qcscine / xtb_wrapper Goto Github PK
View Code? Open in Web Editor NEWHome Page: https://scine.ethz.ch
License: BSD 3-Clause "New" or "Revised" License
xtb_wrapper's People
Contributors
Stargazers
Watchers
xtb_wrapper's Issues
xtb library is not recognized but downloaded
Trying to build this wrapper against the conda-forge xtb distribution currently fails to pickup the installed library. Instead xtb is downloaded and build again:
❯ cmake -B _build -G Ninja -DCMAKE_INSTALL_PREFIX=$PWD/PREFIX -DSCINE_MARCH=""
-- The C compiler identification is GNU 11.1.0
-- The CXX compiler identification is GNU 11.1.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- The Fortran compiler identification is GNU 11.1.0
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /usr/bin/gfortran - skipped
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP_Fortran: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - not found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - found
-- Found BLAS: /opt/intel/mkl/lib/intel64_lin/libmkl_gf_lp64.so;/opt/intel/mkl/lib/intel64_lin/libmkl_gnu_thread.so;/opt/intel/mkl/lib/intel64_lin/libmkl_core.so;/usr/lib/libgomp.so;-lpthread;-lm;-ldl
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- Found LAPACK: /opt/intel/mkl/lib/intel64_lin/libmkl_gf_lp64.so;/opt/intel/mkl/lib/intel64_lin/libmkl_gnu_thread.so;/opt/intel/mkl/lib/intel64_lin/libmkl_core.so;/usr/lib/libgomp.so;-lpthread;-lm;-ldl;-lpthread;-lm;-ldl
-- xtb was not found in your PATH, so it was downloaded.
-- Setting build type to default 'RelWithDebInfo'
-- Scine::UtilsOS found locally at /home/awvwgk/software/opt/conda/envs/scine/lib/cmake/ScineUtilsOS
-- Configuring done
CMake Warning at src/Xtb/CMakeLists.txt:10 (add_library):
Cannot generate a safe runtime search path for target Xtb because files in
some directories may conflict with libraries in implicit directories:
runtime library [libgomp.so.1] in /usr/lib may be hidden by files in:
/home/awvwgk/software/opt/conda/envs/scine/lib
Some of these libraries may not be found correctly.
-- Generating done
-- Build files have been written to: /home/awvwgk/projects/src/git/scine/xtb_wrapper/_build
mamba list
❯ mamba list
# packages in environment at /home/awvwgk/software/opt/conda/envs/scine:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
boost-cpp 1.74.0 h6cacc03_7 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2021.10.8 ha878542_0 conda-forge
cereal 1.3.2 hd8ed1ab_0 conda-forge
eigen 3.4.0 h4bd325d_0 conda-forge
icu 69.1 h9c3ff4c_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
libblas 3.9.0 13_linux64_openblas conda-forge
libcblas 3.9.0 13_linux64_openblas conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 11.2.0 h1d223b6_14 conda-forge
libgfortran-ng 11.2.0 h69a702a_14 conda-forge
libgfortran5 11.2.0 h5c6108e_14 conda-forge
libgomp 11.2.0 h1d223b6_14 conda-forge
liblapack 3.9.0 13_linux64_openblas conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.18 pthreads_h8fe5266_0 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_14 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libzlib 1.2.11 h166bdaf_1014 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
numpy 1.22.3 py310h45f3432_1 conda-forge
openssl 3.0.2 h166bdaf_1 conda-forge
pip 22.0.4 pyhd8ed1ab_0 conda-forge
pkg-config 0.29.2 h36c2ea0_1008 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
python 3.10.4 h2660328_0_cpython conda-forge
python_abi 3.10 2_cp310 conda-forge
readline 8.1 h46c0cb4_0 conda-forge
scine-core 4.0.0 h6e2fe03_0 conda-forge
scine-sparrow 3.0.0 h108e910_0 conda-forge
scine-utilities-python 4.0.0 py310hdda0239_1 conda-forge
scine-utilsos 4.0.0 hab723ef_0 conda-forge
scipy 1.8.0 py310hea5193d_1 conda-forge
setuptools 62.0.0 py310hff52083_0 conda-forge
sqlite 3.37.1 h4ff8645_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tzdata 2022a h191b570_0 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xtb 6.4.1 hf06ca72_2 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yaml-cpp 0.6.3 he1b5a44_4 conda-forge
zlib 1.2.11 h166bdaf_1014 conda-forge
zstd 1.5.2 ha95c52a_0 conda-forge
mamba info
❯ mamba info
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (0.22.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
active environment : scine
active env location : /home/awvwgk/software/opt/conda/envs/scine
shell level : 2
user config file : /home/awvwgk/.condarc
populated config files : /home/awvwgk/software/opt/conda/.condarc
/home/awvwgk/.condarc
conda version : 4.12.0
conda-build version : not installed
python version : 3.9.12.final.0
virtual packages : __linux=5.10.93=0
__glibc=2.33=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/awvwgk/software/opt/conda (writable)
conda av data dir : /home/awvwgk/software/opt/conda/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /home/awvwgk/software/opt/conda/pkgs
/home/awvwgk/.conda/pkgs
envs directories : /home/awvwgk/software/opt/conda/envs
/home/awvwgk/.conda/envs
platform : linux-64
user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.12 Linux/5.10.93-1-MANJARO manjaro/21.2.2 glibc/2.33
UID:GID : 1000:1000
netrc file : None
offline mode : False
pkg-config detected `xtb` dependency fails to link
Building this project against
boost-cpp: 1.74.0
eigen: 3.4.0
scine-core: 4.0.2
scine-utilsos: 5.0.0
xtb: 6.5.1
yaml-cpp: 0.7.0
fails to link with
[8/8] Linking CXX shared library src/Xtb/xtb.module.so
FAILED: src/Xtb/xtb.module.so
: && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c++ -fPIC -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/scine-xtb-1.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wpedantic -O2 -g -DNDEBUG -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib -Wl,--no-as-needed -shared -Wl,-soname,xtb.module.so -o src/Xtb/xtb.module.so src/Xtb/CMakeFiles/Xtb.dir/Xtb/Wrapper/GFN0Wrapper.cpp.o src/Xtb/CMakeFiles/Xtb.dir/Xtb/Wrapper/GFN1Wrapper.cpp.o src/Xtb/CMakeFiles/Xtb.dir/Xtb/Wrapper/GFN2Wrapper.cpp.o src/Xtb/CMakeFiles/Xtb.dir/Xtb/Wrapper/GFNFFWrapper.cpp.o src/Xtb/CMakeFiles/Xtb.dir/Xtb/Wrapper/XtbCalculatorBase.cpp.o src/Xtb/CMakeFiles/Xtb.dir/Xtb/Wrapper/XtbSettings.cpp.o src/Xtb/CMakeFiles/Xtb.dir/Xtb/XtbModule.cpp.o $PREFIX/lib/libutilsos.so -llib-xtb-static -lgfortran $PREFIX/lib/libboost_filesystem.so.1.74.0 $PREFIX/lib/libboost_system.so.1.74.0 $PREFIX/lib/libblas.so && :
$BUILD_PREFIX/bin/../lib/gcc/x86_64-conda-linux-gnu/10.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -llib-xtb-static
collect2: error: ld returned 1 exit status
Due to using the lib-xtb-static target rather than the generated interface library from pkg-config finder.
platform info
active environment : base
active env location : /opt/conda
shell level : 1
user config file : /home/conda/.condarc
populated config files : /opt/conda/.condarc
/home/conda/.condarc
conda version : 4.13.0
conda-build version : 3.22.0
python version : 3.9.13.final.0
virtual packages : __linux=5.15.0=0
__glibc=2.17=0
__unix=0=0
__archspec=1=x86_64
base environment : /opt/conda (writable)
conda av data dir : /opt/conda/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /home/conda/feedstock_root/build_artifacts/pkg_cache
/opt/conda/pkgs
envs directories : /opt/conda/envs
/home/conda/.conda/envs
platform : linux-64
user-agent : conda/4.13.0 requests/2.28.1 CPython/3.9.13 Linux/5.15.0-1014-azure centos/7.9.2009 glibc/2.17
UID:GID : 1001:1001
netrc file : None
offline mode : False
Linking fails with clang 12
Another issue with the LLVM toolchain, linking with the clang and the ld on MacOS (LLVM based) I get an error because the --no-as-needed option is unknown.
[8/8] Linking CXX shared library src/Xtb/xtb.module.dylib
FAILED: src/Xtb/xtb.module.dylib
: && $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang++ -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/scine-xtb-1.0.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -Wall -Wextra -Wpedantic -O3 -DNDEBUG -isysroot /Applications/Xcode_12.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -mmacosx-version-min=10.9 -dynamiclib -Wl,-headerpad_max_install_names -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,--no-as-needed -o src/Xtb/xtb.module.dylib -install_name @rpath/xtb.module.dylib src/Xtb/CMakeFiles/Xtb.dir/Xtb/Wrapper/GFN0Wrapper.cpp.o src/Xtb/CMakeFiles/Xtb.dir/Xtb/Wrapper/GFN1Wrapper.cpp.o src/Xtb/CMakeFiles/Xtb.dir/Xtb/Wrapper/GFN2Wrapper.cpp.o src/Xtb/CMakeFiles/Xtb.dir/Xtb/Wrapper/GFNFFWrapper.cpp.o src/Xtb/CMakeFiles/Xtb.dir/Xtb/Wrapper/XtbCalculatorBase.cpp.o src/Xtb/CMakeFiles/Xtb.dir/Xtb/Wrapper/XtbSettings.cpp.o src/Xtb/CMakeFiles/Xtb.dir/Xtb/XtbModule.cpp.o $PREFIX/lib/libutilsos.dylib -lgfortran $PREFIX/lib/libboost_filesystem.dylib $PREFIX/lib/libboost_system.dylib -framework Accelerate $PREFIX/lib/libxtb.dylib && :
ld: unknown option: --no-as-needed
clang-12: error: linker command failed with exit code 1 (use -v to see invocation)
ninja: build stopped: subcommand failed.
System info
active environment : base
active env location : /Users/runner/mambaforge
shell level : 1
user config file : /Users/runner/.condarc
populated config files : /Users/runner/mambaforge/.condarc
conda version : 4.12.0
conda-build version : 3.21.8
python version : 3.9.10.final.0
virtual packages : __osx=10.15.7=0
__unix=0=0
__archspec=1=x86_64
base environment : /Users/runner/mambaforge (writable)
conda av data dir : /Users/runner/mambaforge/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/osx-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /Users/runner/mambaforge/pkgs
/Users/runner/.conda/pkgs
envs directories : /Users/runner/mambaforge/envs
/Users/runner/.conda/envs
platform : osx-64
user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.10 Darwin/19.6.0 OSX/10.15.7
UID:GID : 501:20
netrc file : None
offline mode : False
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.