Environment creation on Midway (wheel.py error)
pdeperio opened this issue · comments
Trying to create a new conda environment for pax on Midway with e.g.:
conda env create -f /project/lgrandi/deployHQ/head.yml -n pax_v6.2.1
results in error:
Exception:
Traceback (most recent call last):
File "/project/lgrandi/anaconda3/envs/pax_v6.2.1/lib/python3.4/site-packages/pip/basecommand.py", line 209, in main
status = self.run(options, args)
File "/project/lgrandi/anaconda3/envs/pax_v6.2.1/lib/python3.4/site-packages/pip/commands/install.py", line 317, in run
prefix=options.prefix_path,
File "/project/lgrandi/anaconda3/envs/pax_v6.2.1/lib/python3.4/site-packages/pip/req/req_set.py", line 732, in install
**kwargs
File "/project/lgrandi/anaconda3/envs/pax_v6.2.1/lib/python3.4/site-packages/pip/req/req_install.py", line 835, in install
self.move_wheel_files(self.source_dir, root=root, prefix=prefix)
File "/project/lgrandi/anaconda3/envs/pax_v6.2.1/lib/python3.4/site-packages/pip/req/req_install.py", line 1030, in move_wheel_files
isolated=self.isolated,
File "/project/lgrandi/anaconda3/envs/pax_v6.2.1/lib/python3.4/site-packages/pip/wheel.py", line 344, in move_wheel_files
clobber(source, lib_dir, True)
File "/project/lgrandi/anaconda3/envs/pax_v6.2.1/lib/python3.4/site-packages/pip/wheel.py", line 328, in clobber
os.utime(destfile, (st.st_atime, st.st_mtime))
PermissionError: [Errno 1] Operation not permitted
This pip issue suggests it's due to multiple users installing in the same anaconda3 folder.
Not sure what the best solution is right now; maybe just nuke it and reinstall everything again and make sure nobody else installs in there.
Until the issue is solved, use the following command (which ensures you take the versions from the NLeSC channel) for creating new environments:
PAX_VERSION=v6.2.1
conda create -n pax_${PAX_VERSION} python=3.4 root=6 numpy scipy=0.18.1 pyqt=4.11 matplotlib pandas cython h5py numba pip python-snappy pytables scikit-learn rootpy pymongo psutil jupyter dask root_pandas jpeg=8d isl=0.12.2 gmp=5.1.2 glibc=2.12.2 graphviz=2.38.0=4 gsl=1.16 linux-headers=2.6.32 mpc=1.0.1 mpfr=3.1.2 pcre=8.37 python-snappy=0.5 pyopenssl=0.15.1
ln /project/lgrandi/anaconda3/envs/pax_head/etc/conda/activate.d/*.sh /project/lgrandi/anaconda3/envs/pax_${PAX_VERSION}/etc/conda/activate.d/.
I'm not sure that root=6 is a good version. I knew that it was still under development version. I suggest to use root=5.34
where do you see that? should be stable, we've been using it since the beginning thanks to a lot of work from @remenska to make it work with pax/Python
Is ROOT still under development? This isn't really pax....
@pdeperio can you update README?