Help about the Segmentation fault (core dumped) #171

xialang2012 · 2015-09-15T10:11:15Z

I installed the OpenDroneMap on my Ubuntu12.04, the installation worked well. When I used the test data download from the https://github.com/OpenDroneMap/odm_data to run the software. It showed the following errors:
O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
;login: The USENIX Magazine, February 2011:42-47.

This helps funding further development; and it won't cost you a cent.
Or you can get GNU Parallel without this requirement by paying 10000 EUR.

To silence this citation notice run 'parallel --bibtex' once or use '--no-notice'.

running bundler - Tue Sep 15 02:55:17 PDT 2015

Segmentation fault (core dumped)

quitting cause:
"/home/xl/opendronemap/OpenDroneMap-gh-pages/bin/bundler" "/home/xl/opendronemap/OpenDroneMap-gh-pages/reconstruction-with-image-size-2400/list.txt" --options_file "/home/xl/opendronemap/OpenDroneMap-gh-pages/reconstruction-with-image-size-2400/options.txt" > bundle/out
returned with code 35584
xl@ubuntu:~/opendronemap/

So, What should I do to resolve the problem. Thank you.
My Ubuntu owns 5GB RAM and 2 cores.

dakotabenjamin · 2015-09-15T12:47:08Z

Try running install.sh again, then if you still have issues, try the users list to help you continue to troubleshoot:
http://lists.osgeo.org/cgi-bin/mailman/listinfo/opendronemap-users

dakotabenjamin · 2015-09-15T16:13:09Z

Scratch that. Switch to the python-port branch and install that. Then use run.py, not run.pl.

smathermather · 2015-09-17T00:57:54Z

Are we ready for existing features to merge in python-port?

xialang2012 · 2015-09-17T04:10:31Z

I download the python-port, and it showed me some errors in apt-get_install.log: E: Unable to locate package libgoogle-glog-dev.
......
Can't find Google Log. Please set GLOG_INCLUDE_DIR & GLOG_LIBRARY or
enable MINIGLOG option to use minimal glog implementation.

I found that the libgoogle-glog-dev was not available on 12.04 (http://askubuntu.com/questions/312173/installing-gflags-12-04). So, May be I should to change to Ubuntu 12.10.

xialang2012 · 2015-09-17T14:04:06Z

I build the google golg on Ubuntu12.04, and run the install shell, it showed me:

LAStools
- installing LAStools
< done - Thu Sep 17 06:52:43 PDT 2015

cmvs/pmvs
- cleaning cmvs
- building cmvs
- make depend cmvs
< done - Thu Sep 17 06:52:56 PDT 2015

bundler
./install.sh: line 394: cd: /home/xl/Desktop/1/OpenDroneMap-python-port/src/bundler: No such file or directory

I tried to copy the bundler.zip from master branches and unzioed it into the src directory, and run it again. But it did not work. Could you give me some suggestions?

dakotabenjamin · 2015-09-17T14:24:23Z

I'm installing 12.04 right now to look into this.

dakotabenjamin · 2015-09-17T15:10:16Z

While I get this worked out, I would recommend updating to 14.04, which is definitely supported.

dakotabenjamin · 2015-09-17T15:38:39Z

Progress so far:

I had to manually build google-glog, then remove it from apt-get install
I had to add python-pip to apt-get install
ceres failed to build:

/odm_app/src/ceres-solver/internal/ceres/covariance_impl.cc:42:28: fatal error: Eigen/SparseCore: No such file or directory
compilation terminated.
make[2]: *** [internal/ceres/CMakeFiles/ceres.dir/covariance_impl.cc.o] Error 1
make[1]: *** [internal/ceres/CMakeFiles/ceres.dir/all] Error 2
make: *** [all] Error 2

This is failing because I can't install gflags. Because gflags and glog are unavailable as a package for precise64, I would recommend to @smathermather that we update the OS requirements to reflect this lack of support. Minimum requirements should be Ubuntu 14.04 LTS.

One thing to note: It looks like ceres wasn't showing up in your install. Make sure you have the latest merge by calling git pull before installing.

xialang2012 · 2015-09-19T14:07:30Z

Thank you, now I can sucessfully built it on Ubuntu14.04. I think if we change the line 116 in install.pl to "sudo apt-get update -y > "$TOOLS_LOG_PATH/apt-get_get.log" 2>&1". So the installation shell may provide better experience for the users.

Besides, I have some troubles when I run the program. I used image of IMG_9374.JPG IMG_9375.JPG IMG_9376.JPG IMG_9377.JPG IMG_9378.JPG IMG_9379 in https://github.com/OpenDroneMap/odm_data_caliterra as the input images, and I have checked those images which can be stitched well. Then I run the run.py, it showed me as below:

.......
Error in OdmExtractUtm:
No valid GPS position found
.......
running echo "4 5" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt" && cat "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/4-5.txt" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt"
b

running bundler - Sat Sep 19 06:44:55 2015
running echo "--match_table matches.init.txt
--output bundle.out
--output_all bundle_
--output_dir bundle
--variable_focal_length
--use_focal_estimate
--constrain_focal
--constrain_focal_weight 0.0
--estimate_distortion
--run_bundle" > "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/options.txt"
b
running "/home/xl/open/OpenDroneMap/bin/bundler" "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/list.txt" --options_file "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/options.txt" > bundle/out
Segmentation fault (core dumped)
b

quitting cause:
"/home/xl/open/OpenDroneMap/bin/bundler" "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/list.txt" --options_file "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/options.txt" > bundle/out
returned with code 35584.

The program did not regonized the GPS info in exif, and the bundle module failed to perform well. Thank you for your time.

smathermather · 2015-09-19T17:14:02Z

I'm not near my computer to verify, but are we sure that Caliterra has embedded GPS? Not all datasets do.

Fi156 · 2015-09-19T20:04:24Z

Caliterra has GPS Tags in the EXIF Data.

smathermather · 2015-09-19T23:25:34Z

Hi @xialang2012, did you use all the images in the Caliterra dataset, or a subset? Using a subset could easily result in a failure at the bundler step, as bundler will require 3 camera positions for each location in the output dataset. A subset of Caliterra has no guarantees of this completeness.

xialang2012 · 2015-09-20T02:10:05Z

@smathermather I used 6 images in the Caliterrra dataset, and all of those images are joint. Besides, I used Pix4d to process those images, and Pix4d could work well.

dakotabenjamin · 2015-09-21T17:11:46Z

I was able to run the caliterra dataset (both the complete dataset and the images @xialang2012 selected) without error, at least through the pmvs step. However I was running at 9 cores and 12GB RAM, so I pulled up a vagrant machine with 2 cores and 5GB RAM, and again found no errors in bundler.

At what step of the process did you get the Extract UTM error?

xialang2012 · 2015-09-22T01:44:29Z

@dakotabenjamin Below is the running log:

configuration:
{'start_with': 'resize', 'end_with': 'odm_orthophoto', 'force_focal': None, 'odm_texturing_textureWithSize': 3600, 'matcher_threshold': 2.0, 'cmvs_maxImages': 500, 'zip_results': False, 'pmvs_threshold': 0.7, 'matcher_preselect': True, 'resize_to': 2400, 'odm_meshing_solverDivide': 9, 'use_opensfm': False, 'pmvs_wsize': 7, 'odm_texturing_textureResolution': 4096, 'matcher_ratio': 0.6, 'odm_meshing_samplesPerNode': 1, 'odm_meshing_maxVertexCount': 100000, 'pmvs_level': 1, 'run_only': None, 'odm_meshing_octreeDepth': 9, 'pmvs_csize': 2, 'matcher_kDistance': 20, 'odm_georeferencing_useGcp': False, 'odm_georeferencing_gcpFile': 'gcp_list.txt', 'matcher_useKnn': True, 'pmvs_minImageNum': 3, 'force_ccd': None}

source files - Mon Sep 21 18:19:36 2015
using IMG_9374.JPG dimensions: 4000x3000 / focal: 4.5mm / ccd: 6.2mm
using IMG_9375.JPG dimensions: 4000x3000 / focal: 4.5mm / ccd: 6.2mm
using IMG_9376.JPG dimensions: 4000x3000 / focal: 4.5mm / ccd: 6.2mm
using IMG_9377.JPG dimensions: 4000x3000 / focal: 4.5mm / ccd: 6.2mm
using IMG_9378.JPG dimensions: 4000x3000 / focal: 4.5mm / ccd: 6.2mm
using IMG_9379.JPG dimensions: 4000x3000 / focal: 4.5mm / ccd: 6.2mm

found 6 usable images

using max image size of 2400 x 2400

preparing images - Mon Sep 21 18:19:36 2015
resizing IMG_9374.JPG to /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/IMG_9374.JPGrunning convert -resize 2400x2400 -quality 100 "/home/xl/open/OpenDroneMap/IMG_9374.JPG" "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/IMG_9374.JPG"
b
(2400 x 1800)
resizing IMG_9375.JPG to /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/IMG_9375.JPGrunning convert -resize 2400x2400 -quality 100 "/home/xl/open/OpenDroneMap/IMG_9375.JPG" "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/IMG_9375.JPG"
b
(2400 x 1800)
resizing IMG_9376.JPG to /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/IMG_9376.JPGrunning convert -resize 2400x2400 -quality 100 "/home/xl/open/OpenDroneMap/IMG_9376.JPG" "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/IMG_9376.JPG"
b
(2400 x 1800)
resizing IMG_9377.JPG to /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/IMG_9377.JPGrunning convert -resize 2400x2400 -quality 100 "/home/xl/open/OpenDroneMap/IMG_9377.JPG" "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/IMG_9377.JPG"
b
(2400 x 1800)
resizing IMG_9378.JPG to /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/IMG_9378.JPGrunning convert -resize 2400x2400 -quality 100 "/home/xl/open/OpenDroneMap/IMG_9378.JPG" "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/IMG_9378.JPG"
b
(2400 x 1800)
resizing IMG_9379.JPG to /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/IMG_9379.JPGrunning convert -resize 2400x2400 -quality 100 "/home/xl/open/OpenDroneMap/IMG_9379.JPG" "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/IMG_9379.JPG"
b
(2400 x 1800)

finding keypoints - Mon Sep 21 18:19:42 2015
running "/home/xl/open/OpenDroneMap/bin/parallel" --no-notice --halt-on-error 1 -j+0 < "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/_vlsift.templist.txt"
1/6 - 524852/6 - 519584/6 - 500823/6 - 509476/6 - 412415/6 - 47311b

matching keypoints - Mon Sep 21 18:21:11 2015
Error when performing utm_extraction, dumping log file:

Error : No such file
in file '/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/IMG_9374.jpg'
Error in OdmExtractUtm:
No valid GPS position found
For more detailed information, see log file.

running "/home/xl/open/OpenDroneMap/bin/parallel" --no-notice --halt-on-error 1 -j+0 < "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/_matches_jobs.templist.txt"
.
5950 matches (11.5%) took 3.46s for /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/0-1.txt .
3948 matches ( 7.7%) took 3.52s for /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/0-2.txt .
2238 matches ( 4.5%) took 3.52s for /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/0-3.txt ...
6649 matches (13.1%) took 3.54s for /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/1-2.txt .
4116 matches ( 8.2%) took 3.45s for /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/1-3.txt .
1932 matches ( 4.1%) took 3.33s for /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/1-4.txt ..
6297 matches (12.6%) took 3.44s for /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/2-3.txt .
3226 matches ( 6.8%) took 3.43s for /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/2-4.txt .
1626 matches ( 3.9%) took 3.23s for /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/2-5.txt .
3049 matches ( 7.4%) took 3.17s for /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/3-5.txt .
5072 matches (10.7%) took 3.41s for /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/3-4.txt .
5969 matches (14.5%) took 2.63s for /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/4-5.txt b
running rm -f "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt"
b
running echo "0 1" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt" && cat "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/0-1.txt" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt"
b
running echo "0 2" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt" && cat "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/0-2.txt" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt"
b
running echo "0 3" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt" && cat "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/0-3.txt" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt"
b
running echo "1 2" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt" && cat "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/1-2.txt" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt"
b
running echo "1 3" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt" && cat "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/1-3.txt" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt"
b
running echo "1 4" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt" && cat "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/1-4.txt" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt"
b
running echo "2 3" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt" && cat "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/2-3.txt" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt"
b
running echo "2 4" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt" && cat "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/2-4.txt" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt"
b
running echo "2 5" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt" && cat "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/2-5.txt" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt"
b
running echo "3 4" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt" && cat "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/3-4.txt" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt"
b
running echo "3 5" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt" && cat "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/3-5.txt" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt"
b
running echo "4 5" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt" && cat "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches/4-5.txt" >> "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/matches.init.txt"
b

running bundler - Mon Sep 21 18:21:54 2015
running echo "--match_table matches.init.txt
--output bundle.out
--output_all bundle_
--output_dir bundle
--variable_focal_length
--use_focal_estimate
--constrain_focal
--constrain_focal_weight 0.0
--estimate_distortion
--run_bundle" > "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/options.txt"
b
running "/home/xl/open/OpenDroneMap/bin/bundler" "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/list.txt" --options_file "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/options.txt" > bundle/out
Segmentation fault (core dumped)
b

quitting cause:
"/home/xl/open/OpenDroneMap/bin/bundler" "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/list.txt" --options_file "/home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400/options.txt" > bundle/out
returned with code 35584.

In odm_extracting_utm_log.txt:

imagesPath was set to: /home/xl/open/OpenDroneMap/reconstruction-with-image-size-2400
imageListFile was set to: image_list_tmp.txt
outputCoordFile was set to: utm_coord_tmp.txt
Error in OdmExtractUtm:
No valid GPS position found

dakotabenjamin · 2015-09-22T19:37:17Z

At first glance, it looks to me like the file capitalization issue hasn't been fixed in python-port.

dakotabenjamin · 2015-09-22T19:41:43Z

Try this on the images:

rename 'y/A-Z/a-z/' *

if you run into 'file already exists' errors, use the -f tag.

xialang2012 · 2015-09-25T02:51:29Z

@dakotabenjamin It can work well, thank you.

dakotabenjamin · 2015-09-25T15:44:29Z

NP

dakotabenjamin closed this as completed Sep 25, 2015

dakotabenjamin mentioned this issue Oct 1, 2015

Segmentation fault (core dumped) #77

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Help about the Segmentation fault (core dumped) #171

Help about the Segmentation fault (core dumped) #171

xialang2012 commented Sep 15, 2015

dakotabenjamin commented Sep 15, 2015

dakotabenjamin commented Sep 15, 2015

smathermather commented Sep 17, 2015

xialang2012 commented Sep 17, 2015

xialang2012 commented Sep 17, 2015

dakotabenjamin commented Sep 17, 2015

dakotabenjamin commented Sep 17, 2015

dakotabenjamin commented Sep 17, 2015

xialang2012 commented Sep 19, 2015

smathermather commented Sep 19, 2015

Fi156 commented Sep 19, 2015

smathermather commented Sep 19, 2015

xialang2012 commented Sep 20, 2015

dakotabenjamin commented Sep 21, 2015

xialang2012 commented Sep 22, 2015

dakotabenjamin commented Sep 22, 2015

dakotabenjamin commented Sep 22, 2015

xialang2012 commented Sep 25, 2015

dakotabenjamin commented Sep 25, 2015

Help about the Segmentation fault (core dumped) #171

Help about the Segmentation fault (core dumped) #171

Comments

xialang2012 commented Sep 15, 2015

dakotabenjamin commented Sep 15, 2015

dakotabenjamin commented Sep 15, 2015

smathermather commented Sep 17, 2015

xialang2012 commented Sep 17, 2015

xialang2012 commented Sep 17, 2015

dakotabenjamin commented Sep 17, 2015

dakotabenjamin commented Sep 17, 2015

dakotabenjamin commented Sep 17, 2015

xialang2012 commented Sep 19, 2015

smathermather commented Sep 19, 2015

Fi156 commented Sep 19, 2015

smathermather commented Sep 19, 2015

xialang2012 commented Sep 20, 2015

dakotabenjamin commented Sep 21, 2015

xialang2012 commented Sep 22, 2015

dakotabenjamin commented Sep 22, 2015

dakotabenjamin commented Sep 22, 2015

xialang2012 commented Sep 25, 2015

dakotabenjamin commented Sep 25, 2015