l2gen failed on ubuntu 16

[clebreton]

Hello,
i have just re-installed my seadas on a new Ubuntu machine, and took first the meris bundle for testing.
I first had to run the install_ocssw script twice, the first time crashed while installing the scripts.bundle:
error: Operation timed out after 0 milliseconds with 0 out of 0 bytes received (curl_result = 28, http_code = 0, sha1 = 373787f15153d418c70e3fd85c5a5c0cd22c3f8d)
error: Unable to find 2d6109bad8ba822a6b7725c036eeef5d7c356260 under https://oceandata.sci.gsfc.nasa.gov/ocssw/scripts.git
Cannot obtain needed blob 2d6109bad8ba822a6b7725c036eeef5d7c356260
while processing commit 459d2264d4222a7ebab84302feaef0ba154f45b1.
error: fetch failed.
Error - Could not run "cd /home/carole/seadas-7.3.2/ocssw/run/scripts; git fetch -q > /dev/null"
But then I just ran, the install_ocssw.py script a second time and everything when fine.

However when I now try run l2gen, I get :
*** stack smashing detected ***: l2gen terminated
Segmentation fault (core dumped)

Do you have an idea what went wrong? Any help is much appreciated

I am on
Ubuntu 16.04.2 LTS
Codename:  xenial
kernel: 4.4.0-62-generic
git version 2.7.4

thanks in advance,
cheers, Carole

[OB.DAACx - SeanBailey]

Carole,
We'll need a little more information...
How did you call l2gen?  What data were you processing? What parameters did you pass it?

Sean

[clebreton]

Hi Sean,
sure :-)
I called l2gen from the command line, after having set my environment properly (export OCSSWROOT=$HOME/seadas-7.3.2/ocssw and $ .ocssw/OCSSW_bash.env )
I wanted to test process a MERIS FR product and this was my call:
l2gen ifile=~/MER_FSG_1PPEPA20050420_102153_000003662036_00323_16409_4543.N1 ofile=~/MER_FSG_1PPEPA20050420_102153_000003662036_00323_16409_4543.nc aer_opt=-10 rad_opt=1 'l2prod=angstrom Rrs_vvv chlor_a Kd_490 cdom_index par sst Zeu_lee Kd_vvv_lee'

hope this helps
cheers,
Carole

(btw if I try calling from the GUI, when loading the file I get the error message: problem creating Parameter XML file: l2gen failed to run. And if I then click on Run, this is what I get:
execution exception: java.io.IOException: l2gen failed with exit code 139.
Check log for more details.
/home/carole/seadas-7.3.2/ocssw/run/scripts/ocssw_runner: line 22:  7880 Segmentation fault      (core dumped) $*))

[OB.DAACx - SeanBailey]

What is the output if you simply run l2gen on the command line without any calling arguments, e.g.:

$ cd $HOME/seadas-7.3.2/ocssw/run/bin/linux_64
$ ./l2gen

While you're there run:

$ git status

and post the output.

Sean

[clebreton]

Yes this was also my first test, if I simply run l2gen on the command line, I get the l2gen help, which I would expect.
And git status gives:
On branch v7.3
Your branch is up-to-date with 'origin/v7.3'.
nothing to commit, working directory clean

In the meantime, I'm installing the modis bundle to test on a L1B product as well, since this has always worked for me until now.
Carole
EDIT:
After successful aqua.bundle installation, I also successfully ran l2gen with a MODISA L1B product, with the simplest command: l2gen ifile=A2014071122000.L1B_LAC geofile=A2014071122000.GEO
So is this a MERIS problem maybe?

[OB.DAACx - SeanBailey]

> So is this a MERIS problem maybe?

Possibly, although that's still puzzling.  I  tried grabbing the same file you listed, but our archive doesn't have it.
We do have a very similar file:
https://oceandata.sci.gsfc.nasa.gov/echo/getfile/MER_FRS_1PPEPA20050420_102153_000004392036_00323_16409_4543.N1.bz2

which did process properly on my Ubuntu16.04 machine...

Sean

[gnwiii]

You mentioned: "(export OCSSWROOT=$HOME/seadas-7.3.2/ocssw and $ .ocssw/OCSSW_bash.env )".   It isn't clear that the second command is equivalent to
"source $OCSSWROOT/OCSSW_bash.env" or ". $OCSSWROOT/OCSSW_bash.env".   If you have more than one ocssw directory then l2gen might get confused by a mix of versions.  This can happen if your original installation using the GUI gave "$HOME/seadas-7.3.2/ocssw" but the command-line installer used the default "$HOME/ocssw".

[clebreton]

Hi Sean,
I did indeed manage to process the scene you mentioned, as well as other MERIS FRS scenes I had on hand.
I think then that the problem comes from the MERIS_FSG files, which l2gen is not happy with.
In any case, for now I can work with the FRS files :-)

thanks again for the help,
Carole

[clebreton]

It was not the case here since I only had one SeaDAS instance installed, but I keep the tip in mind for when we are testing things, thanks!