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
>
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>
>
>
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Received on Mon Oct 25 2021 - 08:00:02 PDT
