Volume viewer error - 4.6.2

Hi

I know there is the thread Volume viewer error but i don’t want to take that over as the last post indicates that the problem is fixed.

Unfortunately this is not the case in our infrastructure with cryosparc 4.6.2

When someone opens the volume viewer it just shows:

Webtools shows:
image

When i check the command_vis.log i can see that the last entry is 4 days old.

2025-01-17 15:16:02,454 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:16:02,457 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:16:02,474 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:16:02,474 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:16:11,641 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:16:11,644 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:16:11,647 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:16:11,664 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:16:11,665 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:16:13,655 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:16:13,658 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:16:13,663 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:16:13,680 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:16:13,680 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:16:25,797 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:16:25,799 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:16:25,804 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:16:25,821 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:16:25,821 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:16:32,859 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:16:32,861 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:16:32,865 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:16:32,882 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:16:32,883 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:16:34,873 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:16:34,876 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:16:34,880 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:16:34,897 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:16:34,897 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:16:44,980 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:16:44,982 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:16:44,986 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:16:45,003 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:16:45,003 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:16:53,051 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:16:53,054 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:16:53,058 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:16:53,074 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:16:53,074 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:16:55,077 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:16:55,080 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:16:55,084 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:16:55,101 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:16:55,101 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:17:05,155 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:17:05,158 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:17:05,162 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:17:05,178 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:17:05,178 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:17:14,233 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:17:14,235 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:17:14,239 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:17:14,256 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:17:14,256 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:17:16,252 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:17:16,254 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:17:16,258 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:17:16,275 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:17:16,275 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:17:22,329 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:17:22,332 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:17:22,336 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:17:22,353 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:17:22,353 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:17:23,341 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:17:23,344 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:17:23,347 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:17:23,364 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:17:23,364 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:17:35,464 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:17:35,467 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:17:35,470 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:17:35,487 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:17:35,487 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:17:43,534 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:17:43,537 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:17:43,540 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:17:43,557 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:17:43,557 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:17:44,546 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:17:44,549 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:17:44,553 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:17:44,570 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:17:44,570 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:17:53,625 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:17:53,628 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:17:53,631 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:17:53,648 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:17:53,648 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:17:54,632 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:17:54,635 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:17:54,639 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:17:54,656 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:17:54,656 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:18:05,724 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:18:05,727 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:18:05,731 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:18:05,748 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:18:05,748 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:18:13,808 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:18:13,811 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:18:13,815 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:18:13,832 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:18:13,832 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:18:14,818 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:18:14,821 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:18:14,824 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:18:14,841 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:18:14,841 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:18:25,904 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:18:25,906 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:18:25,910 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:18:25,928 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:18:25,928 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:18:35,104 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:18:35,107 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:18:35,111 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:18:35,128 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:18:35,128 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:18:37,120 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:18:37,123 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:18:37,128 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:18:37,145 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:18:37,145 request_handler      INFO     | Completed request for get_individual_data_mic in 0.03s
2025-01-17 15:18:42,176 request_handler      INFO     | Received request for get_individual_data_mic
[2025-01-17 15:18:42,177] ERROR in app: Exception on /get_individual_data_mic [POST]
Traceback (most recent call last):
  File "/opt/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/flask/app.py", line 2528, in wsgi_app
    response = self.full_dispatch_request()
  File "/opt/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/flask/app.py", line 1825, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/opt/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/flask/app.py", line 1823, in full_dispatch_request
    rv = self.dispatch_request()
  File "/opt/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/site-packages/flask/app.py", line 1799, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)
  File "/opt/cryosparc/cryosparc_master/cryosparc_command/command_vis/viscommon.py", line 58, in request_handler
    res = func(*args, **kwargs)
  File "/opt/cryosparc/cryosparc_master/cryosparc_command/command_vis/__init__.py", line 679, in get_individual_data_mic
    micrograph_blob = mongo.db['exposures'].find_one({'project_uid' : project_uid, 'session_uid' : session_uid, 'uid' : exposure_uid}, {'groups.exposure.micrograph_blob_thumb' : 1})['groups']['exposure']['micrograph_blob_thumb']
KeyError: 'micrograph_blob_thumb'
2025-01-17 15:18:46,206 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:18:46,210 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:18:46,214 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:18:46,231 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:18:46,231 request_handler      INFO     | Completed request for get_individual_data_mic in 0.03s
2025-01-17 15:18:55,080 recreate_mesh        INFO     | Loading mesh for [P19 J401.volume_class_0.map]
2025-01-17 15:18:55,087 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] volume path: /mnt/cryosparc/P63/J401/J401_class_00_02800_volume.mrc
2025-01-17 15:18:55,087 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] starting MRC read: J401/J401_class_00_02800_volume.mrc
2025-01-17 15:18:55,146 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] done reading MRC
2025-01-17 15:18:55,146 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] computing mesh...
2025-01-17 15:18:55,150 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] done computing mesh
2025-01-17 15:18:55,150 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] mesh response complete
2025-01-17 15:18:55,373 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:18:55,376 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:18:55,379 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:18:55,396 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:18:55,396 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:18:58,405 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:18:58,408 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:18:58,412 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:18:58,429 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:18:58,429 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:19:00,446 recreate_mesh        INFO     | Loading mesh for [P19 J401.volume_class_0.map]
2025-01-17 15:19:00,453 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] volume path: /mnt/cryosparc/P63/J401/J401_class_00_02800_volume.mrc
2025-01-17 15:19:00,453 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] starting MRC read: J401/J401_class_00_02800_volume.mrc
2025-01-17 15:19:00,453 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] done reading MRC
2025-01-17 15:19:00,453 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] computing mesh...
2025-01-17 15:19:00,457 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] done computing mesh
2025-01-17 15:19:00,457 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] mesh response complete
2025-01-17 15:19:04,658 recreate_mesh        INFO     | Loading mesh for [P19 J401.volume_class_0.map]
2025-01-17 15:19:04,664 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] volume path: /mnt/cryosparc/P63/J401/J401_class_00_02800_volume.mrc
2025-01-17 15:19:04,664 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] starting MRC read: J401/J401_class_00_02800_volume.mrc
2025-01-17 15:19:04,664 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] done reading MRC
2025-01-17 15:19:04,664 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] computing mesh...
2025-01-17 15:19:04,668 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] done computing mesh
2025-01-17 15:19:04,669 recreate_mesh        INFO     | [P19 J401.volume_class_0.map] mesh response complete
2025-01-17 15:19:08,477 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:19:08,480 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:19:08,484 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:19:08,500 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:19:08,501 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:19:14,049 recreate_mesh        INFO     | Loading mesh for [P19 J401.volume_class_1.map]
2025-01-17 15:19:14,056 recreate_mesh        INFO     | [P19 J401.volume_class_1.map] volume path: /mnt/cryosparc/P63/J401/J401_class_01_02800_volume.mrc
2025-01-17 15:19:14,056 recreate_mesh        INFO     | [P19 J401.volume_class_1.map] starting MRC read: J401/J401_class_01_02800_volume.mrc
2025-01-17 15:19:14,112 recreate_mesh        INFO     | [P19 J401.volume_class_1.map] done reading MRC
2025-01-17 15:19:14,112 recreate_mesh        INFO     | [P19 J401.volume_class_1.map] computing mesh...
2025-01-17 15:19:14,116 recreate_mesh        INFO     | [P19 J401.volume_class_1.map] done computing mesh
2025-01-17 15:19:14,116 recreate_mesh        INFO     | [P19 J401.volume_class_1.map] mesh response complete
2025-01-17 15:19:15,533 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:19:15,536 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:19:15,539 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:19:15,556 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:19:15,556 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:19:17,312 recreate_mesh        INFO     | Loading mesh for [P19 J401.volume_class_1.map]
2025-01-17 15:19:17,317 recreate_mesh        INFO     | [P19 J401.volume_class_1.map] volume path: /mnt/cryosparc/P63/J401/J401_class_01_02800_volume.mrc
2025-01-17 15:19:17,317 recreate_mesh        INFO     | [P19 J401.volume_class_1.map] starting MRC read: J401/J401_class_01_02800_volume.mrc
2025-01-17 15:19:17,317 recreate_mesh        INFO     | [P19 J401.volume_class_1.map] done reading MRC
2025-01-17 15:19:17,318 recreate_mesh        INFO     | [P19 J401.volume_class_1.map] computing mesh...
2025-01-17 15:19:17,322 recreate_mesh        INFO     | [P19 J401.volume_class_1.map] done computing mesh
2025-01-17 15:19:17,322 recreate_mesh        INFO     | [P19 J401.volume_class_1.map] mesh response complete
2025-01-17 15:19:20,588 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:19:20,591 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:19:20,595 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:19:20,612 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:19:20,612 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:19:22,604 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:19:22,607 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:19:22,610 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:19:22,627 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:19:22,627 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:19:29,531 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:19:29,534 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:19:29,537 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:19:29,554 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:19:29,554 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:19:29,906 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:19:29,909 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:19:29,911 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:19:29,928 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:19:29,928 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:19:43,342 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:19:43,345 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:19:43,349 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:19:43,368 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.03s
2025-01-17 15:19:43,368 request_handler      INFO     | Completed request for get_individual_data_mic in 0.03s
2025-01-17 15:19:45,360 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:19:45,363 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:19:45,366 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:19:45,383 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:19:45,383 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:19:52,543 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:19:52,546 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:19:52,549 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:19:52,566 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:19:52,567 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:19:54,554 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:19:54,556 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:19:54,560 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:19:54,577 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:19:54,577 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:20:01,757 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:20:01,760 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:20:01,763 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:20:01,780 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:20:01,780 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:20:02,781 request_handler      INFO     | Received request for get_individual_data_mic
2025-01-17 15:20:02,784 read_mrc_image_data  INFO     | Current exposure viewer cache size: 10 micrographs
2025-01-17 15:20:02,787 read_mrc_image_data  INFO     | Pruned exposure viewer cache. New size: 10 micrographs
2025-01-17 15:20:02,804 read_mrc_image_data  INFO     | Micrograph for exposure view ready in 0.02s
2025-01-17 15:20:02,804 request_handler      INFO     | Completed request for get_individual_data_mic in 0.02s
2025-01-17 15:20:12,084 recreate_mesh        INFO     | Loading mesh for [P35 J2687.volume.map]
2025-01-17 15:20:12,090 recreate_mesh        INFO     | [P35 J2687.volume.map] volume path: /mnt/cryosparc/CS-xxx/J2687/J2687_005_volume_map.mrc
2025-01-17 15:20:12,090 recreate_mesh        INFO     | [P35 J2687.volume.map] starting MRC read: J2687/J2687_005_volume_map.mrc
2025-01-17 15:20:13,658 recreate_mesh        INFO     | [P35 J2687.volume.map] done reading MRC
2025-01-17 15:20:13,658 recreate_mesh        INFO     | [P35 J2687.volume.map] computing mesh...
2025-01-17 15:20:14,978 recreate_mesh        INFO     | [P35 J2687.volume.map] done computing mesh
2025-01-17 15:20:14,979 recreate_mesh        INFO     | [P35 J2687.volume.map] mesh response complete

Of course it works for sometime when i restart cryosparc. But after sometimes we are back in the same state.

Not quite sure if it happens when this “exposure viewer cache” is full or when two users opening the volumes viewer at the same time.

Any idea?

3 posts were split to a new topic: Moved to new topic

How long as CryoSparc been running ? I sometimes get the issue were volume viewer will not load anything. This usually comes back if the admin can restart CryoSparc. Also different results with small maps vs. full box volumes

$ cryosparcm restart

I also think that having more resources for CryoSparc helps i.e. in the cryosparc_master there is config.sh

I like to add

export CRYOSPARC_CACHE_NUM_THREADS=8

it could be 4,6,8,more depending on your system, sometimes it helps

I have also the impression it is due how long cryosparc is running. Maybe a memory leak?

I don’t think that

export CRYOSPARC_CACHE_NUM_THREADS=8

has an impact to it. According to the doc this only defines how many threads are used when filling the local ssd cache on a worker.

@wtempel

Can we also check my issue? Thanks :slight_smile:

@biocit Please can you try if a restart of the command_vis server resolves the volume viewer issue:

cryosparcm restart command_vis

sure that helps but i need to do it frequently

Hi,

At risk of potentially muddying the waters, we have had a long-standing issue first documented in Jun 2024, but extending back further, that appears superficially similar.

Therein, volumes cannot be retrieved in the Volumes tab, concomitant with failure to retrieve micrograph (images) in cryoSPARC-Live. These activities stall indefinitely rather than display an error. In addition, while retrieval is on-going (and failing), independent attempts to access the cryoSPARC and cryoSPARC-Live webpages stall as well, and instantly resume when said retrieval is aborted.

Please ignore if unrelated.

Cheers,
Yang

With retrieval, are you referring to displaying and/or downloading a volume?

@leetleyang Does running the command

cryosparcm restart command_vis

when you observe these stalls have any effect?

Hi @wtempel

Displaying, in both scenarios–Volumes tab in cryoSPARC and the downscaled images of averaged micrographs in cryoSPARC-Live. The latter affects both Individual Exposure and the interactive picking interface. I believe downloading works fine, as far as I can remember.

We have resorted to restarting all cryosparcm services–this is effective–but will try restarting just command_vis the next time it happens. It pops up every month or two depending on usage.

I believe our sysadmin has contacted Structura separately with service logs, which we captured during the most recent occurrence. However, I thought to take the opportunity to raise it again given the apparent relevance.

Cheers,
Yang

Thanks for reporting your observation. The periodic crash of the volume viewer (and failures to display micrograph thumbnails in CryoSPARC Live) is a known issue that we plan to address in a future CryoSPARC release. For now (as of CryoSPARC v4.6.2), we recommend restarting the command_vis server with the command
cryosparcm restart command_vis
either periodically (via crontab or similar) or when the issue is observed. A restart limited to command_vis is not expected to disrupt running CryoSPARC jobs.

2 Likes

Thank you for the clarification, @wtempel. We’ll make a note of it.

Cheers,
Yang

This issue pops up weekly for us on 4.6.0, and the command_vis restart is a lifesaver in the interim. thanks!