[ncl-talk] Missing color fill when using gsn_csm_contour_map (ncl V 6.4.0)
Mary Haley
haley at ucar.edu
Tue Sep 4 14:03:22 MDT 2018
Dear Adriana,
Yes, you need to type:
source activate ncl_stable
before you can use NCL.
There are a couple of ways you can make this easier.
[1] You could put the command in your .bashrc (or equivalent file) in your
home directory so this gets executed automatically every time you login.
[2] You could also create an alias that is easier to type:
alias myncl='source activate ncl_stable'
and then all you need to type is "myncl"
to activate the NCL environment.
--Mary
On Mon, Sep 3, 2018 at 6:11 AM, <adriana.bossolasco at cnrs-orleans.fr> wrote:
> Dear Mary and all!!!
>
> Finally!!!! ncl works! I have installed ncl with conda as you recommend me
> and follow the instructions from the web page:
> http://www.ncl.ucar.edu/Download/conda.shtml
> And now works!!! I am very happy
> So that's mean that is a problem with the cairo library (maybe they are
> too new)
> And also now every time that I want to work with ncl I need to lunch:
> source activate ncl_stable
> Right?
> Because now I get the fill color plot
> Other wise if I just run from the UNIX terminal doesn't work!
>
> I will attach the plot!
>
> Thank you very much
>
>
> Le 24/08/2018 16:26, Mary Haley a écrit :
>
>> 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] [1]"
>>> SUPPORT_URL="https://help.ubuntu.com/ [2] [2]"
>>> BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/ [3] [3]"
>>>
>>>
>>> PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-
>> policies/privacy-policy
>>
>>> [4]
>>> [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] [5]
>>> [1]","r")
>>> ;u = a->U(0,35,:,:)
>>> a = addfile("uwnd.2008.nc [6] [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] [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] [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] [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] [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] [7] [1] [3] [8]
>>> anonymous
>>> your_email
>>> cd incoming
>>> put MAM_GEOS_1anee.cam.h0.2000-12-07-00000.nc [5] [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] [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] [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] [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, subscribe
>>> <https://maps.google.com/?q=subscribe&entry=gmail&source=g>r options,
>>> unsubscribe:
>>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk [11] [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] [11] [7] [2]
>>> Links:
>>> ------
>>> [1] http://MAM_GEOS_1anee.cam.h0.2000-12-07-00000.nc [5] [5] [3] [1]
>>>
>>> [2] http://mailman.ucar.edu/mailman/listinfo/ncl-talk [11] [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] [12] [8]
>>> [7] http://www.ncl.ucar.edu/Applications/cylineq.shtml [13] [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] [5]
>>> [2] http://uwnd.2008.nc
>>> [3] http://ftp.cgd.ucar.edu
>>> [4] HTTP://WWW.NCL.UCAR.EDU/DOCUMENT/MANUALS/ [8] [8]
>>> [5] HTTP://WWW.NCL.UCAR.EDU/APPLICATIONS/CYLINEQ.SHTML [9] [9]
>>> [6] http://www.toni-klemm.de
>>> [7] http://mailman.ucar.edu/mailman/listinfo/ncl-talk [11] [11]
>>> [8] http://www.ncl.ucar.edu/Document/Manuals/ [12] [12]
>>> [9] http://www.ncl.ucar.edu/Applications/cylineq.shtml [13] [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] [11]
>>>
>>> Guido Cioni
>>> http://guidocioni.altervista.org [14] [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] [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/ [3]
>>> [4] https://www.ubuntu.com/legal/terms-and-policies/privacy-policy
>>> [4]
>>> [5] http://MAM_GEOS_1anee.cam.h0.2000-12-07-00000.nc [5]
>>> [6] http://uwnd.2008.nc
>>> [7] http://ftp.cgd.ucar.edu
>>> [8] HTTP://WWW.NCL.UCAR.EDU/DOCUMENT/MANUALS/ [8]
>>> [9] HTTP://WWW.NCL.UCAR.EDU/APPLICATIONS/CYLINEQ.SHTML [9]
>>> [10] http://www.toni-klemm.de
>>> [11] http://mailman.ucar.edu/mailman/listinfo/ncl-talk [11]
>>> [12] http://www.ncl.ucar.edu/Document/Manuals/ [12]
>>> [13] http://www.ncl.ucar.edu/Applications/cylineq.shtml [13]
>>> [14] http://guidocioni.altervista.org [14]
>>> [15] 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
>> _______________________________________________
>> ncl-talk mailing list
>> ncl-talk at ucar.edu
>> List instructions, subscriber options, unsubscribe:
>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk [11]
>>
>>
>>
>> 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
>
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