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Package Details: ambertools 25.00-1

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Git Clone URL:	https://aur.archlinux.org/ambertools.git (read-only, click to copy)
Package Base:	ambertools
Description:	Biomolecular simulation package (tools only)
Upstream URL:	http://ambermd.org/
Licenses:	GPL-3.0-or-later AND LGPL-3.0-or-later AND BSD-3-Clause AND MIT
Submitter:	dviktor
Maintainer:	yitzi (vedranmiletic)
Last Packager:	vedranmiletic
Votes:	2
Popularity:	0.000000
First Submitted:	2019-05-05 18:23 (UTC)
Last Updated:	2025-05-05 07:48 (UTC)

Dependencies (19)

blas (blis-cblas-openmp^AUR, blis-cblas^AUR, aocl-blis-aocc^AUR, blas-git^AUR, atlas-lapack^AUR, blas-aocl-gcc^AUR, blas-aocl-aocc^AUR, blis-git^AUR, blis^AUR, blas-mkl^AUR, openblas-lapack^AUR, aocl-blis^AUR, blas-openblas)
boost (boost-git^AUR)
bzip2 (bzip2-git^AUR)
fftw (fftw-amd^AUR)
gcc14-libs
lapack (aocl-libflame-aocc^AUR, lapack-git^AUR, atlas-lapack^AUR, blas-aocl-gcc^AUR, blas-aocl-aocc^AUR, blas-mkl^AUR, openblas-lapack^AUR, aocl-libflame^AUR, blas-openblas)
netcdf (netcdf-openmpi)
python-matplotlib (python-matplotlib-git^AUR)
python-scipy (python-scipy-git^AUR, python-scipy-mkl-bin^AUR, python-scipy-mkl-tbb^AUR, python-scipy-mkl^AUR)
readline (readline-git^AUR)
tk (tk-fossil^AUR)
zlib (zlib-ng-compat-git^AUR, zlib-git^AUR, zlib-ng-compat)
cmake (cmake-git^AUR, cmake3^AUR) (make)
cython (cython-git^AUR) (make)
gcc14-fortran (make)
cuda (cuda11.1^AUR, cuda-12.2^AUR, cuda12.0^AUR, cuda11.4^AUR, cuda11.4-versioned^AUR, cuda12.0-versioned^AUR) (optional) – GPU acceleration support
mpich^AUR (optional) – MPI support
openmpi (openmpi-git^AUR) (optional) – MPI support
python-mpi4py (python-mpi4py-intel^AUR) (optional) – MPI support (Python tools)

Required by (0)

Sources (4)

Latest Comments

1 2 3 Next › Last »

vedranmiletic commented on 2025-02-13 07:13 (UTC)

Latest PKGBUILD should support Python 3.13 and NumPy 2.0. Let me know in the comments if you encounter any issues.

vedranmiletic commented on 2024-12-23 08:19 (UTC)

AmberTools currently fails to build with Python 3.13 due to pytraj build failure: https://github.com/Amber-MD/pytraj/issues/1677

vedranmiletic commented on 2024-09-24 06:19 (UTC)

Version is now upgraded to 24.

@sstac it seems that ParmEd is bundled with AmberTools, but that version is likely incompatible with Arch Linux's NumPy version: https://github.com/ParmEd/ParmEd/issues/1364 I will consider the options (patching bundled version vs providing a separate package), but I can't promise an ETA.

vedranmiletic commented on 2024-08-26 08:42 (UTC)

@sstac It should run out of the box, but there are obviously edge cases like the one you mention. Since there is no python-parmed package at the moment, ambertools package can't depend on it.

There is a link to AmberTools24 archive in the following issue: https://github.com/conda-forge/ambertools-feedstock/issues/135 I am working on getting it packaged in the near future.

sstac commented on 2024-07-02 09:15 (UTC)

Hello!

Launching 'pdb4amber' utility reports a missing parmed module error. The issue gets resolved after manually installing that python module and adding it to $PYTHONPATH. Are the issues of missing modules which have to be added later normal or should the package run out of the box?

vedranmiletic commented on 2024-05-06 18:58 (UTC)

I am aware that AmberTools 24 is out.

I am just waiting for it to be released on Conda to get a proper download URL like https://ambermd.org/downloads/AmberTools23_rc6.tar.bz2 for the release tarball.

vedranmiletic commented on 2022-01-31 17:34 (UTC)

I get a different build failure:

[ 17%] Building mpi4py
running build
running build_src
running build_py
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py
copying src/mpi4py/run.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py
copying src/mpi4py/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py
copying src/mpi4py/bench.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py
copying src/mpi4py/__main__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/futures
copying src/mpi4py/futures/_base.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/futures
copying src/mpi4py/futures/server.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/futures
copying src/mpi4py/futures/__init__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/futures
copying src/mpi4py/futures/pool.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/futures
copying src/mpi4py/futures/aplus.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/futures
copying src/mpi4py/futures/__main__.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/futures
copying src/mpi4py/futures/_lib.py -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/futures
copying src/mpi4py/__init__.pxd -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py
copying src/mpi4py/libmpi.pxd -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py
copying src/mpi4py/MPI.pxd -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/include
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.MPI.h -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.MPI_api.h -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.h -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi4py.i -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/include/mpi4py
copying src/mpi4py/include/mpi4py/mpi.pxi -> /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/include/mpi4py
running build_clib
MPI configuration: [cmake-mpi] from '/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/mpi.cfg'
MPI C compiler:    /usr/bin/gcc-10
MPI C++ compiler:  /usr/bin/g++-10
checking for library 'lmpe' ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include -c _configtest.c -o _configtest.o
/usr/bin/gcc-10 -pthread -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread _configtest.o -L/usr/lib/openmpi -llmpe -lmpi -o _configtest
/usr/bin/ld: cannot find -llmpe
collect2: greška: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'mpe' dylib library
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10/src
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10/src/lib-pmpi
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include -c src/lib-pmpi/mpe.c -o /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10/src/lib-pmpi/mpe.o
creating /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/lib-pmpi
/usr/bin/gcc-10 -pthread -shared -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread -Wl,--no-as-needed /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10/src/lib-pmpi/mpe.o -L/usr/lib/openmpi -lmpi -o /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/lib-pmpi/libmpe.so
checking for library 'vt-mpi' ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include -c _configtest.c -o _configtest.o
/usr/bin/gcc-10 -pthread -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread _configtest.o -L/usr/lib/openmpi -lvt-mpi -lmpi -o _configtest
/usr/bin/ld: cannot find -lvt-mpi
collect2: greška: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.mpi' ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include -c _configtest.c -o _configtest.o
/usr/bin/gcc-10 -pthread -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread _configtest.o -L/usr/lib/openmpi -lvt.mpi -lmpi -o _configtest
/usr/bin/ld: cannot find -lvt.mpi
collect2: greška: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt' dylib library
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include -c src/lib-pmpi/vt.c -o /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10/src/lib-pmpi/vt.o
/usr/bin/gcc-10 -pthread -shared -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread -Wl,--no-as-needed /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10/src/lib-pmpi/vt.o -L/usr/lib/openmpi -lmpi -o /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/lib-pmpi/libvt.so
checking for library 'vt-mpi' ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include -c _configtest.c -o _configtest.o
/usr/bin/gcc-10 -pthread -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread _configtest.o -L/usr/lib/openmpi -lvt-mpi -lmpi -o _configtest
/usr/bin/ld: cannot find -lvt-mpi
collect2: greška: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.mpi' ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include -c _configtest.c -o _configtest.o
/usr/bin/gcc-10 -pthread -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread _configtest.o -L/usr/lib/openmpi -lvt.mpi -lmpi -o _configtest
/usr/bin/ld: cannot find -lvt.mpi
collect2: greška: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt-mpi' dylib library
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include -c src/lib-pmpi/vt-mpi.c -o /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10/src/lib-pmpi/vt-mpi.o
/usr/bin/gcc-10 -pthread -shared -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread -Wl,--no-as-needed /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10/src/lib-pmpi/vt-mpi.o -L/usr/lib/openmpi -lmpi -o /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/lib-pmpi/libvt-mpi.so
checking for library 'vt-hyb' ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include -c _configtest.c -o _configtest.o
/usr/bin/gcc-10 -pthread -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread _configtest.o -L/usr/lib/openmpi -lvt-hyb -lmpi -o _configtest
/usr/bin/ld: cannot find -lvt-hyb
collect2: greška: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
checking for library 'vt.ompi' ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include -c _configtest.c -o _configtest.o
/usr/bin/gcc-10 -pthread -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread _configtest.o -L/usr/lib/openmpi -lvt.ompi -lmpi -o _configtest
/usr/bin/ld: cannot find -lvt.ompi
collect2: greška: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
building 'vt-hyb' dylib library
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include -c src/lib-pmpi/vt-hyb.c -o /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10/src/lib-pmpi/vt-hyb.o
/usr/bin/gcc-10 -pthread -shared -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread -Wl,--no-as-needed /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10/src/lib-pmpi/vt-hyb.o -L/usr/lib/openmpi -lmpi -o /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/lib-pmpi/libvt-hyb.so
running build_ext
MPI configuration: [cmake-mpi] from '/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/mpi.cfg'
MPI C compiler:    /usr/bin/gcc-10
MPI C++ compiler:  /usr/bin/g++-10
checking for dlopen() availability ...
checking for header 'dlfcn.h' ...
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -I/usr/include/python3.10 -c _configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
success!
checking for library 'dl' ...
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -I/usr/include/python3.10 -c _configtest.c -o _configtest.o
gcc -pthread _configtest.o -L/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'dlopen' ...
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -I/usr/include/python3.10 -c _configtest.c -o _configtest.o
gcc -pthread _configtest.o -L/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10 -ldl -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
building 'mpi4py.dl' extension
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/usr/include/python3.10 -c src/dynload.c -o /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10/src/dynload.o
gcc -pthread -shared -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -flto /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10/src/dynload.o -L/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10 -ldl -o /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/lib.linux-x86_64-3.10/mpi4py/dl.cpython-310-x86_64-linux-gnu.so
checking for MPI compile and link ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include/python3.10 -I/usr/include -c_configtest.c -o _configtest.o
success!
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/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include/python3.10 -I/usr/include -c_configtest.c -o _configtest.o
/usr/bin/gcc-10 -pthread -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread _configtest.o -L/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10 -L/usr/lib/openmpi -lmpi -o _configtest
success!
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checking for missing MPI functions/symbols ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include/python3.10 -I/usr/include -c_configtest.c -o _configtest.o
success!
removing: _configtest.c _configtest.o
checking for function 'MPI_Type_create_f90_integer' ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include/python3.10 -I/usr/include -c_configtest.c -o _configtest.o
/usr/bin/gcc-10 -pthread -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread _configtest.o -L/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10 -L/usr/lib/openmpi -lmpi -o _configtest
success!
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checking for function 'MPI_Type_create_f90_real' ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include/python3.10 -I/usr/include -c_configtest.c -o _configtest.o
/usr/bin/gcc-10 -pthread -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread _configtest.o -L/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10 -L/usr/lib/openmpi -lmpi -o _configtest
success!
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checking for function 'MPI_Type_create_f90_complex' ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include/python3.10 -I/usr/include -c_configtest.c -o _configtest.o
/usr/bin/gcc-10 -pthread -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread _configtest.o -L/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10 -L/usr/lib/openmpi -lmpi -o _configtest
success!
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checking for function 'MPI_Status_c2f' ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include/python3.10 -I/usr/include -c_configtest.c -o _configtest.o
/usr/bin/gcc-10 -pthread -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread _configtest.o -L/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10 -L/usr/lib/openmpi -lmpi -o _configtest
success!
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checking for function 'MPI_Status_f2c' ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include/python3.10 -I/usr/include -c_configtest.c -o _configtest.o
/usr/bin/gcc-10 -pthread -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread _configtest.o -L/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10 -L/usr/lib/openmpi -lmpi -o _configtest
success!
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checking for symbol 'MPI_LB' ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include/python3.10 -I/usr/include -c_configtest.c -o _configtest.o
In file included from _configtest.c:2:
_configtest.c: In function „main”:
_configtest.c:5:23: greška: static assertion failed: "MPI_LB was removed in MPI-3.0.  Use MPI_Type_create_resized instead."
5 |   MPI_Datatype s; s = MPI_LB; (void)s;
|                       ^~~~~~
failure.
removing: _configtest.c _configtest.o
checking for symbol 'MPI_UB' ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include/python3.10 -I/usr/include -c_configtest.c -o _configtest.o
In file included from _configtest.c:2:
_configtest.c: In function „main”:
_configtest.c:5:23: greška: static assertion failed: "MPI_UB was removed in MPI-3.0.  Use MPI_Type_create_resized instead."
5 |   MPI_Datatype s; s = MPI_UB; (void)s;
|                       ^~~~~~
failure.
removing: _configtest.c _configtest.o
checking for dlopen() availability ...
checking for header 'dlfcn.h' ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include/python3.10 -I/usr/include -c_configtest.c -o _configtest.o
success!
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success!
checking for library 'dl' ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include/python3.10 -I/usr/include -c_configtest.c -o _configtest.o
/usr/bin/gcc-10 -pthread -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread _configtest.o -L/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10 -L/usr/lib/openmpi -ldl -lmpi -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'dlopen' ...
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -I/usr/include/python3.10 -I/usr/include -c_configtest.c -o _configtest.o
/usr/bin/gcc-10 -pthread -Wl,-rpath -Wl,/usr/lib/openmpi -Wl,--enable-new-dtags -pthread _configtest.o -L/home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10 -L/usr/lib/openmpi -ldl -lmpi -o _configtest
success!
removing: _configtest.c _configtest.o _configtest
building 'mpi4py.MPI' extension
/usr/bin/gcc-10 -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -flto -fPIC -pthread -DPyMPI_MISSING_MPI_LB=1 -DPyMPI_MISSING_MPI_UB=1 -DHAVE_DLFCN_H=1 -DHAVE_DLOPEN=1 -I/usr/include/python3.10 -I/usr/include -c src/MPI.c -o /home/vedranmiletic/.cache/paru/clone/ambertools/src/amber20_src/build/AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-3.10/src/MPI.o
In file included from src/MPI.c:4:
src/mpi4py.MPI.c: In function „__pyx_tp_dealloc_6mpi4py_3MPI_Datatype”:
src/mpi4py.MPI.c:154210:5: greška: lvalue required as increment operand
154210 |     ++Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c:154212:5: greška: lvalue required as decrement operand
154212 |     --Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c: In function „__pyx_tp_dealloc_6mpi4py_3MPI_Request”:
src/mpi4py.MPI.c:154500:5: greška: lvalue required as increment operand
154500 |     ++Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c:154502:5: greška: lvalue required as decrement operand
154502 |     --Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c: In function „__pyx_tp_dealloc_6mpi4py_3MPI_Message”:
src/mpi4py.MPI.c:154880:5: greška: lvalue required as increment operand
154880 |     ++Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c:154882:5: greška: lvalue required as decrement operand
154882 |     --Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c: In function „__pyx_tp_dealloc_6mpi4py_3MPI_Op”:
src/mpi4py.MPI.c:155076:5: greška: lvalue required as increment operand
155076 |     ++Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c:155078:5: greška: lvalue required as decrement operand
155078 |     --Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c: In function „__pyx_tp_dealloc_6mpi4py_3MPI_Group”:
src/mpi4py.MPI.c:155263:5: greška: lvalue required as increment operand
155263 |     ++Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c:155265:5: greška: lvalue required as decrement operand
155265 |     --Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c: In function „__pyx_tp_dealloc_6mpi4py_3MPI_Info”:
src/mpi4py.MPI.c:155459:5: greška: lvalue required as increment operand
155459 |     ++Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c:155461:5: greška: lvalue required as decrement operand
155461 |     --Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c: In function „__pyx_tp_dealloc_6mpi4py_3MPI_Errhandler”:
src/mpi4py.MPI.c:155678:5: greška: lvalue required as increment operand
155678 |     ++Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c:155680:5: greška: lvalue required as decrement operand
155680 |     --Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c: In function „__pyx_tp_dealloc_6mpi4py_3MPI_Comm”:
src/mpi4py.MPI.c:155848:5: greška: lvalue required as increment operand
155848 |     ++Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c:155850:5: greška: lvalue required as decrement operand
155850 |     --Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c: In function „__pyx_tp_dealloc_6mpi4py_3MPI_Win”:
src/mpi4py.MPI.c:156863:5: greška: lvalue required as increment operand
156863 |     ++Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c:156865:5: greška: lvalue required as decrement operand
156865 |     --Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c: In function „__pyx_tp_dealloc_6mpi4py_3MPI_File”:
src/mpi4py.MPI.c:157169:5: greška: lvalue required as increment operand
157169 |     ++Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c:157171:5: greška: lvalue required as decrement operand
157171 |     --Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c: In function „__pyx_tp_dealloc_6mpi4py_3MPI_memory”:
src/mpi4py.MPI.c:157439:5: greška: lvalue required as increment operand
157439 |     ++Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c:157441:5: greška: lvalue required as decrement operand
157441 |     --Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c: In function „__pyx_tp_dealloc_6mpi4py_3MPI__p_mem”:
src/mpi4py.MPI.c:157612:5: greška: lvalue required as increment operand
157612 |     ++Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c:157614:5: greška: lvalue required as decrement operand
157614 |     --Py_REFCNT(o);
|     ^~
src/mpi4py.MPI.c: In function „__Pyx_ParseOptionalKeywords”:
src/mpi4py.MPI.c:174420:21: upozorenje: „_PyUnicode_get_wstr_length” is deprecated [-Wdeprecated-declarations]
174420 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
|                     ^
In file included from /usr/include/python3.10/unicodeobject.h:1046,
from /usr/include/python3.10/Python.h:83,
from src/mpi4py.MPI.c:4,
from src/MPI.c:4:
/usr/include/python3.10/cpython/unicodeobject.h:446:26: napomena: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
|                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/MPI.c:4:
src/mpi4py.MPI.c:174420:21: upozorenje: „PyUnicode_AsUnicode” is deprecated [-Wdeprecated-declarations]
174420 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
|                     ^
In file included from /usr/include/python3.10/unicodeobject.h:1046,
from /usr/include/python3.10/Python.h:83,
from src/mpi4py.MPI.c:4,
from src/MPI.c:4:
/usr/include/python3.10/cpython/unicodeobject.h:580:45: napomena: declared here
580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
|                                             ^~~~~~~~~~~~~~~~~~~
In file included from src/MPI.c:4:
src/mpi4py.MPI.c:174420:21: upozorenje: „_PyUnicode_get_wstr_length” is deprecated [-Wdeprecated-declarations]
174420 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
|                     ^
In file included from /usr/include/python3.10/unicodeobject.h:1046,
from /usr/include/python3.10/Python.h:83,
from src/mpi4py.MPI.c:4,
from src/MPI.c:4:
/usr/include/python3.10/cpython/unicodeobject.h:446:26: napomena: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
|                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/MPI.c:4:
src/mpi4py.MPI.c:174420:21: upozorenje: „_PyUnicode_get_wstr_length” is deprecated [-Wdeprecated-declarations]
174420 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
|                     ^
In file included from /usr/include/python3.10/unicodeobject.h:1046,
from /usr/include/python3.10/Python.h:83,
from src/mpi4py.MPI.c:4,
from src/MPI.c:4:
/usr/include/python3.10/cpython/unicodeobject.h:446:26: napomena: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
|                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/MPI.c:4:
src/mpi4py.MPI.c:174420:21: upozorenje: „PyUnicode_AsUnicode” is deprecated [-Wdeprecated-declarations]
174420 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
|                     ^
In file included from /usr/include/python3.10/unicodeobject.h:1046,
from /usr/include/python3.10/Python.h:83,
from src/mpi4py.MPI.c:4,
from src/MPI.c:4:
/usr/include/python3.10/cpython/unicodeobject.h:580:45: napomena: declared here
580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
|                                             ^~~~~~~~~~~~~~~~~~~
In file included from src/MPI.c:4:
src/mpi4py.MPI.c:174420:21: upozorenje: „_PyUnicode_get_wstr_length” is deprecated [-Wdeprecated-declarations]
174420 |                     (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
|                     ^
In file included from /usr/include/python3.10/unicodeobject.h:1046,
from /usr/include/python3.10/Python.h:83,
from src/mpi4py.MPI.c:4,
from src/MPI.c:4:
/usr/include/python3.10/cpython/unicodeobject.h:446:26: napomena: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
|                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/MPI.c:4:
src/mpi4py.MPI.c:174436:25: upozorenje: „_PyUnicode_get_wstr_length” is deprecated [-Wdeprecated-declarations]
174436 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
|                         ^
In file included from /usr/include/python3.10/unicodeobject.h:1046,
from /usr/include/python3.10/Python.h:83,
from src/mpi4py.MPI.c:4,
from src/MPI.c:4:
/usr/include/python3.10/cpython/unicodeobject.h:446:26: napomena: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
|                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/MPI.c:4:
src/mpi4py.MPI.c:174436:25: upozorenje: „PyUnicode_AsUnicode” is deprecated [-Wdeprecated-declarations]
174436 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
|                         ^
In file included from /usr/include/python3.10/unicodeobject.h:1046,
from /usr/include/python3.10/Python.h:83,
from src/mpi4py.MPI.c:4,
from src/MPI.c:4:
/usr/include/python3.10/cpython/unicodeobject.h:580:45: napomena: declared here
580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
|                                             ^~~~~~~~~~~~~~~~~~~
In file included from src/MPI.c:4:
src/mpi4py.MPI.c:174436:25: upozorenje: „_PyUnicode_get_wstr_length” is deprecated [-Wdeprecated-declarations]
174436 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
|                         ^
In file included from /usr/include/python3.10/unicodeobject.h:1046,
from /usr/include/python3.10/Python.h:83,
from src/mpi4py.MPI.c:4,
from src/MPI.c:4:
/usr/include/python3.10/cpython/unicodeobject.h:446:26: napomena: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
|                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/MPI.c:4:
src/mpi4py.MPI.c:174436:25: upozorenje: „_PyUnicode_get_wstr_length” is deprecated [-Wdeprecated-declarations]
174436 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
|                         ^
In file included from /usr/include/python3.10/unicodeobject.h:1046,
from /usr/include/python3.10/Python.h:83,
from src/mpi4py.MPI.c:4,
from src/MPI.c:4:
/usr/include/python3.10/cpython/unicodeobject.h:446:26: napomena: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
|                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/MPI.c:4:
src/mpi4py.MPI.c:174436:25: upozorenje: „PyUnicode_AsUnicode” is deprecated [-Wdeprecated-declarations]
174436 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
|                         ^
In file included from /usr/include/python3.10/unicodeobject.h:1046,
from /usr/include/python3.10/Python.h:83,
from src/mpi4py.MPI.c:4,
from src/MPI.c:4:
/usr/include/python3.10/cpython/unicodeobject.h:580:45: napomena: declared here
580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
|                                             ^~~~~~~~~~~~~~~~~~~
In file included from src/MPI.c:4:
src/mpi4py.MPI.c:174436:25: upozorenje: „_PyUnicode_get_wstr_length” is deprecated [-Wdeprecated-declarations]
174436 |                         (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
|                         ^
In file included from /usr/include/python3.10/unicodeobject.h:1046,
from /usr/include/python3.10/Python.h:83,
from src/mpi4py.MPI.c:4,
from src/MPI.c:4:
/usr/include/python3.10/cpython/unicodeobject.h:446:26: napomena: declared here
446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) {
|                          ^~~~~~~~~~~~~~~~~~~~~~~~~~
error: command '/usr/bin/gcc-10' failed with exit code 1
make[2]: *** [AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py.dir/build.make:288: AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py-build/mpi4py-build.stamp] Greška 1
make[1]: *** [CMakeFiles/Makefile2:4425: AmberTools/src/mpi4py-3.0.3/CMakeFiles/mpi4py.dir/all] Greška 2
make: *** [Makefile:156: all] Greška 2
==> ERROR: A failure occurred in build().
Aborting...
error: failed to build 'ambertools-21-2':
error: packages failed to build: ambertools-21-2

Any ideas?

Maxwell23 commented on 2021-08-24 08:59 (UTC)

@dviktor Relevant part of log with error when compiling in single thread (with makepkg, building by hand):

[100%] Building Fortran object AmberTools/src/packmol_memgen/packmol_memgen/lib/packmol/CMakeFiles/packmol.dir/polartocart.f90.o
[100%] Building Fortran object AmberTools/src/packmol_memgen/packmol_memgen/lib/packmol/CMakeFiles/packmol.dir/resetboxes.f90.o
[100%] Building Fortran object AmberTools/src/packmol_memgen/packmol_memgen/lib/packmol/CMakeFiles/packmol.dir/tobar.f90.o
[100%] Building Fortran object AmberTools/src/packmol_memgen/packmol_memgen/lib/packmol/CMakeFiles/packmol.dir/setijk.f90.o
[100%] Building Fortran object AmberTools/src/packmol_memgen/packmol_memgen/lib/packmol/CMakeFiles/packmol.dir/setibox.f90.o
[100%] Building Fortran object AmberTools/src/packmol_memgen/packmol_memgen/lib/packmol/CMakeFiles/packmol.dir/restmol.f90.o
[100%] Building Fortran object AmberTools/src/packmol_memgen/packmol_memgen/lib/packmol/CMakeFiles/packmol.dir/swaptype.f90.o
[100%] Building Fortran object AmberTools/src/packmol_memgen/packmol_memgen/lib/packmol/CMakeFiles/packmol.dir/heuristics.f90.o
[100%] Building Fortran object AmberTools/src/packmol_memgen/packmol_memgen/lib/packmol/CMakeFiles/packmol.dir/flashsort.f90.o
[100%] Building Fortran object AmberTools/src/packmol_memgen/packmol_memgen/lib/packmol/CMakeFiles/packmol.dir/jacobi.f90.o
[100%] Building Fortran object AmberTools/src/packmol_memgen/packmol_memgen/lib/packmol/CMakeFiles/packmol.dir/random.f90.o
[100%] Building Fortran object AmberTools/src/packmol_memgen/packmol_memgen/lib/packmol/CMakeFiles/packmol.dir/computef.f90.o
[100%] Building Fortran object AmberTools/src/packmol_memgen/packmol_memgen/lib/packmol/CMakeFiles/packmol.dir/computeg.f90.o
[100%] Linking Fortran executable packmol
[100%] Built target packmol
[100%] Building CXX object AmberTools/src/moft/CMakeFiles/metatwist.dir/metatwist.cpp.o
In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /usr/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /usr/include/boost/shared_ptr.hpp:17,
                 from /usr/include/boost/program_options/options_description.hpp:16,
                 from /usr/include/boost/program_options.hpp:15,
                 from /home/max/ambertools/src/amber20_src/AmberTools/src/moft/metatwist/boosthead.hpp:19,
                 from /home/max/ambertools/src/amber20_src/AmberTools/src/moft/metatwist.cpp:49:
/usr/include/boost/detail/iterator.hpp:13:1: замечание: «#pragma message: This header is deprecated. Use <iterator> instead.»
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
[100%] Linking CXX executable metatwist
/usr/bin/ld: /usr/lib/libboost_program_options.so.1.76.0: неопределённая ссылка на «std::__throw_bad_array_new_length()@GLIBCXX_3.4.29»
collect2: ошибка: выполнение ld завершилось с кодом возврата 1
make[2]: *** [AmberTools/src/moft/CMakeFiles/metatwist.dir/build.make:109: AmberTools/src/moft/metatwist] Ошибка 1
make[1]: *** [CMakeFiles/Makefile2:9426: AmberTools/src/moft/CMakeFiles/metatwist.dir/all] Ошибка 2
make: *** [Makefile:156: all] Ошибка 2
==> ОШИБКА: Произошел сбой в build().
    Прерывание...

dviktor commented on 2021-08-23 19:23 (UTC)

@Maxwell23 can you try to build by hand, with makepkg, without using AUR helpers?

Maxwell23 commented on 2021-08-22 21:54 (UTC) (edited on 2021-08-22 21:55 (UTC) by Maxwell23)

Relevant part of log with error when compiling in single thread (sorry for russian part):

[100%] Linking Fortran executable packmol
[100%] Built target packmol
[100%] Building CXX object AmberTools/src/moft/CMakeFiles/metatwist.dir/metatwist.cpp.o
In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /usr/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /usr/include/boost/shared_ptr.hpp:17,
                 from /usr/include/boost/program_options/options_description.hpp:16,
                 from /usr/include/boost/program_options.hpp:15,
                 from /var/tmp/pamac-build-max/ambertools/src/amber20_src/AmberTools/src/moft/metatwist/boosthead.hpp:19,
                 from /var/tmp/pamac-build-max/ambertools/src/amber20_src/AmberTools/src/moft/metatwist.cpp:49:
/usr/include/boost/detail/iterator.hpp:13:1: замечание: «#pragma message: This header is deprecated. Use <iterator> instead.»
   13 | BOOST_HEADER_DEPRECATED("<iterator>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
[100%] Linking CXX executable metatwist
/usr/bin/ld: /usr/lib/libboost_program_options.so.1.76.0: неопределённая ссылка на «std::__throw_bad_array_new_length()@GLIBCXX_3.4.29»
collect2: ошибка: выполнение ld завершилось с кодом возврата 1
make[2]: *** [AmberTools/src/moft/CMakeFiles/metatwist.dir/build.make:109: AmberTools/src/moft/metatwist] Ошибка 1
make[1]: *** [CMakeFiles/Makefile2:9426: AmberTools/src/moft/CMakeFiles/metatwist.dir/all] Ошибка 2
make: *** [Makefile:156: all] Ошибка 2
==> ОШИБКА: Произошел сбой в build().
    Прерывание...