No light on most plants

[Emblanc]

I noticed that some plants in my simulations never intercept light : in the PAR_per_axes.csv output file, their value for Sum_PAR is always 0.

For example, when I run sim_scheme_test.txt, (which is the simulation we use for tests but with 50 plants instead of 4), plants 11 to 50 never intercept any light ! (see PAR_per_axes.txt)

I think this might be related to Pull request #10 , when we removed mapping_table @christian34, @chrlecarpentier. Before #10 , PAR intercepted by each organ was extracted using mapping_table :

for id in mapping_table.keys():
  if new_lstring[id].name == "Blade" and new_lstring[id][0].photosynthetic == True or new_lstring[id].name == "Sheath" or new_lstring[id].name == "Internode" or new_lstring[id].name == "Peduncle" or new_lstring[id].name == "Ear" and new_lstring[id][0].emerged == True:
    if new_lstring[id][0].tiller in axis_census[new_lstring[id][0].num_plante].keys():
      Debug_PAR_dico_df["Ei"].append(res_sky["Ei"][mapping_table[id]])
      if res_sky["Ei"][mapping_table[id]] < 0:
        new_lstring[id][0].PAR = 0
      else:
        new_lstring[id][0].PAR = res_sky["Ei"][mapping_table[id]] * res_sky["area"][mapping_table[id]]

Now we no longer use mapping_table. Instead, ids are extracted from res_sky dictionary :

for id in res_sky['Ei'].keys():
  new_ = lstring[id]
  if ((new_.name == "Blade" and new_[0].photosynthetic == True) or (new_.name in ("Sheath", "Internode", "Peduncle")) or (new_.name == "Ear" and new_[0].emerged)):
    if new_[0].tiller in axis_census[new_[0].num_plante].keys():
      Debug_PAR_dico_df["Ei"].append(res_sky["Ei"][id])
      if res_sky["Ei"][id] < 0:
        new_[0].PAR = 0
      else:
        new_[0].PAR = res_sky["Ei"][id] * res_sky["area"][id]

It is my understanding that res_sky['Ei'] has 1 key for each organ in the simulation. However, there are more objects in lstring because there are one object for each organ + other objects ("[" and "]" for example). I checked, and it seems that lstring always has between 6 times and 12 times more ids than res_sky['Ei']. This is why I think res_sky["Ei"][id] does not refer to the same organ as lstring[id]. As I see it, when all ids in res_sky['Ei'].keys() have been used, there are still organs in lstring that have not been considered.

[christian34]

I try to reproduce the bug on in the test file developed on branch used for PR #34. For me runing the test_zero_light() test complete without error (all 50 plants have light). @Emblanc : could you run that test on your machine ?

[Emblanc]

I ran the tests of PR #34 and it failed :

FAIL: test.test_light_interception.test_zero_light Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/home/emmanuelle/WALTer_Dvpt/test/test_light_interception.py", line 17, in test_zero_light assert all(PAR > 0) AssertionError:

[christian34]

ok ! Can you remind me the way you install lpy and caribu ?

[Emblanc]

For lpy, I simply installed Openalea. I might not have the right version of CARIBU. I think I'd better re-install it to be sure. Could you remind me how I should install the right version please ?

[pradal]

I would do something like that on Linux:

conda create -n walter -c openalea openlea.lpy 'boost =1.66.0' openalea.plantgl alinea.caribu alinea.astk

I create a walter env. in conda. I force the boost version due to a bug on Linux. If you depends on other packages (numpy, scipy, pandas) you may leter install them

To activate your env: source activate walter

To install other packages: conda install numpy scipy pandas

[pradal]

I will also test walter on my computer

[Emblanc]

Thank you for your help. I created a new env. as you advised and I ran the test again in this new env. but it is still failing.

[christian34]

Hi ! The (good ?) news is that I can reproduce the bug (test fails) on my second machine (win64 with agreenium conda install). I will continue investigating ....

[christian34]

Okay ! The bug came from...the correction of the lpy cut bug in newest version of lpy. I switch the flag to lpy_cut_bug=false and it fix the caribu bug. I've commited the switch in the branch #34 @Emblanc : can you test again ?

[pradal]

Sure. I will launch the tests. Stay tuned...

[Emblanc]

Unfortunately the test is still failing on my computer (as well as the test_cut_module now, but that was to be expected)

[pfernique]

Fresh new installation works. Did you try to remove all environment depending on LPy, clean the cache and re-install ? i.e.

conda env remove -n walter
conda clean --all -y
conda create -n walter boost=1.66 openlea.lpy alinea.caribu openalea.mtg scipy pandas nose  -c openalea

[Emblanc]

I did as you advised and the test is no longer failing !

[Emblanc]

There is something that I do not understand though : I tried to run a simulation (the same as the test simulation) and when I look at the PAR_per_axes.csv output file, 2 out of 4 plants receive 0 light. I might be doing something wrong. I ran my simulation in the walter environment and my WALTer repository was on the PR34 branch.

[christian34]

very good news for the test (the merge is close) !

Can you describe a bit more how you launch the last test :within a python session with commands similar to the test (if yes, you can probably write /sketch a new failing test, to be investigated/debugged) , or do you do something else ?

[Emblanc]

Yes, very good news for the test indeed !

To run my last simulation, I just opened a terminal on my computer and then :

source activate walter walter -p my_project walter -i sim_scheme_test.csv

[christian34]

Too bad: I run these commands on my two windows machine and cannot reproduce your results (all plants receive light in the PAR_per_axes.csv). May be walter command is pointing to a wrong script ? You may try to re-run at walter root dir:

source activate walter
python setup.py install --prefix=$CONDA_PREFIX

[Emblanc]

I tried but there is an error with python setup.py install --prefix=$CONDA_PREFIX

running install Checking .pth file support in /home/emmanuelle/miniconda2/envs/walter/lib/python2.7/site-packages/ /usr/bin/python -E -c pass TEST FAILED: /home/emmanuelle/miniconda2/envs/walter/lib/python2.7/site-packages/ does NOT support .pth files error: bad install directory or PYTHONPATH You are attempting to install a package to a directory that is not on PYTHONPATH and which Python does not read ".pth" files from. The installation directory you specified (via --install-dir, --prefix, or the distutils default setting) was: /home/emmanuelle/miniconda2/envs/walter/lib/python2.7/site-packages/ and your PYTHONPATH environment variable currently contains: '' Here are some of your options for correcting the problem: You can choose a different installation directory, i.e., one that is on PYTHONPATH or supports .pth files You can add the installation directory to the PYTHONPATH environment variable. (It must then also be on PYTHONPATH whenever you run Python and want to use the package(s) you are installing.) *You can set up the installation directory to support ".pth" files by using one of the approaches described here: https://pythonhosted.org/setuptools/easy_install.html#custom-installation-locations

[pradal]

Are you in your conda environment (activate walter)?

Le 27/03/2018 à 09:56, Emmanuelle Blanc a écrit :

I tried but there is an error with |python setup.py install --prefix=$CONDA_PREFIX|

running install
Checking .pth file support in
/home/emmanuelle/miniconda2/envs/walter/lib/python2.7/site-packages/
/usr/bin/python -E -c pass
TEST FAILED:
/home/emmanuelle/miniconda2/envs/walter/lib/python2.7/site-packages/
does NOT support .pth files
error: bad install directory or PYTHONPATH
You are attempting to install a package to a directory that is not
on PYTHONPATH and which Python does not read ".pth" files from. The
installation directory you specified (via --install-dir, --prefix, or
the distutils default setting) was:
/home/emmanuelle/miniconda2/envs/walter/lib/python2.7/site-packages/
and your PYTHONPATH environment variable currently contains:
''
Here are some of your options for correcting the problem:
*You can choose a different installation directory, i.e., one that is
on PYTHONPATH or supports .pth files
*You can add the installation directory to the PYTHONPATH environment
variable. (It must then also be on PYTHONPATH whenever you run
Python and want to use the package(s) you are installing.)
*You can set up the installation directory to support ".pth" files by
using one of the approaches described here:
https://pythonhosted.org/setuptools/easy_install.html#custom-installation-locations

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[Emblanc]

Yes, I am in my conda environment walter

[pradal]

What is the python which is used?

Get me the result of:

which python

Le 27/03/2018 à 10:32, Emmanuelle Blanc a écrit :

Yes, I am in my conda environment walter

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[Emblanc]

The result of which python is :

/home/emmanuelle/miniconda2/envs/walter/bin/python

[pradal]

Strange. Send me the result of the command conda info --all

[Emblanc]

 active environment : walter
active env location : /home/emmanuelle/miniconda2/envs/walter
        shell level : 1
   user config file : /home/emmanuelle/.condarc

populated config files : conda version : 4.4.10 conda-build version : not installed python version : 2.7.14.final.0 base environment : /home/emmanuelle/miniconda2 (writable) channel URLs : https://repo.continuum.io/pkgs/main/linux-64 https://repo.continuum.io/pkgs/main/noarch https://repo.continuum.io/pkgs/free/linux-64 https://repo.continuum.io/pkgs/free/noarch https://repo.continuum.io/pkgs/r/linux-64 https://repo.continuum.io/pkgs/r/noarch https://repo.continuum.io/pkgs/pro/linux-64 https://repo.continuum.io/pkgs/pro/noarch package cache : /home/emmanuelle/miniconda2/pkgs /home/emmanuelle/.conda/pkgs envs directories : /home/emmanuelle/miniconda2/envs /home/emmanuelle/.conda/envs platform : linux-64 user-agent : conda/4.4.10 requests/2.18.4 CPython/2.7.14 Linux/4.4.0-116-generic ubuntu/14.04 glibc/2.19 UID:GID : 1001:1001 netrc file : None offline mode : False

conda environments:

# base /home/emmanuelle/miniconda2 walter * /home/emmanuelle/miniconda2/envs/walter

sys.version: 2.7.14 |Anaconda, Inc.| (default, Dec 7... sys.prefix: /home/emmanuelle/miniconda2 sys.executable: /home/emmanuelle/miniconda2/bin/python conda location: /home/emmanuelle/miniconda2/lib/python2.7/site-packages/conda conda-build: None conda-env: /home/emmanuelle/miniconda2/bin/conda-env user site dirs:

CIO_TEST: CONDA_DEFAULT_ENV: walter CONDA_PREFIX: /home/emmanuelle/miniconda2/envs/walter CONDA_PROMPT_MODIFIER: (walter) CONDA_PYTHON_EXE: /home/emmanuelle/miniconda2/bin/python CONDA_ROOT: /home/emmanuelle/miniconda2 CONDA_SHLVL: 1 DEFAULTS_PATH: /usr/share/gconf/ubuntu.default.path LD_LIBRARY_PATH: /usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/local/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/lib/python2.7/dist-packages/lib:/usr/local/lib MANDATORY_PATH: /usr/share/gconf/ubuntu.mandatory.path PATH: /home/emmanuelle/miniconda2/envs/walter/bin:/home/emmanuelle/miniconda2/bin:/usr/lib/python2.7/dist-packages/bin:/usr/lib/python2.7/dist-packages/bin:/usr/lib/python2.7/dist-packages/bin:/usr/lib/python2.7/dist-packages/bin:/usr/local/lib/python2.7/dist-packages/alinea.caribu-7.1.0-py2.7-linux-x86_64.egg/bin:/usr/lib/python2.7/dist-packages/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin REQUESTS_CA_BUNDLE: SSL_CERT_FILE: XDG_SEAT_PATH: /org/freedesktop/DisplayManager/Seat0 XDG_SESSION_PATH: /org/freedesktop/DisplayManager/Session0

WARNING: could not import _license.show_info

try:

$ conda install -n root _license

[pradal]

You have to unset your LD_LIBRARY_PATH export LD_LIBRARY_PATH=

Can you try just: python setup.py install

[Emblanc]

I ran both lines. python setup.py install seemed to work

[Emblanc]

Should I try to run python setup.py install --prefix=$CONDA_PREFIX again ?

[pradal]

No. If it succeed, you do not need to rerun the command.

Le 27/03/2018 à 11:27, Emmanuelle Blanc a écrit :

Should I try to run |python setup.py install --prefix=$CONDA_PREFIX| again ?

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[Emblanc]

I can no longer create a project to run my simulation :

walter -p my_project returns the error

Traceback (most recent call last): File "/usr/local/bin/walter", line 9, in load_entry_point('walter==2.0.1', 'console_scripts', 'walter')() File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 351, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 2363, in load_entry_point return ep.load() File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 2088, in load entry = import(self.module_name, globals(),globals(), ['name']) File "/usr/local/lib/python2.7/dist-packages/walter-2.0.1-py2.7.egg/walter/project.py", line 15, in from openalea.lpy import Lsystem File "/usr/lib/python2.7/dist-packages/openalea/lpy/init.py", line 2, in from __lpy_kernel__ import * ImportError: liblpy.so: cannot open shared object file: No such file or directory

[Emblanc]

I can create a project if I run my command in a new terminal (still in the walter environment). But the results of my simulations are still wrong (plants with 0 light)

[pradal]

In your new ternimal, can you run export LD_LIBRARY_PATH=

[Emblanc]

I ran export LD_LIBRARY_PATH= in my new terminal and then tried to create a project. It returned the same error message as in the first terminal

[......] ImportError: liblpy.so: cannot open shared object file: No such file or directory

[pradal]

This is strange. It seems that you use a library that is in your system (not in conda). Do you have the lib in

ls $CONDA_PREFIX/lib/liblpy.so

[Emblanc]

When I run ls $CONDA_PREFIX/lib/liblpy.so, the result is

/home/emmanuelle/miniconda2/envs/walter/lib/liblpy.so

[pradal]

and can you run smth like

ldd /home/emmanuelle/miniconda2/envs/walter/lib/liblpy.so

Le 27/03/2018 à 11:50, Emmanuelle Blanc a écrit :

When I run |ls $CONDA_PREFIX/lib/liblpy.so|, the result is

/home/emmanuelle/miniconda2/envs/walter/lib/liblpy.so

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[Emblanc]

ldd /home/emmanuelle/miniconda2/envs/walter/lib/liblpy.so

linux-vdso.so.1 => (0x00007ffc43fce000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f0df9e00000) libpython2.7.so.1.0 => /home/emmanuelle/miniconda2/envs/walter/lib/./libpython2.7.so.1.0 (0x00007f0df9a23000) libboost_python.so.1.66.0 => /home/emmanuelle/miniconda2/envs/walter/lib/./libboost_python.so.1.66.0 (0x00007f0df97e0000) libQtCore.so.4 => /home/emmanuelle/miniconda2/envs/walter/lib/./libQtCore.so.4 (0x00007f0df92d1000) libpgltool.so => /home/emmanuelle/miniconda2/envs/walter/lib/./libpgltool.so (0x00007f0df90c2000) libpglmath.so => /home/emmanuelle/miniconda2/envs/walter/lib/./libpglmath.so (0x00007f0df8ea4000) libpglsg.so => /home/emmanuelle/miniconda2/envs/walter/lib/./libpglsg.so (0x00007f0df8aed000) libpglalgo.so => /home/emmanuelle/miniconda2/envs/walter/lib/./libpglalgo.so (0x00007f0df825b000) libpglgui.so => /home/emmanuelle/miniconda2/envs/walter/lib/./libpglgui.so (0x00007f0df7e40000) libstdc++.so.6 => /home/emmanuelle/miniconda2/envs/walter/lib/./libstdc++.so.6 (0x00007f0df7b06000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f0df7800000) libgcc_s.so.1 => /home/emmanuelle/miniconda2/envs/walter/lib/./libgcc_s.so.1 (0x00007f0df75ee000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f0df7225000) /lib64/ld-linux-x86-64.so.2 (0x00007f0dfa368000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f0df7021000) libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f0df6e1e000) libz.so.1 => /home/emmanuelle/miniconda2/envs/walter/lib/././libz.so.1 (0x00007f0df6c07000) libgthread-2.0.so.0 => /usr/lib/x86_64-linux-gnu/libgthread-2.0.so.0 (0x00007f0df6a05000) libglib-2.0.so.0 => /lib/x86_64-linux-gnu/libglib-2.0.so.0 (0x00007f0df66fd000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f0df64f5000) libGLU.so.1 => /usr/lib/x86_64-linux-gnu/libGLU.so.1 (0x00007f0df6287000) libqhull.so.7 => /home/emmanuelle/miniconda2/envs/walter/lib/././libqhull.so.7 (0x00007f0df6017000) libboost_thread.so.1.66.0 => /home/emmanuelle/miniconda2/envs/walter/lib/././libboost_thread.so.1.66.0 (0x00007f0df5df5000) libann.so => /home/emmanuelle/miniconda2/envs/walter/lib/././libann.so (0x00007f0df5be2000) libgmp.so.10 => /home/emmanuelle/miniconda2/envs/walter/lib/././libgmp.so.10 (0x00007f0df594e000) libCGAL.so.13 => /home/emmanuelle/miniconda2/envs/walter/lib/././libCGAL.so.13 (0x00007f0df5727000) libmpfr.so.4 => /home/emmanuelle/miniconda2/envs/walter/lib/././libmpfr.so.4 (0x00007f0df54c3000) libQtOpenGL.so.4 => /home/emmanuelle/miniconda2/envs/walter/lib/././libQtOpenGL.so.4 (0x00007f0df51b8000) libQtGui.so.4 => /home/emmanuelle/miniconda2/envs/walter/lib/././libQtGui.so.4 (0x00007f0df445e000) libQtNetwork.so.4 => /home/emmanuelle/miniconda2/envs/walter/lib/././libQtNetwork.so.4 (0x00007f0df40f9000) libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007f0df3ebb000) libGL.so.1 => /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1 (0x00007f0df3c53000) libboost_system.so.1.66.0 => /home/emmanuelle/miniconda2/envs/walter/lib/./././libboost_system.so.1.66.0 (0x00007f0df3a4e000) libfreetype.so.6 => /home/emmanuelle/miniconda2/envs/walter/lib/./././libfreetype.so.6 (0x00007f0df37b4000) libXrender.so.1 => /usr/lib/x86_64-linux-gnu/libXrender.so.1 (0x00007f0df35aa000) libfontconfig.so.1 => /home/emmanuelle/miniconda2/envs/walter/lib/./././libfontconfig.so.1 (0x00007f0df3367000) libXext.so.6 => /usr/lib/x86_64-linux-gnu/libXext.so.6 (0x00007f0df3155000) libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007f0df2e20000) libpng16.so.16 => /home/emmanuelle/miniconda2/envs/walter/lib/./././libpng16.so.16 (0x00007f0df2be9000) libgobject-2.0.so.0 => /usr/lib/x86_64-linux-gnu/libgobject-2.0.so.0 (0x00007f0df2998000) libSM.so.6 => /usr/lib/x86_64-linux-gnu/libSM.so.6 (0x00007f0df2790000) libICE.so.6 => /usr/lib/x86_64-linux-gnu/libICE.so.6 (0x00007f0df2574000) libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1 (0x00007f0df234a000) libxcb-dri3.so.0 => /usr/lib/x86_64-linux-gnu/libxcb-dri3.so.0 (0x00007f0df2147000) libxcb-present.so.0 => /usr/lib/x86_64-linux-gnu/libxcb-present.so.0 (0x00007f0df1f44000) libxcb-sync.so.1 => /usr/lib/x86_64-linux-gnu/libxcb-sync.so.1 (0x00007f0df1d3e000) libxshmfence.so.1 => /usr/lib/x86_64-linux-gnu/libxshmfence.so.1 (0x00007f0df1b3c000) libglapi.so.0 => /usr/lib/x86_64-linux-gnu/libglapi.so.0 (0x00007f0df190e000) libXdamage.so.1 => /usr/lib/x86_64-linux-gnu/libXdamage.so.1 (0x00007f0df170b000) libXfixes.so.3 => /usr/lib/x86_64-linux-gnu/libXfixes.so.3 (0x00007f0df1505000) libX11-xcb.so.1 => /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1 (0x00007f0df1303000) libxcb-glx.so.0 => /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0 (0x00007f0df10ec000) libxcb-dri2.so.0 => /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0 (0x00007f0df0ee7000) libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f0df0cc8000) libXxf86vm.so.1 => /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1 (0x00007f0df0ac2000) libdrm.so.2 => /usr/lib/x86_64-linux-gnu/libdrm.so.2 (0x00007f0df08b4000) libxml2.so.2 => /home/emmanuelle/miniconda2/envs/walter/lib/././././libxml2.so.2 (0x00007f0df0559000) libiconv.so.2 => /home/emmanuelle/miniconda2/envs/walter/lib/././././libiconv.so.2 (0x00007f0df026a000) libffi.so.6 => /home/emmanuelle/miniconda2/envs/walter/lib/./././libffi.so.6 (0x00007f0df0061000) libuuid.so.1 => /lib/x86_64-linux-gnu/libuuid.so.1 (0x00007f0defe5c000) libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007f0defc58000) libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007f0defa52000)

[pradal]

Nice. if you run lpy, what happens?

[Emblanc]

lpy opened normally

[pradal]

With export LD_LIBRARY_PATH= ?

[Emblanc]

Yes, lpy opens normally right after I run export LD_LIBRARY_PATH=

[pradal]

Do not use sudo python setup.py in conda...