[MacPorts] #53031: macports ncl fails, mac install of ncarg works

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[MacPorts] #53031: macports ncl fails, mac install of ncarg works

MacPorts
#53031: macports ncl fails, mac install of ncarg works
--------------------+-------------------
 Reporter:  basmac  |      Owner:
     Type:  defect  |     Status:  new
 Priority:  Normal  |  Milestone:
Component:  ports   |    Version:  2.3.5
 Keywords:  ncl     |       Port:  ncarg
--------------------+-------------------
 Running the same script the macports /opt/local crashes with an error,
 whereas a separate default install of ncarg/ncl works from /usr/local.

 Attached is the log, running /opt/local ncl first then /usr/local ncl
 second using ( ncarg @6.3.0_8+gcc6 (active))

 macports fails on ElCap or new install on Sierra. The attached log is
 Sierra, but has the same error, on ElCap (ncarg @6.3.0_9+gcc5 (active))

 The library script ESMF_regridding.ncl are the same size in
 /usr/local/ncl/ as under /opt/local.

--
Ticket URL: <https://trac.macports.org/ticket/53031>
MacPorts <https://www.macports.org/>
Ports system for macOS
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Re: [MacPorts] #53031: macports ncl fails, mac install of ncarg works

MacPorts
#53031: macports ncl fails, mac install of ncarg works
---------------------+-------------------
  Reporter:  basmac  |      Owner:
      Type:  defect  |     Status:  new
  Priority:  Normal  |  Milestone:
 Component:  ports   |    Version:  2.3.5
Resolution:          |   Keywords:  ncl
      Port:  ncarg   |
---------------------+-------------------
Changes (by basmac):

 * Attachment "ncl.mac27.log" added.


--
Ticket URL: <https://trac.macports.org/ticket/53031>
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Re: [MacPorts] #53031: macports ncl fails, mac install of ncarg works

MacPorts
In reply to this post by MacPorts
#53031: macports ncl fails, mac install of ncarg works
---------------------+----------------------
  Reporter:  basmac  |      Owner:  tenomoto
      Type:  defect  |     Status:  assigned
  Priority:  Normal  |  Milestone:
 Component:  ports   |    Version:  2.3.5
Resolution:          |   Keywords:
      Port:  ncarg   |
---------------------+----------------------
Changes (by mf2k):

 * cc: takeshi@… (removed)
 * status:  new => assigned
 * owner:   => tenomoto
 * keywords:  ncl =>


--
Ticket URL: <https://trac.macports.org/ticket/53031#comment:1>
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Re: [MacPorts] #53031: macports ncl fails, mac install of ncarg works

MacPorts
In reply to this post by MacPorts
#53031: macports ncl fails, mac install of ncarg works
---------------------+----------------------
  Reporter:  basmac  |      Owner:  tenomoto
      Type:  defect  |     Status:  assigned
  Priority:  Normal  |  Milestone:
 Component:  ports   |    Version:  2.3.5
Resolution:          |   Keywords:
      Port:  ncarg   |
---------------------+----------------------

Comment (by tenomoto):

 Thanks for reporting. I was able to reproduce the problem, but I don't
 have a solution at the moment.

 It appears that {{{setfileoption}}} break the symbol table and {{{Opt}}}
 becomes undefined,
 I attach the simple script to cause the error.

 BTW, I'd like to draw your attention the warning message on line 47.

 {{{
 warning:["Palette.c":1850]:NhlLoadColormapFiles: Invalid colormap
 directory: /opt/local/ncl/lib/ncarg/colormaps
 }}}


 The default {{{NCARG_COLORMAPS}}} should be
 {{{/opt/local/lib/ncarg/colormaps}}}.

--
Ticket URL: <https://trac.macports.org/ticket/53031#comment:2>
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Re: [MacPorts] #53031: macports ncl fails, mac install of ncarg works

MacPorts
In reply to this post by MacPorts
#53031: macports ncl fails, mac install of ncarg works
---------------------+----------------------
  Reporter:  basmac  |      Owner:  tenomoto
      Type:  defect  |     Status:  assigned
  Priority:  Normal  |  Milestone:
 Component:  ports   |    Version:  2.3.5
Resolution:          |   Keywords:
      Port:  ncarg   |
---------------------+----------------------
Changes (by tenomoto):

 * Attachment "bar.ncl" added.


--
Ticket URL: <https://trac.macports.org/ticket/53031>
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Re: [MacPorts] #53031: macports ncl fails, mac install of ncarg works

MacPorts
In reply to this post by MacPorts
#53031: macports ncl fails, mac install of ncarg works
---------------------+----------------------
  Reporter:  basmac  |      Owner:  tenomoto
      Type:  defect  |     Status:  assigned
  Priority:  Normal  |  Milestone:
 Component:  ports   |    Version:  2.3.5
Resolution:          |   Keywords:
      Port:  ncarg   |
---------------------+----------------------

Comment (by basmac):

 Hi,
 thanks for finding the issue, when I run your bar.ncl I get the following.
 Is this what we are supposed to get ?

 [mac27:~] bmcinnes% ncl bar.ncl
  Copyright (C) 1995-2015 - All Rights Reserved
  University Corporation for Atmospheric Research
  NCAR Command Language Version 6.3.0
  The use of this software is governed by a License Agreement.
  See http://www.ncl.ucar.edu/ for more details.


 Variable: nc_file_type
 Type: string
 Total Size: 8 bytes
             1 values
 Number of Dimensions: 1
 Dimensions and sizes:    [1]
 Coordinates:
 (0)    netcdf3
 fatal:Variable (nc_file_type) is undefined
 fatal:["Execute.c":8575]:Execute: Error occurred at or near line 10 in
 file bar.ncl

 fatal:["Execute.c":8575]:Execute: Error occurred at or near line 16 in
 file bar.ncl

 [mac27:~] bmcinnes%

 I am not sure if this is related, but the user also has this issue, for
 your information

 I made a script that tests both the regridding and the ability to plot
 .png files. Here is the output when I try to run it using the /usr/local
 NCL version:

 [mac72:~/NCL/NCLtalk/NCLmacports] mgehne% setenv NCARG_ROOT /usr/local

 [mac72:~/NCL/NCLtalk/NCLmacports] mgehne% setenv PATH /usr/local/$PATH

 [mac72:~/NCL/NCLtalk/NCLmacports] mgehne% source ~/.tcshrc

 [mac72:~/NCL/NCLtalk/NCLmacports] mgehne% ncl test_regrid_plot.ncl

  Copyright (C) 1995-2015 - All Rights Reserved

  University Corporation for Atmospheric Research

  NCAR Command Language Version 6.3.0

  The use of this software is governed by a License Agreement.

  See http://www.ncl.ucar.edu/ for more details.

 (0)     Regrid option is on.

 (0)     Plot option is on.

 (0)     defining data array


 Variable: data

 Type: float

 Total Size: 259200 bytes

             64800 values

 Number of Dimensions: 2

 Dimensions and sizes:   [lat | 180] x [lon | 360]

 Coordinates:

             lat: [-89.5..89.5]

             lon: [ 0..359]

 (0)     Regridding!

 (0)     defining new lat and lon arrays

 (0)     defining options for regridding

 (0)     Regridding using method = neareststod

 dyld: Library not loaded: /usr/local/lib/libgfortran.3.dylib

   Referenced from: /usr/local/ncl/bin/ESMF_RegridWeightGen

   Reason: image not found

 fatal:The result of the conditional expression yields a missing value. NCL
 can not determine branch, see ismissing function

 fatal:["Execute.c":8575]:Execute: Error occurred at or near line 2938 in
 file $NCARG_ROOT/lib/ncarg/nclscripts/esmf/ESMF_regridding.ncl


 fatal:["Execute.c":8575]:Execute: Error occurred at or near line 4027 in
 file $NCARG_ROOT/lib/ncarg/nclscripts/esmf/ESMF_regridding.ncl


 fatal:["Execute.c":8575]:Execute: Error occurred at or near line 69 in
 file test_regrid_plot.ncl


 [mac72:~/NCL/NCLtalk/NCLmacports] mgehne% which ncl

 /usr/local/bin/ncl

 [mac72:~/NCL/NCLtalk/NCLmacports] mgehne% env | grep NCARG

 NCARG_ROOT=/usr/local

 NCARG_COLORMAPS=/Users/mgehne/NCL/Colormaps:/usr/local/lib/ncarg/colormaps


 This is a slightly different error message than I have been getting
 previously.


 I also attached the test script if you feel like running that on your
 machine. Setting the options at the beginning to False turns off the
 regridding or plotting.

--
Ticket URL: <https://trac.macports.org/ticket/53031#comment:3>
MacPorts <https://www.macports.org/>
Ports system for macOS
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Re: [MacPorts] #53031: macports ncl fails, mac install of ncarg works

MacPorts
In reply to this post by MacPorts
#53031: macports ncl fails, mac install of ncarg works
---------------------+----------------------
  Reporter:  basmac  |      Owner:  tenomoto
      Type:  defect  |     Status:  assigned
  Priority:  Normal  |  Milestone:
 Component:  ports   |    Version:  2.3.5
Resolution:          |   Keywords:
      Port:  ncarg   |
---------------------+----------------------
Changes (by basmac):

 * Attachment "test_regrid_plot.ncl" added.


--
Ticket URL: <https://trac.macports.org/ticket/53031>
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Re: [MacPorts] #53031: macports ncl fails, mac install of ncarg works

MacPorts
In reply to this post by MacPorts
#53031: macports ncl fails, mac install of ncarg works
---------------------+----------------------
  Reporter:  basmac  |      Owner:  tenomoto
      Type:  defect  |     Status:  assigned
  Priority:  Normal  |  Milestone:
 Component:  ports   |    Version:  2.3.5
Resolution:          |   Keywords:
      Port:  ncarg   |
---------------------+----------------------

Comment (by basmac):

 On clean mac Sierra and ncl 6.3.0 in /usr/local/, your test fails for
 /opt/local version of ncl and works on /usr/local version which is 10.10.

 [mac27:~] bmcinnes% cd
 [mac27:~] bmcinnes% setenv NCARG_ROOT /opt/local
 [mac27:~] bmcinnes% ncl bar.ncl
  Copyright (C) 1995-2015 - All Rights Reserved
  University Corporation for Atmospheric Research
  NCAR Command Language Version 6.3.0
  The use of this software is governed by a License Agreement.
  See http://www.ncl.ucar.edu/ for more details.


 Variable: nc_file_type
 Type: string
 Total Size: 8 bytes
             1 values
 Number of Dimensions: 1
 Dimensions and sizes:   [1]
 Coordinates:
 (0)     netcdf3
 fatal:Variable (nc_file_type) is undefined
 fatal:["Execute.c":8575]:Execute: Error occurred at or near line 10 in
 file bar.ncl

 fatal:["Execute.c":8575]:Execute: Error occurred at or near line 16 in
 file bar.ncl

 [mac27:~] bmcinnes% /usr/local/bin/ncl bar.ncl
  Copyright (C) 1995-2015 - All Rights Reserved
  University Corporation for Atmospheric Research
  NCAR Command Language Version 6.3.0
  The use of this software is governed by a License Agreement.
  See http://www.ncl.ucar.edu/ for more details.


 Variable: nc_file_type
 Type: string
 Total Size: 8 bytes
             1 values
 Number of Dimensions: 1
 Dimensions and sizes:   [1]
 Coordinates:
 (0)     netcdf3


 Variable: nc_file_type
 Type: string
 Total Size: 8 bytes
             1 values
 Number of Dimensions: 1
 Dimensions and sizes:   [1]
 Coordinates:
 (0)     netcdf4


 Variable: nc_file_type
 Type: string
 Total Size: 8 bytes
             1 values
 Number of Dimensions: 1
 Dimensions and sizes:   [1]
 Coordinates:
 (0)     netcdf3
 [mac27:~] bmcinnes%

--
Ticket URL: <https://trac.macports.org/ticket/53031#comment:4>
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Re: [MacPorts] #53031: macports ncl fails, mac install of ncarg works

MacPorts
In reply to this post by MacPorts
#53031: macports ncl fails, mac install of ncarg works
---------------------+----------------------
  Reporter:  basmac  |      Owner:  tenomoto
      Type:  defect  |     Status:  assigned
  Priority:  Normal  |  Milestone:
 Component:  ports   |    Version:  2.3.5
Resolution:          |   Keywords:
      Port:  ncarg   |
---------------------+----------------------

Comment (by basmac):

 The latest binary of ncarg 6.4.0 does not give the error using the test
 bar.ncl.

 Can we get that installed into macports ?

 thanks

--
Ticket URL: <https://trac.macports.org/ticket/53031#comment:5>
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Re: [MacPorts] #53031: macports ncl fails, mac install of ncarg works

MacPorts
In reply to this post by MacPorts
#53031: macports ncl fails, mac install of ncarg works
---------------------+----------------------
  Reporter:  basmac  |      Owner:  tenomoto
      Type:  defect  |     Status:  assigned
  Priority:  Normal  |  Milestone:
 Component:  ports   |    Version:  2.3.5
Resolution:          |   Keywords:
      Port:  ncarg   |
---------------------+----------------------
Changes (by Dave-Allured):

 * Attachment "test3.setfileoption.ncl" added.

 Reduced bug demo script

--
Ticket URL: <https://trac.macports.org/ticket/53031>
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Re: [MacPorts] #53031: macports ncl fails, mac install of ncarg works

MacPorts
In reply to this post by MacPorts
#53031: macports ncl fails, mac install of ncarg works
---------------------+----------------------
  Reporter:  basmac  |      Owner:  tenomoto
      Type:  defect  |     Status:  assigned
  Priority:  Normal  |  Milestone:
 Component:  ports   |    Version:  2.3.5
Resolution:          |   Keywords:
      Port:  ncarg   |
---------------------+----------------------

Comment (by Dave-Allured):

 Here is a more reduced demo for the `setfileoption` bug:

 {{{
 procedure test3 ()
 begin
   setfileoption ("nc", "Format", "Classic")
   x = 99
   print (x+"")
 end

 begin
   test3 ()
 end
 }}}

 This should just print "99" if NCL is working correctly.  With current
 build ncarg.6.4.0_9 it gets this error, which is equivalent to the
 previously reported errors:

 {{{
 > ncl test3.setfileoption.ncl
  NCAR Command Language Version 6.4.0
 fatal:Variable (x) is undefined
 fatal:["Execute.c":8640]:Execute: Error occurred at or near line 5 in file
 test3.setfileoption.ncl
 fatal:["Execute.c":8640]:Execute: Error occurred at or near line 9 in file
 test3.setfileoption.ncl
 }}}

 The previous test script, bar.ncl, is longer than needed, and it contains
 an unrelated bug that can also corrupt NCL execution and print more
 confusing errors.  The problem is a missing "undef" statement at the top,
 not related to the current issue.

 I agree with Takeshi's previous observation that `setfileoption` appears
 to break the symbol table.

--
Ticket URL: <https://trac.macports.org/ticket/53031#comment:6>
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Re: [MacPorts] #53031: macports ncl fails, mac install of ncarg works

MacPorts
In reply to this post by MacPorts
#53031: macports ncl fails, mac install of ncarg works
---------------------+----------------------
  Reporter:  basmac  |      Owner:  tenomoto
      Type:  defect  |     Status:  assigned
  Priority:  Normal  |  Milestone:
 Component:  ports   |    Version:  2.3.5
Resolution:          |   Keywords:
      Port:  ncarg   |
---------------------+----------------------

Comment (by tenomoto):

 `setfileoption` in ncarg 6.5.0 causes Segmentation Fault 11 on High
 Sierra. In the past the problem disappeared with some compilers #38687. So
 I tried a few versions of gcc only to fail. I have no idea how to fix this
 at the moment. I decided to revert to 6.4.0.
 [cdde049ce2176cdef35c2e8737f718b9d4dae9d2/macports-ports].

--
Ticket URL: <https://trac.macports.org/ticket/53031#comment:8>
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Re: [MacPorts] #53031: macports ncl fails, mac install of ncarg works

MacPorts
In reply to this post by MacPorts
#53031: macports ncl fails, mac install of ncarg works
---------------------+----------------------
  Reporter:  basmac  |      Owner:  tenomoto
      Type:  defect  |     Status:  closed
  Priority:  Normal  |  Milestone:
 Component:  ports   |    Version:  2.3.5
Resolution:  fixed   |   Keywords:
      Port:  ncarg   |
---------------------+----------------------
Changes (by tenomoto):

 * status:  assigned => closed
 * resolution:   => fixed


Comment:

 In [changeset:"278e517b8e560b682d4a9c5ed79f9ee74530482f/macports-ports"
 278e517b8e560b682d4a9c5ed79f9ee74530482f/macports-ports] (master):
 {{{
 #!ConfigurableCommitTicketReference repository="macports-ports"
 revision="278e517b8e560b682d4a9c5ed79f9ee74530482f"
 ncarg: update (again) to 6.5.0

 Closes: https://trac.macports.org/ticket/53031
 Closes: https://trac.macports.org/ticket/56870
 }}}

--
Ticket URL: <https://trac.macports.org/ticket/53031#comment:9>
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Re: [MacPorts] #53031: macports ncl fails, mac install of ncarg works

MacPorts
In reply to this post by MacPorts
#53031: macports ncl fails, mac install of ncarg works
---------------------+----------------------
  Reporter:  basmac  |      Owner:  tenomoto
      Type:  defect  |     Status:  closed
  Priority:  Normal  |  Milestone:
 Component:  ports   |    Version:  2.3.5
Resolution:  fixed   |   Keywords:
      Port:  ncarg   |
---------------------+----------------------

Comment (by Dave-Allured):

 For the record only, I got this information from an NCARG/NCL developer a
 while back:

   "The one library that I see that could potentially be an issue is HDF5
 1.10.x.  You cannot build or link NCL V6.4.0 against this version of HDF5.
 You must use HDF 1.8.x. All the other libraries look okay to me, but I
 have to admit that I haven't tried this exact pairing of everything, so
 there could be something I'm not aware of.  HDF5 1.10 just flat out
 shouldn't work with NCL640, so I'm a bit surprised to see that and not
 have heard from more people running into problems."

   "In NCL V6.5.0, you *can* link against HDF5 1.10.x."

 When this ticket #53031 was active (2016 Dec. to 2018 Aug.), MacPorts
 NCARG V6.4.0 was indeed building against HDF5 1.10.x.  Therefore I think
 it is likely that this version incompatibility was behind the
 `setfileoption` bug and other problems.

--
Ticket URL: <https://trac.macports.org/ticket/53031#comment:10>
MacPorts <https://www.macports.org/>
Ports system for macOS