Dear David,
Thank you very much for your help.
When I changed the version of gcc and also g++ from 11 to 9. The
installation was finished without errors.
Best regards,
Victor
пн, 25 окт. 2021 г. в 17:36, Victor Nazarychev <nazarychev.imc.macro.ru>:
> Dear David,
>
> Thank you very much for your help.
> After replacing the file, the installation continued until 98%, but again
> error appeared:
>
> [ 98%] Building parmed native library
> running build
> running build_py
> UPDATING
> /home/victor/src/amber20_src/build/AmberTools/src/parmed/CMakeFiles/parmed-build/lib.linux-x86_64-3.9/parmed/_version.py
> set
> /home/victor/src/amber20_src/build/AmberTools/src/parmed/CMakeFiles/parmed-build/lib.linux-x86_64-3.9/parmed/_version.py
> to '3.4.1'
> running build_ext
> building 'parmed.amber._rdparm' extension
> gcc -pthread -B
> /home/victor/src/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat
> -Wl,--sysroot=/ -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC
> -O2 -isystem
> /home/victor/src/amber20_src/build/CMakeFiles/miniconda/install/include
> -fPIC -O2 -isystem
> /home/victor/src/amber20_src/build/CMakeFiles/miniconda/install/include
> -fPIC -I/home/victor/src/amber20_src/AmberTools/src/parmed/src
> -I/home/victor/src/amber20_src/build/CMakeFiles/miniconda/install/include/python3.9
> -c src/_rdparm.cpp -o
> /home/victor/src/amber20_src/build/AmberTools/src/parmed/CMakeFiles/parmed-build/temp.linux-x86_64-3.9/src/_rdparm.o
> gcc: fatal error: cannot execute ‘cc1plus’: execvp: Нет такого файла или
> каталога
> compilation terminated.
> error: command '/usr/bin/gcc' failed with exit code 1
> make[2]: *** [AmberTools/src/parmed/CMakeFiles/parmed.dir/build.make:216:
> AmberTools/src/parmed/CMakeFiles/parmed-build/parmed-build.stamp] Ошибка 1
> make[1]: *** [CMakeFiles/Makefile2:6596:
> AmberTools/src/parmed/CMakeFiles/parmed.dir/all] Ошибка 2
> make: *** [Makefile:156: all] Ошибка 2
>
> Best regards,
> Victor
>
>
>>
>> От кого: David A Case <david.case.rutgers.edu>
>> Кому: AMBER Mailing List <amber.ambermd.org>
>> Дата: Понедельник, 25 октября 2021, 16:43 +03:00
>> Тема: Re: [AMBER] Fwd: Ambertools21 installation problems
>>
>> On Mon, Oct 25, 2021, Victor Nazarychev wrote:
>>
>> >> >I tried to install AmberTools21 using Option 1 in the instruction
>> manual
>> >> >from the website https://ambermd.org/GetAmber.php#ambertools .
>>
>> >> > [ 94%] Building C object
>> >>
>> >AmberTools/src/leap/src/leap/CMakeFiles/leap_common_obj.dir/getline.c.o
>> >> >
>> >>
>> >>
>> >/home/victor/src/amber20_src/AmberTools/src/leap/src/leap/getline.c:117:17:
>> >> >error: conflicting types for ‘write’
>> >> >
>> >> >117 | extern int write();
>>
>> Can you try the following: replace the file,
>>
>> amber20_src/AmberTools/src/leap/src/leap/getline.c
>>
>> with the one in the attachment? The code you have is clearly outdated, but
>> I'm not yet sure why no one else has reported this problem -- it could be
>> related to your use of the very recent ubuntu 21.10 release, or it could
>> be
>> something else.
>>
>> ....thanks...dave case
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org <http:///compose?To=AMBER.ambermd.org>
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>
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Received on Wed Oct 27 2021 - 03:00:02 PDT
