Problems installing/running when locating database on NTFS volume

olibclarke · August 22, 2019, 1:21am

Hi,

I’m attempting to install cryosparc 2.9 on a new GPU workstation (OS Ubuntu 18.04 LTS, CUDA 10.1)

This workstation has a partition for the OS and software (ext4, SSD) and a RAID array which is NTFS, in order to maintain compatibility with Windows (it is a dual boot setup).

It installs and starts up fine if I locate the database on the home partition (ext4, SSD), but it fails if I locate the database on the NTFS volume (or if I move it there post install).

Looking at the logs it seems to be a permissions issue of some kind, but I have permission to write to the directory, so I am a little stumped, and running chmod/chown on the database dir doesn’t help. Any help or suggestions appreciated

Cheers
Oli

Output of cryosparcm log database:

2019-08-21T21:03:08.580-0400 I NETWORK  [signalProcessingThread] shutdown: going to close listening sockets...
2019-08-21T21:03:08.580-0400 I NETWORK  [signalProcessingThread] closing listening socket: 6
2019-08-21T21:03:08.580-0400 I NETWORK  [signalProcessingThread] closing listening socket: 7
2019-08-21T21:03:08.580-0400 I NETWORK  [signalProcessingThread] removing socket file: /tmp/mongodb-39001.sock
2019-08-21T21:03:08.580-0400 I NETWORK  [signalProcessingThread] shutdown: going to flush diaglog...
2019-08-21T21:03:08.580-0400 I REPL     [signalProcessingThread] shutting down replication subsystems
2019-08-21T21:03:08.580-0400 I REPL     [signalProcessingThread] Stopping replication reporter thread
2019-08-21T21:03:08.580-0400 I REPL     [signalProcessingThread] Stopping replication fetcher thread
2019-08-21T21:03:08.580-0400 I REPL     [signalProcessingThread] Stopping replication applier thread
2019-08-21T21:03:08.586-0400 I -        [conn4] end connection 127.0.0.1:45312 (7 connections now open)
2019-08-21T21:03:08.586-0400 I -        [conn5] end connection 127.0.0.1:45318 (7 connections now open)
2019-08-21T21:03:08.587-0400 I -        [conn6] end connection 127.0.0.1:45324 (5 connections now open)
2019-08-21T21:03:08.588-0400 I -        [conn9] end connection 127.0.0.1:45334 (4 connections now open)
2019-08-21T21:03:08.588-0400 I -        [conn10] end connection 127.0.0.1:45336 (4 connections now open)
2019-08-21T21:03:08.588-0400 I -        [conn7] end connection 127.0.0.1:45330 (3 connections now open)
2019-08-21T21:03:09.291-0400 I -        [conn8] end connection 127.0.0.1:45332 (1 connection now open)
2019-08-21T21:03:09.301-0400 I REPL     [signalProcessingThread] Stopping replication storage threads
2019-08-21T21:03:09.302-0400 I FTDC     [signalProcessingThread] Shutting down full-time diagnostic data capture
2019-08-21T21:03:09.306-0400 I STORAGE  [signalProcessingThread] WiredTigerKVEngine shutting down
2019-08-21T21:03:09.437-0400 I STORAGE  [signalProcessingThread] shutdown: removing fs lock...
2019-08-21T21:03:09.437-0400 I CONTROL  [signalProcessingThread] now exiting
2019-08-21T21:03:09.437-0400 I CONTROL  [signalProcessingThread] shutting down with code:0
2019-08-21T21:03:09.437-0400 I CONTROL  [initandlisten] shutting down with code:0
2019-08-21T21:03:11.374-0400 I CONTROL  [initandlisten] MongoDB starting : pid=38381 port=39001 dbpath=/home/user/software/cryosparc/cryosparc2_database 64-bit host=ubuntu
2019-08-21T21:03:11.374-0400 I CONTROL  [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-08-21T21:03:11.374-0400 I CONTROL  [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-08-21T21:03:11.374-0400 I CONTROL  [initandlisten] OpenSSL version: OpenSSL 1.0.2p  14 Aug 2018
2019-08-21T21:03:11.374-0400 I CONTROL  [initandlisten] allocator: tcmalloc
2019-08-21T21:03:11.374-0400 I CONTROL  [initandlisten] modules: none
2019-08-21T21:03:11.374-0400 I CONTROL  [initandlisten] build environment:
2019-08-21T21:03:11.374-0400 I CONTROL  [initandlisten]     distarch: x86_64
2019-08-21T21:03:11.374-0400 I CONTROL  [initandlisten]     target_arch: x86_64
2019-08-21T21:03:11.374-0400 I CONTROL  [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/user/software/cryosparc/cryosparc2_database", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-08-21T21:03:11.374-0400 W -        [initandlisten] Detected unclean shutdown - /home/user/software/cryosparc/cryosparc2_database/mongod.lock is not empty.
2019-08-21T21:03:11.402-0400 I -        [initandlisten] Detected data files in /home/user/software/cryosparc/cryosparc2_database created by the 'wiredTiger' storage engine, so setting the active storage engine to 'wiredTiger'.
2019-08-21T21:03:11.402-0400 W STORAGE  [initandlisten] Recovering data from the last clean checkpoint.
2019-08-21T21:03:11.402-0400 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),
2019-08-21T21:03:11.417-0400 E STORAGE  [initandlisten] WiredTiger error (1) [1566435791:417120][38381:0x7f0fe1ca6d40], file:WiredTiger.wt, connection: /home/user/software/cryosparc/cryosparc2_database/WiredTiger.wt: handle-open: open: Operation not permitted
2019-08-21T21:03:11.417-0400 I -        [initandlisten] Assertion: 28595:1: Operation not permitted src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-08-21T21:03:11.417-0400 I STORAGE  [initandlisten] exception in initAndListen: 28595 1: Operation not permitted, terminating
2019-08-21T21:03:11.417-0400 I NETWORK  [initandlisten] shutdown: going to close listening sockets...
2019-08-21T21:03:11.417-0400 I NETWORK  [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-08-21T21:03:11.417-0400 I NETWORK  [initandlisten] shutdown: going to flush diaglog...
2019-08-21T21:03:11.417-0400 I CONTROL  [initandlisten] now exiting
2019-08-21T21:03:11.417-0400 I CONTROL  [initandlisten] shutting down with code:100
2019-08-21T21:03:12.474-0400 I CONTROL  [initandlisten] MongoDB starting : pid=38384 port=39001 dbpath=/home/user/software/cryosparc/cryosparc2_database 64-bit host=ubuntu
2019-08-21T21:03:12.474-0400 I CONTROL  [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-08-21T21:03:12.474-0400 I CONTROL  [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-08-21T21:03:12.474-0400 I CONTROL  [initandlisten] OpenSSL version: OpenSSL 1.0.2p  14 Aug 2018
2019-08-21T21:03:12.474-0400 I CONTROL  [initandlisten] allocator: tcmalloc
2019-08-21T21:03:12.474-0400 I CONTROL  [initandlisten] modules: none
2019-08-21T21:03:12.474-0400 I CONTROL  [initandlisten] build environment:
2019-08-21T21:03:12.474-0400 I CONTROL  [initandlisten]     distarch: x86_64
2019-08-21T21:03:12.474-0400 I CONTROL  [initandlisten]     target_arch: x86_64
2019-08-21T21:03:12.474-0400 I CONTROL  [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/user/software/cryosparc/cryosparc2_database", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-08-21T21:03:12.475-0400 W -        [initandlisten] Detected unclean shutdown - /home/user/software/cryosparc/cryosparc2_database/mongod.lock is not empty.
2019-08-21T21:03:12.502-0400 I -        [initandlisten] Detected data files in /home/user/software/cryosparc/cryosparc2_database created by the 'wiredTiger' storage engine, so setting the active storage engine to 'wiredTiger'.
2019-08-21T21:03:12.503-0400 W STORAGE  [initandlisten] Recovering data from the last clean checkpoint.
2019-08-21T21:03:12.503-0400 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),
2019-08-21T21:03:12.517-0400 E STORAGE  [initandlisten] WiredTiger error (1) [1566435792:517679][38384:0x7f3ac32dad40], file:WiredTiger.wt, connection: /home/user/software/cryosparc/cryosparc2_database/WiredTiger.wt: handle-open: open: Operation not permitted
2019-08-21T21:03:12.518-0400 I -        [initandlisten] Assertion: 28595:1: Operation not permitted src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-08-21T21:03:12.518-0400 I STORAGE  [initandlisten] exception in initAndListen: 28595 1: Operation not permitted, terminating
2019-08-21T21:03:12.518-0400 I NETWORK  [initandlisten] shutdown: going to close listening sockets...
2019-08-21T21:03:12.518-0400 I NETWORK  [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-08-21T21:03:12.518-0400 I NETWORK  [initandlisten] shutdown: going to flush diaglog...
2019-08-21T21:03:12.518-0400 I CONTROL  [initandlisten] now exiting
2019-08-21T21:03:12.518-0400 I CONTROL  [initandlisten] shutting down with code:100
2019-08-21T21:03:14.574-0400 I CONTROL  [initandlisten] MongoDB starting : pid=38393 port=39001 dbpath=/home/user/software/cryosparc/cryosparc2_database 64-bit host=ubuntu
2019-08-21T21:03:14.574-0400 I CONTROL  [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-08-21T21:03:14.574-0400 I CONTROL  [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-08-21T21:03:14.574-0400 I CONTROL  [initandlisten] OpenSSL version: OpenSSL 1.0.2p  14 Aug 2018
2019-08-21T21:03:14.574-0400 I CONTROL  [initandlisten] allocator: tcmalloc
2019-08-21T21:03:14.574-0400 I CONTROL  [initandlisten] modules: none
2019-08-21T21:03:14.574-0400 I CONTROL  [initandlisten] build environment:
2019-08-21T21:03:14.574-0400 I CONTROL  [initandlisten]     distarch: x86_64
2019-08-21T21:03:14.574-0400 I CONTROL  [initandlisten]     target_arch: x86_64
2019-08-21T21:03:14.574-0400 I CONTROL  [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/user/software/cryosparc/cryosparc2_database", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-08-21T21:03:14.574-0400 W -        [initandlisten] Detected unclean shutdown - /home/user/software/cryosparc/cryosparc2_database/mongod.lock is not empty.
2019-08-21T21:03:14.602-0400 I -        [initandlisten] Detected data files in /home/user/software/cryosparc/cryosparc2_database created by the 'wiredTiger' storage engine, so setting the active storage engine to 'wiredTiger'.
2019-08-21T21:03:14.602-0400 W STORAGE  [initandlisten] Recovering data from the last clean checkpoint.
2019-08-21T21:03:14.602-0400 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),
2019-08-21T21:03:14.616-0400 E STORAGE  [initandlisten] WiredTiger error (1) [1566435794:616511][38393:0x7f3dc7b3bd40], file:WiredTiger.wt, connection: /home/user/software/cryosparc/cryosparc2_database/WiredTiger.wt: handle-open: open: Operation not permitted
2019-08-21T21:03:14.616-0400 I -        [initandlisten] Assertion: 28595:1: Operation not permitted src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-08-21T21:03:14.617-0400 I STORAGE  [initandlisten] exception in initAndListen: 28595 1: Operation not permitted, terminating
2019-08-21T21:03:14.617-0400 I NETWORK  [initandlisten] shutdown: going to close listening sockets...
2019-08-21T21:03:14.617-0400 I NETWORK  [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-08-21T21:03:14.670-0400 I NETWORK  [initandlisten] shutdown: going to flush diaglog...
2019-08-21T21:03:14.670-0400 I CONTROL  [initandlisten] now exiting
2019-08-21T21:03:14.670-0400 I CONTROL  [initandlisten] shutting down with code:100
2019-08-21T21:03:17.726-0400 I CONTROL  [initandlisten] MongoDB starting : pid=38396 port=39001 dbpath=/home/user/software/cryosparc/cryosparc2_database 64-bit host=ubuntu
2019-08-21T21:03:17.726-0400 I CONTROL  [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-08-21T21:03:17.726-0400 I CONTROL  [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-08-21T21:03:17.726-0400 I CONTROL  [initandlisten] OpenSSL version: OpenSSL 1.0.2p  14 Aug 2018
2019-08-21T21:03:17.726-0400 I CONTROL  [initandlisten] allocator: tcmalloc
2019-08-21T21:03:17.726-0400 I CONTROL  [initandlisten] modules: none
2019-08-21T21:03:17.726-0400 I CONTROL  [initandlisten] build environment:
2019-08-21T21:03:17.726-0400 I CONTROL  [initandlisten]     distarch: x86_64
2019-08-21T21:03:17.726-0400 I CONTROL  [initandlisten]     target_arch: x86_64
2019-08-21T21:03:17.726-0400 I CONTROL  [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/user/software/cryosparc/cryosparc2_database", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-08-21T21:03:17.727-0400 W -        [initandlisten] Detected unclean shutdown - /home/user/software/cryosparc/cryosparc2_database/mongod.lock is not empty.
2019-08-21T21:03:17.755-0400 I -        [initandlisten] Detected data files in /home/user/software/cryosparc/cryosparc2_database created by the 'wiredTiger' storage engine, so setting the active storage engine to 'wiredTiger'.
2019-08-21T21:03:17.755-0400 W STORAGE  [initandlisten] Recovering data from the last clean checkpoint.
2019-08-21T21:03:17.755-0400 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),
2019-08-21T21:03:17.769-0400 E STORAGE  [initandlisten] WiredTiger error (1) [1566435797:769655][38396:0x7f8923601d40], file:WiredTiger.wt, connection: /home/user/software/cryosparc/cryosparc2_database/WiredTiger.wt: handle-open: open: Operation not permitted
2019-08-21T21:03:17.770-0400 I -        [initandlisten] Assertion: 28595:1: Operation not permitted src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-08-21T21:03:17.770-0400 I STORAGE  [initandlisten] exception in initAndListen: 28595 1: Operation not permitted, terminating
2019-08-21T21:03:17.770-0400 I NETWORK  [initandlisten] shutdown: going to close listening sockets...
2019-08-21T21:03:17.770-0400 I NETWORK  [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-08-21T21:03:17.770-0400 I NETWORK  [initandlisten] shutdown: going to flush diaglog...
2019-08-21T21:03:17.770-0400 I CONTROL  [initandlisten] now exiting
2019-08-21T21:03:17.770-0400 I CONTROL  [initandlisten] shutting down with code:100
2019-08-21T21:04:02.038-0400 I CONTROL  [initandlisten] MongoDB starting : pid=38509 port=39001 dbpath=/home/user/software/cryosparc/cryosparc2_database 64-bit host=ubuntu
2019-08-21T21:04:02.038-0400 I CONTROL  [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-08-21T21:04:02.038-0400 I CONTROL  [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-08-21T21:04:02.038-0400 I CONTROL  [initandlisten] OpenSSL version: OpenSSL 1.0.2p  14 Aug 2018
2019-08-21T21:04:02.038-0400 I CONTROL  [initandlisten] allocator: tcmalloc
2019-08-21T21:04:02.038-0400 I CONTROL  [initandlisten] modules: none
2019-08-21T21:04:02.038-0400 I CONTROL  [initandlisten] build environment:
2019-08-21T21:04:02.038-0400 I CONTROL  [initandlisten]     distarch: x86_64
2019-08-21T21:04:02.038-0400 I CONTROL  [initandlisten]     target_arch: x86_64
2019-08-21T21:04:02.038-0400 I CONTROL  [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/user/software/cryosparc/cryosparc2_database", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-08-21T21:04:02.038-0400 W -        [initandlisten] Detected unclean shutdown - /home/user/software/cryosparc/cryosparc2_database/mongod.lock is not empty.
2019-08-21T21:04:02.066-0400 I -        [initandlisten] Detected data files in /home/user/software/cryosparc/cryosparc2_database created by the 'wiredTiger' storage engine, so setting the active storage engine to 'wiredTiger'.
2019-08-21T21:04:02.066-0400 W STORAGE  [initandlisten] Recovering data from the last clean checkpoint.
2019-08-21T21:04:02.066-0400 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),
2019-08-21T21:04:02.080-0400 E STORAGE  [initandlisten] WiredTiger error (1) [1566435842:80535][38509:0x7fde905bed40], file:WiredTiger.wt, connection: /home/user/software/cryosparc/cryosparc2_database/WiredTiger.wt: handle-open: open: Operation not permitted
2019-08-21T21:04:02.081-0400 I -        [initandlisten] Assertion: 28595:1: Operation not permitted src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-08-21T21:04:02.081-0400 I STORAGE  [initandlisten] exception in initAndListen: 28595 1: Operation not permitted, terminating
2019-08-21T21:04:02.081-0400 I NETWORK  [initandlisten] shutdown: going to close listening sockets...
2019-08-21T21:04:02.081-0400 I NETWORK  [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-08-21T21:04:02.081-0400 I NETWORK  [initandlisten] shutdown: going to flush diaglog...
2019-08-21T21:04:02.081-0400 I CONTROL  [initandlisten] now exiting
2019-08-21T21:04:02.081-0400 I CONTROL  [initandlisten] shutting down with code:100
2019-08-21T21:04:03.138-0400 I CONTROL  [initandlisten] MongoDB starting : pid=38512 port=39001 dbpath=/home/user/software/cryosparc/cryosparc2_database 64-bit host=ubuntu
2019-08-21T21:04:03.138-0400 I CONTROL  [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-08-21T21:04:03.138-0400 I CONTROL  [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-08-21T21:04:03.138-0400 I CONTROL  [initandlisten] OpenSSL version: OpenSSL 1.0.2p  14 Aug 2018
2019-08-21T21:04:03.138-0400 I CONTROL  [initandlisten] allocator: tcmalloc
2019-08-21T21:04:03.138-0400 I CONTROL  [initandlisten] modules: none
2019-08-21T21:04:03.138-0400 I CONTROL  [initandlisten] build environment:
2019-08-21T21:04:03.138-0400 I CONTROL  [initandlisten]     distarch: x86_64
2019-08-21T21:04:03.138-0400 I CONTROL  [initandlisten]     target_arch: x86_64
2019-08-21T21:04:03.138-0400 I CONTROL  [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/user/software/cryosparc/cryosparc2_database", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-08-21T21:04:03.139-0400 W -        [initandlisten] Detected unclean shutdown - /home/user/software/cryosparc/cryosparc2_database/mongod.lock is not empty.
2019-08-21T21:04:03.166-0400 I -        [initandlisten] Detected data files in /home/user/software/cryosparc/cryosparc2_database created by the 'wiredTiger' storage engine, so setting the active storage engine to 'wiredTiger'.
2019-08-21T21:04:03.167-0400 W STORAGE  [initandlisten] Recovering data from the last clean checkpoint.
2019-08-21T21:04:03.167-0400 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),
2019-08-21T21:04:03.181-0400 E STORAGE  [initandlisten] WiredTiger error (1) [1566435843:181458][38512:0x7f5907daed40], file:WiredTiger.wt, connection: /home/user/software/cryosparc/cryosparc2_database/WiredTiger.wt: handle-open: open: Operation not permitted
2019-08-21T21:04:03.181-0400 I -        [initandlisten] Assertion: 28595:1: Operation not permitted src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-08-21T21:04:03.182-0400 I STORAGE  [initandlisten] exception in initAndListen: 28595 1: Operation not permitted, terminating
2019-08-21T21:04:03.182-0400 I NETWORK  [initandlisten] shutdown: going to close listening sockets...
2019-08-21T21:04:03.182-0400 I NETWORK  [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-08-21T21:04:03.182-0400 I NETWORK  [initandlisten] shutdown: going to flush diaglog...
2019-08-21T21:04:03.182-0400 I CONTROL  [initandlisten] now exiting
2019-08-21T21:04:03.182-0400 I CONTROL  [initandlisten] shutting down with code:100
2019-08-21T21:04:05.238-0400 I CONTROL  [initandlisten] MongoDB starting : pid=38521 port=39001 dbpath=/home/user/software/cryosparc/cryosparc2_database 64-bit host=ubuntu
2019-08-21T21:04:05.238-0400 I CONTROL  [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-08-21T21:04:05.238-0400 I CONTROL  [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-08-21T21:04:05.238-0400 I CONTROL  [initandlisten] OpenSSL version: OpenSSL 1.0.2p  14 Aug 2018
2019-08-21T21:04:05.238-0400 I CONTROL  [initandlisten] allocator: tcmalloc
2019-08-21T21:04:05.238-0400 I CONTROL  [initandlisten] modules: none
2019-08-21T21:04:05.238-0400 I CONTROL  [initandlisten] build environment:
2019-08-21T21:04:05.238-0400 I CONTROL  [initandlisten]     distarch: x86_64
2019-08-21T21:04:05.238-0400 I CONTROL  [initandlisten]     target_arch: x86_64
2019-08-21T21:04:05.238-0400 I CONTROL  [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/user/software/cryosparc/cryosparc2_database", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-08-21T21:04:05.238-0400 W -        [initandlisten] Detected unclean shutdown - /home/user/software/cryosparc/cryosparc2_database/mongod.lock is not empty.
2019-08-21T21:04:05.266-0400 I -        [initandlisten] Detected data files in /home/user/software/cryosparc/cryosparc2_database created by the 'wiredTiger' storage engine, so setting the active storage engine to 'wiredTiger'.
2019-08-21T21:04:05.266-0400 W STORAGE  [initandlisten] Recovering data from the last clean checkpoint.
2019-08-21T21:04:05.266-0400 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),
2019-08-21T21:04:05.281-0400 E STORAGE  [initandlisten] WiredTiger error (1) [1566435845:281218][38521:0x7f902d8a5d40], file:WiredTiger.wt, connection: /home/user/software/cryosparc/cryosparc2_database/WiredTiger.wt: handle-open: open: Operation not permitted
2019-08-21T21:04:05.281-0400 I -        [initandlisten] Assertion: 28595:1: Operation not permitted src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-08-21T21:04:05.281-0400 I STORAGE  [initandlisten] exception in initAndListen: 28595 1: Operation not permitted, terminating
2019-08-21T21:04:05.281-0400 I NETWORK  [initandlisten] shutdown: going to close listening sockets...
2019-08-21T21:04:05.281-0400 I NETWORK  [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-08-21T21:04:05.281-0400 I NETWORK  [initandlisten] shutdown: going to flush diaglog...
2019-08-21T21:04:05.281-0400 I CONTROL  [initandlisten] now exiting
2019-08-21T21:04:05.281-0400 I CONTROL  [initandlisten] shutting down with code:100
2019-08-21T21:04:08.338-0400 I CONTROL  [initandlisten] MongoDB starting : pid=38524 port=39001 dbpath=/home/user/software/cryosparc/cryosparc2_database 64-bit host=ubuntu
2019-08-21T21:04:08.338-0400 I CONTROL  [initandlisten] db version v3.4.10-4-g67ee356c6b
2019-08-21T21:04:08.338-0400 I CONTROL  [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2019-08-21T21:04:08.338-0400 I CONTROL  [initandlisten] OpenSSL version: OpenSSL 1.0.2p  14 Aug 2018
2019-08-21T21:04:08.338-0400 I CONTROL  [initandlisten] allocator: tcmalloc
2019-08-21T21:04:08.338-0400 I CONTROL  [initandlisten] modules: none
2019-08-21T21:04:08.338-0400 I CONTROL  [initandlisten] build environment:
2019-08-21T21:04:08.338-0400 I CONTROL  [initandlisten]     distarch: x86_64
2019-08-21T21:04:08.338-0400 I CONTROL  [initandlisten]     target_arch: x86_64
2019-08-21T21:04:08.338-0400 I CONTROL  [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/user/software/cryosparc/cryosparc2_database", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2019-08-21T21:04:08.338-0400 W -        [initandlisten] Detected unclean shutdown - /home/user/software/cryosparc/cryosparc2_database/mongod.lock is not empty.
2019-08-21T21:04:08.366-0400 I -        [initandlisten] Detected data files in /home/user/software/cryosparc/cryosparc2_database created by the 'wiredTiger' storage engine, so setting the active storage engine to 'wiredTiger'.
2019-08-21T21:04:08.367-0400 W STORAGE  [initandlisten] Recovering data from the last clean checkpoint.
2019-08-21T21:04:08.367-0400 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),
2019-08-21T21:04:08.381-0400 E STORAGE  [initandlisten] WiredTiger error (1) [1566435848:381526][38524:0x7f2c739d1d40], file:WiredTiger.wt, connection: /home/user/software/cryosparc/cryosparc2_database/WiredTiger.wt: handle-open: open: Operation not permitted
2019-08-21T21:04:08.382-0400 I -        [initandlisten] Assertion: 28595:1: Operation not permitted src/mongo/db/storage/wiredtiger/wiredtiger_kv_engine.cpp 276
2019-08-21T21:04:08.382-0400 I STORAGE  [initandlisten] exception in initAndListen: 28595 1: Operation not permitted, terminating
2019-08-21T21:04:08.382-0400 I NETWORK  [initandlisten] shutdown: going to close listening sockets...
2019-08-21T21:04:08.382-0400 I NETWORK  [initandlisten] removing socket file: /tmp/mongodb-39001.sock
2019-08-21T21:04:08.382-0400 I NETWORK  [initandlisten] shutdown: going to flush diaglog...
2019-08-21T21:04:08.382-0400 I CONTROL  [initandlisten] now exiting
2019-08-21T21:04:08.382-0400 I CONTROL  [initandlisten] shutting down with code:100

Output of cryosparcm log command_core:

*** BG WORKER START
[JSONRPC ERROR  2019-08-21 20:55:53.031294  at  set_config_var ]
-----------------------------------------------------
Traceback (most recent call last):
  File "cryosparc2_command/command_core/__init__.py", line 106, in wrapper
    res = func(*args, **kwargs)
  File "cryosparc2_command/command_core/__init__.py", line 372, in set_config_var
    mongo.db[colname].update_one({'name' : name}, {op : {'name' : name, 'value' : value}}, upsert=True)
  File "/home/user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/collection.py", line 894, in update_one
    collation=collation)
  File "/home/user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/collection.py", line 753, in _update
    codec_options=self.__write_response_codec_options).copy()
  File "/home/user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/pool.py", line 424, in command
    self._raise_connection_failure(error)
  File "/home/user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/pool.py", line 552, in _raise_connection_failure
    raise error
NotMasterError: not master
-----------------------------------------------------
[2019-08-21 20:55:53,033] ERROR in app: Exception on /startup [GET]
Traceback (most recent call last):
  File "/home/user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/flask/app.py", line 1982, in wsgi_app
    response = self.full_dispatch_request()
  File "/home/user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/flask/app.py", line 1614, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/home/user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/flask/app.py", line 1517, in handle_user_exception
    reraise(exc_type, exc_value, tb)
  File "/home/user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/flask/app.py", line 1612, in full_dispatch_request
    rv = self.dispatch_request()
  File "/home/user/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/flask/app.py", line 1598, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "cryosparc2_command/command_core/__init__.py", line 238, in startup
    set_config_var('running_version', versionfile.read().strip())
  File "cryosparc2_command/command_core/__init__.py", line 115, in wrapper
    raise e
NotMasterError: not master
COMMAND CORE STARTED ===  2019-08-21 21:01:09.737596  ==========================
*** BG WORKER START

olibclarke · August 22, 2019, 1:34am

Ah seems like it is a known issue with ntfs… ugh:

Seems like I might need to do some fiddling around with /etc/fstab/, but have a starting point at least…

Oli

Update:
The second link above, followed by chown-ing and chmod-ing the cryosparc database directory ultimately fixed the issue. Initially it was still giving the same database error, so I nuked everything in the database directory. Then, cryosparc could start successfully, but I couldn’t log in (it couldn’t find me as a user). So I deleted the master, worker, and database directories, and performed a fresh install. That terminated with the error below. Turned out this was because a cryosparcm process was still running from the previous install; killing that process and rerunning the install script gave a working installation.

Update 2:
On this system, I have five GPUs, of which I want to use four for compute and one to drive the display. I was able to list the gpus using bin/cryosparcw gpulist, and enable the specific GPUs I wanted by running:
bin/cryosparcw connect --update --master ubuntu --worker ubuntu --gpus 0,1,2,3