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Author Topic: Bad performance (only single core used) on gradual selection tool (45k images)  (Read 2715 times)

andyroo

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I'm processing a dataset with about 45k images and I notice that the gradual selection operations take several hours per iteration. My first Reconstruction uncertainty filter took about 8 hrs on a sparse cloud with 172M points, and it looks like most of that time there is only a single CPU core working.

Wondering if there's a way to parallelize the gradual selection tools so they use all available cores, or even offload to the GPU.

Andy

Alexey Pasumansky

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Hello Andy,

Which version of Metashape you are using? Also can you please post a screenshot of the Chunk Info dialog?
Best regards,
Alexey Pasumansky,
Agisoft LLC

andyroo

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HI Alexey,

I'm using Metashape 1.5.5 build 9097.  Save keypoints is enabled.  I attached a screenshot of the chunk info dialog, and included relevant logfile output from (scipted) generic selection filtering below

Code: [Select]
2019-10-29 21:52:09 Finished processing in 9549.9 sec (exit code 1)
2019-10-29 21:54:49 59160567  points selected
2019-10-29 21:54:49 RU threshold  10.0 selected  59160567 / 172014583 ( 34.3928  %) of  points. Adjusting
2019-10-29 21:57:29 RU threshold  11.0 selected  54139925 / 172014583 ( 31.474  %) of  points. Adjusting
2019-10-29 22:00:08 RU threshold  12.0 selected  44628315 / 172014583 ( 25.9445  %) of  points. Adjusting
2019-10-29 22:02:46 RU threshold  13.0  is  18.9606 % of total points. Ready to delete
2019-10-29 22:02:49 RU 13.0 deleted 32615010 points
2019-10-29 22:02:49 OptimizeCameras: f, cx, cy, k1-k3, p1, p2, adaptive fitting = 0
2019-10-29 22:02:50 Optimizing camera locations...
2019-10-29 22:07:24 removed 2 cameras: 29296, 41560
2019-10-29 22:07:24 removed 2 stations
2019-10-29 22:08:45 adjusting: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 0.117036 -> 0.115838
2019-10-30 01:23:12 coordinates applied in 0 sec
2019-10-30 01:23:30 Finished processing in 12041.3 sec (exit code 1)
2019-10-30 01:23:30 completed optimization # 1
2019-10-30 01:23:31 initializing with RU = 10.0
2019-10-30 01:23:31 Analyzing point cloud...
2019-10-30 03:24:49 Finished processing in 7277.72 sec (exit code 1)
2019-10-30 03:26:57 26545093  points selected
2019-10-30 03:26:57 RU threshold  10.0  is  19.0424 % of total points. Ready to delete
2019-10-30 03:26:59 RU 10.0 deleted 26545093 points
2019-10-30 03:26:59 OptimizeCameras: f, cx, cy, k1-k3, p1, p2, adaptive fitting = 0
2019-10-30 03:27:00 Optimizing camera locations...
2019-10-30 03:31:45 removed 8 cameras: 27741, 28752, 29297, 35695, 35722, 36602, 39689, 39691
2019-10-30 03:31:45 removed 8 stations
2019-10-30 03:31:45 removed 1 points
2019-10-30 03:33:00 adjusting: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 0.116194 -> 0.116075
2019-10-30 06:54:56 coordinates applied in 0 sec
2019-10-30 06:55:11 Finished processing in 12491.8 sec (exit code 1)
2019-10-30 06:55:11 completed optimization # 2
2019-10-30 06:55:12 initializing with RU = 10.0
2019-10-30 06:55:12 Analyzing point cloud...
2019-10-30 08:32:50 Finished processing in 5858.23 sec (exit code 1)
2019-10-30 08:34:33 163  points selected
2019-10-30 08:34:33 RU threshold  10.0  is  0.0001 % of total points. Ready to delete
2019-10-30 08:34:35 RU 10.0 deleted 163 points
2019-10-30 08:34:35 OptimizeCameras: f, cx, cy, k1-k3, p1, p2, adaptive fitting = 0
2019-10-30 08:34:35 Optimizing camera locations...
2019-10-30 08:39:11 removed 2 cameras: 31292, 31294
2019-10-30 08:39:11 removed 2 stations
2019-10-30 08:39:11 removed 1 points
2019-10-30 08:40:24 adjusting: !xxxxxxxxxxxx!xx!x!x!x!x!x!x!x!!xx!x!x!x!x!x!!x!x! 0.116274 -> 0.115059
2019-10-30 11:07:04 LM singular S
2019-10-30 11:07:16 coordinates applied in 0 sec
2019-10-30 11:07:32 Finished processing in 9177.12 sec (exit code 1)
2019-10-30 11:07:32 completed optimization # 3
2019-10-30 11:07:32 initializing with RU = 10.0
2019-10-30 11:07:32 Analyzing point cloud...
2019-10-30 12:45:45 Finished processing in 5892.99 sec (exit code 1)
2019-10-30 12:47:28 805  points selected
2019-10-30 12:47:28 RU threshold  10.0  is  0.0007 % of total points. Ready to delete
2019-10-30 12:47:29 RU 10.0 deleted 805 points
2019-10-30 12:47:29 OptimizeCameras: f, cx, cy, k1-k3, p1, p2, adaptive fitting = 0
2019-10-30 12:47:30 Optimizing camera locations...
2019-10-30 12:53:13 adjusting: !xxxxxxxxxxxx!xx!!xx!x!!xx!x!!xx!x!x!x!!xx!x!x!x!x 0.116108 -> 0.115059
2019-10-30 15:25:53 LM singular S
2019-10-30 15:26:07 coordinates applied in 0 sec
2019-10-30 15:26:21 Finished processing in 9531.87 sec (exit code 1)
2019-10-30 15:26:21 completed optimization # 4
2019-10-30 15:26:22 initializing with RU = 10.0
2019-10-30 15:26:22 Analyzing point cloud...
2019-10-30 17:03:45 Finished processing in 5843.01 sec (exit code 1)
2019-10-30 17:05:27 3  points selected
2019-10-30 17:05:27 RU threshold  10.0  is  0.0 % of total points. Ready to delete
2019-10-30 17:05:28 RU 10.0 deleted 3 points
2019-10-30 17:05:28 OptimizeCameras: f, cx, cy, k1-k3, p1, p2, adaptive fitting = 0
2019-10-30 17:05:28 Optimizing camera locations...
2019-10-30 17:11:11 adjusting: !xxxxxxxxxxxxxx!!x!!xx!x!x!x!x!!xx!x!x!x!x!x!x!x!x 0.116108 -> 0.115059
2019-10-30 19:43:02 LM singular S
2019-10-30 19:43:15 coordinates applied in 0 sec
2019-10-30 19:43:30 Finished processing in 9482.14 sec (exit code 1)
2019-10-30 19:43:30 completed optimization # 5
2019-10-30 19:43:31 initializing with RU = 10.0
2019-10-30 19:43:31 Analyzing point cloud...
2019-10-30 21:21:37 Finished processing in 5885.84 sec (exit code 1)
2019-10-30 21:23:20 0  points selected
2019-10-30 21:25:03 Reconstruction Uncertainty optimization completed.
2019-10-30 21:25:03 59161074 of 172014583 removed in 5 optimizations on chunk "Chunk 1_RU10.0".
2019-10-30 21:25:03
2019-10-30 21:25:03 SaveProject: path = SfM:/Dorian/All_Dorian_4D_finalPositions.psx
2019-10-30 21:25:03 Saving project...
2019-10-30 21:30:33 saved project in 329.8 sec
2019-10-30 21:30:33 Finished processing in 329.8 sec (exit code 1)
2019-10-30 21:30:33 DuplicateChunk: items = (keypoints, depth maps, dense cloud, model, DEM, orthomosaic, tiled model)
2019-10-30 21:30:33 Duplicating chunk...
2019-10-30 22:31:23 Finished processing in 3625.46 sec (exit code 1)
2019-10-30 22:31:23 Copied chunk Chunk 1_RU10.0 to chunk Chunk 1_RU10.0_PA3.0
2019-10-30 22:31:23 Running Projection Accuracy optimization
2019-10-30 22:33:18 initializing with PA = 3.0
2019-10-30 22:33:22 Analyzing point cloud...
2019-10-31 00:08:59 Finished processing in 5740.74 sec (exit code 1)
2019-10-31 00:10:46 55240979  points selected
2019-10-31 00:10:46 PA threshold  3.0  is  48.9493 % of total points. Ready to delete
2019-10-31 00:10:49 PA 3.0 deleted 55240979 points
2019-10-31 00:10:49 OptimizeCameras: f, cx, cy, k1-k3, p1, p2, adaptive fitting = 0
2019-10-31 00:10:49 Optimizing camera locations...
2019-10-31 00:15:28 removed 167 cameras: 499, 500, 501, 502, 598, 599, 621, 622, 623, 627, 628, 629, 630, 631, 632, 633, 634, 635, 636, 637, 638, 639, 640, 641, 642, 2272, 2273, 2274, 2275, 2276, 2277, 2278, 2279, 2280, 2281, 2282, 2283, 2284, 2285, 2287, 2288, 2289, 2935, 2936, 2937, 2938, 2939, 2940, 2941, 2942, 2943, 2944, 2945, 2946, 4184, 4185, 4186, 4187, 4188, 4879, 4884, 4885, 4886, 4887, 4888, 4889, 4890, 4891, 4892, 4893, 4894, 4895, 4896, 5366, 5367, 5371, 5386, 5387, 6137, 6138, 6139, 6141, 6143, 6144, 6169, 6171, 6172, 6173, 6174, 6215, 6220, 6221, 6222, 6603, 6632, 8493, 8494, 10593, 27745, 27746, 27747, 27750, 27752, 27753, 28753, 28754, 28755, 28756, 28757, 28759, 28761, 28763, 28764, 29298, 29306, 29307, 29439, 31291, 31293, 31305, 31318, 31326, 31327, 31328, 31332, 31343, 31349, 31350, 31851, 32437, 32881, 32882, 35694, 35721, 36279, 36549, 36550, 36551, 36603, 36604, 39682, 39687, 39692, 40154, 40155, 40882, 41541, 41542, 41561, 41562, 41702, 41703, 42287, 44476, 44937, 44954, 44979, 2286, 2947, 27748, 28758, 28762, 29304, 29305, 39690, 28760, 29303
2019-10-31 00:15:28 removed 167 stations
2019-10-31 00:15:28 removed 78 points
2019-10-31 00:16:13 adjusting: !xxxxxxxxxxxx!xx!x!x!x!x!x!!x!xx!x!!xx!x!x!x!x!x!x 0.133599 -> 0.131582
2019-10-31 01:40:02 LM singular S
2019-10-31 01:40:10 coordinates applied in 0 sec
2019-10-31 01:40:19 Finished processing in 5369.24 sec (exit code 1)
2019-10-31 01:40:19 completed optimization # 1
2019-10-31 01:40:20 initializing with PA = 3.0
2019-10-31 01:40:20 Analyzing point cloud...
2019-10-31 02:29:29 Finished processing in 2948.8 sec (exit code 1)
2019-10-31 02:30:22 0  points selected
2019-10-31 02:31:13 Projection Accuracy optimization completed.
2019-10-31 02:31:13 55240979 of 112853507 removed in 1 optimizations on chunk "Chunk 1_RU10.0_PA3.0".
2019-10-31 02:31:13
2019-10-31 02:31:13 SaveProject: path = SfM:/Dorian/All_Dorian_4D_finalPositions.psx
2019-10-31 02:31:13 Saving project...
2019-10-31 02:36:24 saved project in 310.708 sec
2019-10-31 02:36:24 Finished processing in 310.708 sec (exit code 1)

andyroo

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I could upload the last five days of logs if it helps. Mostly confused about low CPU usage during depth filtering and point extraction, and wondering how/if I can optimize somehow.

We had a power outage after about 4 days that made me lose my progress on the big chunk so I split the project into 15 chunks thinking it would be faster and am running dense cloud on these smaller area chunks in series.

Interestingly things are still going pretty slowly (1/15 chunks done, first chunk took 5.6 days to finish, which is about how long I thought the original 45k chunk was going to finish in). I'm suspicious that the total number of photos per chunk (even though ~80-90% are disabled) , or maybe even the total size of the project (~20 chunks, 150k  - 200k images) is affecting the processing time, rather than the number of active images in the current chunk.

The whole 45k image chunk has 23478 active cameras and took 1.47 days to complete the GPU Depth reconstruction, and was interrupted during filtering stage after 1.63 days

The first chunk after splitting contains 9316 active cameras, and took 0.74 days to complete GPU depth reconst., 1.02d to complete depth filtering, and 3.83d to extract points.

I should have results on the second chunk tomorrow. At this rate though it looks like it's taking about 5-6 days per chunk.
« Last Edit: November 18, 2019, 11:38:35 PM by andyroo »

andyroo

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Updating this because it's still an issue for me. I would love to see the gradual selection use all of my cores and/or the GPUs.

I'm working on a chunk with ~62k images and it is taking ~2.5h and only using a single core just to show me the gradual selection slider (just the first "Analyzing point cloud step") after I select the gradual selection parameter (Reconstruction Uncertainty).

The sparse cloud (tiepoints) is ~286 million points covering ~500 linear km with 2-6 adjacent lines, being processed in EPSG:6318.

The gradual selection tools are important in our workflow and this makes them a significant part of the processing time for large projects.

I attached some images of CPU usage and progress time. Happy to provide more info if it's useful.