libSystem not found using gfortran

Chris Jones jonesc at hep.phy.cam.ac.uk
Fri Oct 11 13:36:21 UTC 2019 


On 11/10/2019 2:30 pm, Guillaume Houzeaux @ BSC wrote:
> Ok Chris,
> 
> I'm installing xcode 11.1 from the app store. Should I go through the 
> migration steps again afterwards?

yes. See my previous mail I just sent. All your ports need to be 
uninstalled, then rebuilt from source natively for Darwin19.

Chris

> 
> Guillaume
>>
>>
>> On 11/10/2019 2:22 pm, Guillaume Houzeaux @ BSC wrote:
>>> Chris,
>>>>
>>>>
>>>> On 11/10/2019 1:41 pm, Guillaume Houzeaux @ BSC wrote:
>>>>> Chris, thanks a lot for your very quick answer!
>>>>>
>>>>> 1. I followed the path for migration and reinstalled all packages. 
>>>>> I will try to do it once more to be sure.
>>>>> 2. Xcode version: 11.0
>>>>
>>>> Please update to 11.1. 11.0 indeed has a number of issues since fixed.
>>>
>>> I get no updates available :o(
>>
>> I think I saw the same. try a search for Xcode in the App store and 
>> update from there....
>>
>>>
>>> I will try from developer.apple.com
>>>
>>>>
>>>>> Reading specs from 
>>>>> /opt/local/lib/gcc9/gcc/x86_64-apple-darwin18/9.2.0/../../../libgfortran.spec
>>>>> rename spec lib to liborig
>>>>> COLLECT_GCC_OPTIONS='-v' '-mmacosx-version-min=10.15.0' 
>>>>> '-shared-libgcc' '-mtune=core2'
>>>>> COMPILER_PATH=/opt/local/libexec/gcc/x86_64-apple-darwin18/9.2.0/:/opt/local/libexec/gcc/x86_64-apple-darwin18/9.2.0/:/opt/local/libexec/gcc/x86_64-apple-darwin18/:/opt/local/lib/gcc9/gcc/x86_64-apple-darwin18/9.2.0/:/opt/local/lib/gcc9/gcc/x86_64-apple-darwin18/ 
>>>>>
>>>>> LIBRARY_PATH=/usr/lib/:/opt/local/lib/gcc9/gcc/x86_64-apple-darwin18/9.2.0/:/opt/local/lib/gcc9/gcc/x86_64-apple-darwin18/9.2.0/../../../ 
>>>>>
>>>>> COLLECT_GCC_OPTIONS='-v' '-mmacosx-version-min=10.15.0' 
>>>>> '-shared-libgcc' '-mtune=core2'
>>>>>   /opt/local/libexec/gcc/x86_64-apple-darwin18/9.2.0/collect2 
>>>>> -syslibroot 
>>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/ 
>>>>> -dynamic -arch x86_64 -macosx_version_min 10.15.0 
>>>>> -weak_reference_mismatches non-weak -o a.out 
>>>>> -L/opt/local/lib/gcc9/gcc/x86_64-apple-darwin18/9.2.0 
>>>>> -L/opt/local/lib/gcc9/gcc/x86_64-apple-darwin18/9.2.0/../../.. 
>>>>> /var/folders/1z/j0r1q88d2_95cj4fd50r39mr0000gr/T//cce0rRJI.o 
>>>>> -lgfortran -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc 
>>>>> -lquadmath -lm -lgcc_ext.10.5 -lgcc -lSystem -v
>>>>> collect2 version 9.2.0
>>>>> /opt/local/bin/ld -syslibroot 
>>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/ 
>>>>
>>>>
>>>>
>>>> This I think is your problem. You are using the 10.14 SDK, not the 
>>>> 10.15 one. Does
>>>>
>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk 
>>>>
>>>>
>>>> even exist on your system ? I guess not.
>>> nope, it does not exist
>>>>
>>>> Chris
>>>>
>>>>> -dynamic -arch x86_64 -macosx_version_min 10.15.0 
>>>>> -weak_reference_mismatches non-weak -o a.out 
>>>>> -L/opt/local/lib/gcc9/gcc/x86_64-apple-darwin18/9.2.0 
>>>>> -L/opt/local/lib/gcc9/gcc/x86_64-apple-darwin18/9.2.0/../../.. 
>>>>> /var/folders/1z/j0r1q88d2_95cj4fd50r39mr0000gr/T//cce0rRJI.o 
>>>>> -lgfortran -no_compact_unwind -lSystem -lgcc_ext.10.5 -lgcc 
>>>>> -lquadmath -lm -lgcc_ext.10.5 -lgcc -lSystem -v
>>>>> @(#)PROGRAM:ld  PROJECT:ld64-512.4
>>>>> BUILD 05:06:53 Aug 16 2019
>>>>> configured to support archs: armv6 armv7 armv7s arm64 arm64e 
>>>>> arm64_32 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em
>>>>> Library search paths:
>>>>>      /opt/local/lib/gcc9/gcc/x86_64-apple-darwin18/9.2.0
>>>>>      /opt/local/lib/gcc9
>>>>> Framework search paths:
>>>>> ld: library not found for -lSystem
>>>>> collect2: error: ld returned 1 exit status
>>>>>
>>>>>
>>>>>>
>>>>>> one more request.
>>>>>>
>>>>>> please post the full output from compiling your test code with the 
>>>>>> -v option.
>>>>>>
>>>>>> cheers Chris
>>>>>>
>>>>>> On 11/10/2019 12:59 pm, Chris Jones wrote:
>>>>>>>
>>>>>>> can you please direct us to the exact test application code you 
>>>>>>> are using ?
>>>>>>>
>>>>>>> Also, can you confirm the exact Xcode version you are using ?
>>>>>>>
>>>>>>> Have you correctly followed the macports migration guide after 
>>>>>>> updating your OS ?
>>>>>>>
>>>>>>> https://trac.macports.org/wiki/Migration
>>>>>>>
>>>>>>> cheers Chris
>>>>>>>
>>>>>>> On 11/10/2019 12:55 pm, Guillaume Houzeaux @ BSC wrote:
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I'm compiling with gfortran9 on catalina and get this error:
>>>>>>>>
>>>>>>>> gfortran test.f90
>>>>>>>> ld: library not found for -lSystem
>>>>>>>> collect2: error: ld returned 1 exit status
>>>>>>>>
>>>>>>>> Seems that it does not find the library libSystem. I changed all 
>>>>>>>> the library paths in my bash_profile
>>>>>>>>
>>>>>>>> to include /usr/lib but does not work. The only solution for the 
>>>>>>>> moment is to compile with
>>>>>>>>
>>>>>>>> gfortran test.f90-L/usr/lib
>>>>>>>>
>>>>>>>> but this is not a practical option... Any idea on how to fix this?
>>>>>>>>
>>>>>>>> Thanks in advance
>>>>>>>>
>>>>>>>> -- 
>>>>>>>> Guillaume Houzeaux
>>>>>>>> Team Leader
>>>>>>>> Dpt. Computer Applications in Science and Engineering
>>>>>>>> Barcelona Supercomputing Center (BSC-CNS)
>>>>>>>> Edificio NEXUS II - Office 3A, c) Jordi Girona 29
>>>>>>>> 08034 Barcelona, Spain
>>>>>>>>
>>>>>>>> Location: 
>>>>>>>> <https://www.google.es/maps/place/Carrer+de+Jordi+Girona,+08034+Barcelona/@41.3881175,2.1132195,17z/data=!3m1!4b1!4m8!1m2!10m1!1e2!3m4!1s0x12a4985099390467:0xd9abcf1987739b3e!8m2!3d41.3881175!4d2.1154135?hl=en> 
>>>>>>>>
>>>>>>>> Tel: +34 93 413 7781
>>>>>>>> Skype user: guillaume_houzeaux_bsc
>>>>>>>> WWW: BSC profile <https://www.bsc.es/houzeaux-guillaume>
>>>>>>>> ResearcherID: D-4950-2012
>>>>>>>> Scientific Profile: 
>>>>>>>> <https://www.researchgate.net/profile/Guillaume_Houzeaux> 
>>>>>>>> <http://scholar.google.es/citations?user=cL9khdYAAAAJ&hl=en> 
>>>>>>>> <http://orcid.org/0000-0002-2592-1426> 
>>>>>>>> <http://www.researcherid.com/rid/D-4950-2012>
>>>>>>>>
>>>>>
>>>>> -- 
>>>>> Guillaume Houzeaux
>>>>> Team Leader
>>>>> Dpt. Computer Applications in Science and Engineering
>>>>> Barcelona Supercomputing Center (BSC-CNS)
>>>>> Edificio NEXUS II - Office 3A, c) Jordi Girona 29
>>>>> 08034 Barcelona, Spain
>>>>>
>>>>> Location: 
>>>>> <https://www.google.es/maps/place/Carrer+de+Jordi+Girona,+08034+Barcelona/@41.3881175,2.1132195,17z/data=!3m1!4b1!4m8!1m2!10m1!1e2!3m4!1s0x12a4985099390467:0xd9abcf1987739b3e!8m2!3d41.3881175!4d2.1154135?hl=en> 
>>>>>
>>>>> Tel: +34 93 413 7781
>>>>> Skype user: guillaume_houzeaux_bsc
>>>>> WWW: BSC profile <https://www.bsc.es/houzeaux-guillaume>
>>>>> ResearcherID: D-4950-2012
>>>>> Scientific Profile: 
>>>>> <https://www.researchgate.net/profile/Guillaume_Houzeaux> 
>>>>> <http://scholar.google.es/citations?user=cL9khdYAAAAJ&hl=en> 
>>>>> <http://orcid.org/0000-0002-2592-1426> 
>>>>> <http://www.researcherid.com/rid/D-4950-2012>
>>>>>
>>> Thanks again,
>>>
>>> g.
>>>
>>> -- 
>>> Guillaume Houzeaux
>>> Team Leader
>>> Dpt. Computer Applications in Science and Engineering
>>> Barcelona Supercomputing Center (BSC-CNS)
>>> Edificio NEXUS II - Office 3A, c) Jordi Girona 29
>>> 08034 Barcelona, Spain
>>>
>>> Location: 
>>> <https://www.google.es/maps/place/Carrer+de+Jordi+Girona,+08034+Barcelona/@41.3881175,2.1132195,17z/data=!3m1!4b1!4m8!1m2!10m1!1e2!3m4!1s0x12a4985099390467:0xd9abcf1987739b3e!8m2!3d41.3881175!4d2.1154135?hl=en> 
>>>
>>> Tel: +34 93 413 7781
>>> Skype user: guillaume_houzeaux_bsc
>>> WWW: BSC profile <https://www.bsc.es/houzeaux-guillaume>
>>> ResearcherID: D-4950-2012
>>> Scientific Profile: 
>>> <https://www.researchgate.net/profile/Guillaume_Houzeaux> 
>>> <http://scholar.google.es/citations?user=cL9khdYAAAAJ&hl=en> 
>>> <http://orcid.org/0000-0002-2592-1426> 
>>> <http://www.researcherid.com/rid/D-4950-2012>
>>>
> 
> -- 
> Guillaume Houzeaux
> Team Leader
> Dpt. Computer Applications in Science and Engineering
> Barcelona Supercomputing Center (BSC-CNS)
> Edificio NEXUS II - Office 3A, c) Jordi Girona 29
> 08034 Barcelona, Spain
> 
> Location: 
> <https://www.google.es/maps/place/Carrer+de+Jordi+Girona,+08034+Barcelona/@41.3881175,2.1132195,17z/data=!3m1!4b1!4m8!1m2!10m1!1e2!3m4!1s0x12a4985099390467:0xd9abcf1987739b3e!8m2!3d41.3881175!4d2.1154135?hl=en> 
> 
> Tel: +34 93 413 7781
> Skype user: guillaume_houzeaux_bsc
> WWW: BSC profile <https://www.bsc.es/houzeaux-guillaume>
> ResearcherID: D-4950-2012
> Scientific Profile: 
> <https://www.researchgate.net/profile/Guillaume_Houzeaux> 
> <http://scholar.google.es/citations?user=cL9khdYAAAAJ&hl=en> 
> <http://orcid.org/0000-0002-2592-1426> 
> <http://www.researcherid.com/rid/D-4950-2012>
>

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