Cryosparc cannot start after updating to V2.11.0

chenzhao · October 4, 2019, 4:52am

Today I have tried to update cryosparc V2.9.0 to V2.11.0. I first just ran cryosparcm update, however, after the update is successfully finished, I cannot start cryosparc, which gives me an error of:
pymongo.errors.ServerSelectionTimeoutError: localhost:39001: [Errno 111] Connection refused

I did not find a way to solve this problem, and to save time, I decided that I would just update by directly reinstall cryosparc from scratch. The installation procedure looks very normal without any error. However, when I ran cryosparcm start, the only line that shows in the command line window is:
Starting cryoSPARC System master process…
which then returns the command line prompt.
It seems that cryosparc somehow cannot complete the start process.

I then tried to revert to version V2.9.0 by running cryosparcm update --version=2.9.0. However, it just shows:
CryoSPARC current version v2.11.0
update starting on Fri Oct 4 00:49:44 EDT 2019

`=============================

Updating to version 2.9.0.
=============================`
then it returns the command line prompt.

I have never encountered such problems before and I do not know how to trouble shoot. I would really appreciate it if anyone could give me any suggestions.

Sincerely,
Chen

chenzhao · October 4, 2019, 7:23pm

I have tried a couple of more things and now I am having a different problem. Because I was seriously stuck yesterday, today I switched to a new directory for installing cryosparc V2.11.0. This time I again got the connection error when starting the master process:
pymongo.errors.ServerSelectionTimeoutError: localhost:39001: [Errno 111] Connection refused

I then ran cryosparcm log database, and saw something like this:

2019-10-04T14:57:06.747-0400 I - [conn1343] end connection 129.85.13.82:39194 (17 connections now open)
2019-10-04T14:57:13.230-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39236 #1344 (17 connections now open)
2019-10-04T14:57:13.230-0400 I NETWORK [conn1344] received client metadata from 129.85.13.82:39236 conn1344: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:57:13.267-0400 I - [conn1344] end connection 129.85.13.82:39236 (17 connections now open)
2019-10-04T14:57:19.651-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39278 #1345 (17 connections now open)
2019-10-04T14:57:19.652-0400 I NETWORK [conn1345] received client metadata from 129.85.13.82:39278 conn1345: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:57:19.687-0400 I - [conn1345] end connection 129.85.13.82:39278 (17 connections now open)
2019-10-04T14:57:26.045-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39320 #1346 (17 connections now open)
2019-10-04T14:57:26.046-0400 I NETWORK [conn1346] received client metadata from 129.85.13.82:39320 conn1346: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:57:26.082-0400 I - [conn1346] end connection 129.85.13.82:39320 (17 connections now open)
2019-10-04T14:57:32.452-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39368 #1347 (17 connections now open)
2019-10-04T14:57:32.452-0400 I NETWORK [conn1347] received client metadata from 129.85.13.82:39368 conn1347: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:57:32.485-0400 I - [conn1347] end connection 129.85.13.82:39368 (17 connections now open)
2019-10-04T14:57:38.824-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39404 #1348 (17 connections now open)
2019-10-04T14:57:38.824-0400 I NETWORK [conn1348] received client metadata from 129.85.13.82:39404 conn1348: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:57:38.861-0400 I - [conn1348] end connection 129.85.13.82:39404 (17 connections now open)
2019-10-04T14:57:45.197-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39446 #1349 (17 connections now open)
2019-10-04T14:57:45.197-0400 I NETWORK [conn1349] received client metadata from 129.85.13.82:39446 conn1349: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:57:45.232-0400 I - [conn1349] end connection 129.85.13.82:39446 (17 connections now open)
2019-10-04T14:57:51.587-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39488 #1350 (17 connections now open)
2019-10-04T14:57:51.587-0400 I NETWORK [conn1350] received client metadata from 129.85.13.82:39488 conn1350: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:57:51.623-0400 I - [conn1350] end connection 129.85.13.82:39488 (17 connections now open)
2019-10-04T14:57:57.996-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39530 #1351 (17 connections now open)
2019-10-04T14:57:57.996-0400 I NETWORK [conn1351] received client metadata from 129.85.13.82:39530 conn1351: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:57:58.032-0400 I - [conn1351] end connection 129.85.13.82:39530 (17 connections now open)
2019-10-04T14:58:04.384-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39572 #1352 (17 connections now open)
2019-10-04T14:58:04.384-0400 I NETWORK [conn1352] received client metadata from 129.85.13.82:39572 conn1352: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:58:04.420-0400 I - [conn1352] end connection 129.85.13.82:39572 (17 connections now open)
2019-10-04T14:58:10.903-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39618 #1353 (17 connections now open)
2019-10-04T14:58:10.903-0400 I NETWORK [conn1353] received client metadata from 129.85.13.82:39618 conn1353: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:58:10.937-0400 I - [conn1353] end connection 129.85.13.82:39618 (17 connections now open)
2019-10-04T14:58:17.438-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39656 #1354 (17 connections now open)
2019-10-04T14:58:17.438-0400 I NETWORK [conn1354] received client metadata from 129.85.13.82:39656 conn1354: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:58:17.473-0400 I - [conn1354] end connection 129.85.13.82:39656 (17 connections now open)
2019-10-04T14:58:23.895-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39698 #1355 (17 connections now open)
2019-10-04T14:58:23.895-0400 I NETWORK [conn1355] received client metadata from 129.85.13.82:39698 conn1355: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:58:23.933-0400 I - [conn1355] end connection 129.85.13.82:39698 (17 connections now open)
2019-10-04T14:58:30.264-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39741 #1356 (17 connections now open)
2019-10-04T14:58:30.264-0400 I NETWORK [conn1356] received client metadata from 129.85.13.82:39741 conn1356: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:58:30.300-0400 I - [conn1356] end connection 129.85.13.82:39741 (17 connections now open)
2019-10-04T14:58:36.630-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39782 #1357 (17 connections now open)
2019-10-04T14:58:36.630-0400 I NETWORK [conn1357] received client metadata from 129.85.13.82:39782 conn1357: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:58:36.666-0400 I - [conn1357] end connection 129.85.13.82:39782 (17 connections now open)
2019-10-04T14:58:42.970-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39824 #1358 (17 connections now open)
2019-10-04T14:58:42.970-0400 I NETWORK [conn1358] received client metadata from 129.85.13.82:39824 conn1358: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:58:43.007-0400 I - [conn1358] end connection 129.85.13.82:39824 (17 connections now open)
2019-10-04T14:58:49.333-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39866 #1359 (17 connections now open)
2019-10-04T14:58:49.334-0400 I NETWORK [conn1359] received client metadata from 129.85.13.82:39866 conn1359: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:58:49.370-0400 I - [conn1359] end connection 129.85.13.82:39866 (17 connections now open)
2019-10-04T14:58:55.688-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39914 #1360 (17 connections now open)
2019-10-04T14:58:55.688-0400 I NETWORK [conn1360] received client metadata from 129.85.13.82:39914 conn1360: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:58:55.718-0400 I - [conn1360] end connection 129.85.13.82:39914 (17 connections now open)
2019-10-04T14:59:02.072-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39950 #1361 (17 connections now open)
2019-10-04T14:59:02.072-0400 I NETWORK [conn1361] received client metadata from 129.85.13.82:39950 conn1361: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:59:02.108-0400 I - [conn1361] end connection 129.85.13.82:39950 (17 connections now open)
2019-10-04T14:59:08.454-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:39992 #1362 (17 connections now open)
2019-10-04T14:59:08.454-0400 I NETWORK [conn1362] received client metadata from 129.85.13.82:39992 conn1362: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:59:08.491-0400 I - [conn1362] end connection 129.85.13.82:39992 (17 connections now open)
2019-10-04T14:59:14.831-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:40034 #1363 (17 connections now open)
2019-10-04T14:59:14.831-0400 I NETWORK [conn1363] received client metadata from 129.85.13.82:40034 conn1363: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:59:14.867-0400 I - [conn1363] end connection 129.85.13.82:40034 (17 connections now open)
2019-10-04T14:59:21.183-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:40078 #1364 (17 connections now open)
2019-10-04T14:59:21.183-0400 I NETWORK [conn1364] received client metadata from 129.85.13.82:40078 conn1364: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:59:21.220-0400 I - [conn1364] end connection 129.85.13.82:40078 (17 connections now open)
2019-10-04T14:59:27.516-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:40120 #1365 (17 connections now open)
2019-10-04T14:59:27.516-0400 I NETWORK [conn1365] received client metadata from 129.85.13.82:40120 conn1365: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:59:27.552-0400 I - [conn1365] end connection 129.85.13.82:40120 (17 connections now open)
2019-10-04T14:59:33.940-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:40162 #1366 (17 connections now open)
2019-10-04T14:59:33.940-0400 I NETWORK [conn1366] received client metadata from 129.85.13.82:40162 conn1366: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:59:33.975-0400 I - [conn1366] end connection 129.85.13.82:40162 (17 connections now open)
2019-10-04T14:59:40.322-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:40204 #1367 (17 connections now open)
2019-10-04T14:59:40.322-0400 I NETWORK [conn1367] received client metadata from 129.85.13.82:40204 conn1367: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:59:40.358-0400 I - [conn1367] end connection 129.85.13.82:40204 (17 connections now open)
2019-10-04T14:59:46.849-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:40250 #1368 (17 connections now open)
2019-10-04T14:59:46.850-0400 I NETWORK [conn1368] received client metadata from 129.85.13.82:40250 conn1368: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:59:46.887-0400 I - [conn1368] end connection 129.85.13.82:40250 (17 connections now open)
2019-10-04T14:59:53.230-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:40294 #1369 (17 connections now open)
2019-10-04T14:59:53.230-0400 I NETWORK [conn1369] received client metadata from 129.85.13.82:40294 conn1369: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:59:53.266-0400 I - [conn1369] end connection 129.85.13.82:40294 (17 connections now open)
2019-10-04T14:59:59.630-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:40336 #1370 (17 connections now open)
2019-10-04T14:59:59.630-0400 I NETWORK [conn1370] received client metadata from 129.85.13.82:40336 conn1370: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T14:59:59.666-0400 I - [conn1370] end connection 129.85.13.82:40336 (17 connections now open)
2019-10-04T15:00:06.161-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:40378 #1371 (17 connections now open)
2019-10-04T15:00:06.161-0400 I NETWORK [conn1371] received client metadata from 129.85.13.82:40378 conn1371: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T15:00:06.196-0400 I - [conn1371] end connection 129.85.13.82:40378 (17 connections now open)
2019-10-04T15:00:12.614-0400 I NETWORK [thread1] connection accepted from 129.85.13.82:40424 #1372 (17 connections now open)
2019-10-04T15:00:12.614-0400 I NETWORK [conn1372] received client metadata from 129.85.13.82:40424 conn1372: { driver: { name: “PyMongo”, version: “3.4.0” }, os: { type: “Linux”, name: “Scientific Linux 7.4 Nitrogen”, architecture: “x86_64”, version: “3.10.0-693.2.2.el7.x86_64” }, platform: “CPython 2.7.15.final.0” }
2019-10-04T15:00:12.647-0400 I - [conn1372] end connection 129.85.13.82:40424 (17 connections now open)
2019-10-04T15:00:15.194-0400 I CONTROL [signalProcessingThread] got signal 15 (Terminated), will terminate after current cmd ends
2019-10-04T15:00:15.194-0400 I NETWORK [signalProcessingThread] shutdown: going to close listening sockets…
2019-10-04T15:00:15.194-0400 I NETWORK [signalProcessingThread] closing listening socket: 6
2019-10-04T15:00:15.194-0400 I NETWORK [signalProcessingThread] closing listening socket: 7
2019-10-04T15:00:15.194-0400 I NETWORK [signalProcessingThread] removing socket file: /tmp/mongodb-39001.sock
2019-10-04T15:00:15.194-0400 I NETWORK [signalProcessingThread] shutdown: going to flush diaglog…
2019-10-04T15:00:15.194-0400 I REPL [signalProcessingThread] shutting down replication subsystems
2019-10-04T15:00:15.194-0400 I REPL [signalProcessingThread] Stopping replication reporter thread
2019-10-04T15:00:15.194-0400 I REPL [signalProcessingThread] Stopping replication fetcher thread
2019-10-04T15:00:15.194-0400 I REPL [signalProcessingThread] Stopping replication applier thread
2019-10-04T15:00:15.205-0400 I - [conn6] end connection 129.85.13.82:39740 (16 connections now open)
2019-10-04T15:00:15.205-0400 I - [conn12] end connection 129.85.13.82:39832 (15 connections now open)
2019-10-04T15:00:15.205-0400 I - [conn8] end connection 129.85.13.82:39744 (15 connections now open)
2019-10-04T15:00:15.205-0400 I - [conn9] end connection 129.85.13.82:39746 (14 connections now open)
2019-10-04T15:00:15.205-0400 I - [conn16] end connection 129.85.13.82:39968 (14 connections now open)
2019-10-04T15:00:15.205-0400 I - [conn34] end connection 129.85.13.82:40612 (13 connections now open)
2019-10-04T15:00:15.205-0400 I - [conn439] end connection 129.85.13.82:57514 (13 connections now open)
2019-10-04T15:00:15.205-0400 I - [conn82] end connection 129.85.13.82:42588 (13 connections now open)
2019-10-04T15:00:15.205-0400 I - [conn440] end connection 129.85.13.82:57516 (13 connections now open)
2019-10-04T15:00:15.205-0400 I - [conn438] end connection 129.85.13.82:57512 (13 connections now open)
2019-10-04T15:00:15.205-0400 I - [conn441] end connection 129.85.13.82:57518 (12 connections now open)
2019-10-04T15:00:15.207-0400 I - [conn5] end connection 129.85.13.82:39736 (5 connections now open)
2019-10-04T15:00:15.207-0400 I - [conn23] end connection 129.85.13.82:40190 (4 connections now open)
2019-10-04T15:00:15.207-0400 I - [conn4] end connection 129.85.13.82:39718 (4 connections now open)
2019-10-04T15:00:15.208-0400 I - [conn21] end connection 129.85.13.82:40142 (2 connections now open)
2019-10-04T15:00:15.518-0400 I REPL [signalProcessingThread] Stopping replication storage threads
2019-10-04T15:00:15.518-0400 I FTDC [signalProcessingThread] Shutting down full-time diagnostic data capture
2019-10-04T15:00:15.523-0400 I STORAGE [signalProcessingThread] WiredTigerKVEngine shutting down
2019-10-04T15:00:15.922-0400 I STORAGE [signalProcessingThread] shutdown: removing fs lock…
2019-10-04T15:00:15.922-0400 I CONTROL [signalProcessingThread] now exiting
2019-10-04T15:00:15.922-0400 I CONTROL [signalProcessingThread] shutting down with code:0
2019-10-04T15:00:15.922-0400 I CONTROL [initandlisten] shutting down with code:0
2019-10-04T15:00:33.205-0400 I CONTROL [initandlisten] MongoDB starting : pid=3649 port=39001 dbpath=/home/data0/data0/cryosparc2_database 64-bit host=patriot.rockfeller.edu
2019-10-04T15:00:33.205-0400 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-10-04T15:00:33.205-0400 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-10-04T15:00:33.205-0400 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2019-10-04T15:00:33.205-0400 I CONTROL [initandlisten] allocator: tcmalloc
2019-10-04T15:00:33.205-0400 I CONTROL [initandlisten] modules: none
2019-10-04T15:00:33.205-0400 I CONTROL [initandlisten] build environment:
2019-10-04T15:00:33.205-0400 I CONTROL [initandlisten] distarch: x86_64
2019-10-04T15:00:33.205-0400 I CONTROL [initandlisten] target_arch: x86_64
2019-10-04T15:00:33.205-0400 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/home/data0/data0/cryosparc2_database”, journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-10-04T15:00:33.252-0400 I - [initandlisten] Detected data files in /home/data0/data0/cryosparc2_database created by the ‘wiredTiger’ storage engine, so setting the active storage engine to ‘wiredTiger’.
2019-10-04T15:00:33.252-0400 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=4096M,session_max=20000,eviction=(threads_min=4,threads_max=4),config_base=false,statistics=(fast),log=(enabled=true,archive=true,path=journal,compressor=snappy),file_manager=(close_idle_time=100000),checkpoint=(wait=60,log_size=2GB),statistics_log=(wait=0),log=(enabled=false),
2019-10-04T15:00:33.260-0400 E STORAGE [initandlisten] WiredTiger error (13) [1570215633:260135][3649:0x7f9baede9d40], file:WiredTiger.wt, connection: /home/data0/data0/cryosparc2_database/WiredTiger.turtle: handle-open: open: Permission denied
2019-10-04T15:00:33.260-0400 I - [initandlisten] Assertion: 28595:13: Permission denied src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-10-04T15:00:33.260-0400 I STORAGE [initandlisten] exception in initAndListen: 28595 13: Permission denied, terminating
2019-10-04T15:00:33.260-0400 I NETWORK [initandlisten] shutdown: going to close listening sockets…
2019-10-04T15:00:33.260-0400 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-10-04T15:00:33.260-0400 I NETWORK [initandlisten] shutdown: going to flush diaglog…
2019-10-04T15:00:33.260-0400 I CONTROL [initandlisten] now exiting
2019-10-04T15:00:33.260-0400 I CONTROL [initandlisten] shutting down with code:100
2019-10-04T15:00:34.294-0400 I CONTROL [initandlisten] MongoDB starting : pid=3652 port=39001 dbpath=/home/data0/data0/cryosparc2_database 64-bit host=patriot.rockfeller.edu
2019-10-04T15:00:34.294-0400 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-10-04T15:00:34.294-0400 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-10-04T15:00:34.294-0400 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2019-10-04T15:00:34.294-0400 I CONTROL [initandlisten] allocator: tcmalloc
2019-10-04T15:00:34.294-0400 I CONTROL [initandlisten] modules: none
2019-10-04T15:00:34.294-0400 I CONTROL [initandlisten] build environment:
2019-10-04T15:00:34.294-0400 I CONTROL [initandlisten] distarch: x86_64
2019-10-04T15:00:34.294-0400 I CONTROL [initandlisten] target_arch: x86_64
2019-10-04T15:00:34.295-0400 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/home/data0/data0/cryosparc2_database”, journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-10-04T15:00:34.322-0400 I - [initandlisten] Detected data files in /home/data0/data0/cryosparc2_database created by the ‘wiredTiger’ storage engine, so setting the active storage engine to ‘wiredTiger’.
2019-10-04T15:00:34.323-0400 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=4096M,session_max=20000,eviction=(threads_min=4,threads_max=4),config_base=false,statistics=(fast),log=(enabled=true,archive=true,path=journal,compressor=snappy),file_manager=(close_idle_time=100000),checkpoint=(wait=60,log_size=2GB),statistics_log=(wait=0),log=(enabled=false),
2019-10-04T15:00:34.329-0400 E STORAGE [initandlisten] WiredTiger error (13) [1570215634:329119][3652:0x7f3d500f9d40], file:WiredTiger.wt, connection: /home/data0/data0/cryosparc2_database/WiredTiger.turtle: handle-open: open: Permission denied
2019-10-04T15:00:34.329-0400 I - [initandlisten] Assertion: 28595:13: Permission denied src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-10-04T15:00:34.329-0400 I STORAGE [initandlisten] exception in initAndListen: 28595 13: Permission denied, terminating
2019-10-04T15:00:34.329-0400 I NETWORK [initandlisten] shutdown: going to close listening sockets…
2019-10-04T15:00:34.329-0400 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-10-04T15:00:34.329-0400 I NETWORK [initandlisten] shutdown: going to flush diaglog…
2019-10-04T15:00:34.329-0400 I CONTROL [initandlisten] now exiting
2019-10-04T15:00:34.329-0400 I CONTROL [initandlisten] shutting down with code:100
2019-10-04T15:00:36.368-0400 I CONTROL [initandlisten] MongoDB starting : pid=3661 port=39001 dbpath=/home/data0/data0/cryosparc2_database 64-bit host=patriot.rockfeller.edu
2019-10-04T15:00:36.368-0400 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-10-04T15:00:36.368-0400 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-10-04T15:00:36.368-0400 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2019-10-04T15:00:36.368-0400 I CONTROL [initandlisten] allocator: tcmalloc
2019-10-04T15:00:36.368-0400 I CONTROL [initandlisten] modules: none
2019-10-04T15:00:36.368-0400 I CONTROL [initandlisten] build environment:
2019-10-04T15:00:36.368-0400 I CONTROL [initandlisten] distarch: x86_64
2019-10-04T15:00:36.368-0400 I CONTROL [initandlisten] target_arch: x86_64
2019-10-04T15:00:36.368-0400 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/home/data0/data0/cryosparc2_database”, journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-10-04T15:00:36.396-0400 I - [initandlisten] Detected data files in /home/data0/data0/cryosparc2_database created by the ‘wiredTiger’ storage engine, so setting the active storage engine to ‘wiredTiger’.
2019-10-04T15:00:36.396-0400 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=4096M,session_max=20000,eviction=(threads_min=4,threads_max=4),config_base=false,statistics=(fast),log=(enabled=true,archive=true,path=journal,compressor=snappy),file_manager=(close_idle_time=100000),checkpoint=(wait=60,log_size=2GB),statistics_log=(wait=0),log=(enabled=false),
2019-10-04T15:00:36.405-0400 E STORAGE [initandlisten] WiredTiger error (13) [1570215636:405044][3661:0x7f4c38739d40], file:WiredTiger.wt, connection: /home/data0/data0/cryosparc2_database/WiredTiger.turtle: handle-open: open: Permission denied
2019-10-04T15:00:36.405-0400 I - [initandlisten] Assertion: 28595:13: Permission denied src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-10-04T15:00:36.405-0400 I STORAGE [initandlisten] exception in initAndListen: 28595 13: Permission denied, terminating
2019-10-04T15:00:36.405-0400 I NETWORK [initandlisten] shutdown: going to close listening sockets…
2019-10-04T15:00:36.405-0400 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-10-04T15:00:36.405-0400 I NETWORK [initandlisten] shutdown: going to flush diaglog…
2019-10-04T15:00:36.405-0400 I CONTROL [initandlisten] now exiting
2019-10-04T15:00:36.405-0400 I CONTROL [initandlisten] shutting down with code:100
2019-10-04T15:00:39.442-0400 I CONTROL [initandlisten] MongoDB starting : pid=3667 port=39001 dbpath=/home/data0/data0/cryosparc2_database 64-bit host=patriot.rockfeller.edu
2019-10-04T15:00:39.442-0400 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-10-04T15:00:39.442-0400 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-10-04T15:00:39.442-0400 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2019-10-04T15:00:39.442-0400 I CONTROL [initandlisten] allocator: tcmalloc
2019-10-04T15:00:39.442-0400 I CONTROL [initandlisten] modules: none
2019-10-04T15:00:39.442-0400 I CONTROL [initandlisten] build environment:
2019-10-04T15:00:39.442-0400 I CONTROL [initandlisten] distarch: x86_64
2019-10-04T15:00:39.442-0400 I CONTROL [initandlisten] target_arch: x86_64
2019-10-04T15:00:39.442-0400 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/home/data0/data0/cryosparc2_database”, journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-10-04T15:00:39.470-0400 I - [initandlisten] Detected data files in /home/data0/data0/cryosparc2_database created by the ‘wiredTiger’ storage engine, so setting the active storage engine to ‘wiredTiger’.
2019-10-04T15:00:39.470-0400 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=4096M,session_max=20000,eviction=(threads_min=4,threads_max=4),config_base=false,statistics=(fast),log=(enabled=true,archive=true,path=journal,compressor=snappy),file_manager=(close_idle_time=100000),checkpoint=(wait=60,log_size=2GB),statistics_log=(wait=0),log=(enabled=false),
2019-10-04T15:00:39.478-0400 E STORAGE [initandlisten] WiredTiger error (13) [1570215639:478334][3667:0x7efe601dbd40], file:WiredTiger.wt, connection: /home/data0/data0/cryosparc2_database/WiredTiger.turtle: handle-open: open: Permission denied
2019-10-04T15:00:39.478-0400 I - [initandlisten] Assertion: 28595:13: Permission denied src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-10-04T15:00:39.478-0400 I STORAGE [initandlisten] exception in initAndListen: 28595 13: Permission denied, terminating
2019-10-04T15:00:39.478-0400 I NETWORK [initandlisten] shutdown: going to close listening sockets…
2019-10-04T15:00:39.478-0400 I NETWORK [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-10-04T15:00:39.478-0400 I NETWORK [initandlisten] shutdown: going to flush diaglog…
2019-10-04T15:00:39.478-0400 I CONTROL [initandlisten] now exiting
2019-10-04T15:00:39.478-0400 I CONTROL [initandlisten] shutting down with code:100

Because I saw the permission denied error, I then tried to start cryosparc as a root. This time I could successfully start cryosparc V2.11 and access it through a browser. When I get in, it says it is in the process of exporting an old project, however, the progress bar did not seem to be moving. I ignored this and started a new project and workspace. I was able to import particle stacks as previously, however, when I tried to run a 2D classification, I saw the following error:
[Errno 2] No such file or directory (on the top)
Job directory /home/data0/data0/czhao/100119Krios/processing/P16/J4 is not empty (in the job log)

I am currently stuck again and I am wondering whether anyone has any clue of how to solve this problem.

stephan · October 11, 2019, 3:49pm

Hi @chenzhao,

Are you still having this issue?

chenzhao · October 18, 2019, 2:08am

Sorry for my delayed reply. I solved this issue by a complete reinstall but keep the root folder name for cryosparc the same. The original error is due to the fact that I changed the root folder name after reinstall cryosparc.