conda_environments issueshttps://git.geomar.de/python/conda_environments/-/issues2017-04-18T10:31:26Zhttps://git.geomar.de/python/conda_environments/-/issues/9aospy2017-04-18T10:31:26ZAnnika DrewsaospyHallo Willi,
kannst du bitte ``aospy`` für die Python2.7 Umgebung installieren?
Danke!
AnnikaHallo Willi,
kannst du bitte ``aospy`` für die Python2.7 Umgebung installieren?
Danke!
AnnikaWilli RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/10Pymatlab2017-04-18T10:31:19ZRafael AbelPymatlabHallo Willi,
da man ja immerwieder mal das problem hat matlab routinen zu haben, die irgendwas fuer einen erledigen und keine Lust die komplett umzuschreiben oder das gar nicht so einfach ist...
Dann scheint pymatlab eine alternative zu ...Hallo Willi,
da man ja immerwieder mal das problem hat matlab routinen zu haben, die irgendwas fuer einen erledigen und keine Lust die komplett umzuschreiben oder das gar nicht so einfach ist...
Dann scheint pymatlab eine alternative zu sein. Wir haben ja matlab versionen auf der NESH und anderen systemen...
Koenntest du pymatlab bitte installieren auf der NESH?
VIelen Dank fuer Deine Hilfe!
https://pypi.python.org/pypi/pymatlab
Beste Gruesse,
RafaelWilli RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/11Add eofs2017-04-18T10:32:49ZWilli RathAdd eofshttp://ajdawson.github.io/eofs/ says that there is a conda-forge package for Python 2 and 3.
(cc: @patrick-wagner )http://ajdawson.github.io/eofs/ says that there is a conda-forge package for Python 2 and 3.
(cc: @patrick-wagner )Willi RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/12Fortran magic2017-10-02T10:40:15ZRafael AbelFortran magichttps://github.com/mgaitan/fortran_magic
DANKE :)https://github.com/mgaitan/fortran_magic
DANKE :)Willi RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/13netCDF4 in py3_std on HLRN is not working2017-10-02T10:40:15ZJan Klaus RiecknetCDF4 in py3_std on HLRN is not working```python
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-5-f731da2de255> in <module>()
----> 1 import netCDF4
/home/...```python
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-5-f731da2de255> in <module>()
----> 1 import netCDF4
/home/b/shkifmwr/TM/software/miniconda3_20170516/envs/py3_std/lib/python3.6/site-packages/netCDF4/__init__.py in <module>()
1 # init for netCDF4. package
2 # Docstring comes from extension module _netCDF4.
----> 3 from ._netCDF4 import *
4 # Need explicit imports for names beginning with underscores
5 from ._netCDF4 import __doc__, __pdoc__
ImportError: libmfhdf.so.0: cannot open shared object file: No such file or directory
```https://git.geomar.de/python/conda_environments/-/issues/14HTTPS-Error on Nesh2017-05-17T13:15:46ZWilli RathHTTPS-Error on Nesh(Currently preventing fix of #13 on Nesh.)
Add nesh envs to `locations.ini` and use SSH with agent forwarding instead.(Currently preventing fix of #13 on Nesh.)
Add nesh envs to `locations.ini` and use SSH with agent forwarding instead.Willi RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/15Spyder not working on py2_std on taurus?2017-10-02T10:40:15ZWilli RathSpyder not working on py2_std on taurus?Willi RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/16py3_std at HLRN2017-10-24T12:44:12ZJan Klaus Rieckpy3_std at HLRNWhile py2_std works really well at HLRN during the last weeks, py3_std has some problems. Starting the kernel from the notebook one quickly gets a connection but then the kernel is never ready...Basically the same problem that has always...While py2_std works really well at HLRN during the last weeks, py3_std has some problems. Starting the kernel from the notebook one quickly gets a connection but then the kernel is never ready...Basically the same problem that has always been an issue with HLRN but for py2_std it does not seem to be an issue anymore. (Tried all the usual workarounds, deleting old jobs and kernels and activating the environment at HLRN before <- no problems there, just from the notebook)
Sorry for being so vague, but I couldn't pin it down any furtherhttps://git.geomar.de/python/conda_environments/-/issues/17python basemap needs increased resolution of landmask2017-09-07T08:13:22ZRafael Abelpython basemap needs increased resolution of landmaskHi Willi,
bei Gelegenheit koennte man nochmal die hochaufgeloesten Kuestenlinien fuer basemap interstallien...
Vielen Dank!
conda install -c conda-forge basemap-data-hires
Beste Gruesse,
RafaelHi Willi,
bei Gelegenheit koennte man nochmal die hochaufgeloesten Kuestenlinien fuer basemap interstallien...
Vielen Dank!
conda install -c conda-forge basemap-data-hires
Beste Gruesse,
Rafaelhttps://git.geomar.de/python/conda_environments/-/issues/18Scipy stats fail for masked arrays (was: Scipy linear regression fails for la...2017-09-12T08:50:43ZWilli RathScipy stats fail for masked arrays (was: Scipy linear regression fails for large N on Nesh?)(cc: @rafael-abel)(cc: @rafael-abel)Willi RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/19Add python-cdo.2017-09-19T11:37:07ZWilli RathAdd python-cdo.https://github.com/conda-forge/python-cdo-feedstock
Check if this works with Py3.
(cc: @klaus-getzlaff @sebastian-wahl )https://github.com/conda-forge/python-cdo-feedstock
Check if this works with Py3.
(cc: @klaus-getzlaff @sebastian-wahl )Willi RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/20add iris2017-09-19T11:37:05ZPatrick Wagneradd irisCould the package iris be added on HLRN?
https://pypi.python.org/pypi/Iris/2.0Could the package iris be added on HLRN?
https://pypi.python.org/pypi/Iris/2.0https://git.geomar.de/python/conda_environments/-/issues/21Update everywhere2017-09-21T17:03:24ZWilli RathUpdate everywhere- [x] Add new packages (#19, #20)
- [x] Fix #22 first
- [x] Fix #23 first
- [x] Update conda mirrors
- [x] Propagate conda mirrors to
- [x] Hannover
- [x] Berlin (down atm)
- [x] Deploy
- [x] Hannover
- [x] Berlin
- [x] Nesh
...- [x] Add new packages (#19, #20)
- [x] Fix #22 first
- [x] Fix #23 first
- [x] Update conda mirrors
- [x] Propagate conda mirrors to
- [x] Hannover
- [x] Berlin (down atm)
- [x] Deploy
- [x] Hannover
- [x] Berlin
- [x] Nesh
- [x] taurus / ursusWilli RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/22Pin monitoring.yml, netcdf4=1.2.82017-09-19T18:41:33ZWilli RathPin monitoring.yml, netcdf4=1.2.8See TM/Monitoring#109 ...
(do this before #21!)See TM/Monitoring#109 ...
(do this before #21!)Willi RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/23Ping netCDF4=1.2.8 everywhere2017-09-21T15:39:08ZWilli RathPing netCDF4=1.2.8 everywhereThe Auto-Masking which was more widely rolled out in v1.2.9 has consequences all over the place. Pin to v1.2.8 until this settles.The Auto-Masking which was more widely rolled out in v1.2.9 has consequences all over the place. Pin to v1.2.8 until this settles.Willi RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/24Add pyngl and pynio to the Std environments again?2017-10-02T12:26:18ZWilli RathAdd pyngl and pynio to the Std environments again?There's a recent update to both feedstocks. Let's see if they are less restrictive wrt pinned versions now.
And let's see if there's py3 support.There's a recent update to both feedstocks. Let's see if they are less restrictive wrt pinned versions now.
And let's see if there's py3 support.Willi RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/25add python gsw2017-11-06T10:24:22ZJan Klaus Rieckadd python gswIt would be nice to add python gsw to the standard environments. https://github.com/TEOS-10/python-gsw/
I know this package will be deprecated in favor of this: https://github.com/TEOS-10/GSW-Python, however, not all functionality is imp...It would be nice to add python gsw to the standard environments. https://github.com/TEOS-10/python-gsw/
I know this package will be deprecated in favor of this: https://github.com/TEOS-10/GSW-Python, however, not all functionality is implemented in the new package yet and it apparently does not work with python2.* . So it might be best to use the older package for now.https://git.geomar.de/python/conda_environments/-/issues/26Deploy to HLRN2018-03-14T11:02:27ZWilli RathDeploy to HLRN1. [ ] Update local mirrors
2. [ ] Sync mirror to HLRN
- [ ] Berlin
- [ ] Hannover
3. [ ] Update conda
- [ ] Berlin
- [ ] Hannover
- [ ] taurus / ursus
- [ ] nesh1. [ ] Update local mirrors
2. [ ] Sync mirror to HLRN
- [ ] Berlin
- [ ] Hannover
3. [ ] Update conda
- [ ] Berlin
- [ ] Hannover
- [ ] taurus / ursus
- [ ] neshWilli RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/27Add memory_profiler to py3_std at HLRN2018-03-14T11:02:18ZPatrick WagnerAdd memory_profiler to py3_std at HLRNIt's available with the py2_std but not with the py3_std. Could it be added?It's available with the py2_std but not with the py3_std. Could it be added?https://git.geomar.de/python/conda_environments/-/issues/28Update xarray to 0.10.02018-01-09T11:07:01ZPatrick WagnerUpdate xarray to 0.10.0There's a new xarray release with some useful updates on indexing and resampling.There's a new xarray release with some useful updates on indexing and resampling.https://git.geomar.de/python/conda_environments/-/issues/29Pin CDO to 1.82018-03-14T11:15:19ZWilli RathPin CDO to 1.8At HLRN, `cdo=1.9` with our pinned `netcdf4=1.2.8` leads to missing shared HDF5 libraries. Pinning to `cdo=1.8` works.
- [x] Manual hot-fix: install `cdo=1.8`
- [x] Hannover
- [x] `py2_std`
- [x] `py3_std`
- [x] Ber...At HLRN, `cdo=1.9` with our pinned `netcdf4=1.2.8` leads to missing shared HDF5 libraries. Pinning to `cdo=1.8` works.
- [x] Manual hot-fix: install `cdo=1.8`
- [x] Hannover
- [x] `py2_std`
- [x] `py3_std`
- [x] Berlin
- [x] `py2_std`
- [x] `py3_std`
- [x] Taurus
- [x] `py2_std`
- [x] `py3_std`
- [x] Nesh
- [x] `py2_std`
- [x] `py3_std`
- [x] Pin in `_env_templates`
(cc: @sebastian-wahl )Willi RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/30pyferret: HDF5 library version mismatched error2018-04-24T10:54:05ZKlaus Getzlaffpyferret: HDF5 library version mismatched errorafter pyferret environment is activated "conda list" gives this result:
[conda_list.txt](/uploads/1c46bf97eefcbd074637462f30fc8d9a/conda_list.txt)after pyferret environment is activated "conda list" gives this result:
[conda_list.txt](/uploads/1c46bf97eefcbd074637462f30fc8d9a/conda_list.txt)Willi RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/31Add sklearn to standard environments2018-06-12T09:10:28ZMartin ClausAdd sklearn to standard environmentsMight be useful to add [scikit-learn](http://scikit-learn.org/stable/) to the standard environments. The size seems to be about 15 MB.Might be useful to add [scikit-learn](http://scikit-learn.org/stable/) to the standard environments. The size seems to be about 15 MB.https://git.geomar.de/python/conda_environments/-/issues/32HLRN Hannover hlogin: library issues using py3_std environment2018-07-11T13:04:42ZChristina RothHLRN Hannover hlogin: library issues using py3_std environment```bash
from matplotlib import pyplot as plt
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/h/shkifmwr/TM/software/miniconda3_20180110/envs/py3_std/lib/python3.5/site-packages/matplotlib/pyplot.py"...```bash
from matplotlib import pyplot as plt
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/h/shkifmwr/TM/software/miniconda3_20180110/envs/py3_std/lib/python3.5/site-packages/matplotlib/pyplot.py", line 116, in <module>
_backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()
File "/home/h/shkifmwr/TM/software/miniconda3_20180110/envs/py3_std/lib/python3.5/site-packages/matplotlib/backends/__init__.py", line 60, in pylab_setup
[backend_name], 0)
File "/home/h/shkifmwr/TM/software/miniconda3_20180110/envs/py3_std/lib/python3.5/site-packages/matplotlib/backends/backend_qt5agg.py", line 16, in <module>
from .backend_qt5 import (
File "/home/h/shkifmwr/TM/software/miniconda3_20180110/envs/py3_std/lib/python3.5/site-packages/matplotlib/backends/backend_qt5.py", line 18, in <module>
import matplotlib.backends.qt_editor.figureoptions as figureoptions
File "/home/h/shkifmwr/TM/software/miniconda3_20180110/envs/py3_std/lib/python3.5/site-packages/matplotlib/backends/qt_editor/figureoptions.py", line 20, in <module>
import matplotlib.backends.qt_editor.formlayout as formlayout
File "/home/h/shkifmwr/TM/software/miniconda3_20180110/envs/py3_std/lib/python3.5/site-packages/matplotlib/backends/qt_editor/formlayout.py", line 56, in <module>
from matplotlib.backends.qt_compat import QtGui, QtWidgets, QtCore
File "/home/h/shkifmwr/TM/software/miniconda3_20180110/envs/py3_std/lib/python3.5/site-packages/matplotlib/backends/qt_compat.py", line 137, in <module>
from PyQt5 import QtCore, QtGui, QtWidgets
ImportError: /lib64/libpthread.so.0: version `GLIBC_2.12' not found (required by /home/h/shkifmwr/TM/software/miniconda3_20180110/envs/py3_std/lib/python3.5/site-packages/PyQt5/../../.././libglib-2.0.so.0)
```
I am running `python` interactively, before I activated `py3_std` via `source /gfs1/work/shkifmwr/TM/software/miniconda3_latest/bin/activate py3_std`https://git.geomar.de/python/conda_environments/-/issues/33update x-array to version 0.10.4 or later2018-06-12T09:10:12ZSebastian Wahlupdate x-array to version 0.10.4 or laterThe version which is currently used (`0.10.2`) has a bug in handling axis labelling when using subplots with simple line plots. Since it took me 4 hours to find out about this on Friday it might be helpful to update soonish to avoid othe...The version which is currently used (`0.10.2`) has a bug in handling axis labelling when using subplots with simple line plots. Since it took me 4 hours to find out about this on Friday it might be helpful to update soonish to avoid others to run into the same error. Thanks @martin-claus for the help.Willi RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/34matplotlib errors in env py3_std at HLRN2018-07-11T14:07:58ZJan Klaus Rieckmatplotlib errors in env py3_std at HLRNWhen I start an Ipython kernel at HLRN (say bdata1) in the py3_std environment, everything works as expected. However, when I activate that environment interactively at HLRN and then try to import e.g. pyplot from matplotlib, I get the f...When I start an Ipython kernel at HLRN (say bdata1) in the py3_std environment, everything works as expected. However, when I activate that environment interactively at HLRN and then try to import e.g. pyplot from matplotlib, I get the following error:
```python
ImportError Traceback (most recent call last)
<ipython-input-1-9fd843dc79b6> in <module>()
8 from xorca.xorca.lib import load_xorca_dataset
9 import xgcm
---> 10 from matplotlib import pyplot as plt
11 from cmocean import cm
12 from matplotlib import colors
/gfs1/work/shkifmwr/_TM/software/miniconda3_20180131/envs/py3_std/lib/python3.6/site-packages/matplotlib/pyplot.py in <module>()
114 ## Global ##
115
--> 116 _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup()
117
118 _IP_REGISTERED = None
/gfs1/work/shkifmwr/_TM/software/miniconda3_20180131/envs/py3_std/lib/python3.6/site-packages/matplotlib/backends/__init__.py in pylab_setup(name)
58 # imports. 0 means only perform absolute imports.
59 backend_mod = __import__(backend_name, globals(), locals(),
---> 60 [backend_name], 0)
61
62 # Things we pull in from all backends
/gfs1/work/shkifmwr/_TM/software/miniconda3_20180131/envs/py3_std/lib/python3.6/site-packages/matplotlib/backends/backend_qt5agg.py in <module>()
14
15 from .backend_agg import FigureCanvasAgg
---> 16 from .backend_qt5 import (
17 QtCore, QtGui, QtWidgets, _BackendQT5, FigureCanvasQT, FigureManagerQT,
18 NavigationToolbar2QT, backend_version)
/gfs1/work/shkifmwr/_TM/software/miniconda3_20180131/envs/py3_std/lib/python3.6/site-packages/matplotlib/backends/backend_qt5.py in <module>()
16 _Backend, FigureCanvasBase, FigureManagerBase, NavigationToolbar2,
17 TimerBase, cursors)
---> 18 import matplotlib.backends.qt_editor.figureoptions as figureoptions
19 from matplotlib.backends.qt_editor.formsubplottool import UiSubplotTool
20 from matplotlib.figure import Figure
/gfs1/work/shkifmwr/_TM/software/miniconda3_20180131/envs/py3_std/lib/python3.6/site-packages/matplotlib/backends/qt_editor/figureoptions.py in <module>()
18 import matplotlib
19 from matplotlib import cm, colors as mcolors, markers, image as mimage
---> 20 import matplotlib.backends.qt_editor.formlayout as formlayout
21 from matplotlib.backends.qt_compat import QtGui
22
/gfs1/work/shkifmwr/_TM/software/miniconda3_20180131/envs/py3_std/lib/python3.6/site-packages/matplotlib/backends/qt_editor/formlayout.py in <module>()
54
55 from matplotlib import colors as mcolors
---> 56 from matplotlib.backends.qt_compat import QtGui, QtWidgets, QtCore
57
58
/gfs1/work/shkifmwr/_TM/software/miniconda3_20180131/envs/py3_std/lib/python3.6/site-packages/matplotlib/backends/qt_compat.py in <module>()
135 if QT_API == QT_API_PYQT5:
136 try:
--> 137 from PyQt5 import QtCore, QtGui, QtWidgets
138 _getSaveFileName = QtWidgets.QFileDialog.getSaveFileName
139 except ImportError:
ImportError: /lib64/libpthread.so.0: version `GLIBC_2.12' not found (required by /gfs1/work/shkifmwr/_TM/software/miniconda3_20180131/envs/py3_std/lib/python3.6/site-packages/PyQt5/../../.././libglib-2.0.so.0)
```
I am not sure whether this is a known behavior, as I think I never tried to use matplotlib within these environments interactively before.
[Note that this also applies to the py2_std environment.]
[[Also note, that I already tried to use different backends with `matplotlib.use(<backend_name>)`, they all produce some kind of error....]]https://git.geomar.de/python/conda_environments/-/issues/35xgcm error2018-09-12T08:37:56ZJan Klaus Rieckxgcm errorDid something change on the HLRN Berlin between Sep 10 and Sep 11? I had a script that worked perfectly fine and after changing nothing, xgcm has some problems:
```python
------------------------------------------------------------------...Did something change on the HLRN Berlin between Sep 10 and Sep 11? I had a script that worked perfectly fine and after changing nothing, xgcm has some problems:
```python
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-78-d3d23357ec67> in <module>()
----> 1 dgrid = xgcm.Grid(dbox, periodic=['X', 'Y'])
/gfs1/work/shkifmwr/_TM/software/miniconda3_20180131/envs/py3_std/lib/python3.6/site-packages/xgcm/grid.py in __init__(self, ds, check_dims, periodic, default_shifts)
503 axis_default_shifts = {}
504 self.axes[axis_name] = Axis(ds, axis_name, is_periodic,
--> 505 default_shifts=axis_default_shifts)
506
507
/gfs1/work/shkifmwr/_TM/software/miniconda3_20180131/envs/py3_std/lib/python3.6/site-packages/xgcm/grid.py in __init__(self, ds, axis_name, periodic, default_shifts)
109 if len(coords_without_axis_shift) == 0:
110 raise ValueError("Couldn't find a center coordinate for axis %s"
--> 111 % axis_name)
112 elif len(coords_without_axis_shift) > 1:
113 raise ValueError("Found two coordinates without "
ValueError: Couldn't find a center coordinate for axis Z
```
`dbox`, from which I want to construct the `Grid` instance looks like this:
```python
<xarray.Dataset>
Dimensions: (t: 6, x_c: 47, x_r: 47, y_c: 73, y_r: 73, z_c: 35, z_l: 36)
Coordinates:
* y_c (y_c) int64 147 148 149 150 151 152 153 154 155 156 157 158 ...
* x_c (x_c) int64 236 237 238 239 240 241 242 243 244 245 246 247 ...
llat_cc (y_c, x_c) float32 dask.array<shape=(73, 47), chunksize=(54, 47)>
llon_cc (y_c, x_c) float32 dask.array<shape=(73, 47), chunksize=(54, 47)>
* t (t) datetime64[ns] 1985-02-02T12:00:00 1985-02-07T12:00:00 ...
e1t (y_c, x_c) float64 dask.array<shape=(73, 47), chunksize=(54, 47)>
e2t (y_c, x_c) float64 dask.array<shape=(73, 47), chunksize=(54, 47)>
* z_c (z_c) int64 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 ...
depth_c (z_c) float64 dask.array<shape=(35,), chunksize=(23,)>
e3t (z_c, y_c, x_c) float64 dask.array<shape=(35, 73, 47), chunksize=(23, 54, 47)>
tmask (z_c, y_c, x_c) int8 dask.array<shape=(35, 73, 47), chunksize=(23, 54, 47)>
* z_l (z_l) float64 0.5 1.5 2.5 3.5 4.5 5.5 6.5 7.5 8.5 9.5 10.5 ...
depth_l (z_l) float64 dask.array<shape=(36,), chunksize=(23,)>
e3w (z_l, y_c, x_c) float64 dask.array<shape=(36, 73, 47), chunksize=(23, 54, 47)>
box_tmask (z_c, y_c, x_c) float64 dask.array<shape=(35, 73, 47), chunksize=(23, 54, 47)>
* x_r (x_r) float64 236.5 237.5 238.5 239.5 240.5 241.5 242.5 243.5 ...
llat_cr (y_c, x_r) float32 dask.array<shape=(73, 47), chunksize=(54, 47)>
llon_cr (y_c, x_r) float32 dask.array<shape=(73, 47), chunksize=(54, 47)>
e1u (y_c, x_r) float64 dask.array<shape=(73, 47), chunksize=(54, 47)>
e2u (y_c, x_r) float64 dask.array<shape=(73, 47), chunksize=(54, 47)>
e3u (z_c, y_c, x_r) float64 dask.array<shape=(35, 73, 47), chunksize=(23, 54, 47)>
umask (z_c, y_c, x_r) int8 dask.array<shape=(35, 73, 47), chunksize=(23, 54, 47)>
box_umask (z_c, y_c, x_r) float64 dask.array<shape=(35, 73, 47), chunksize=(23, 54, 47)>
* y_r (y_r) float64 147.5 148.5 149.5 150.5 151.5 152.5 153.5 154.5 ...
llat_rc (y_r, x_c) float32 dask.array<shape=(73, 47), chunksize=(54, 47)>
llon_rc (y_r, x_c) float32 dask.array<shape=(73, 47), chunksize=(54, 47)>
e1v (y_r, x_c) float64 dask.array<shape=(73, 47), chunksize=(54, 47)>
e2v (y_r, x_c) float64 dask.array<shape=(73, 47), chunksize=(54, 47)>
e3v (z_c, y_r, x_c) float64 dask.array<shape=(35, 73, 47), chunksize=(23, 54, 47)>
vmask (z_c, y_r, x_c) int8 dask.array<shape=(35, 73, 47), chunksize=(23, 54, 47)>
box_vmask (z_c, y_r, x_c) float64 dask.array<shape=(35, 73, 47), chunksize=(23, 54, 47)>
llat_rr (y_r, x_r) float32 dask.array<shape=(73, 47), chunksize=(54, 47)>
llon_rr (y_r, x_r) float32 dask.array<shape=(73, 47), chunksize=(54, 47)>
e1f (y_r, x_r) float64 dask.array<shape=(73, 47), chunksize=(54, 47)>
e2f (y_r, x_r) float64 dask.array<shape=(73, 47), chunksize=(54, 47)>
fmask (z_c, y_r, x_r) int8 dask.array<shape=(35, 73, 47), chunksize=(23, 54, 47)>
box_fmask (z_c, y_r, x_r) float64 dask.array<shape=(35, 73, 47), chunksize=(23, 54, 47)>
e3f (z_c, y_r, x_r) float64 6.191 6.191 6.191 6.191 6.191 6.191 ...
Data variables:
sobowlin (t, y_c, x_c) float64 dask.array<shape=(6, 73, 47), chunksize=(1, 54, 47)>
sohefldo (t, y_c, x_c) float64 dask.array<shape=(6, 73, 47), chunksize=(1, 54, 47)>
sohefldp (t, y_c, x_c) float64 dask.array<shape=(6, 73, 47), chunksize=(1, 54, 47)>
somixhgt (t, y_c, x_c) float64 dask.array<shape=(6, 73, 47), chunksize=(1, 54, 47)>
soshfldo (t, y_c, x_c) float64 dask.array<shape=(6, 73, 47), chunksize=(1, 54, 47)>
sowafldp (t, y_c, x_c) float64 dask.array<shape=(6, 73, 47), chunksize=(1, 54, 47)>
sowaflup (t, y_c, x_c) float64 dask.array<shape=(6, 73, 47), chunksize=(1, 54, 47)>
sowindsp (t, y_c, x_c) float64 dask.array<shape=(6, 73, 47), chunksize=(1, 54, 47)>
vosaline (t, z_c, y_c, x_c) float64 dask.array<shape=(6, 35, 73, 47), chunksize=(1, 23, 54, 47)>
votemper (t, z_c, y_c, x_c) float64 dask.array<shape=(6, 35, 73, 47), chunksize=(1, 23, 54, 47)>
vosigma0 (t, z_c, y_c, x_c) float64 dask.array<shape=(6, 35, 73, 47), chunksize=(1, 23, 54, 47)>
vosigma1 (t, z_c, y_c, x_c) float64 dask.array<shape=(6, 35, 73, 47), chunksize=(1, 23, 54, 47)>
vosigma2 (t, z_c, y_c, x_c) float64 dask.array<shape=(6, 35, 73, 47), chunksize=(1, 23, 54, 47)>
vototvor (t, z_l, y_c, x_c) float64 dask.array<shape=(6, 36, 73, 47), chunksize=(1, 23, 54, 47)>
vorelvor (t, z_l, y_c, x_c) float64 dask.array<shape=(6, 36, 73, 47), chunksize=(1, 23, 54, 47)>
vostrvor (t, z_l, y_c, x_c) float64 dask.array<shape=(6, 36, 73, 47), chunksize=(1, 23, 54, 47)>
sozotaux (t, y_c, x_r) float64 dask.array<shape=(6, 73, 47), chunksize=(1, 54, 47)>
vozocrtx (t, z_c, y_c, x_r) float64 dask.array<shape=(6, 35, 73, 47), chunksize=(1, 23, 54, 47)>
sometauy (t, y_r, x_c) float64 dask.array<shape=(6, 73, 47), chunksize=(1, 54, 47)>
vomecrty (t, z_c, y_r, x_c) float64 dask.array<shape=(6, 35, 73, 47), chunksize=(1, 23, 54, 47)>
```
Looks like everything required for a successful definition of a grid is there....https://git.geomar.de/python/conda_environments/-/issues/36How to run a Jupyter notebook on background ?2019-03-05T12:24:45ZArthur PrigentHow to run a Jupyter notebook on background ?As I get disconnected from HLRN roughly every 20 min I can't leave a code running for a while using the ./run_chromium_through_ssh_tunnel.sh script.
![Screenshot_2019-03-05_at_13.06.33](/uploads/f1d406b9baff55032f35de0a4ca34826/Screens...As I get disconnected from HLRN roughly every 20 min I can't leave a code running for a while using the ./run_chromium_through_ssh_tunnel.sh script.
![Screenshot_2019-03-05_at_13.06.33](/uploads/f1d406b9baff55032f35de0a4ca34826/Screenshot_2019-03-05_at_13.06.33.png)
![Screenshot_2019-03-05_at_13.03.30](/uploads/c3df7ffe97de90be89954883bbf67092/Screenshot_2019-03-05_at_13.03.30.png)
The disconnection problem occurs whether I use the Wifi or the LAN.
This is why I am wondering if it is possible to start a Jupyter notebook on a screen on HLRN in order to leave a script running for a long time.
I tried to launch my notebook converted into a .py file on a screen on HLRN :
python campo_bootstrap.py
I get the error : segmentation fault
![Screenshot_2019-03-05_at_12.57.44](/uploads/8d8f7b50e499820f98f331914998fd3f/Screenshot_2019-03-05_at_12.57.44.png)
If you have any idea or solution I would be grateful.https://git.geomar.de/python/conda_environments/-/issues/5TeX?2017-03-30T15:23:41ZWilli RathTeX?https://github.com/conda-forge/texlive-core-feedstock seems to lead to a proper LaTeX-Feedstock.
@annika-drews tried
```python
import matplotlib as mpl
mpl.use("pgf")
fontsize=10
width = 25/2.54 # cm to inch usually 10
he...https://github.com/conda-forge/texlive-core-feedstock seems to lead to a proper LaTeX-Feedstock.
@annika-drews tried
```python
import matplotlib as mpl
mpl.use("pgf")
fontsize=10
width = 25/2.54 # cm to inch usually 10
height = 7/2.54
pgf_with_pdflatex = {
"pgf.texsystem": "pdflatex",
"pgf.preamble": [
r"\usepackage[utf8x]{inputenc}",
r"\usepackage[T1]{fontenc}",
r"\usepackage{lmodern}",
# r"\usepackage{siunitx}"
],
"axes.labelsize": fontsize, # LaTeX default is 10pt font.
"font.size": fontsize,
"legend.fontsize": fontsize,
"xtick.labelsize": fontsize,
"ytick.labelsize": fontsize,
"lines.linewidth": 1,
"figure.figsize" : [width, height],
# "savefig.bbox" : 'tight',
# "savefig.pad_inches" : 0.01
}
mpl.rcParams.update(pgf_with_pdflatex)
```
and failed with `py2_std` on `taurus`.Willi RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/1Download all cartopy features2017-02-05T19:21:56ZWilli RathDownload all cartopy featuresSee: https://github.com/conda-forge/cartopy-feedstock/issues/27
Implement this as a script for now.See: https://github.com/conda-forge/cartopy-feedstock/issues/27
Implement this as a script for now.Willi RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/3seawater module at HLRN2017-03-01T16:22:10ZJan Klaus Rieckseawater module at HLRNThe seawater module is not installed in the `py2_std` and `py3_std` environments on HLRNThe seawater module is not installed in the `py2_std` and `py3_std` environments on HLRNhttps://git.geomar.de/python/conda_environments/-/issues/6pyNGL2017-03-20T11:58:05ZAnnika DrewspyNGLI am missing the module ``Ngl`` in ``py2_std``. Can it be added?
Thank you!I am missing the module ``Ngl`` in ``py2_std``. Can it be added?
Thank you!Willi RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/8Pin Python2 to 2.7.122017-04-18T10:31:33ZWilli RathPin Python2 to 2.7.12On taurus, importing `matplotlib` may throw a `NameError: name 'PROTOCOL_TLS' is not defined`.
https://github.com/owtf/owtf/issues/815 suggests updating the distro packages and PyOpenSSL. As a hotfix, pinning to Python 2.7.12 in `py2_s...On taurus, importing `matplotlib` may throw a `NameError: name 'PROTOCOL_TLS' is not defined`.
https://github.com/owtf/owtf/issues/815 suggests updating the distro packages and PyOpenSSL. As a hotfix, pinning to Python 2.7.12 in `py2_std` on taurus helped.Willi RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/4cf_units for conda2017-03-07T11:19:18ZRafael Abelcf_units for condaHi Willi,
koenntest du bitte fuer py_std2 "cf_units" hinzufuegen?
Vielen dank!
Beste Gruesse
RafaelHi Willi,
koenntest du bitte fuer py_std2 "cf_units" hinzufuegen?
Vielen dank!
Beste Gruesse
Rafaelhttps://git.geomar.de/python/conda_environments/-/issues/2Be able to pick envs in setup script2017-02-19T14:01:48ZWilli RathBe able to pick envs in setup scriptAdd input args to setup script which allow for picking envs to be installed.Add input args to setup script which allow for picking envs to be installed.Willi RathWilli Rathhttps://git.geomar.de/python/conda_environments/-/issues/7Pin Matplotlib everywhere2017-03-31T12:51:58ZWilli RathPin Matplotlib everywhereIn python/doc#2, we found that Matplotlib 2.0 behaves weird with LaTeX output. As this is only one of many subtleties w.r.t. Matplotlib 2.0, pin it to 1.5.3 everywhere for now.In python/doc#2, we found that Matplotlib 2.0 behaves weird with LaTeX output. As this is only one of many subtleties w.r.t. Matplotlib 2.0, pin it to 1.5.3 everywhere for now.Willi RathWilli Rath2017-03-31