Problem with installing QML on MAC

[yghadar]

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.

[andersx]

The FORTRAN variable should be "f90" and is used to tell setuptools the fortran version - you should NOT change this variable in setup.py.

[andersx]

You should not change anything in setup.py.
Please follow the instructions here: http://www.qmlcode.org/installation.html

Feel free to open another issue if the instructions do not work.

[yghadar]

Hi Anders, I have use export path to provide the path with my working gfortran directory. I have also tried installing qml without chaninging anything in setup.py. It still can't find my gfortran. It would be good if instruction could be provided for Mac users. Thank you, *Yasaman Ghadar, PhD* *Postdoctoral Scholar* *Argonne National Laboratory* *Leadership Computing FacilityEmail: ghadar@anl.gov <ghadar@anl.gov> * *Phone: 630-252-1398 <630-252-1398>*

…

On Wed, Aug 30, 2017 at 1:02 PM, Anders Steen Christensen < ***@***.***> wrote: The FORTRAN variable should be "f90" and is used to tell setuptools the fortran version - you should NOT change this variable in setup.py. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#32 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AYjqF0bZEdjP_4rr4RA6rnA2oNKoZ-Ywks5sdaOZgaJpZM4PGKiu> .

[andersx]

Ok, are you able to install qml via pip (simply "pip install qml")? Or does that yield the same error?

[yghadar]

On Mac that results to the same error. *Yasaman Ghadar, PhD* *Postdoctoral Scholar* *Argonne National Laboratory* *Leadership Computing FacilityEmail: ghadar@anl.gov <ghadar@anl.gov> * *Phone: 630-252-1398 <630-252-1398>*

…

On Wed, Aug 30, 2017 at 2:18 PM, Anders Steen Christensen < ***@***.***> wrote: Ok, are you able to install qml via pip (simply "pip install qml")? Or does that yield the same error? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#32 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AYjqFymvRUToBsdmMygXede-P3JwbPq0ks5sdbV0gaJpZM4PGKiu> .

[andersx]

Could you post the output from the following command:

pip install git+https://github.com/qmlcode/qml@develop --user -U

[yghadar]

Please see the following: Thanks pip install git+https://github.com/qmlcode/qml@develop --user -U Collecting git+https://github.com/qmlcode/qml@develop Cloning https://github.com/qmlcode/qml (to develop) to /private/var/folders/d2/n_zzmk5561927yl3r7w5zwkm0000gq/T/pip-GoZ2Nj-build Installing collected packages: qml Running setup.py install for qml ... error Complete output from command /Users/yghadar/miniconda2/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/d2/n_zzmk5561927yl3r7w5zwkm0000gq/T/pip-GoZ2Nj-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/d2/n_zzmk5561927yl3r7w5zwkm0000gq/T/pip-Q1tsFy-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 "farad_kernels" sources f2py options: ['--quiet'] adding 'build/src.macosx-10.7-x86_64-2.7/build/src.macosx-10.7-x86_64-2.7/fortranobject.c' to sources. adding 'build/src.macosx-10.7-x86_64-2.7/build/src.macosx-10.7-x86_64-2.7' to include_dirs. adding 'build/src.macosx-10.7-x86_64-2.7/farad_kernels-f2pywrappers.f' to sources. adding 'build/src.macosx-10.7-x86_64-2.7/farad_kernels-f2pywrappers2.f90' to sources. building extension "fcho_solve" sources f2py options: ['--quiet'] adding 'build/src.macosx-10.7-x86_64-2.7/build/src.macosx-10.7-x86_64-2.7/fortranobject.c' to sources. adding 'build/src.macosx-10.7-x86_64-2.7/build/src.macosx-10.7-x86_64-2.7' to include_dirs. adding 'build/src.macosx-10.7-x86_64-2.7/fcho_solve-f2pywrappers.f' to sources. building extension "fdistance" sources f2py options: ['--quiet'] adding 'build/src.macosx-10.7-x86_64-2.7/build/src.macosx-10.7-x86_64-2.7/fortranobject.c' to sources. adding 'build/src.macosx-10.7-x86_64-2.7/build/src.macosx-10.7-x86_64-2.7' to include_dirs. adding 'build/src.macosx-10.7-x86_64-2.7/fdistance-f2pywrappers.f' to sources. building extension "fkernels" sources f2py options: ['--quiet'] adding 'build/src.macosx-10.7-x86_64-2.7/build/src.macosx-10.7-x86_64-2.7/fortranobject.c' to sources. adding 'build/src.macosx-10.7-x86_64-2.7/build/src.macosx-10.7-x86_64-2.7' to include_dirs. adding 'build/src.macosx-10.7-x86_64-2.7/fkernels-f2pywrappers.f' to sources. building extension "fslatm" sources f2py options: ['--quiet'] adding 'build/src.macosx-10.7-x86_64-2.7/build/src.macosx-10.7-x86_64-2.7/fortranobject.c' to sources. adding 'build/src.macosx-10.7-x86_64-2.7/build/src.macosx-10.7-x86_64-2.7' to include_dirs. adding 'build/src.macosx-10.7-x86_64-2.7/fslatm-f2pywrappers.f' to sources. adding 'build/src.macosx-10.7-x86_64-2.7/fslatm-f2pywrappers2.f90' to sources. building extension "frepresentations" sources f2py options: ['--quiet'] adding 'build/src.macosx-10.7-x86_64-2.7/build/src.macosx-10.7-x86_64-2.7/fortranobject.c' to sources. adding 'build/src.macosx-10.7-x86_64-2.7/build/src.macosx-10.7-x86_64-2.7' to include_dirs. adding 'build/src.macosx-10.7-x86_64-2.7/frepresentations-f2pywrappers.f' to sources. adding 'build/src.macosx-10.7-x86_64-2.7/frepresentations-f2pywrappers2.f90' to sources. build_src: building npy-pkg config files running build_py creating build/lib.macosx-10.7-x86_64-2.7 creating build/lib.macosx-10.7-x86_64-2.7/qml copying qml/__init__.py -> build/lib.macosx-10.7-x86_64-2.7/qml copying qml/arad.py -> build/lib.macosx-10.7-x86_64-2.7/qml copying qml/compound.py -> build/lib.macosx-10.7-x86_64-2.7/qml copying qml/data.py -> build/lib.macosx-10.7-x86_64-2.7/qml copying qml/distance.py -> build/lib.macosx-10.7-x86_64-2.7/qml copying qml/kernels.py -> build/lib.macosx-10.7-x86_64-2.7/qml copying qml/math.py -> build/lib.macosx-10.7-x86_64-2.7/qml copying qml/representations.py -> build/lib.macosx-10.7-x86_64-2.7/qml copying qml/slatm.py -> build/lib.macosx-10.7-x86_64-2.7/qml copying qml/wrappers.py -> build/lib.macosx-10.7-x86_64-2.7/qml running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext 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. warning: build_ext: f90_compiler=None is not available. building 'farad_kernels' extension error: extension 'farad_kernels' has Fortran sources but no Fortran compiler found

…

---------------------------------------- Command "/Users/yghadar/miniconda2/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/d2/n_zzmk5561927yl3r7w5zwkm0000gq/T/pip-GoZ2Nj-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/d2/n_zzmk5561927yl3r7w5zwkm0000gq/T/pip-Q1tsFy-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /private/var/folders/d2/n_zzmk5561927yl3r7w5zwkm0000gq/T/pip-GoZ2Nj-build/ *Yasaman Ghadar, PhD* *Postdoctoral Scholar* *Argonne National Laboratory* *Leadership Computing FacilityEmail: ghadar@anl.gov <ghadar@anl.gov> * *Phone: 630-252-1398 <630-252-1398>*

On Wed, Aug 30, 2017 at 2:26 PM, Anders Steen Christensen < ***@***.***> wrote: Could you post the output from the following command: pip install ***@***.*** --user -U — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#32 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AYjqF60XUDE44uLTWoqXXdTpY0iCEamwks5sdbd6gaJpZM4PGKiu> .

[andersx]

Looks like a problem with your f compiler - what happens if you write:
which gfortran

Also try updating your gcc:

# Update brew
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

# Install GCC
brew install gcc

[yghadar]

Hi, I have installed gfortran from macports, I have also export path in my bashrc file but that does not seem to help. work:~ yghadar$ which gfortran work:~ yghadar$ which gfortran-mp-6 /opt/local/bin/gfortran-mp-6 *Yasaman Ghadar, PhD* *Postdoctoral Scholar* *Argonne National Laboratory* *Leadership Computing FacilityEmail: ghadar@anl.gov <ghadar@anl.gov> * *Phone: 630-252-1398 <630-252-1398>*

…

On Thu, Aug 31, 2017 at 3:28 AM, Anders Steen Christensen < ***@***.***> wrote: Looks like a problem with your f compiler - what happens if you write: which fortran Also try updating your gcc: # Update brew /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" # Install GCC brew install gcc — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#32 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AYjqF27Z82ElxoKrDoAPFHw9wX0ysB9vks5sdm6igaJpZM4PGKiu> .

[andersx]

I think I understand the root of your problem now. This seems to be a limitations in python's setuptools, that it only looks for execuatbles named gfortran, but it should be possible to install a package regardless.

Can you run the following command:
python setup.py build --help-fcompiler

This should give you a list of all f-compilers can find. I assume the list will be empty.

[yghadar]

Yes, you are right. Here is the output generated from python setup.py build --help-fcompiler $ python setup.py build --help-fcompiler Fortran compilers found: 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=gnu95 GNU Fortran 95 compiler

--fcompiler=ibm IBM XL Fortran Compiler

--fcompiler=intel Intel Fortran Compiler for 32-bit apps

--fcompiler=nag NAGWare Fortran 95 Compiler

--fcompiler=pg Portland Group Fortran Compiler Compilers not available on this platform:

--fcompiler=compaq Compaq 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=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. *Yasaman Ghadar, PhD* *Postdoctoral Scholar* *Argonne National Laboratory* *Leadership Computing FacilityEmail: ghadar@anl.gov <ghadar@anl.gov> * *Phone: 630-252-1398 <630-252-1398>*

On Thu, Aug 31, 2017 at 10:13 AM, Anders Steen Christensen < ***@***.***> wrote: I think I understand the root of your problem now. This seems to be a limitations in python's setuptools, that it only looks for execuatbles named gfortran, but it should be possible to install a package regardless. Can you run the following command: python setup.py build --help-fcompiler This should give you a list of all f-compilers can find. I assume the list will be empty. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#32 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AYjqF1USXGhGX8FI8JmZSRwzY68DlkQjks5sds2LgaJpZM4PGKiu> .

[andersx]

Looks like you need to set up a symlink to gcc and gfortran, there are instructions here:
https://stackoverflow.com/questions/8361002/how-to-use-the-gcc-installed-in-macports/8372496#8372496

Once you setup the symlinks, I think setup.py should be able to find the right gfortran. Let me know how it goes!

[yghadar]

Hi, So it looks working but it is not here is the output of python install setup.py ( last lines) byte-compiling /Users/yghadar/miniconda2/lib/python2.7/site-packages/qml/__init__.py to __init__.pyc byte-compiling /Users/yghadar/miniconda2/lib/python2.7/site-packages/qml/arad.py to arad.pyc byte-compiling /Users/yghadar/miniconda2/lib/python2.7/site-packages/qml/compound.py to compound.pyc byte-compiling /Users/yghadar/miniconda2/lib/python2.7/site-packages/qml/data.py to data.pyc byte-compiling /Users/yghadar/miniconda2/lib/python2.7/site-packages/qml/distance.py to distance.pyc byte-compiling /Users/yghadar/miniconda2/lib/python2.7/site-packages/qml/kernels.py to kernels.pyc byte-compiling /Users/yghadar/miniconda2/lib/python2.7/site-packages/qml/math.py to math.pyc byte-compiling /Users/yghadar/miniconda2/lib/python2.7/site-packages/qml/representations.py to representations.pyc byte-compiling /Users/yghadar/miniconda2/lib/python2.7/site-packages/qml/slatm.py to slatm.pyc byte-compiling /Users/yghadar/miniconda2/lib/python2.7/site-packages/qml/wrappers.py to wrappers.pyc running install_egg_info Writing /Users/yghadar/miniconda2/lib/python2.7/site-packages/qml-0.3.1-py2.7.egg-info running install_clib customize UnixCCompiler Here is the output of:

>> import qml

Traceback (most recent call last): File "<stdin>", line 1, in <module> File "qml/__init__.py", line 37, in <module> from .compound import Compound File "qml/compound.py", line 30, in <module> from .representations import generate_coulomb_matrix File "qml/representations.py", line 28, in <module> from .frepresentations import fgenerate_coulomb_matrix ImportError: No module named frepresentations *Yasaman Ghadar, PhD* *Postdoctoral Scholar* *Argonne National Laboratory* *Leadership Computing FacilityEmail: ghadar@anl.gov <ghadar@anl.gov> * *Phone: 630-252-1398 <630-252-1398>*

…

On Thu, Aug 31, 2017 at 10:25 AM, Anders Steen Christensen < ***@***.***> wrote: Looks like you need to set up a symlink to gcc and gfortran, there are instructions here: https://stackoverflow.com/questions/8361002/how-to-use- the-gcc-installed-in-macports/8372496#8372496 Once you setup the symlinks, I think setup.py should be able to find the right gfortran. Let me know how it goes! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#32 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AYjqFx-oGtj9NAJ1trvLq63Extmatl36ks5sdtBVgaJpZM4PGKiu> .

[andersx]

Based on

File "qml/__init__.py", line 37, in <module>

it looks like you were probably in the source folder, which you cloned from github. In this case the qml/ folder only contains the source (it is not where setup.py places the compiled code), but this is the folder that python searches first.

Can you try from another folder?

[yghadar]

I removed the qml folder ls Miniconda2-latest-MacOSX-x86_64.sh conda lammps-16Feb16 lammps-31Mar17 packmol then I run this command: pip install git+ https://github.com/qmlcode/qml@develop --user -U This is what I get: error: Command "gcc -fno-strict-aliasing -I/Users/yghadar/miniconda2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ibuild/src.macosx-10.7-x86_64-2.7/build/src.macosx-10.7-x86_64-2.7 -I/Users/yghadar/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/Users/yghadar/miniconda2/include/python2.7 -c build/src.macosx-10.7-x86_64-2.7/farad_kernelsmodule.c -o build/temp.macosx-10.7-x86_64-2.7/build/src.macosx-10.7-x86_64-2.7/farad_kernelsmodule.o -MMD -MF build/temp.macosx-10.7-x86_64-2.7/build/src.macosx-10.7-x86_64-2.7/farad_kernelsmodule.o.d -O3 -m64 -march=native -fPIC" failed with exit status 1

…

---------------------------------------- Command "/Users/yghadar/miniconda2/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/d2/n_zzmk5561927yl3r7w5zwkm0000gq/T/pip-rCYaDb-build/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/d2/n_zzmk5561927yl3r7w5zwkm0000gq/T/pip-qWGJyX-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /private/var/folders/d2/n_zzmk5561927yl3r7w5zwkm0000gq/T/pip-rCYaDb-build/ *Yasaman Ghadar, PhD* *Postdoctoral Scholar* *Argonne National Laboratory* *Leadership Computing FacilityEmail: ghadar@anl.gov <ghadar@anl.gov> * *Phone: 630-252-1398 <630-252-1398>*

On Thu, Aug 31, 2017 at 11:52 AM, Anders Steen Christensen < ***@***.***> wrote: Based on File "qml/__init__.py", line 37, in <module> it looks like you were probably in the source folder, which you cloned from github. In this case the qml/ folder only contains the source (it is not where setup.py places the compiled code), but this is the folder that python searches first. Can you try from another folder? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#32 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AYjqF2UoMn_5jNJ9af_V035p7QuFUeVsks5sduThgaJpZM4PGKiu> .

[andersx]

Difficult to say what your problem is here. But it looks like a problem with your environments. Really difficult to say from my end - you could try installing gcc from homebrew maybe.