Matthew,
This is a problem associated with the miniconda install of python 3.11 and
can be mitigated by going up to 3.10 and not further; see
http://archive.ambermd.org/202312/0054.html for more information.
Set -DDOWNLOAD_MINICONDA=FALSE in your run_cmake script - and ensure that
your system python version is 3.10 at most.
Cheers,
Todd
On Wed, Jan 3, 2024 at 12:55 AM Matthew Guberman-Pfeffer via AMBER <
amber.ambermd.org> wrote:
> Dear Amber Community,
>
> Compillation is failing at the very end with the following message. I
> previously compiled Amber22 without a problem not he same workstation. Can
> you please help me resolve the issue?
>
> [ 92%] Building pytraj native library
> sys.argv ['setup.py', 'build', '--disable-openmp']
> Original compiler envs
> CXX = /usr/bin/g++
> CC = /usr/bin/gcc
> COMPILER =
> use_pip = False, cpptraj_home =
> compile_c_extension = True
> 2.0.6
> use_prebuilt_cythonized_files = False
> pytraj is inside AMBERHOME
> using environment: CC=/usr/bin/gcc, CXX=/usr/bin/g++
> using CC=/usr/bin/gcc, CXX=/usr/bin/g++
> Final compiler envs
> CXX = /usr/bin/g++
> CC = /usr/bin/gcc
> COMPILER =
> install = True
> set rpath to
> /usr/local/amber22_cphmd/amber22_src/build/AmberTools/src/cpptraj/src
> /usr/local/amber22_cphmd/amber22_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/dist.py:498:
> SetuptoolsDeprecationWarning: Invalid dash-separated options
> !!
>
>
> ********************************************************************************
> Usage of dash-separated 'description-file' will not be supported
> in future
> versions. Please use the underscore name 'description_file'
> instead.
>
> This deprecation is overdue, please update your project and remove
> deprecated
> calls to avoid build errors in the future.
>
> See
> https://setuptools.pypa.io/en/latest/userguide/declarative_config.html
> for details.
>
> ********************************************************************************
>
> !!
> opt = self.warn_dash_deprecation(opt, section)
> running build
> running build_py
> copying pytraj/version.py -> build/lib.linux-x86_64-cpython-311/pytraj
> running build_ext
> building 'pytraj.core.parameter_types' extension
> /usr/bin/gcc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem
> /usr/local/amber22_cphmd/amber22_src/build/CMakeFiles/miniconda/install/include
> -fPIC -O2 -isystem
> /usr/local/amber22_cphmd/amber22_src/build/CMakeFiles/miniconda/install/include
> -fPIC
> -I/usr/local/amber22_cphmd/amber22_src/AmberTools/src/pytraj/../cpptraj/src
> -I/usr/local/amber22_cphmd/amber22_src/AmberTools/src/pytraj/pytraj
> -I/usr/local/amber22_cphmd/amber22_src/build/CMakeFiles/miniconda/install/include/python3.11
> -c pytraj/core/parameter_types.cpp -o
> build/temp.linux-x86_64-cpython-311/pytraj/core/parameter_types.o -O0 -ggdb
> -Wl,-rpath=/usr/local/amber22_cphmd/amber22_src/build/AmberTools/src/cpptraj/src
> pytraj/core/parameter_types.cpp:212:12: fatal error: longintrepr.h: No
> such file or directory
> 212 | #include "longintrepr.h"
> | ^~~~~~~~~~~~~~~
> compilation terminated.
> error: command '/usr/bin/gcc' failed with exit code 1
> make[2]: *** [AmberTools/src/pytraj/CMakeFiles/pytraj.dir/build.make:521:
> AmberTools/src/pytraj/CMakeFiles/python-build/pytraj-build.stamp] Error 1
> make[1]: *** [CMakeFiles/Makefile2:7203:
> AmberTools/src/pytraj/CMakeFiles/pytraj.dir/all] Error 2
> make: *** [Makefile:152: all] Error 2
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jan 03 2024 - 06:00:02 PST
