[Met_help] [rt.rap.ucar.edu #77118] History for compiling METv5.1 - issue linking gsl
Julie Prestopnik via RT
met_help at ucar.edu
Thu Jul 28 12:44:44 MDT 2016
----------------------------------------------------------------
Initial Request
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Dear Met Help,
I am trying to compile METv5.1 on a new Linux system ( 2.6.32-573.7.1.el6.x86_64 GNU/Linux). I have disabled all options except mode and mode_analysis. From what I can tell, make install runs without error (I attached the make.log file), but the GSL library is never correctly linked in, and so the mode and mode_analysis executables fail with the following error:
./mode_analysis: error while loading shared libraries: libgsl.so.19: cannot open shared object file: No such file or directory
GSL is correctly installed, the libraries in question are on the system, and MET_GSLLIB and MET_GSLINC are defined variables before running configure. When I look at the make.log file, the libraries appear to be linked in correctly. Any idea what I’m doing wrong?
Thanks,
Becky Adams-Selin, Ph.D.
Staff Scientist II
Atmospheric and Environmental Research, Inc.
________________________________
This email is intended solely for the recipient. It may contain privileged, proprietary or confidential information or material. If you are not the intended recipient, please delete this email and any attachments and notify the sender of the error.
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Complete Ticket History
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Subject: Re: [rt.rap.ucar.edu #77118] compiling METv5.1 - issue linking gsl
From: Julie Prestopnik
Time: Wed Jul 13 10:27:53 2016
Hi Becky.
By default, MET version 5.1 is compiled using dynamic linking. Rather
than compiling the external library code in with the MET executables,
which is called static linking, it looks for them at runtime. And it
is looking for those "shared object" (.so) library files.
This should be easy to fix, we just need to tell it where to find
them, and we do that by setting (or adding to) the LD_LIBRARY_PATH.
Look in your ~/.cshrc file (or other shell startup configuration
file). If LD_LIBRARY_PATH is already defined in there, add
"/network/home/rselin/MET/gsl-2.1/lib" to the end of it. If not, add:
setenv LD_LIBRARY_PATH /network/home/rselin/MET/gsl-2.1/lib
Then, save that change and source that file:
source ~/.cshrc
Please give that a try, and let me know if that fixes the issue.
Thanks,
Julie
On Tue, Jul 12, 2016 at 2:31 PM, Adams-Selin, Becky via RT
<met_help at ucar.edu> wrote:
>
> Tue Jul 12 14:31:52 2016: Request 77118 was acted upon.
> Transaction: Ticket created by RSelin at aer.com
> Queue: met_help
> Subject: compiling METv5.1 - issue linking gsl
> Owner: Nobody
> Requestors: RSelin at aer.com
> Status: new
> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=77118 >
>
>
> Dear Met Help,
>
> I am trying to compile METv5.1 on a new Linux system ( 2.6.32-
573.7.1.el6.x86_64 GNU/Linux). I have disabled all options except
mode and mode_analysis. From what I can tell, make install runs
without error (I attached the make.log file), but the GSL library is
never correctly linked in, and so the mode and mode_analysis
executables fail with the following error:
>
> ./mode_analysis: error while loading shared libraries: libgsl.so.19:
cannot open shared object file: No such file or directory
>
> GSL is correctly installed, the libraries in question are on the
system, and MET_GSLLIB and MET_GSLINC are defined variables before
running configure. When I look at the make.log file, the libraries
appear to be linked in correctly. Any idea what I’m doing wrong?
>
> Thanks,
>
> Becky Adams-Selin, Ph.D.
> Staff Scientist II
> Atmospheric and Environmental Research, Inc.
>
>
> ________________________________
>
> This email is intended solely for the recipient. It may contain
privileged, proprietary or confidential information or material. If
you are not the intended recipient, please delete this email and any
attachments and notify the sender of the error.
>
--
Julie Prestopnik
National Center for Atmospheric Research
Research Applications Laboratory
Phone: 303.497.8399
Email: jpresto at ucar.edu
------------------------------------------------
Subject: Re: [rt.rap.ucar.edu #77118] compiling METv5.1 - issue linking gsl
From: Adams-Selin, Becky
Time: Wed Jul 13 12:08:13 2016
That worked, thanks Julie! I¹d recommend editing Section 2.9 of the
MET
users¹ guide to include that helpful tip.
Becky Adams-Selin, Ph.D.
Staff Scientist II
Atmospheric and Environmental Research, Inc.
On 7/13/16, 11:27 AM, "Julie Prestopnik via RT" <met_help at ucar.edu>
wrote:
>Hi Becky.
>
>By default, MET version 5.1 is compiled using dynamic linking.
Rather
>than compiling the external library code in with the MET executables,
>which is called static linking, it looks for them at runtime. And it
>is looking for those "shared object" (.so) library files.
>
>This should be easy to fix, we just need to tell it where to find
>them, and we do that by setting (or adding to) the LD_LIBRARY_PATH.
>Look in your ~/.cshrc file (or other shell startup configuration
>file). If LD_LIBRARY_PATH is already defined in there, add
>"/network/home/rselin/MET/gsl-2.1/lib" to the end of it. If not,
add:
>
> setenv LD_LIBRARY_PATH /network/home/rselin/MET/gsl-2.1/lib
>
>Then, save that change and source that file:
>
> source ~/.cshrc
>
>Please give that a try, and let me know if that fixes the issue.
>
>Thanks,
>Julie
>
>On Tue, Jul 12, 2016 at 2:31 PM, Adams-Selin, Becky via RT
><met_help at ucar.edu> wrote:
>>
>> Tue Jul 12 14:31:52 2016: Request 77118 was acted upon.
>> Transaction: Ticket created by RSelin at aer.com
>> Queue: met_help
>> Subject: compiling METv5.1 - issue linking gsl
>> Owner: Nobody
>> Requestors: RSelin at aer.com
>> Status: new
>> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=77118 >
>>
>>
>> Dear Met Help,
>>
>> I am trying to compile METv5.1 on a new Linux system (
>>2.6.32-573.7.1.el6.x86_64 GNU/Linux). I have disabled all options
>>except mode and mode_analysis. From what I can tell, make install
runs
>>without error (I attached the make.log file), but the GSL library is
>>never correctly linked in, and so the mode and mode_analysis
executables
>>fail with the following error:
>>
>> ./mode_analysis: error while loading shared libraries:
libgsl.so.19:
>>cannot open shared object file: No such file or directory
>>
>> GSL is correctly installed, the libraries in question are on the
>>system, and MET_GSLLIB and MET_GSLINC are defined variables before
>>running configure. When I look at the make.log file, the libraries
>>appear to be linked in correctly. Any idea what I¹m doing wrong?
>>
>> Thanks,
>>
>> Becky Adams-Selin, Ph.D.
>> Staff Scientist II
>> Atmospheric and Environmental Research, Inc.
>>
>>
>> ________________________________
>>
>> This email is intended solely for the recipient. It may contain
>>privileged, proprietary or confidential information or material. If
you
>>are not the intended recipient, please delete this email and any
>>attachments and notify the sender of the error.
>>
>
>
>
>--
>Julie Prestopnik
>National Center for Atmospheric Research
>Research Applications Laboratory
>Phone: 303.497.8399
>Email: jpresto at ucar.edu
>
>
________________________________
This email is intended solely for the recipient. It may contain
privileged, proprietary or confidential information or material. If
you are not the intended recipient, please delete this email and any
attachments and notify the sender of the error.
------------------------------------------------
Subject: Re: [rt.rap.ucar.edu #77118] compiling METv5.1 - issue linking gsl
From: Julie Prestopnik
Time: Wed Jul 13 12:13:26 2016
I'm glad that worked! Thank you for the suggestion, Becky. We always
appreciate that kind of feedback.
Julie
On Wed, Jul 13, 2016 at 12:08 PM, Adams-Selin, Becky via RT
<met_help at ucar.edu> wrote:
>
> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=77118 >
>
> That worked, thanks Julie! I¹d recommend editing Section 2.9 of the
MET
> users¹ guide to include that helpful tip.
>
> Becky Adams-Selin, Ph.D.
> Staff Scientist II
> Atmospheric and Environmental Research, Inc.
>
>
>
>
>
> On 7/13/16, 11:27 AM, "Julie Prestopnik via RT" <met_help at ucar.edu>
wrote:
>
>>Hi Becky.
>>
>>By default, MET version 5.1 is compiled using dynamic linking.
Rather
>>than compiling the external library code in with the MET
executables,
>>which is called static linking, it looks for them at runtime. And
it
>>is looking for those "shared object" (.so) library files.
>>
>>This should be easy to fix, we just need to tell it where to find
>>them, and we do that by setting (or adding to) the LD_LIBRARY_PATH.
>>Look in your ~/.cshrc file (or other shell startup configuration
>>file). If LD_LIBRARY_PATH is already defined in there, add
>>"/network/home/rselin/MET/gsl-2.1/lib" to the end of it. If not,
add:
>>
>> setenv LD_LIBRARY_PATH /network/home/rselin/MET/gsl-2.1/lib
>>
>>Then, save that change and source that file:
>>
>> source ~/.cshrc
>>
>>Please give that a try, and let me know if that fixes the issue.
>>
>>Thanks,
>>Julie
>>
>>On Tue, Jul 12, 2016 at 2:31 PM, Adams-Selin, Becky via RT
>><met_help at ucar.edu> wrote:
>>>
>>> Tue Jul 12 14:31:52 2016: Request 77118 was acted upon.
>>> Transaction: Ticket created by RSelin at aer.com
>>> Queue: met_help
>>> Subject: compiling METv5.1 - issue linking gsl
>>> Owner: Nobody
>>> Requestors: RSelin at aer.com
>>> Status: new
>>> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=77118 >
>>>
>>>
>>> Dear Met Help,
>>>
>>> I am trying to compile METv5.1 on a new Linux system (
>>>2.6.32-573.7.1.el6.x86_64 GNU/Linux). I have disabled all options
>>>except mode and mode_analysis. From what I can tell, make install
runs
>>>without error (I attached the make.log file), but the GSL library
is
>>>never correctly linked in, and so the mode and mode_analysis
executables
>>>fail with the following error:
>>>
>>> ./mode_analysis: error while loading shared libraries:
libgsl.so.19:
>>>cannot open shared object file: No such file or directory
>>>
>>> GSL is correctly installed, the libraries in question are on the
>>>system, and MET_GSLLIB and MET_GSLINC are defined variables before
>>>running configure. When I look at the make.log file, the libraries
>>>appear to be linked in correctly. Any idea what I¹m doing wrong?
>>>
>>> Thanks,
>>>
>>> Becky Adams-Selin, Ph.D.
>>> Staff Scientist II
>>> Atmospheric and Environmental Research, Inc.
>>>
>>>
>>> ________________________________
>>>
>>> This email is intended solely for the recipient. It may contain
>>>privileged, proprietary or confidential information or material. If
you
>>>are not the intended recipient, please delete this email and any
>>>attachments and notify the sender of the error.
>>>
>>
>>
>>
>>--
>>Julie Prestopnik
>>National Center for Atmospheric Research
>>Research Applications Laboratory
>>Phone: 303.497.8399
>>Email: jpresto at ucar.edu
>>
>>
>
>
> ________________________________
>
> This email is intended solely for the recipient. It may contain
privileged, proprietary or confidential information or material. If
you are not the intended recipient, please delete this email and any
attachments and notify the sender of the error.
>
>
>
--
Julie Prestopnik
National Center for Atmospheric Research
Research Applications Laboratory
Phone: 303.497.8399
Email: jpresto at ucar.edu
------------------------------------------------
Subject: Re: [rt.rap.ucar.edu #77118] compiling METv5.1 - issue linking gsl
From: Julie Prestopnik
Time: Tue Jul 19 12:59:48 2016
Hi Becky. I just wanted to follow up. I added information about this
problem to section 2.9 and also to the troubleshooting section, so
future versions of the MET User's Guide (in future releases) will
contain this information. Thanks for the feedback and for trying to
troubleshoot using the MET User's Guide. I'll go ahead and close this
ticket for now. Please let us know if you run into any other
difficulties.
Julie
On Wed, Jul 13, 2016 at 12:13 PM, Julie Prestopnik <jpresto at ucar.edu>
wrote:
> I'm glad that worked! Thank you for the suggestion, Becky. We
always
> appreciate that kind of feedback.
>
> Julie
>
> On Wed, Jul 13, 2016 at 12:08 PM, Adams-Selin, Becky via RT
> <met_help at ucar.edu> wrote:
>>
>> <URL: https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=77118 >
>>
>> That worked, thanks Julie! I¹d recommend editing Section 2.9 of
the MET
>> users¹ guide to include that helpful tip.
>>
>> Becky Adams-Selin, Ph.D.
>> Staff Scientist II
>> Atmospheric and Environmental Research, Inc.
>>
>>
>>
>>
>>
>> On 7/13/16, 11:27 AM, "Julie Prestopnik via RT" <met_help at ucar.edu>
wrote:
>>
>>>Hi Becky.
>>>
>>>By default, MET version 5.1 is compiled using dynamic linking.
Rather
>>>than compiling the external library code in with the MET
executables,
>>>which is called static linking, it looks for them at runtime. And
it
>>>is looking for those "shared object" (.so) library files.
>>>
>>>This should be easy to fix, we just need to tell it where to find
>>>them, and we do that by setting (or adding to) the LD_LIBRARY_PATH.
>>>Look in your ~/.cshrc file (or other shell startup configuration
>>>file). If LD_LIBRARY_PATH is already defined in there, add
>>>"/network/home/rselin/MET/gsl-2.1/lib" to the end of it. If not,
add:
>>>
>>> setenv LD_LIBRARY_PATH /network/home/rselin/MET/gsl-2.1/lib
>>>
>>>Then, save that change and source that file:
>>>
>>> source ~/.cshrc
>>>
>>>Please give that a try, and let me know if that fixes the issue.
>>>
>>>Thanks,
>>>Julie
>>>
>>>On Tue, Jul 12, 2016 at 2:31 PM, Adams-Selin, Becky via RT
>>><met_help at ucar.edu> wrote:
>>>>
>>>> Tue Jul 12 14:31:52 2016: Request 77118 was acted upon.
>>>> Transaction: Ticket created by RSelin at aer.com
>>>> Queue: met_help
>>>> Subject: compiling METv5.1 - issue linking gsl
>>>> Owner: Nobody
>>>> Requestors: RSelin at aer.com
>>>> Status: new
>>>> Ticket <URL:
https://rt.rap.ucar.edu/rt/Ticket/Display.html?id=77118 >
>>>>
>>>>
>>>> Dear Met Help,
>>>>
>>>> I am trying to compile METv5.1 on a new Linux system (
>>>>2.6.32-573.7.1.el6.x86_64 GNU/Linux). I have disabled all options
>>>>except mode and mode_analysis. From what I can tell, make install
runs
>>>>without error (I attached the make.log file), but the GSL library
is
>>>>never correctly linked in, and so the mode and mode_analysis
executables
>>>>fail with the following error:
>>>>
>>>> ./mode_analysis: error while loading shared libraries:
libgsl.so.19:
>>>>cannot open shared object file: No such file or directory
>>>>
>>>> GSL is correctly installed, the libraries in question are on the
>>>>system, and MET_GSLLIB and MET_GSLINC are defined variables before
>>>>running configure. When I look at the make.log file, the
libraries
>>>>appear to be linked in correctly. Any idea what I¹m doing wrong?
>>>>
>>>> Thanks,
>>>>
>>>> Becky Adams-Selin, Ph.D.
>>>> Staff Scientist II
>>>> Atmospheric and Environmental Research, Inc.
>>>>
>>>>
>>>> ________________________________
>>>>
>>>> This email is intended solely for the recipient. It may contain
>>>>privileged, proprietary or confidential information or material.
If you
>>>>are not the intended recipient, please delete this email and any
>>>>attachments and notify the sender of the error.
>>>>
>>>
>>>
>>>
>>>--
>>>Julie Prestopnik
>>>National Center for Atmospheric Research
>>>Research Applications Laboratory
>>>Phone: 303.497.8399
>>>Email: jpresto at ucar.edu
>>>
>>>
>>
>>
>> ________________________________
>>
>> This email is intended solely for the recipient. It may contain
privileged, proprietary or confidential information or material. If
you are not the intended recipient, please delete this email and any
attachments and notify the sender of the error.
>>
>>
>>
>
>
>
> --
> Julie Prestopnik
> National Center for Atmospheric Research
> Research Applications Laboratory
> Phone: 303.497.8399
> Email: jpresto at ucar.edu
--
Julie Prestopnik
National Center for Atmospheric Research
Research Applications Laboratory
Phone: 303.497.8399
Email: jpresto at ucar.edu
------------------------------------------------
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