isayev
problem installing ASED3
Hello,
I am trying to setting up ASE-ANI in my box with Linux Mint 19.1
When I run the test, I got:
python3 ~/bin/ASE_ANI/examples/ani_quicktest.py van Der Waals correction will be unavailable. Please install ased3 Traceback (most recent call last): File "/home/icamps/bin/ASE_ANI/examples/ani_quicktest.py", line 16, in <module> mol = read('data/water.xyz') File "/usr/lib/python3/dist-packages/ase/io/formats.py", line 428, in read parallel=parallel, **kwargs)) File "/usr/lib/python3/dist-packages/ase/io/formats.py", line 475, in _iread fd = open_with_compression(filename) File "/usr/lib/python3/dist-packages/ase/io/formats.py", line 286, in open_with_compression return open(filename, mode) FileNotFoundError: [Errno 2] No such file or directory: 'data/water.xyz'
But trying to install ASED3, I got then (with python setup.py install):
gfortran: error: build/temp.linux-x86_64-2.7/ased3/_d3params.o: No such file or directory gfortran: error: build/temp.linux-x86_64-2.7/ased3/_d3.o: No such file or directory gfortran: error: build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ased3/_d3-f2pywrappers2.o: No such file or directory
If I execute python3 setup.py install
I got:
build/src.linux-x86_64-3.6/ased3/_d3module.c:17:10: fatal error: Python.h: No such file or directory #include "Python.h" ^~~~~~~~~~ compilation terminated. build/src.linux-x86_64-3.6/ased3/_d3module.c:17:10: fatal error: Python.h: No such file or directory #include "Python.h" ^~~~~~~~~~ compilation terminated. error: Command "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 -Ibuild/src.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ased3 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.6m -c build/src.linux-x86_64-3.6/ased3/_d3module.c -o build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ased3/_d3module.o -MMD -MF build/temp.linux-x86_64-3.6/build/src.linux-x86_64-3.6/ased3/_d3module.o.d" failed with exit status 1
I appreciate any help.
Regards,
Camps
@icamps there are two separate errors. First "file not found" because in example ani_quicktest.py we use a relative path. Go to "~/bin/ASE_ANI/" and execute python3 examples/ani_quicktest.py one more time.
Second, D3 correction is totally optional, but if you'd like to have it, please try:
git clone https://github.com/isayev/ased3
cd ased3
python setup.py install
@isayev Thanks for the quick response!
I continue getting errors.
As I am beginning to play with ASE_ANI, I am not really sure if I will make use of D3 correction (probably yes), but at this time, I am just running the tests to see if the installation is ok, and I do not know how to disable the use of D3 in the examples.
I am confused. When I execute python3 examples/ani_quicktest.py, Iḿ using python3, but when installing ASED3 executing python setup.py install I am using python2.7, right?
Installing ASED3 with python, I got a different error now:
fortran:f90: build/src.linux-x86_64-2.7/ased3/_d3-f2pywrappers2.f90 /usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ased3/_d3module.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ased3/fortranobject.o build/temp.linux-x86_64-2.7/ased3/_d3params.o build/temp.linux-x86_64-2.7/ased3/_d3.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ased3/_d3-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -liomp5 -lgfortran -o build/lib.linux-x86_64-2.7/ased3/_d3.so /usr/bin/ld: cannot find -liomp5 collect2: error: ld returned 1 exit status error: Command "/usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ased3/_d3module.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ased3/fortranobject.o build/temp.linux-x86_64-2.7/ased3/_d3params.o build/temp.linux-x86_64-2.7/ased3/_d3.o build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/ased3/_d3-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/7 -L/usr/lib/gcc/x86_64-linux-gnu/7 -liomp5 -lgfortran -o build/lib.linux-x86_64-2.7/ased3/_d3.so" failed with exit status 1
If I try to install with python3, the error is the same as before: the file Python.h is missing.
A rapid googling about /usr/bin/ld: cannot find -liomp5 give that it could be related with python2-numpy-mkl
I suppose that in order to use ASE_ANI (that is developed for Python3, I have to configure ASED3 with Python3 too, right?
- No everything in python3.6!
- Yes, you are missing liomp5, check if you have Intel MKL, or any other custom BLAS library installed. Often the problem is that your
$LD_LIBRARY_PATHvariable is not defined.
For the missing Python.h file; you might be missing some system package:
$ locate Python.h
[...]
/usr/include/python3.10/Python.h
[...]
$ dpkg -S /usr/include/python3.10/Python.h
libpython3.10-dev:amd64: /usr/include/python3.10/Python.h
I assume you are under a Debian-like Linux; if not then adapt commands to your Linux distro.
