Re: [spdlib-develop] Vegetation Metrics-Segementation Fault - Conda?

Pete Bunting [pfb] Tue, 10 Feb 2015 01:29:06 -0800

Hi Ramiro,

Could you try running spdmetrics with just the height metric MaxH? Just 
wondering if it is one of the metrics which is failing or if it fails before 
starting the calculation.

Something else you could try is to copy your conda installation which is
working from your laptop to the other machine as you know that is fully
configured. Doesn’t sound like it is the issue but just eliminates it further.

Cheers, Pete

****************************************************
* Dr Pete Bunting
* Senior Lecturer in Remote Sensing
* Earth Observation and Ecosystem Dynamics Group
* Department of Geography and Earth Sciences
* Aberystwyth University
* Aberystwyth
* Ceredigion
* SY23 3DB
* UK
*
* Ph: +44 (0) 1970 622615
* Mob: +44 (0) 7917 842743
* Email: p...@aber.ac.uk<mailto:p...@aber.ac.uk>
* ORCID: http://orcid.org/0000-0002-7435-0148
****************************************************

On 10 Feb 2015, at 09:05, Ramiro Silveyra González
<rasil...@gmail.com<mailto:rasil...@gmail.com>> wrote:

Hi Pete,

yes, both 64bit linux versions. My laptop has Ubuntu 14.04 "Trusty Tahr".
The other... I think that it has the same version, I can check it out later.

SPDlib works well, the problem is only spdmetrics.
I am running all spd commands (translate, ground class, noise, height, interp
for dtm, chm, and so on...) and they all work.

Thanks,

Ramiro

2015-02-10 9:59 GMT+01:00 Ramiro Silveyra González
<rasil...@gmail.com<mailto:rasil...@gmail.com>>:
Hi Dan,

II have created a new environment. It didn't work for me as you suggested.
I have created first a python 3 env and then install spdmetrics. I also had to
install kealib, since spdlib doesn't demand it.
I have tried to run spdmetrics from this new environment but I get the same
error: segemtation fault: <seg_fault.png>

and here is the code (the xml I have already sent it to you):

#!/bin/bash
############# export Environment and GDAL_DRIVER_KEA #############
source activate /home/trashtos/anaconda/envs/spdtest
export GDAL_DRIVER_PATH=~/anaconda/envs/spdtest/gdalplugins:$GDAL_DRIVER_PATH
export GDAL_DATA=~/anaconda/envs/spdtest/share/gdal:$GDAL_DATA
############# METRICS #############
spdmetrics --image -f KEA -b 1 -c 50 -r 50 -m
/media/trashtos/INTENSO/Ramiro_Masterarbeit/metrics2.xml -o
/media/trashtos/INTENSO/Ramiro_Masterarbeit/Tiles/Rows1/Cols29/als_dr_opt3_row1col29_2013_nztm_rmn_pmfmccgrd_10m_metrics.kea
-i
/media/trashtos/INTENSO/Ramiro_Masterarbeit/Tiles/Rows1/Cols29/als_dr_opt3_row1col29_2013_nztm_10m_rmn_pmfmccgrd_h.spd
###########################################

Thanks,

Ramiro

2015-02-09 22:18 GMT+01:00 Pete Bunting [pfb]
<p...@aber.ac.uk<mailto:p...@aber.ac.uk>>:
Hi Ramiro,

Can you let me know which flavour of Linux the machine which is failing to run
spdlib has installed? Is it the same and your laptop? I assume they are both
running 64bit linux versions?

Many thanks,

Pete

****************************************************
* Dr Pete Bunting
* Senior Lecturer in Remote Sensing
* Earth Observation and Ecosystem Dynamics Group
* Department of Geography and Earth Sciences
* Aberystwyth University
* Aberystwyth
* Ceredigion
* SY23 3DB
* UK
*
* Ph: +44 (0) 1970 622615<tel:%2B44%20%280%29%201970%20622615>
* Mob: +44 (0) 7917 842743<tel:%2B44%20%280%29%207917%20842743>
* Email: p...@aber.ac.uk<mailto:p...@aber.ac.uk>
* ORCID: http://orcid.org/0000-0002-7435-0148
****************************************************

On 9 Feb 2015, at 20:57, Daniel Clewley
<daniel.clew...@gmail.com<mailto:daniel.clew...@gmail.com>> wrote:

Hi Ramiro,

Didn’t think it would be that simple but good to get the obvious out of the way
first.

I take it you’re using Python 3 not 2 (we don’t keep the 2 builds as up to
date). Creating a new conda environment is a good way to test. You can use:

conda create -n spdtest spdlib

To create a new conda environment with just SPDLib.

If this doesn’t work you can try going back to an older version using:

conda create -n spdtest spdlib=3.1.3

Thanks,

Dan

On 9 Feb 2015, at 20:28, Ramiro Silveyra González
<rasil...@gmail.com<mailto:rasil...@gmail.com>> wrote:

Hi Daniel,

I have shorten the paths for the email. Input, output and XML file are written
with full path. The command is part of sh script I have created with an adapted
version of Pete's multi SPD tiles processing. Tile scripts are created by a
Python script and then submitted to the CPU cores.

It has worked previously without troubles on my laptop in both ways, single
file processing and multiprocessing, exactly the same command with same files,
so memory allocation shouldn't be a problem. Now it doesn't.

On the big computer there is a newer installed version of anaconda, and there
it has never work, no matter what script, input, output, XML file I submit to
spdmetrics.

I have noticed that depending on which order I installed packages with
anaconda, spdlib fails to open files. However, I have tried to reinstall the
packages but I didn't work out. My next idea is to create an anaconda
environment for the spdlib and try to run the scripts from there, in case some
packages dependencies were the source of the problem.

Best,

Ramiro

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Re: [spdlib-develop] Vegetation Metrics-Segementation Fault - Conda?

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