: adriana.bossolasco at cnrs-orleans.fr
>>> Links:
>>> ------
>>> [1] http://MAM_GEOS_1anee.cam.h0.2000-12-07-00000.nc [5]
>>> [2] http://uwnd.2008.nc
>>> [3] http://ftp.cgd.ucar.edu
>>> [4] HTTP://WWW.NCL.UCAR.EDU/DOCUMENT/MANUALS/ [8]
>>> [5] HTTP://WWW.NCL.UCAR.EDU/APPLICATIONS/CYLINEQ.SHTML [9]
>>> [6] http://www.toni-klemm.de
>>> [7] http://mailman.ucar.edu/mailman/listinfo/ncl-talk [11]
>>> [8] http://www.ncl.ucar.edu/Document/Manuals/ [12]
>>> [9] http://www.ncl.ucar.edu/Applications/cylineq.shtml [13]
>>>
>>> --
>>> Adriana Bossolasco
>>> LPC2E UMR 7328 (CNRS, Université d'Orléans)
>>> 3A avenue de la Recherche Scientifique
>>> 45071 Orléans Cedex 2 - FRANCE
>>> Tel +33 (0)2 38 25 52 85
>>> e-mail: adriana.bossolasco at cnrs-orleans.fr
>>> _______________________________________________
>>> ncl-talk mailing list
>>> ncl-talk at ucar.edu
>>> List instructions, subscriber options, unsubscribe:
>>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk [11]
>>>
>>> Guido Cioni
>>> http://guidocioni.altervista.org [14]
>>>
>>> Links:
>>> ------
>>> [1] http://ftp.cgd.ucar.edu
>>> [2] http://www.toni-klemm.de
>>> [3] http://mam_geos_1anee.cam.h0.2000-12-07-00000.nc [15]
>>>
>>
>> --
>> Adriana Bossolasco
>> LPC2E UMR 7328 (CNRS, Université d'Orléans)
>> 3A avenue de la Recherche Scientifique
>> 45071 Orléans Cedex 2 - FRANCE
>> Tel +33 (0)2 38 25 52 85
>> e-mail: adriana.bossolasco at cnrs-orleans.fr
>>
>>
>> Links:
>> ------
>> [1] https://www.ubuntu.com/
>> [2] https://help.ubuntu.com/
>> [3] https://bugs.launchpad.net/ubuntu/
>> [4] https://www.ubuntu.com/legal/terms-and-policies/privacy-policy
>> [5] http://MAM_GEOS_1anee.cam.h0.2000-12-07-00000.nc
>> [6] http://uwnd.2008.nc
>> [7] http://ftp.cgd.ucar.edu
>> [8] HTTP://WWW.NCL.UCAR.EDU/DOCUMENT/MANUALS/
>> [9] HTTP://WWW.NCL.UCAR.EDU/APPLICATIONS/CYLINEQ.SHTML
>> [10] http://www.toni-klemm.de
>> [11] http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>> [12] http://www.ncl.ucar.edu/Document/Manuals/
>> [13] http://www.ncl.ucar.edu/Applications/cylineq.shtml
>> [14] http://guidocioni.altervista.org
>> [15] http://mam_geos_1anee.cam.h0.2000-12-07-00000.nc
>>
>
> --
> Adriana Bossolasco
> LPC2E UMR 7328 (CNRS, Université d'Orléans)
> 3A avenue de la Recherche Scientifique
> 45071 Orléans Cedex 2 - FRANCE
> Tel +33 (0)2 38 25 52 85
> e-mail: adriana.bossolasco at cnrs-orleans.fr
>
> _______________________________________________
> ncl-talk mailing list
> ncl-talk at ucar.edu
> List instructions, subscriber options, unsubscribe:
> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>
>
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