Package Details: ambertools 21-2

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, LGPL
Submitter: dviktor
Maintainer: None
Last Packager: dviktor
Votes: 2
Popularity: 0.000000
First Submitted: 2019-05-05 18:23 (UTC)
Last Updated: 2021-06-21 12:30 (UTC)

Latest Comments

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!
removing: _configtest.c _configtest.o _configtest
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!
removing: _configtest.c _configtest.o _configtest
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!
removing: _configtest.c _configtest.o _configtest
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!
removing: _configtest.c _configtest.o _configtest
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!
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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...

dviktor commented on 2021-08-21 12:20 (UTC)

that error log isn't full. try to compile in single thread (MAKEFLAGS=j1) and post relevant part of log with error, please

Maxwell23 commented on 2021-08-19 21:35 (UTC) (edited on 2021-08-19 21:38 (UTC) by Maxwell23)

Please help me. I get an error when trying to emerge AmberTools:

[ 35%] Built target cpptraj_common_obj

make: *** [Makefile:156: all] Error 2

What should I do?

dviktor commented on 2020-11-15 15:48 (UTC)

@asakurahao I have similar warnings but they shouldn't block xleap from running:

$ xleap
-I: Adding /opt/amber/dat/leap/prep to search path.
-I: Adding /opt/amber/dat/leap/lib to search path.
-I: Adding /opt/amber/dat/leap/parm to search path.
-I: Adding /opt/amber/dat/leap/cmd to search path.
Warning: Cannot convert string "-*-helvetica-medium-r-*-*-18-*-*-*-*-*-*-*" to type FontStruct
Warning: Cannot convert string "-*-helvetica-bold-r-*-14-*" to type FontStruct
Warning: Cannot convert string "-*-helvetica-medium-o-*-*-14-*-*-*-*-*-*-*" to type FontStruct
Warning: Cannot convert string "-*-courier-bold-r-*-*-14-*-*-*-*-*-*-*" to type FontStruct
Warning: Cannot convert string "-*-helvetica-medium-o-*-*-18-*-*-*-*-*-*-*" to type FontStruct
Warning: Cannot convert string "-*-courier-medium-r-*-*-14-*-*-*-*-*-*-*" to type FontStruct

To avoid these messages you can try to install one of the Xorg fonts

asakurahao commented on 2020-11-15 15:47 (UTC)

@dviktor Thanks, it works now!

dviktor commented on 2020-11-15 10:45 (UTC)

@asakurahao it seems like AMBER developers haven't published support patch. I've added one so re-download package and try again

asakurahao commented on 2020-11-14 23:11 (UTC)

@dviktor, It is working now, Thanks.

Now, I'm having problems with version of CUDA. "CUDA version 11.1 detected Error: Unsupported CUDA version. AMBER requires CUDA version >= 7.5 and <= 10.2."

How can I disable it or correct this problem?

dviktor commented on 2020-11-14 19:05 (UTC)

@asakurahao Yes, AMBER developers require that you download sources from their website. Then you should place them in the same directory where your downloaded PKGBUILD resides. After that just run makepkg

asakurahao commented on 2020-11-14 19:03 (UTC)

Dear,

When I try to install, the message is shown: Building ambertools... ==> Making package: ambertools 20-5 (Sat 14 Nov 2020 03:55:49 PM -03) ==> Checking runtime dependencies... ==> Checking buildtime dependencies... ==> Retrieving sources... ==> ERROR: AmberTools20.tar.bz2 was not found in the build directory and is not a URL. Failed to build ambertools

Looking in the source files, there is a "local://AmberTools20.tar.bz2". Should I download the software? If yes, where should I put it?

dviktor commented on 2019-09-19 12:53 (UTC)

@Gusten should be fixed now

Gusten commented on 2019-09-19 11:49 (UTC)

It appears that the md5sums for amber.sh and 19 need to be updated.