New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

x.plot(s,box) error #256

Closed
jaigsingla opened this Issue Sep 13, 2017 · 34 comments

Comments

Projects
None yet
3 participants
@jaigsingla

jaigsingla commented Sep 13, 2017

Hi,

Recently downloaded and configured this sw. All gallery examples are working ok.

While plotting data with box encountered this issue

line 1842 vcs2vtk.py -> colors.InsertNextTypedTuple(vtk_color)
Attribute error : InsertNextTypedTuple

please help

@jypeter

This comment has been minimized.

jypeter commented Sep 13, 2017

Can you be more specific? Which version of uvcdat are you using, and on which platform? If the examples worked, can you post a small script that will reproduce the error, preferably using the test data that you can download with:
python -c 'import vcs; vcs.download_sample_data_files(); print "\nFinished downloading sample data to", vcs.sample_data'

This will help @doutriaux1 check what's wrong

@jaigsingla

This comment has been minimized.

jaigsingla commented Sep 13, 2017

@jypeter

This comment has been minimized.

jypeter commented Sep 13, 2017

I have just run the example in Basic_VCS_demo.html by copy/pasting the relevant parts in my interpreter and just using bg=False instead of True and it worked fine

@jaigsingla you may want to paste the full traceback, instead of just

line 1842 vcs2vtk.py -> colors.InsertNextTypedTuple(vtk_color)
Attribute error : InsertNextTypedTuple

This will help Charles

@jaigsingla

This comment has been minimized.

jaigsingla commented Sep 13, 2017

Hello ,

Pls find attached file for more insight.

trace.txt

@jaigsingla

This comment has been minimized.

jaigsingla commented Sep 14, 2017

Hello Charles,

waiting for your comments on above

@doutriaux1

This comment has been minimized.

Member

doutriaux1 commented Sep 14, 2017

@jaigsingla I just ran this w/o any problem with a 2.12 env, do you mind posting the reslut of

conda list

In particular look at what it says for vtk-cdat. I'm curious if you got the wrong vtk

@doutriaux1

This comment has been minimized.

Member

doutriaux1 commented Sep 14, 2017

For ref this is what my conda list gives with a working 2.12 env:

conda list
# packages in environment at /home/doutriaux1/anaconda2/envs/2.12:
#
acme_diags                v0.1b                hf894526_0    uvcdat
alabaster                 0.7.10                     py_0    conda-forge
asciidata                 2.12             py27hbe9d963_0    uvcdat
asn1crypto                0.22.0                   py27_0    conda-forge
astroid                   1.5.3                    py27_0    conda-forge
autopep8                  1.3.2                    py27_0    conda-forge
babel                     2.4.0                    py27_0    conda-forge
backports.functools_lru_cache 1.4                      py27_0    conda-forge
backports.shutil_get_terminal_size 1.0.0                      py_2    conda-forge
backports_abc             0.5                      py27_0    conda-forge
basemap                   1.1.0                    py27_2    conda-forge
beautifulsoup4            4.6.0                    py27_0    conda-forge
binaryio                  2.12            np113py27h8073811_0    uvcdat
bkcharts                  0.2                      py27_0    conda-forge
bleach                    2.0.0                    py27_0    conda-forge
bokeh                     0.12.6                   py27_0    conda-forge
bzip2                     1.0.6                         1    conda-forge
ca-certificates           2017.7.27.1                   0    conda-forge
cartopy                   0.15.1                   py27_4    conda-forge
cdat_info                 2.12                     py27_1    conda-forge
cdms2                     2.12                np113py27_0    conda-forge
cdp                       1.1.0                         0    uvcdat
cdtime                    2.12                np113py27_2    conda-forge
cdutil                    2.12                     py27_0    conda-forge
certifi                   2017.7.27.1              py27_0    conda-forge
cffi                      1.10.0                   py27_0    conda-forge
chardet                   3.0.4                    py27_0    conda-forge
cibots                    0.2                      py27_0    conda-forge
clapack                   3.2.1                         0    conda-forge
click                     6.7                      py27_0    conda-forge
cloog                     0.18.0                        0  
cloudpickle               0.4.0                    py27_0    conda-forge
configparser              3.5.0                    py27_0    conda-forge
cryptography              2.0.3                    py27_0    conda-forge
cssgrid                   2.12            np113py27h3898552_0    uvcdat
curl                      7.54.1                        0    conda-forge
cycler                    0.10.0                   py27_0    conda-forge
dask                      0.15.2                   py27_0    conda-forge
dask-core                 0.15.2                   py27_0    conda-forge
decorator                 4.1.2                    py27_0    conda-forge
distarray                 2.12                     py27_0    conda-forge
distributed               1.18.3                   py27_0    conda-forge
docutils                  0.14                     py27_0    conda-forge
dsgrid                    2.12            np113py27h9d524be_0    uvcdat
dv3d                      2.12             py27hac3d9b5_0    uvcdat
entrypoints               0.2.3                    py27_1    conda-forge
enum34                    1.1.6                    py27_1    conda-forge
eofs                      1.2.0                    py27_0    conda-forge
esmf                      7.0.0                         6    conda-forge
esmpy                     7.0.0                    py27_1    conda-forge
expat                     2.2.1                         0    conda-forge
ffmpeg                    3.2.4                         1    conda-forge
flake8                    3.4.1                    py27_0    conda-forge
fontconfig                2.12.1                        4    conda-forge
freetype                  2.7                           1    conda-forge
functools32               3.2.3.2                  py27_1    conda-forge
future                    0.16.0                   py27_0    conda-forge
futures                   3.0.5                    py27_0    conda-forge
g2clib                    1.6.0                         3    conda-forge
gcc                       4.8.5                         7  
genutil                   2.12                np113py27_0    conda-forge
geos                      3.5.1                         1    conda-forge
gmp                       6.1.2                         0    conda-forge
hdf4                      4.2.12                        0    conda-forge
hdf5                      1.8.18                        0    conda-forge
hdf5tools                 2.12             py27he5a1532_0    uvcdat
heapdict                  1.0.0                    py27_0    conda-forge
html5lib                  0.999999999              py27_0    conda-forge
icu                       58.1                          1    conda-forge
idna                      2.5                      py27_0    conda-forge
imagesize                 0.7.1                    py27_0    conda-forge
ipaddress                 1.0.18                   py27_0    conda-forge
ipykernel                 4.6.1                    py27_0    conda-forge
ipython                   5.4.1                    py27_0    conda-forge
ipython_genutils          0.2.0                    py27_0    conda-forge
ipywidgets                7.0.0                    py27_1    conda-forge
isl                       0.12.2                        0  
isort                     4.2.15                   py27_0    conda-forge
jasper                    1.900.1                       4    conda-forge
jedi                      0.10.2                   py27_0    conda-forge
jinja2                    2.9.6                    py27_0    conda-forge
jpeg                      9b                            0    conda-forge
jsonschema                2.6.0                    py27_0    conda-forge
jupyter                   1.0.0                    py27_0    conda-forge
jupyter_client            5.1.0                    py27_0    conda-forge
jupyter_console           5.1.0                    py27_0    conda-forge
jupyter_core              4.3.0                    py27_0    conda-forge
krb5                      1.14.2                        0    conda-forge
lapack                    3.6.1                         1    conda-forge
lazy-object-proxy         1.3.1                    py27_0    conda-forge
libcdms                   2.12                          0    conda-forge
libcf                     1.0.1                    py27_0    conda-forge
libdrs                    2.12                          0    conda-forge
libdrs_f                  2.12                          1    conda-forge
libffi                    3.2.1                         3    conda-forge
libgcc                    5.2.0                         0  
libgfortran               3.0.0                         1  
libiconv                  1.14                          4    conda-forge
libnetcdf                 4.4.1.1                       5    conda-forge
libpng                    1.6.28                        0    conda-forge
libsodium                 1.0.10                        0    conda-forge
libssh2                   1.8.0                         1    conda-forge
libtiff                   4.0.6                         7    conda-forge
libxml2                   2.9.5                         0    conda-forge
libxslt                   1.1.29                        5    conda-forge
lmoments                  2.12            np113py27h5574120_0    uvcdat
locket                    0.2.0                    py27_1    conda-forge
lxml                      3.8.0                    py27_0    conda-forge
markupsafe                1.0                      py27_0    conda-forge
matplotlib                1.5.3               np113py27_8    conda-forge
mccabe                    0.6.1                    py27_0    conda-forge
mistune                   0.7.4                    py27_0    conda-forge
mkl                       2017.0.3                      0  
mpc                       1.0.3                         4    conda-forge
mpfr                      3.1.5                         0    conda-forge
mpich                     3.2                           4    conda-forge
msgpack-python            0.4.8                    py27_0    conda-forge
natgrid                   2.12            np113py27h481ab8b_0    uvcdat
nb_conda                  2.2.1                    py27_0    conda-forge
nb_conda_kernels          2.1.0                    py27_0    conda-forge
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                    py27_0    conda-forge
ncurses                   5.9                          10    conda-forge
netcdf-fortran            4.4.4                         3    conda-forge
notebook                  5.0.0                    py27_0    conda-forge
numpy                     1.13.1                   py27_0  
numpydoc                  0.7.0                    py27_0    conda-forge
olefile                   0.44                     py27_0    conda-forge
openssl                   1.0.2l                        0    conda-forge
ort                       2.12            np113py27hd89025a_0    uvcdat
ossuuid                   1.6.2                         0    conda-forge
output_viewer             1.2.2                    py27_0    uvcdat
owslib                    0.15.0                     py_0    conda-forge
pandas                    0.20.3                   py27_1    conda-forge
pandoc                    1.19.2                        0    conda-forge
pandocfilters             1.4.1                    py27_0    conda-forge
partd                     0.3.8                    py27_0    conda-forge
pathlib2                  2.3.0                    py27_0    conda-forge
pexpect                   4.2.1                    py27_0    conda-forge
pickleshare               0.7.4                    py27_0    conda-forge
pillow                    4.2.1                    py27_0    conda-forge
pip                       9.0.1                    py27_0    conda-forge
proj4                     4.9.3                         4    conda-forge
prompt_toolkit            1.0.15                   py27_0    conda-forge
psutil                    5.2.2                    py27_0    conda-forge
ptyprocess                0.5.2                    py27_0    conda-forge
pycodestyle               2.3.1                    py27_0    conda-forge
pycparser                 2.18                     py27_0    conda-forge
pyepsg                    0.3.2                    py27_0    conda-forge
pyflakes                  1.5.0                    py27_0    conda-forge
pygments                  2.2.0                    py27_0    conda-forge
pylint                    1.7.1                    py27_0    conda-forge
pyopenssl                 17.2.0                   py27_0    conda-forge
pyparsing                 2.2.0                    py27_0    conda-forge
pyproj                    1.9.5.1                  py27_0    conda-forge
pyqt                      4.11.3                   py27_1  
pyshp                     1.2.12                     py_0    conda-forge
pysocks                   1.6.7                    py27_0    conda-forge
pyspharm                  1.0.9                    py27_2    conda-forge
python                    2.7.13                        1    conda-forge
python-dateutil           2.6.1                    py27_0    conda-forge
pytz                      2017.2                   py27_0    conda-forge
pyyaml                    3.12                     py27_1    conda-forge
pyzmq                     16.0.2                   py27_2    conda-forge
qt                        4.8.6                         3  
qtawesome                 0.4.4                    py27_0    conda-forge
qtconsole                 4.3.1                    py27_0    conda-forge
qtpy                      1.3.1                    py27_0    conda-forge
readline                  6.2                           0    conda-forge
regridpack                2.12            np113py27hf1cacc0_0    uvcdat
requests                  2.18.4                   py27_1    conda-forge
rope                      0.10.7                   py27_0    conda-forge
scandir                   1.5                      py27_1    conda-forge
scikit-learn              0.19.0              np113py27_0  
scipy                     0.19.1              np113py27_0  
setuptools                36.3.0                   py27_0    conda-forge
shapely                   1.6.1                    py27_1    conda-forge
shgrid                    2.12            np113py27h2504d4d_0    uvcdat
simplegeneric             0.8.1                    py27_0    conda-forge
singledispatch            3.4.0.3                  py27_0    conda-forge
sip                       4.16.5                   py27_0  
six                       1.10.0                   py27_1    conda-forge
snowballstemmer           1.2.1                    py27_0    conda-forge
sortedcontainers          1.5.7                    py27_0    conda-forge
sphinx                    1.6.3                    py27_0    conda-forge
sphinxcontrib-websupport  1.0.1                    py27_0    conda-forge
spyder                    3.2.3                    py27_0    conda-forge
sqlite                    3.13.0                        1    conda-forge
ssl_match_hostname        3.5.0.1                  py27_1    conda-forge
subprocess32              3.2.7                    py27_0    conda-forge
tblib                     1.3.2                    py27_0    conda-forge
terminado                 0.6                      py27_0    conda-forge
testpath                  0.3.1                    py27_0    conda-forge
thermo                    2.12             py27h2ad96b2_0    uvcdat
tk                        8.5.19                        2    conda-forge
toolz                     0.8.2                    py27_0    conda-forge
tornado                   4.5.2                    py27_0    conda-forge
traitlets                 4.3.2                    py27_0    conda-forge
trends                    2.12            np113py27hedb240a_0    uvcdat
typing                    3.6.2                    py27_0    conda-forge
udunits2                  2.2.23                        0    conda-forge
urllib3                   1.22                     py27_0    conda-forge
uvcdat                    2.12                 h5103ec1_0    uvcdat
uvcmetrics                2.2.1           np113py27h151233a_0    uvcdat
vcs                       2.12             py27had75802_0    uvcdat
vcsaddons                 2.12             py27h7706516_0    uvcdat
vistrails                 2.12                 h7b70e8b_0    uvcdat
vtk-cdat                  7.1.0.2.12       py27hd6333ce_0    uvcdat
wcwidth                   0.1.7                    py27_0    conda-forge
webencodings              0.5                      py27_0    conda-forge
wheel                     0.29.0                   py27_0    conda-forge
widgetsnbextension        3.0.2                    py27_0    conda-forge
windspharm                1.5.1                    py27_0    conda-forge
wk                        2.12             py27ha696ee6_0    uvcdat
wrapt                     1.10.11                  py27_0    conda-forge
x264                      20131217                      3    conda-forge
xmgrace                   2.12             py27hb3ccff1_0    uvcdat
xz                        5.2.3                         0    conda-forge
yaml                      0.1.6                         0    conda-forge
zeromq                    4.2.1                         1    conda-forge
zict                      0.1.2                    py27_0    conda-forge
zlib                      1.2.11                        0    conda-forge
zonalmeans                2.12            np113py27h96f9f80_0    uvcdat
@jaigsingla

This comment has been minimized.

jaigsingla commented Sep 15, 2017

Hello ,

I am not getting vtk listing in this list.
actually , I have installed vtk separately.

Please guide for proper installation

@doutriaux1 doutriaux1 added the invalid label Sep 15, 2017

@doutriaux1 doutriaux1 added this to the 3.0 milestone Sep 15, 2017

@doutriaux1

This comment has been minimized.

Member

doutriaux1 commented Sep 15, 2017

@doutriaux1 doutriaux1 closed this Sep 15, 2017

@jaigsingla

This comment has been minimized.

jaigsingla commented Sep 15, 2017

Hi ,

Used creating the conda channel approach.
I think I should try installation from ENV file.

@doutriaux1

This comment has been minimized.

Member

doutriaux1 commented Sep 15, 2017

@jaigsingla that's how I installed it, did you add vtk after the fact? You need to use the vtk-cdat package which IS vtk but we need an much more recent version that what's on conda-forge hence our name. If you install vtk after the fact you will essentially erase vtk-cdat and endup with a lesser vtk.

@jaigsingla

This comment has been minimized.

jaigsingla commented Sep 15, 2017

@jaigsingla

This comment has been minimized.

jaigsingla commented Sep 15, 2017

Shall I reinstall full or shall I download only vtk-cdat package and install the same

@doutriaux1

This comment has been minimized.

Member

doutriaux1 commented Sep 15, 2017

not sure what else vtk brought in, vtk-cdat only only is probably enough, but just to be safe I would start from scratch

@jaigsingla

This comment has been minimized.

jaigsingla commented Sep 15, 2017

@doutriaux1

This comment has been minimized.

Member

doutriaux1 commented Sep 15, 2017

yes rm -rf envs/[name] is enough. You can also use the conda command

conda env remove -n [name]
@jaigsingla

This comment has been minimized.

jaigsingla commented Sep 18, 2017

installation_trace.txt

Hello,
I have recreated env and listed conda list. output is attached in the file.
Facing Import error as vtkIOFFMPEGPython .
Please find attached file for details.

thanks
Jai

@jypeter

This comment has been minimized.

jypeter commented Sep 18, 2017

You have some strange things in your environment, like lots duplicated packages coming from pip

backports-abc             0.5                       <pip>
backports.functools-lru-cache 1.4                       <pip>
backports.functools_lru_cache 1.4                      py27_0    conda-forge
backports.shutil-get-terminal-size 1.0.0                     <pip>
backports.shutil_get_terminal_size 1.0.0                    py27_1    conda-forge
backports.ssl-match-hostname 3.5.0.1                   <pip>
backports_abc             0.5                      py27_0    conda-forge

In my case I have for 2.12

backports.functools_lru_cache 1.3                      py27_0    conda-forge
backports.shutil_get_terminal_size 1.0.0                    py27_1    conda-forge
backports_abc             0.5                      py27_0    conda-forge

What packages did you install with pip?

I suggest you do a standard installation of uvcdat-2.12, then clone it, and install you own stuff in the cloned version. This will make it possible to check how things work in a clean default environment, and in your special one.

You can see how I did it for 2.10 in my 2.10 installation notes.

I have started python with python -v, and I have the following references to vtkIOFFMPEG when I type import vcs

# /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.12/lib/python2.7/site-packages/vtk/vtkIOMovie.pyc matches /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.12/lib/python2.7/site-packages/vtk/vtkIOMovie.py
import vtk.vtkIOMovie # precompiled from /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.12/lib/python2.7/site-packages/vtk/vtkIOMovie.pyc
dlopen("/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.12/lib/python2.7/site-packages/vtk/vtkIOMoviePython.so", 102);
import vtk.vtkIOMoviePython # dynamically loaded from /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.12/lib/python2.7/site-packages/vtk/vtkIOMoviePython.so
# /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.12/lib/python2.7/site-packages/vtk/vtkIOFFMPEG.pyc matches /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.12/lib/python2.7/site-packages/vtk/vtkIOFFMPEG.py
import vtk.vtkIOFFMPEG # precompiled from /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.12/lib/python2.7/site-packages/vtk/vtkIOFFMPEG.pyc
dlopen("/home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.12/lib/python2.7/site-packages/vtk/vtkIOFFMPEGPython.so", 102);
import vtk.vtkIOFFMPEGPython # dynamically loaded from /home/share/unix_files/cdat/miniconda2/envs/uvcdat-2.12/lib/python2.7/site-packages/vtk/vtkIOFFMPEGPython.so
@doutriaux1

This comment has been minimized.

Member

doutriaux1 commented Sep 18, 2017

It seems like you might be have installed vtk in your root environment before, con you do a:

source activate root
conda list

if it show vtk in it, that means you have installed packages in root which are now picked up even though you are in your environment. I ran into this before. I would recommend

  • save/move your envs directory if you have special envs you want to preserve
  • delete your /home/share/unix_files/cdat/miniconda2/ directory
  • reinstall conda fresh

If you don't want to do this right away, try to avoid symlinks by doing

conda create -n uvcdat-2.12-nosymlink -c conda-forge -c uvcdat uvcdat --copy

But there's no warranty that will fix your issue.

@doutriaux1

This comment has been minimized.

Member

doutriaux1 commented Sep 18, 2017

also the fact that you're getting numpy 1.12 is suspicious, it should be 1.13

@jaigsingla

This comment has been minimized.

jaigsingla commented Sep 18, 2017

Hello ,
Earlier there was no vtk in the machine. When above reported error flashed , I installed vtk. But, then it gave boxfill issue. From error logs it looks like it is pointing out vtk dependent module??

@doutriaux1

This comment has been minimized.

Member

doutriaux1 commented Sep 18, 2017

@jaigsingla it's picking up another VTK on your system, one that does not have ffmpeg bindings or was built against an older version of FFMPEG. I'm suspecting you have it installed. Also uvcdat should come with numpy 1.13 on a clean system you're getting 1.12 so something is odd here.
At this point I would recommend either starting fresh or looking at your env maybe your LD_LIBRARY_PATH is set to something that has vtk.

@jaigsingla

This comment has been minimized.

jaigsingla commented Sep 18, 2017

OK Charles. Will check tomorrow and cm back to you. Thanks

@jaigsingla

This comment has been minimized.

jaigsingla commented Sep 19, 2017

Hello Charles,

there is no other vtk in root env installation. There is only a vtk installed in one of envs and its version is 6.3.0 . Is this the suspect but this i have installed in environment after getting vtkFFMEG error.

@jaigsingla

This comment has been minimized.

jaigsingla commented Sep 20, 2017

Hello,
Now when i am trying to execute it says libbz2.so.1.0 import error . can not open object file on line 9 in vtkIOFFMPEG.py

i have one libbz2.so.1.0.6 in /usr/lib64 location.

Pls comment.

@doutriaux1

This comment has been minimized.

Member

doutriaux1 commented Sep 20, 2017

@jaigsingla can you please try this for me,

  • (re)move your miniconda2 directory
  • install a fresh miniconda
  • create an env from this file
conda env create -f 2.12.yml

Please let me know if this helps.

@jaigsingla

This comment has been minimized.

jaigsingla commented Sep 20, 2017

@doutriaux1

This comment has been minimized.

Member

doutriaux1 commented Sep 20, 2017

@jaigsingla it would work too with anaconda, but miniconda is faster

wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh
miniconda.sh
@jaigsingla

This comment has been minimized.

jaigsingla commented Sep 21, 2017

Hello ,
I could get miniconda & install it separately. Can I do offline installation of uvcdat as i dont have internet on my working machine.
How to download all relevant packages and install it on offline machine. or can anyone share full env which i can just download?

@doutriaux1

This comment has been minimized.

Member

doutriaux1 commented Sep 21, 2017

@jaigsingla we have an older page explaining this, please let me know if it is still relevant @jypeter helped write the first page. See: https://github.com/UV-CDAT/uvcdat/wiki/Anaconda_Offline_Installation

@jaigsingla

This comment has been minimized.

jaigsingla commented Sep 22, 2017

Hello All,
thanks for help. I could get through installation issue on linux machine. While rendering heavy data on windows using mobaxterm getting IO: fatal IO error 11 (Resource temporarily unavailable) on X server "localhost:10.0" error?

Is this SW installation can be done on windows also?

@doutriaux1

This comment has been minimized.

Member

doutriaux1 commented Sep 25, 2017

Do you have some sort of X11 installed on your windows machine? Only Windows 10 is supported see: https://github.com/UV-CDAT/uvcdat/wiki/CDAT-under-windows

@jaigsingla

This comment has been minimized.

jaigsingla commented Sep 26, 2017

Using mobaxterm for connectivity to linux. It has X11 feature.
I have win 8.1 currently. Can we generate .exe out of this which shall run on multi platform.

@doutriaux1

This comment has been minimized.

Member

doutriaux1 commented Sep 26, 2017

unfortunately no.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment