Help about the Segmentation fault (core dumped)

[xialang2012]

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]

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]

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

[smathermather]

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

[xialang2012]

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]

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]

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

[dakotabenjamin]

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

[dakotabenjamin]

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]

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 --outputall 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]

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

[Fi156]

Caliterra has GPS Tags in the EXIF Data.

[smathermather]

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]

@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]

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]

@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 --outputall 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]

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

[dakotabenjamin]

Try this on the images:

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

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

[xialang2012]

@dakotabenjamin It can work well, thank you.

[dakotabenjamin]

NP