Sen2cor fails on my linux system

Hello

I have installed sen2corr on linux:

LSB Version: core-9.20160110ubuntu0.2-amd64:core-9.20160110ubuntu0.2-noarch:security-9.20160110ubuntu0.2-amd64:security-9.20160110ubuntu0.2-noarch
Distributor ID: Ubuntu
Description: Ubuntu 16.04.2 LTS
Release:16.04
Codename: xenial

I followed the tutorial described in: Proposition of a step by step tuto to install Sen2cor on Ubuntu VM 16.10 . Also, I have installed it (SEN2COR) as plugin in SNAP (5.0) and I have configured it in Tools/External Tools Sen2cor.

I have tried to execute from terminal, L2A_Process --resolution=10 --GIP_L2A /home/fluxes/sen2cor/cfg/L2A_GIPP.xml S2A_MSIL1C_20170531T115221_N0205_R123_T28RDR_20170531T115242.SAFE
The processing starts, however the execution hangs. Please find enclosed the messages showed in termmial (L2_process_message.txt)

Execution from gpt Sen2cor operator, /home/fluxes/snap/bin/gpt Sen2Cor -SsourceProduct=S2A_MSIL1C_20170531T115221_N0205_R123_T28RDR_20170531T115242.SAFE -PtargetProductFile=prueba.SAFE
also stopps without ending, please find enclosed the output message in this case (gtp_sen2cor_message.txt)

gpt_sen2cor_message.txt (6.8 KB)
L2_process_message.txt (7.5 KB)

I have also tried to execute from Tools/External Tools Sen2cor / run. The execution also fails, please find the output message in the screenshot snap_interactive_sen2cor.jpg

regards
Josep

no module named tables indicates that not all dependencies were installed correctly.

Can you install pytables? In Windows this can be done in the command line by pip install pytables

Hello

pytable are instaled on my python 2.7 system (/home/fluxes/anaconda2/lib/python2.7/site-packages/tables/)

In the manage external tools I have changes de PYTHON_BIN from python to /home/fluxes/anaconda2/bin/python. It is suposed to be the default for python. Now the processing starts and stip at 87%. Please find enclosed the new message in the interactive run.

Josep

You should be able to install pytables using the conda package manager – consult the anaconada Python documentation. A pip should work as well, but could require installing other packages. Conda handles dependencies for you.

Hello

I think that currently the problem is not related to tables. They are available on my system

home/fluxes/anaconda2/lib/python2.7/site-packages/tables/

Nevertheless I already tried to reinstall it
conda install pytables
Fetching package metadata …
Solving package specifications: .

Package plan for installation in environment /home/fluxes/anaconda2:

The following packages will be SUPERSEDED by a higher-priority channel:

conda:     4.3.22-py27_0     anaconda --> 4.3.22-py27_0    
conda-env: 2.6.0-0           anaconda --> 2.6.0-0          
pytables:  3.3.0-np112py27_0 anaconda --> 3.3.0-np112py27_0

Proceed ([y]/n)? y

conda-env-2.6. 100% |########################################################################################################| Time: 0:00:00 915.85 kB/s
pytables-3.3.0 100% |########################################################################################################| Time: 0:00:01 5.55 MB/s
conda-4.3.22-p 100% |########################################################################################################| Time: 0:00:00 12.83 MB/s

The message related to tables only affected the SNAP interactive execution (first post) and the message changed after changing the SNAP interactive configuration (second post)

Thank you
Josep

Hello

I solved the problem, time ago, but I forgot to post the solution. In my case, the problem was solved reading the documentation and install de exact version of anaconda for the sen2cor version, and avoid to update anything.

Regards
josep