[ncl-talk] [ncl-install] Trouble with NCL 6.4.0 (symbol not found _ZdaPvm)

Tue Mar 21 16:29:07 MDT 2017

Andrea,

If this this current installation method of NCL is giving you too much
grief, then you can try the conda installation, which has instructions here:

http://www.ncl.ucar.edu/Download/conda.shtml

Otherwise, I think you are almost there to getting this current version to
work.

What's happening is that you have one version of gfortran (6.3.0) and then
an older version of gcc (4.2.1).  NCL was compiled with gcc 6.3.0, but when
you run it on your system, it's trying to pull in your gcc 4.2.1 libraries
and failing because they are too old.

Do you have gcc installed in /usr/local/bin? You can try this:

/usr/local/bin/gcc --version

If you do have this, and it is echoing 6.3.0, then I believe the solution
is to simply make sure that /usr/local/bin is on your search path before
/usr/bin.  I know this seems a little strange, but this is somewhat how
shared libraries work.

If you don't have /usr/local/bin/gcc, then you will likely need to install
it.  You should use the same method that you used for gfortran, which I'm
guessing is that you downloaded it from hpc.sourceforge.net.  If you go to
that website, you'll see gcc 6.3.0 binaries for both El Capitan and Sierra.
Download the appropriate gcc-6.3.bin.tar.gz file for your system, and then
untar it from "/" since it is going to put everything in /usr/local.

There are instructions here:

http://www.ncl.ucar.edu/Download/macosx.shtml#InstallCompilers

But hpc.sourceforge.net also has instructions.

Good luck,

--Mary

On Tue, Mar 21, 2017 at 12:48 PM, Andrea Jenney <andrea at atmos.colostate.edu>
wrote:

> Here is what you requested:
>
>
> /Users/andrea> which gcc
> /usr/bin/gcc
>
>
> /Users/andrea> gcc --version
> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
> --with-gxx-include-dir=/Applications/Xcode.app/
> Contents/Developer/Platforms/MacOSX.platform/Developer/
> SDKs/MacOSX10.12.sdk/usr/include/c++/4.2.1
> Apple LLVM version 8.0.0 (clang-800.0.42.1)
> Target: x86_64-apple-darwin16.4.0
> Thread model: posix
> InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin
>
>
> /Users/andrea> which gfortran
> /usr/local/bin/gfortran
>
>
> /Users/andrea> gfortran --version
> GNU Fortran (GCC) 6.3.0
> Copyright (C) 2016 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.
>
>
> /Users/andrea> nm /opt/local/lib/libstdc++.6.dylib | grep
> __ZTTNSt7__cxx1118basic_stringstreamIcSt11char_traitsIcESaIcEEE
> /Applications/Xcode.app/Contents/Developer/Toolchains/
> XcodeDefault.xctoolchain/usr/bin/nm: /opt/local/lib/libstdc++.6.dylib: No
> such file or directory.
>
> Andrea
>
> On Mar 21, 2017, at 12:40 PM, Mary Haley <haley at ucar.edu> wrote:
>
> Thanks, that helps narrow it down.
>
> I think this may be an issue with your version of gcc/gfortran.
>
> Can you type the following:
>
> which gcc
> gcc --version
> which gfortran
> gfortran --version
> nm /opt/local/lib/libstdc++.6.dylib | grep __ZTTNSt7__cxx1118basic_
> stringstreamIcSt11char_traitsIcESaIcEEE
>
> and send me all of the output?
>
> If your version of gcc/gfortran is lower than 5.x, then this could be the
> problem.  I used version 5.4 to compile NCL, but I think 5.3 should work
> too, if you have it on your system.
>
>
> --Mary
>
>
>
>
>
> On Tue, Mar 21, 2017 at 12:22 PM, Andrea Jenney <
> andrea at atmos.colostate.edu> wrote:
>
>> Hi Mary,
>>
>> Yes, the new binary was installed. I am cc’ing Kelley, who has been
>> helping me with this. Here is the full text.
>>
>> dyld: Symbol not found: __ZTTNSt7__cxx1118basic_string
>> streamIcSt11char_traitsIcESaIcEEE
>>   Referenced from: /usr/local/bin/ncl
>>   Expected in: /usr/lib/libstdc++.6.dylib
>>  in /usr/local/bin/ncl
>> Abort
>>
>> Andrea
>>
>> On Mar 21, 2017, at 11:59 AM, Mary Haley <haley at ucar.edu> wrote:
>>
>> Hi Andrea,
>>
>> I'm going to take this offline for a bit.
>>
>> Did you download the new binary that I mentioned over the weekend?
>>
>> Is there more to this error message? It would help if I could see the
>> full text, if there's any.
>>
>> Thanks,
>>
>> --Mary
>>
>>
>> On Mon, Mar 20, 2017 at 2:15 PM, Andrea Jenney <
>> andrea at atmos.colostate.edu> wrote:
>>
>>> Mary,
>>>
>>> I tried everything you did here and now I am getting a different error
>>> for a different symbol not found.
>>>
>>> This one is
>>> dyld: Symbol not found: __ZTTNSt7__cxx1118basic_string
>>> streamIcSt11char_traitsIcESaIcEEE
>>>
>>> Andrea
>>>
>>> On Mar 19, 2017, at 11:43 AM, Mary Haley <haley at ucar.edu> wrote:
>>>
>>> Hi everybody,
>>>
>>> This email is for Will and Andrea and everybody else who is running into
>>> the "_ZdaPvm missing symbol" issue with the NCL 6.4.0 MacOS 10.11 (El
>>> Capitan) binary
>>>
>>> This is due to me having built NCL with the 6.1.0 GNU compilers, and
>>> you likely only have GNU 5.4.0 or earlier on your systems. Thanks to Dave
>>> Allured and Will and others who helped me debug this issue!
>>>
>>> After some fisticuffs with my El Capitan system, I was able to download
>>> and use MacPorts GNU 5.4.0 to rebuild NCL. I verified that there are no
>>> references to _ZdaPvm in the binary.
>>>
>>> Please download and try one of these binaries if you have MacOS 10.11
>>> (they can also be used on MacOS 10.12):
>>>
>>> *Non-OPeNDAP enabled binary:*
>>>
>>> https://www.earthsystemgrid.org/dataset/ncl.640.nodap/file.html
>>>
>>> Click on "ncl_ncarg-6.4.0-MacOS_10.11_64bit_nodap_gnu540.tar.gz
>>> <https://www.earthsystemgrid.org/download/fileDownload.html?logicalFileId=48c0481e-0cc9-11e7-9b99-00c0f03d5b7c>
>>> "
>>> https://www.earthsystemgrid.org/download/fileDownload.html?logicalFileId
>>> =48c0481e-0cc9-11e7-9b99-00c0f03d5b7c
>>>
>>> *OPeNDAP enabled binary:*
>>>
>>> https://www.earthsystemgrid.org/dataset/ncl.640.dap/file.html
>>>
>>> Click on "ncl_ncarg-6.4.0-MacOS_10.11_64bit_gnu540.tar.gz
>>> <https://www.earthsystemgrid.org/download/fileDownload.html?logicalFileId=d82e7332-0cc6-11e7-9b99-00c0f03d5b7c>
>>> "
>>>
>>> I would appreciate hearing from anybody who is able to successfully use
>>> these binaries, especially from folks who ran into the "_ZdaPvm" issue,
>>> so I know if I can resolve this.
>>>
>>> Thanks,
>>>
>>> --Mary
>>>
>>>
>>>
>>> On Thu, Mar 16, 2017 at 4:22 PM, Will Hobbs <will.hobbs at utas.edu.au>
>>> wrote:
>>>
>>>> Andrea
>>>>
>>>>
>>>>
>>>> I already responded to Mary; I updated al my Macports stuff but it
>>>> hasn’t helped.
>>>>
>>>>
>>>>
>>>> Will
>>>>
>>>>
>>>>
>>>> *From: *<ncl-install-bounces at ucar.edu> on behalf of Mary Haley <
>>>> haley at ucar.edu>
>>>> *Date: *Friday, 17 March 2017 at 6:36 AM
>>>> *To: *Andrea Jenney <andrea at atmos.colostate.edu>
>>>> *Cc: *"ncl-install at ucar.edu" <ncl-install at ucar.edu>
>>>> *Subject: *Re: [ncl-install] Trouble with NCL 6.4.0 (symbol not found
>>>> _ZdaPvm)
>>>>
>>>>
>>>>
>>>> Andrea,
>>>>
>>>>
>>>>
>>>> You are the third person to report this problem.  The first person said
>>>> that what worked for him was to upgrade his MacPort installation.  I'm
>>>> waiting to hear back from the second person as to whether this solution
>>>> works for him as well.
>>>>
>>>>
>>>>
>>>> I think the issue is that we used the HPC GNU compilers to build NCL,
>>>> and if you have the MacPort version of the compilers, then this missing
>>>> symbol shows up if your MacPorts is old.
>>>>
>>>>
>>>>
>>>> Have you updated MacPorts since upgrading to Sierra?
>>>>
>>>>
>>>>
>>>> The other possible solution is to download the HPC version of the GNU
>>>> compilers, which will get installed to /usr/local and hence won't overwrite
>>>> your MacPorts version that's in /opt/local. Follow this link for more
>>>> details:
>>>>
>>>>
>>>>
>>>> http://www.ncl.ucar.edu/Download/macosx.shtml#InstallCompilers
>>>>
>>>>
>>>>
>>>> If you find the solution, can you let me know so I can make sure other
>>>> users are aware of it?
>>>>
>>>>
>>>> Thanks,
>>>>
>>>>
>>>>
>>>> --Mary
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, Mar 16, 2017 at 11:03 AM, Andrea Jenney <
>>>> andrea at atmos.colostate.edu> wrote:
>>>>
>>>> Hi ncl-install,
>>>>
>>>>
>>>>
>>>> I have been trying to update to the latest release of NCL (6.4.0) and I
>>>> have been encountering this error message when I try to run it:
>>>>
>>>>
>>>>
>>>> dyld: Symbol not found: __ZdaPvm
>>>>   Referenced from: /usr/local/bin/ncl
>>>>   Expected in: /usr/lib/libstdc++.6.dylib
>>>>  in /usr/local/bin/ncl
>>>> Abort
>>>>
>>>>
>>>>
>>>> I have tried updating to the newest operating system (Mac OS
>>>> 10.12.3-Sierra), updating gfortran, and reinstalling the X11 libraries as
>>>> well as updating to the newest Xquartz. What seems to be the problem?
>>>>
>>>>
>>>>
>>>> Thank you!
>>>>
>>>>
>>>>
>>>> Andrea
>>>>
>>>> ---
>>>>
>>>> Andrea Jenney
>>>> Graduate Research Assistant | Randall Group
>>>>
>>>> Colorado State University | Department of Atmospheric Science
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>>
>>>>
>>>>
>>>>
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>>>
>>>
>>> ---
>>> Andrea Jenney
>>> Graduate Research Assistant | Randall Group
>>> Colorado State University | Department of Atmospheric Science
>>>
>>>
>>>
>>>
>>>
>>
>> ---
>> Andrea Jenney
>> Graduate Research Assistant | Randall Group
>> Colorado State University | Department of Atmospheric Science
>>
>>
>>
>>
>>
>
> ---
> Andrea Jenney
> Graduate Research Assistant | Randall Group
> Colorado State University | Department of Atmospheric Science
>
>
>
>
>
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