I have Mac with Sierra OS. I have installed BLAS, LAPACK as well as ASE and gnu compilers from macport. When I try python setup.py install I get: resetting extension 'farad_kernels' language from '/opt/local/bin/gfortran-mp-7' to 'f77'. resetting extension 'fcho_solve' language from '/opt/local/bin/gfortran-mp-7' to 'f77'. resetting extension 'fdistance' language from '/opt/local/bin/gfortran-mp-7' to 'f77'. resetting extension 'fkernels' language from '/opt/local/bin/gfortran-mp-7' to 'f77'. resetting extension 'frepresentations' language from '/opt/local/bin/gfortran-mp-7' to 'f77'. customize Gnu95FCompiler Could not locate executable gfortran Could not locate executable f95 customize NAGFCompiler customize AbsoftFCompiler Could not locate executable f90 Could not locate executable f77 customize IBMFCompiler Could not locate executable xlf90 Could not locate executable xlf customize IntelFCompiler Could not locate executable ifort Could not locate executable ifc customize GnuFCompiler Could not locate executable g77 customize G95FCompiler Could not locate executable g95 customize PGroupFCompiler Could not locate executable pgfortran don't know how to compile Fortran code on platform 'posix' warning: build_ext: f77_compiler=None is not available.

building 'farad_kernels' extension error: extension 'farad_kernels' has Fortran sources but no Fortran compiler found bash-3.2$

I have give the full path in setup.py for FORTRAN = "/opt/local/bin/gfortran-mp-7"

Please let me know what I need to do to resolve the issue.

probably my setup, but happens on both my macbook and linux desktop at work (both with python 3)

p setup.py install --prefix=/Users/strange/qmlcode MKL-discover: MKLROOT was not set Traceback (most recent call last): File "setup.py", line 170, in setup_pepytools() File "setup.py", line 149, in setup_pepytools long_description = readme(), File "setup.py", line 134, in readme return f.read() File "/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/lib/python3.6/encodings/ascii.py", line 26, in decode return codecs.ascii_decode(input, self.errors)[0]

Following seems to fix it:

diff --git a/setup.py b/setup.py
index 495f7e8..2ce0397 100755
--- a/setup.py
+++ b/setup.py
@@ -130,7 +130,7 @@ ext_fslatm = Extension(name = 'fslatm',
 
 # use README.md as long description
 def readme():
-    with open('README.md') as f:
+    with open('README.md', encoding='latin1') as f:
         return f.read()

Hi,

It is a great work of the FCHL19 in https://arxiv.org/pdf/1909.01946.pdf I searched the source code and had no idea where FCHL19 located. Is that possible to provide a basic example of the FCHL19?

Thanks, Xinyu

As said in title. These are superseeded by the QMLearn interface.

This will also remove the dependency on ASE, as far as I can see.

Any downsides to this @larsbratholm ?

Hi all, When attempting to install the QML package for python 3.8.3 an error returned. I've followed the installation guide for intel compilers and have installed ifort, mkl, numpy and scikit-learn. Looking through the message it says that MKLROOT is not set. Checking in system variables confirms this. There is a variable for ifort_compiler20 and mkl_serial, probably indicating succesfull installation.

What should mklroot be set to and is it the problem in this situation?

The error message is:

Collecting qml Using cached https://files.pythonhosted.org/packages/7b/f3/c08d18659054cdf5e5dc531ee32ab20e6aa1d3772545837557828a03b1f5/qml-0.4.0.27.tar.gz Installing collected packages: qml Running setup.py install for qml ... error ERROR: Command errored out with exit status 1: command: 'c:\users\BRS\appdata\local\programs\python\python38\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\BRS\AppData\Local\Temp\pip-install-gn9koii5\qml\setup.py'"'"'; file='"'"'C:\Users\BRS\AppData\Local\Temp\pip-install-gn9koii5\qml\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' build --compiler=intelem --fcompiler=intelem install --record 'C:\Users\BRS\AppData\Local\Temp\pip-record-537c7i8_\install-record.txt' --single-version-externally-managed --compile --user --prefix= cwd: C:\Users\BRS\AppData\Local\Temp\pip-install-gn9koii5\qml
Complete output (103 lines): MKL-discover: MKLROOT was not set running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "ffchl_module" sources f2py options: ['--quiet'] adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8\fortranobject.c' to sources. adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8' to include_dirs. adding 'build\src.win-amd64-3.8\ffchl_module-f2pywrappers.f' to sources. adding 'build\src.win-amd64-3.8\ffchl_module-f2pywrappers2.f90' to sources. building extension "farad_kernels" sources f2py options: ['--quiet'] adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8\fortranobject.c' to sources. adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8' to include_dirs. adding 'build\src.win-amd64-3.8\farad_kernels-f2pywrappers.f' to sources. adding 'build\src.win-amd64-3.8\farad_kernels-f2pywrappers2.f90' to sources. building extension "fcho_solve" sources f2py options: ['--quiet'] adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8\fortranobject.c' to sources. adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8' to include_dirs. adding 'build\src.win-amd64-3.8\fcho_solve-f2pywrappers.f' to sources. building extension "fdistance" sources f2py options: ['--quiet'] adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8\fortranobject.c' to sources. adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8' to include_dirs. adding 'build\src.win-amd64-3.8\fdistance-f2pywrappers.f' to sources. building extension "fkernels" sources f2py options: ['--quiet'] adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8\fortranobject.c' to sources. adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8' to include_dirs. adding 'build\src.win-amd64-3.8\fkernels-f2pywrappers.f' to sources. building extension "fslatm" sources f2py options: ['--quiet'] adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8\fortranobject.c' to sources. adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8' to include_dirs. adding 'build\src.win-amd64-3.8\fslatm-f2pywrappers.f' to sources. adding 'build\src.win-amd64-3.8\fslatm-f2pywrappers2.f90' to sources. building extension "frepresentations" sources f2py options: ['--quiet'] adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8\fortranobject.c' to sources. adding 'build\src.win-amd64-3.8\build\src.win-amd64-3.8' to include_dirs. adding 'build\src.win-amd64-3.8\frepresentations-f2pywrappers.f' to sources. adding 'build\src.win-amd64-3.8\frepresentations-f2pywrappers2.f90' to sources. build_src: building npy-pkg config files running build_py creating build\lib.win-amd64-3.8 creating build\lib.win-amd64-3.8\qml copying qml\alchemy.py -> build\lib.win-amd64-3.8\qml copying qml\arad.py -> build\lib.win-amd64-3.8\qml copying qml\compound.py -> build\lib.win-amd64-3.8\qml copying qml\data.py -> build\lib.win-amd64-3.8\qml copying qml\distance.py -> build\lib.win-amd64-3.8\qml copying qml\fchl.py -> build\lib.win-amd64-3.8\qml copying qml\kernels.py -> build\lib.win-amd64-3.8\qml copying qml\math.py -> build\lib.win-amd64-3.8\qml copying qml\representations.py -> build\lib.win-amd64-3.8\qml copying qml\slatm.py -> build\lib.win-amd64-3.8\qml copying qml\wrappers.py -> build\lib.win-amd64-3.8\qml copying qml_init_.py -> build\lib.win-amd64-3.8\qml running build_ext Could not locate executable icc Could not locate executable ecc customize IntelEM64TCCompiler customize IntelEM64TCCompiler using build_ext customize IntelEM64TFCompiler Could not locate executable ifort Could not locate executable efort Could not locate executable efc Traceback (most recent call last): File "", line 1, in File "C:\Users\BRS\AppData\Local\Temp\pip-install-gn9koii5\qml\setup.py", line 172, in setup_pepytools() File "C:\Users\BRS\AppData\Local\Temp\pip-install-gn9koii5\qml\setup.py", line 140, in setup_pepytools setup( File "c:\users\BRS\appdata\local\programs\python\python38\lib\site-packages\numpy\distutils\core.py", line 171, in setup return old_setup(**new_attr) File "c:\users\BRS\appdata\local\programs\python\python38\lib\site-packages\setuptools_init_.py", line 145, in setup return distutils.core.setup(**attrs) File "c:\users\BRS\appdata\local\programs\python\python38\lib\distutils\core.py", line 148, in setup dist.run_commands() File "c:\users\BRS\appdata\local\programs\python\python38\lib\distutils\dist.py", line 966, in run_commands self.run_command(cmd) File "c:\users\BRS\appdata\local\programs\python\python38\lib\distutils\dist.py", line 985, in run_command cmd_obj.run() File "c:\users\BRS\appdata\local\programs\python\python38\lib\site-packages\numpy\distutils\command\build.py", line 42, in run old_build.run(self) File "c:\users\BRS\appdata\local\programs\python\python38\lib\distutils\command\build.py", line 135, in run self.run_command(cmd_name) File "c:\users\BRS\appdata\local\programs\python\python38\lib\distutils\cmd.py", line 313, in run_command self.distribution.run_command(command) File "c:\users\BRS\appdata\local\programs\python\python38\lib\distutils\dist.py", line 985, in run_command cmd_obj.run() File "c:\users\BRS\appdata\local\programs\python\python38\lib\site-packages\numpy\distutils\command\build_ext.py", line 239, in run fcompiler.customize(self.distribution) File "c:\users\BRS\appdata\local\programs\python\python38\lib\site-packages\numpy\distutils\fcompiler_init_.py", line 463, in customize self.find_executables() File "c:\users\BRS\appdata\local\programs\python\python38\lib\site-packages\numpy\distutils\fcompiler_init_.py", line 352, in find_executables raise CompilerNotFound('%s: f90 nor f77' % ctype) numpy.distutils.fcompiler.CompilerNotFound: intelem: f90 nor f77 ---------------------------------------- ERROR: Command errored out with exit status 1: 'c:\users\BRS\appdata\local\programs\python\python38\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\BRS\AppData\Local\Temp\pip-install-gn9koii5\qml\setup.py'"'"'; file='"'"'C:\Users\BRS\AppData\Local\Temp\pip-install-gn9koii5\qml\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' build --compiler=intelem --fcompiler=intelem install --record 'C:\Users\BRS\AppData\Local\Temp\pip-record-537c7i8_\install-record.txt' --single-version-externally-managed --compile --user --prefix= Check the logs for full command output.

I'm new to python, help would be greatly appreciated.

Hello everyone, I have never had problems installing with pip3 before. I have Ubuntu 18.04.4 LTS. Thanks

Collecting qml Downloading https://files.pythonhosted.org/packages/7b/f3/c08d18659054cdf5e5dc531ee32ab20e6aa1d3772545837557828a03b1f5/qml-0.4.0.27.tar.gz (41kB) 100% |████████████████████████████████| 51kB 1.2MB/s Building wheels for collected packages: qml Running setup.py bdist_wheel for qml ... error Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-b9e7yqyc/qml/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d /tmp/tmpm3f7m3g3pip-wheel- --python-tag cp36: MKL-discover: MKLROOT was not set running bdist_wheel running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "ffchl_module" sources f2py options: ['--quiet'] adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs. adding 'build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers.f' to sources. adding 'build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers2.f90' to sources. building extension "farad_kernels" sources f2py options: ['--quiet'] adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs. adding 'build/src.linux-x86_64-3.6/farad_kernels-f2pywrappers.f' to sources. adding 'build/src.linux-x86_64-3.6/farad_kernels-f2pywrappers2.f90' to sources. building extension "fcho_solve" sources f2py options: ['--quiet'] adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs. adding 'build/src.linux-x86_64-3.6/fcho_solve-f2pywrappers.f' to sources. building extension "fdistance" sources f2py options: ['--quiet'] adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs. adding 'build/src.linux-x86_64-3.6/fdistance-f2pywrappers.f' to sources. building extension "fkernels" sources f2py options: ['--quiet'] adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs. adding 'build/src.linux-x86_64-3.6/fkernels-f2pywrappers.f' to sources. building extension "fslatm" sources f2py options: ['--quiet'] adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs. adding 'build/src.linux-x86_64-3.6/fslatm-f2pywrappers.f' to sources. adding 'build/src.linux-x86_64-3.6/fslatm-f2pywrappers2.f90' to sources. building extension "frepresentations" sources f2py options: ['--quiet'] adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs. adding 'build/src.linux-x86_64-3.6/frepresentations-f2pywrappers.f' to sources. adding 'build/src.linux-x86_64-3.6/frepresentations-f2pywrappers2.f90' to sources. build_src: building npy-pkg config files running build_py creating build/lib.linux-x86_64-3.6 creating build/lib.linux-x86_64-3.6/qml copying qml/compound.py -> build/lib.linux-x86_64-3.6/qml copying qml/representations.py -> build/lib.linux-x86_64-3.6/qml copying qml/data.py -> build/lib.linux-x86_64-3.6/qml copying qml/alchemy.py -> build/lib.linux-x86_64-3.6/qml copying qml/init.py -> build/lib.linux-x86_64-3.6/qml copying qml/fchl.py -> build/lib.linux-x86_64-3.6/qml copying qml/kernels.py -> build/lib.linux-x86_64-3.6/qml copying qml/slatm.py -> build/lib.linux-x86_64-3.6/qml copying qml/distance.py -> build/lib.linux-x86_64-3.6/qml copying qml/math.py -> build/lib.linux-x86_64-3.6/qml copying qml/wrappers.py -> build/lib.linux-x86_64-3.6/qml copying qml/arad.py -> build/lib.linux-x86_64-3.6/qml running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']' customize Gnu95FCompiler Found executable /usr/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using build_ext get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']' customize Gnu95FCompiler customize Gnu95FCompiler customize Gnu95FCompiler using build_ext building 'ffchl_module' extension compiling C sources C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

creating build/temp.linux-x86_64-3.6/build creating build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6 creating build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build creating build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6 compile options: '-Ibuild/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6 -I/home/graggi/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c' extra options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp' x86_64-linux-gnu-gcc: build/src.linux-x86_64-3.6/ffchl_modulemodule.c x86_64-linux-gnu-gcc: build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c compiling Fortran 90 module sources creating build/temp.linux-x86_64-3.6/qml Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops compile options: '-Ibuild/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6 -I/home/graggi/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c' extra options: '-Jbuild/temp.linux-x86_64-3.6/qml -Ibuild/temp.linux-x86_64-3.6/qml' extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp' gfortran:f90: qml/ffchl_module.f90 qml/ffchl_module.f90:275:36:

   & t_width, d_width, cut_distance, order, pd, ang_norm2, &
                                  1

Warning: Unused dummy argument ‘cut_distance’ at (1) [-Wunused-dummy-argument] compiling Fortran sources Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops compile options: '-Ibuild/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6 -I/home/graggi/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c' extra options: '-Jbuild/temp.linux-x86_64-3.6/qml -Ibuild/temp.linux-x86_64-3.6/qml' extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp' gfortran:f90: qml/ffchl_scalar_kernels.f90 extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp' gfortran:f90: build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers2.f90 extra f77 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp' gfortran:f77: build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers.f /usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_modulemodule.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.o build/temp.linux-x86_64-3.6/qml/ffchl_module.o build/temp.linux-x86_64-3.6/qml/ffchl_scalar_kernels.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran -o build/lib.linux-x86_64-3.6/qml/ffchl_module.cpython-36m-x86_64-linux-gnu.so -lgomp -lblas -llapack /usr/bin/ld: cannot find -lblas /usr/bin/ld: cannot find -llapack collect2: error: ld returned 1 exit status error: Command "/usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_modulemodule.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.o build/temp.linux-x86_64-3.6/qml/ffchl_module.o build/temp.linux-x86_64-3.6/qml/ffchl_scalar_kernels.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran -o build/lib.linux-x86_64-3.6/qml/ffchl_module.cpython-36m-x86_64-linux-gnu.so -lgomp -lblas -llapack" failed with exit status 1

Failed building wheel for qml Running setup.py clean for qml Failed to build qml Installing collected packages: qml Running setup.py install for qml ... error Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-b9e7yqyc/qml/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-0kdli_b1-record/install-record.txt --single-version-externally-managed --compile --user --prefix=: MKL-discover: MKLROOT was not set running install running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "ffchl_module" sources f2py options: ['--quiet'] adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs. adding 'build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers.f' to sources. adding 'build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers2.f90' to sources. building extension "farad_kernels" sources f2py options: ['--quiet'] adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs. adding 'build/src.linux-x86_64-3.6/farad_kernels-f2pywrappers.f' to sources. adding 'build/src.linux-x86_64-3.6/farad_kernels-f2pywrappers2.f90' to sources. building extension "fcho_solve" sources f2py options: ['--quiet'] adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs. adding 'build/src.linux-x86_64-3.6/fcho_solve-f2pywrappers.f' to sources. building extension "fdistance" sources f2py options: ['--quiet'] adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs. adding 'build/src.linux-x86_64-3.6/fdistance-f2pywrappers.f' to sources. building extension "fkernels" sources f2py options: ['--quiet'] adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs. adding 'build/src.linux-x86_64-3.6/fkernels-f2pywrappers.f' to sources. building extension "fslatm" sources f2py options: ['--quiet'] adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs. adding 'build/src.linux-x86_64-3.6/fslatm-f2pywrappers.f' to sources. adding 'build/src.linux-x86_64-3.6/fslatm-f2pywrappers2.f90' to sources. building extension "frepresentations" sources f2py options: ['--quiet'] adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c' to sources. adding 'build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6' to include_dirs. adding 'build/src.linux-x86_64-3.6/frepresentations-f2pywrappers.f' to sources. adding 'build/src.linux-x86_64-3.6/frepresentations-f2pywrappers2.f90' to sources. build_src: building npy-pkg config files running build_py creating build/lib.linux-x86_64-3.6 creating build/lib.linux-x86_64-3.6/qml copying qml/compound.py -> build/lib.linux-x86_64-3.6/qml copying qml/representations.py -> build/lib.linux-x86_64-3.6/qml copying qml/data.py -> build/lib.linux-x86_64-3.6/qml copying qml/alchemy.py -> build/lib.linux-x86_64-3.6/qml copying qml/init.py -> build/lib.linux-x86_64-3.6/qml copying qml/fchl.py -> build/lib.linux-x86_64-3.6/qml copying qml/kernels.py -> build/lib.linux-x86_64-3.6/qml copying qml/slatm.py -> build/lib.linux-x86_64-3.6/qml copying qml/distance.py -> build/lib.linux-x86_64-3.6/qml copying qml/math.py -> build/lib.linux-x86_64-3.6/qml copying qml/wrappers.py -> build/lib.linux-x86_64-3.6/qml copying qml/arad.py -> build/lib.linux-x86_64-3.6/qml running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']' customize Gnu95FCompiler Found executable /usr/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using build_ext get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']' customize Gnu95FCompiler customize Gnu95FCompiler customize Gnu95FCompiler using build_ext building 'ffchl_module' extension compiling C sources C compiler: x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC

creating build/temp.linux-x86_64-3.6/build
creating build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build
creating build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6
compile options: '-Ibuild/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6 -I/home/graggi/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c'
extra options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
x86_64-linux-gnu-gcc: build/src.linux-x86_64-3.6/ffchl_modulemodule.c
x86_64-linux-gnu-gcc: build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.c
compiling Fortran 90 module sources
creating build/temp.linux-x86_64-3.6/qml
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
compile options: '-Ibuild/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6 -I/home/graggi/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c'
extra options: '-Jbuild/temp.linux-x86_64-3.6/qml -Ibuild/temp.linux-x86_64-3.6/qml'
extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
gfortran:f90: qml/ffchl_module.f90
qml/ffchl_module.f90:275:36:

     & t_width, d_width, cut_distance, order, pd, ang_norm2, &
                                    1
Warning: Unused dummy argument ‘cut_distance’ at (1) [-Wunused-dummy-argument]
compiling Fortran sources
Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -O3 -funroll-loops
compile options: '-Ibuild/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6 -I/home/graggi/.local/lib/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c'
extra options: '-Jbuild/temp.linux-x86_64-3.6/qml -Ibuild/temp.linux-x86_64-3.6/qml'
extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
gfortran:f90: qml/ffchl_scalar_kernels.f90
extra f90 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
gfortran:f90: build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers2.f90
extra f77 options: '-O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp'
gfortran:f77: build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers.f
/usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_modulemodule.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.o build/temp.linux-x86_64-3.6/qml/ffchl_module.o build/temp.linux-x86_64-3.6/qml/ffchl_scalar_kernels.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran -o build/lib.linux-x86_64-3.6/qml/ffchl_module.cpython-36m-x86_64-linux-gnu.so -lgomp -lblas -llapack
/usr/bin/ld: cannot find -lblas
/usr/bin/ld: cannot find -llapack
collect2: error: ld returned 1 exit status
error: Command "/usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_modulemodule.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/fortranobject.o build/temp.linux-x86_64-3.6/qml/ffchl_module.o build/temp.linux-x86_64-3.6/qml/ffchl_scalar_kernels.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers.o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ffchl_module-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -lgfortran -o build/lib.linux-x86_64-3.6/qml/ffchl_module.cpython-36m-x86_64-linux-gnu.so -lgomp -lblas -llapack" failed with exit status 1

----------------------------------------

Command "/usr/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-b9e7yqyc/qml/setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record /tmp/pip-0kdli_b1-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /tmp/pip-build-b9e7yqyc/qml/

It's not a bug but rather an enhancement / feature request : when creating mol objects using the Compound class to then generate a Coulomb matrix with mol.generate_coulomb_matrix, we have to specify the desired size of the Coulomb matrix with the size argument. It would be nice if properties such as the number of atoms were available in the Compound class. Currently I'm working around this by reading in the coordinates and atom types from the xyz files myself and generating Coulomb matrices using the representations.generate_coulomb_matrix function instead.

The same fortran function is called two different places in the code, using different parameters.

https://github.com/qmlcode/qml/blob/develop/qml/fchl/fchl_scalar_kernels.py#L132

https://github.com/qmlcode/qml/blob/develop/qml/fchl/fchl_kernels.py#L148

One has a verbose flag and one does not, so one of them must be wrong?

On second thought it seems unnecessary to type qml.ml.respresentations, rather than qml.representations.

Anybody against me moving it back to it's former dir?

Moved the existing QML examples into a notebook and added aglaia examples. The aglaia examples can be run in the notebook. We might have to modify the existing QML examples at some point so that they can be run too.

Also made modifications to the aglaia module so that it is consistent with QML in using the word "representation" instead of "descriptor".

I was looking through the documentation to try it out. :-)

"Clang Fortran compiler" was mentioned here: http://www.qmlcode.org/installation.html#note-on-apple-mac-support

I think you mean that the "GCC Fortran compiler, gfortran" through homebrew does not include OpenMP support.

AFAIK, there is no Clang Fortran compiler.

You can get a gfortran from here, which I think includes the OpenMP support: http://hpc.sourceforge.net

Is there a way to build this into a MacBook Air with Apple Silicon (M1)? I'm trying, but there were a lot of errors complaining the lack of a FORTRAN compiler. Here is my output of python setup.py build --help-fcompiler

Gnu95FCompiler instance properties:
  archiver        = ['/opt/homebrew/bin/gfortran', '-cr']
  compile_switch  = '-c'
  compiler_f77    = ['/opt/homebrew/bin/gfortran', '-Wall', '-g', '-ffixed-
                    form', '-fno-second-underscore', '-fPIC', '-O3', '-funroll
                    -loops']
  compiler_f90    = ['/opt/homebrew/bin/gfortran', '-Wall', '-g', '-fno-
                    second-underscore', '-fPIC', '-O3', '-funroll-loops']
  compiler_fix    = ['/opt/homebrew/bin/gfortran', '-Wall', '-g', '-ffixed-
                    form', '-fno-second-underscore', '-Wall', '-g', '-fno-
                    second-underscore', '-fPIC', '-O3', '-funroll-loops']
  libraries       = ['gfortran']
  library_dirs    =
                    ['/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/
                    aarch64-apple-darwin21/11',
                    '/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/a
                    arch64-apple-darwin21/11/../../..',
                    '/opt/homebrew/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/a
                    arch64-apple-darwin21/11/../../..']
  linker_exe      = ['/opt/homebrew/bin/gfortran', '-Wall', '-Wall']
  linker_so       = ['/opt/homebrew/bin/gfortran', '-Wall', '-g', '-Wall', '
                    -g', '-undefined', 'dynamic_lookup', '-bundle']
  object_switch   = '-o '
  ranlib          = ['/opt/homebrew/bin/gfortran']
  version         = LooseVersion ('11')
  version_cmd     = ['/opt/homebrew/bin/gfortran', '-dumpversion']
Fortran compilers found:
  --fcompiler=gnu95  GNU Fortran 95 compiler (11)
Compilers available for this platform, but not found:
  --fcompiler=absoft  Absoft Corp Fortran Compiler
  --fcompiler=g95     G95 Fortran Compiler
  --fcompiler=gnu     GNU Fortran 77 compiler
  --fcompiler=ibm     IBM XL Fortran Compiler
  --fcompiler=intel   Intel Fortran Compiler for 32-bit apps
  --fcompiler=nag     NAGWare Fortran 95 Compiler
  --fcompiler=nagfor  NAG Fortran Compiler
  --fcompiler=pg      Portland Group Fortran Compiler
Compilers not available on this platform:
  --fcompiler=arm       Arm Compiler
  --fcompiler=compaq    Compaq Fortran Compiler
  --fcompiler=flang     Portland Group Fortran LLVM Compiler
  --fcompiler=fujitsu   Fujitsu Fortran Compiler
  --fcompiler=hpux      HP Fortran 90 Compiler
  --fcompiler=intele    Intel Fortran Compiler for Itanium apps
  --fcompiler=intelem   Intel Fortran Compiler for 64-bit apps
  --fcompiler=intelev   Intel Visual Fortran Compiler for Itanium apps
  --fcompiler=intelv    Intel Visual Fortran Compiler for 32-bit apps
  --fcompiler=intelvem  Intel Visual Fortran Compiler for 64-bit apps
  --fcompiler=lahey     Lahey/Fujitsu Fortran 95 Compiler
  --fcompiler=mips      MIPSpro Fortran Compiler
  --fcompiler=none      Fake Fortran compiler
  --fcompiler=nv        NVIDIA HPC SDK
  --fcompiler=pathf95   PathScale Fortran Compiler
  --fcompiler=sun       Sun or Forte Fortran 95 Compiler
  --fcompiler=vast      Pacific-Sierra Research Fortran 90 Compiler
For compiler details, run 'config_fc --verbose' setup command.```

It's worth to mention that I have `gfortran` installed from `brew`, and an Anaconda environment with many tools, including `pip`.

Python 3.9.9 (main, Dec 1 2021, 16:36:40) [GCC 7.5.0] on linux Type "help", "copyright", "credits" or "license" for more information.

import qml Traceback (most recent call last): File "", line 1, in File "/user/kijsdc/.local/lib/python3.9/site-packages/qml/init.py", line 37, in from .compound import Compound File "/user/kijsdc/.local/lib/python3.9/site-packages/qml/compound.py", line 30, in from .representations import generate_coulomb_matrix File "/user/kijsdc/.local/lib/python3.9/site-packages/qml/representations.py", line 28, in from .frepresentations import fgenerate_coulomb_matrix ImportError: /user/kijsdc/.local/lib/python3.9/site-packages/qml/frepresentations.cpython-39-x86_64-linux-gnu.so: undefined symbol: dsyev_

I need your help. please help me...

When installing qmlcode on a windows system, pip install qml, the installation fails with the error:

 cl : Command line error D8021 : invalid numeric argument '/Wno-maybe-uninitialized'
error: Command "C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.29.30037\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Ibuild\src.win-amd64-3.9\build\src.win-amd64-3.9\fchl -IC:\raghav\env_dftb\lib\site-packages\numpy\core\include -IC:\raghav\env_dftb\include -Ic:\users\davinder kumar\appdata\local\programs\python\python39\include -Ic:\users\davinder kumar\appdata\local\programs\python\python39\include -IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.29.30037\include /Tcbuild\src.win-amd64-3.9\fchl\ffchl_modulemodule.c /Fobuild\temp.win-amd64-3.9\Release\build\src.win-amd64-3.9\fchl\ffchl_modulemodule.obj -O3 -fopenmp -m64 -march=native -fPIC -Wno-maybe-uninitialized -Wno-unused-function -Wno-cpp" failed with exit status 2

Is this a problem due to lack of some installed requirement?

When I run generate_bob, either through the Compound class or just the representation, it is throwing a seg fault. I have installed qml (through pip3) as well as the Fortran compiler (brew install gcc).

The generation of a BoB representation via $ qml.representations.generate_bob requires the variable "atomtypes" as third argument which is not used by the function.