Comments (7)
Yep, thanks.
from cookiecutter-cms.
Possibly need the same compiler toolchain for building the local package as was used to build the env packages. Another suspect is that the c-f compiler toolchain has switched over the past months, so old envs may behave differently than new envs.
from cookiecutter-cms.
I might have an idea, but will need some more information. Can you post your test_env.yaml file?
I will point out that the cookiecutter does not do anything with compilation, so this might be an upstream package issue, not necessarily the cookiecutter itself. For instance, the line /home/davids4/anaconda3/envs/paprika-debug-tleap-dummy/lib/python3.6/site-packages/scipy/sparse/_sparsetools.cpython-36m-x86_64-linux-gnu.so
indicates it might be an issue with the scipy download, which seems unlikely.
Are there additional packages in your base
/root
conda environment which may get overwritten or temporarily removed when you activate the new environment?
from cookiecutter-cms.
Hi Levi, thanks for your thoughts. Here is the test_env.yaml
file:
(paprika-debug-tleap-dummy) [davids4@tscc-login1 pAPRika]$ cat devtools/conda-envs/test_env.yaml
name: paprika-debug-tleap-dummy
channels:
- conda-forge
- omnia
# AmberTools seem to live at this repository...
- http://ambermd.org/downloads/ambertools/conda/
dependencies:
# Base depends
- python=3.6
- pip
- numpy
- scipy
- parmed
- mdtraj
- pymbar
- openmm
# Eventually we can/should migrate away from this, once AMBER gets onto omnia/conda-forge.
# See https://openforcefieldgroup.slack.com/archives/C8NE3J96U/p1549403299386500
- ambertools=18
# Testing
- pytest
- pytest-cov
# Pip-only installs
- pip:
- codecov
I'm not sure if there's anything in base
that might be overwritten by this test environment. It's been a few months since I've worked on TSCC with this code, so I just did a conda update conda
and conda update
before trying to test my cookiecutter
branch. I'm running conda 4.6.3
now. FWIW, here's the output of conda list
in my test environment:
`conda list`
(paprika-debug-tleap-dummy) [davids4@tscc-login1 pAPRika]$ conda list
# packages in environment at /home/davids4/anaconda3/envs/paprika-debug-tleap-dummy:
#
# Name Version Build Channel
ambertools 18.0 0 omnia
atomicwrites 1.3.0 py_0 conda-forge
attrs 18.2.0 py_0 conda-forge
blas 1.1 openblas conda-forge
blosc 1.15.1 hf484d3e_1002 conda-forge
bzip2 1.0.6 h14c3975_1002 conda-forge
ca-certificates 2018.11.29 ha4d7672_0 conda-forge
certifi 2018.11.29 py36_1000 conda-forge
chardet 3.0.4 pypi_0 pypi
codecov 2.0.15 pypi_0 pypi
coverage 4.5.2 py36h14c3975_1000 conda-forge
fftw3f 3.3.4 2 omnia
hdf5 1.10.4 nompi_h11e915b_1105 conda-forge
idna 2.8 pypi_0 pypi
libffi 3.2.1 hf484d3e_1005 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-ng 7.3.0 hdf63c60_0 conda-forge
libgfortran-ng 7.2.0 hdf63c60_3 conda-forge
libstdcxx-ng 7.3.0 hdf63c60_0 conda-forge
lzo 2.10 h14c3975_1000 conda-forge
mdtraj 1.9.2 py36hff88cb2_1000 conda-forge
mmpbsa-py 16.0 pypi_0 pypi
more-itertools 4.3.0 py36_1000 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
numexpr 2.6.9 py36h637b7d7_1000 conda-forge
numpy 1.16.1 py36_blas_openblash1522bff_0 [blas_openblas] conda-forge
openblas 0.3.3 h9ac9557_1001 conda-forge
openmm 7.3.0 py36_cuda92_rc_1 omnia
openssl 1.0.2p h14c3975_1002 conda-forge
packmol-memgen 0.9.9a0 pypi_0 pypi
pandas 0.24.1 py36hf484d3e_0 conda-forge
paprika 0.0.3+87.g1ecf2fe.dirty dev_0 <develop>
parmed 3.0.0+57.g74a84d30 pypi_0 pypi
pdb4amber 1.6.dev0 pypi_0 pypi
pip 19.0.2 py36_0 conda-forge
pluggy 0.8.1 py_0 conda-forge
py 1.7.0 py_0 conda-forge
pymbar 3.0.3 py36h3010b51_3 conda-forge
pymsmt 18.0 pypi_0 pypi
pytables 3.4.4 py36h5d69a80_1004 conda-forge
pytest 4.2.1 py36_0 conda-forge
pytest-cov 2.6.1 py_0 conda-forge
python 3.6.7 hd21baee_1001 conda-forge
python-dateutil 2.8.0 py_0 conda-forge
pytraj 2.0.3 pypi_0 pypi
pytz 2018.9 py_0 conda-forge
readline 7.0 hf8c457e_1001 conda-forge
requests 2.21.0 pypi_0 pypi
sander 16.0 pypi_0 pypi
scipy 1.2.0 py36_blas_openblash1522bff_1201 [blas_openblas] conda-forge
setuptools 40.8.0 py36_0 conda-forge
six 1.12.0 py36_1000 conda-forge
sqlite 3.26.0 h67949de_1000 conda-forge
tk 8.6.9 h84994c4_1000 conda-forge
urllib3 1.24.1 pypi_0 pypi
wheel 0.33.0 py36_0 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
zlib 1.2.11 h14c3975_1004 conda-forge
from cookiecutter-cms.
I think this might actually be an issue with some pointer to old linkers which the scipy library is looking at, but expecting a newer version which should get shipped with Conda.
I don't have a good answer for you, but here is a link to someone having this exact same issue: ContinuumIO/anaconda-issues#5191 (comment)
From what I am reading on that issue, it looks like it might be your LD_LIBRARY_PATH
variable is set to point at some old libgcc files and so the SciPy binaries are looking there first instead of at the ones installed in the Conda Environment.
from cookiecutter-cms.
Hmm, yes indeed, good sleuthing. I didn't have anything overriding LD_LIBRARY_PATH
in my .bashrc
but it is set by the cluster and some of those look kinda old. If I manually add the conda
libraries to the front of that, things do work. For example:
(paprika-debug-tleap-dummy) [davids4@tscc-login1 lib]$ LD_LIBRARY_PATH=/home/davids4/anaconda3/lib:$LD_LIBRARY_PATH
(I guess I could have used the environment specific lib
directory, but the base one worked). It's not ideal, but it's a viable workaround.
from cookiecutter-cms.
Glad to hear. Can we close this issue then as it seems to be beyond the scope of Cookiecutter?
from cookiecutter-cms.
Related Issues (20)
- Switch to mamba + miniforge = mambaforge to speed up CI? HOT 14
- Revisit using src/package_name directory instead of package_name directory HOT 6
- [ALERT TO USERS] Travis CI Security Breach - REMOVE Travis - Cycle Secure Env Vars HOT 3
- Test API Issue Creation
- Where to write the dependency? HOT 4
- Tests folder outside Python package? HOT 1
- Add pre-commit.ci
- PEP 517/518 (pyproject.toml) HOT 8
- Default chron schedule for GHA
- Allow package name to be different from repository name HOT 1
- Update default branch to main instead of master HOT 3
- Remove default channel from conda-forge setting HOT 2
- cruft remains in setup.cfg HOT 2
- Use native config files for coverage, flake8, and yapf HOT 1
- Missing versioneer file?
- Deprecated use of pyyaml's yaml.load function without a Loader argument
- Multiple errors while using cookiecutter for initiating a new repository HOT 2
- `provision-with-micromamba` is deprecated HOT 3
- Python versions falling behind NEP29/SPEC0
- Missing version information in generated Sphinx docs
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.
from cookiecutter-cms.