Database: ERROR (spawn error)

HI,

I have this error when I try to restart cryosparc.

Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: ERROR (spawn error)
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py", line 1149, in database_names
    "listDatabases")["databases"]]
  File "/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/database.py", line 491, in command
    with client._socket_for_reads(read_preference) as (sock_info, slave_ok):
  File "/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/contextlib.py", line 17, in __enter__
    return self.gen.next()
  File "/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py", line 859, in _socket_for_reads
    with self._get_socket(read_preference) as sock_info:
  File "/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/contextlib.py", line 17, in __enter__
    return self.gen.next()
  File "/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py", line 823, in _get_socket
    server = self._get_topology().select_server(selector)
  File "/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 214, in select_server
    address))
  File "/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 189, in select_servers
    self._error_message(selector))
pymongo.errors.ServerSelectionTimeoutError: localhost:39001: [Errno 111] Connection refused

I have try to stop it and check with ps -ax | grep “supervisord” and there is no process.

This is the cryosparc status:

bash-4.2$ cryosparcm status
----------------------------------------------------------------------------
CryoSPARC System master node installed at
/home/binshtem/software/cryosparc/cryosparc2_master
Current cryoSPARC version: v2.12.4
----------------------------------------------------------------------------

cryosparcm is not running.

----------------------------------------------------------------------------

global config variables:

export CRYOSPARC_LICENSE_ID="xxxxxx"
export CRYOSPARC_MASTER_HOSTNAME="xxxxxxx"
export CRYOSPARC_DB_PATH="/home/xxxxxx/software/cryosparc/cryosparc2_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=false

cryosparcm process status after restart with error:

app                              STOPPED   Not started
app_dev                          STOPPED   Not started
command_core                     STOPPED   Not started
command_proxy                    STOPPED   Not started
command_rtp                      STOPPED   Not started
command_vis                      STOPPED   Not started
database                         FATAL     Exited too quickly (process log may have details)
watchdog_dev                     STOPPED   Not started
webapp                           STOPPED   Not started
webapp_dev                       STOPPED   Not started 

this is the database log:

2020-01-02T10:21:25.033-0600 I CONTROL  [initandlisten] MongoDB starting : pid=36141 port=39001 dbpath=/home/binshtem/software/cryosparc/cryosparc2_database 64-bit host=cryogpu2.csb.vanderbilt.edu
2020-01-02T10:21:25.033-0600 I CONTROL  [initandlisten] db version v3.4.10-4-g67ee356c6b
2020-01-02T10:21:25.033-0600 I CONTROL  [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2020-01-02T10:21:25.033-0600 I CONTROL  [initandlisten] OpenSSL version: OpenSSL 1.0.2p  14 Aug 2018
2020-01-02T10:21:25.033-0600 I CONTROL  [initandlisten] allocator: tcmalloc
2020-01-02T10:21:25.033-0600 I CONTROL  [initandlisten] modules: none
2020-01-02T10:21:25.033-0600 I CONTROL  [initandlisten] build environment:
2020-01-02T10:21:25.033-0600 I CONTROL  [initandlisten]     distarch: x86_64
2020-01-02T10:21:25.033-0600 I CONTROL  [initandlisten]     target_arch: x86_64
2020-01-02T10:21:25.033-0600 I CONTROL  [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: "meteor" }, storage: { dbPath: "/home/binshtem/software/cryosparc/cryosparc2_database", journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2020-01-02T10:21:25.036-0600 W -        [initandlisten] Detected unclean shutdown - /home/binshtem/software/cryosparc/cryosparc2_database/mongod.lock is not empty.
2020-01-02T10:21:25.072-0600 I -        [initandlisten] Detected data files in /home/binshtem/software/cryosparc/cryosparc2_database created by the 'wiredTiger' storage engine, so setting the active storage engine to 'wiredTiger'.
2020-01-02T10:21:25.072-0600 W STORAGE  [initandlisten] Recovering data from the last clean checkpoint.
2020-01-02T10:21:25.073-0600 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),
2020-01-02T10:21:25.087-0600 E STORAGE  [initandlisten] WiredTiger error (0) [1577982085:87787][36141:0x2ac87000be00], file:WiredTiger.wt, connection: WiredTiger.turtle: encountered an illegal file format or internal value
2020-01-02T10:21:25.087-0600 E STORAGE  [initandlisten] WiredTiger error (-31804) [1577982085:87825][36141:0x2ac87000be00], file:WiredTiger.wt, connection: the process must exit and restart: WT_PANIC: WiredTiger library panic
2020-01-02T10:21:25.087-0600 I -        [initandlisten] Fatal Assertion 28558 at src/mongo/db/storage/wiredtiger/wiredtiger_util.cpp 361
2020-01-02T10:21:25.087-0600 I -        [initandlisten] 

***aborting after fassert() failure


2020-01-02T10:21:25.095-0600 F -        [initandlisten] Got signal: 6 (Aborted).

 0x55c81c8b5d6b 0x55c81c8b4fe6 0x55c81c8b54c3 0x2ac870f805e0 0x2ac8711c21f7 0x2ac8711c38e8 0x55c81bad4887 0x55c81c5ac597 0x55c81badee75 0x55c81badf08c 0x55c81badf2f5 0x55c81d2ac9d7 0x55c81d2ab1d9 0x55c81d260893 0x55c81d2eb974 0x55c81d2ebf1f 0x55c81d2ec1cc 0x55c81d26e8a9 0x55c81d2e1618 0x55c81d2aa8fe 0x55c81d2aa9eb 0x55c81d25ce6a 0x55c81c591685 0x55c81c5899ca 0x55c81c46f50a 0x55c81bae0bab 0x2ac8711aec05 0x55c81bb44cff
----- BEGIN BACKTRACE -----
{"backtrace":[{"b":"55C81B495000","o":"1420D6B","s":"_ZN5mongo15printStackTraceERSo"},{"b":"55C81B495000","o":"141FFE6"},{"b":"55C81B495000","o":"14204C3"},{"b":"2AC870F71000","o":"F5E0"},{"b":"2AC87118D000","o":"351F7","s":"gsignal"},{"b":"2AC87118D000","o":"368E8","s":"abort"},{"b":"55C81B495000","o":"63F887","s":"_ZN5mongo32fassertFailedNoTraceWithLocationEiPKcj"},{"b":"55C81B495000","o":"1117597"},{"b":"55C81B495000","o":"649E75","s":"__wt_eventv"},{"b":"55C81B495000","o":"64A08C","s":"__wt_err"},{"b":"55C81B495000","o":"64A2F5","s":"__wt_panic"},{"b":"55C81B495000","o":"1E179D7","s":"__wt_turtle_read"},{"b":"55C81B495000","o":"1E161D9","s":"__wt_metadata_search"},{"b":"55C81B495000","o":"1DCB893","s":"__wt_conn_btree_open"},{"b":"55C81B495000","o":"1E56974","s":"__wt_session_get_btree"},{"b":"55C81B495000","o":"1E56F1F","s":"__wt_session_get_btree"},{"b":"55C81B495000","o":"1E571CC","s":"__wt_session_get_btree_ckpt"},{"b":"55C81B495000","o":"1DD98A9","s":"__wt_curfile_open"},{"b":"55C81B495000","o":"1E4C618"},{"b":"55C81B495000","o":"1E158FE","s":"__wt_metadata_cursor_open"},{"b":"55C81B495000","o":"1E159EB","s":"__wt_metadata_cursor"},{"b":"55C81B495000","o":"1DC7E6A","s":"wiredtiger_open"},{"b":"55C81B495000","o":"10FC685","s":"_ZN5mongo18WiredTigerKVEngineC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_PNS_11ClockSourceES8_mbbbb"},{"b":"55C81B495000","o":"10F49CA"},{"b":"55C81B495000","o":"FDA50A","s":"_ZN5mongo20ServiceContextMongoD29initializeGlobalStorageEngineEv"},{"b":"55C81B495000","o":"64BBAB","s":"main"},{"b":"2AC87118D000","o":"21C05","s":"__libc_start_main"},{"b":"55C81B495000","o":"6AFCFF"}],"processInfo":{ "mongodbVersion" : "3.4.10-4-g67ee356c6b", "gitVersion" : "67ee356c6be377cda547d16423daef5beb4e8377", "compiledModules" : [], "uname" : { "sysname" : "Linux", "release" : "3.10.0-957.27.2.el7.x86_64", "version" : "#1 SMP Mon Jul 29 17:46:05 UTC 2019", "machine" : "x86_64" }, "somap" : [ { "b" : "55C81B495000", "elfType" : 3, "buildId" : "A14732EAAA95508462633A5030B501E08B1B106F" }, { "b" : "7FFF486D6000", "elfType" : 3, "buildId" : "88212B24946DE81A7B05A4F4422F5A8B37CBD908" }, { "b" : "2AC86FE12000", "path" : "/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/lib/libpython2.7.so.1.0", "elfType" : 3 }, { "b" : "2AC870014000", "path" : "/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/bin/../lib/libssl.so.1.0.0", "elfType" : 3 }, { "b" : "2AC87028A000", "path" : "/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/bin/../lib/libcrypto.so.1.0.0", "elfType" : 3 }, { "b" : "2AC8706EF000", "path" : "/lib64/librt.so.1", "elfType" : 3, "buildId" : "6D322588B36D2617C03C0F3B93677E62FCFFDA81" }, { "b" : "2AC8708F7000", "path" : "/lib64/libdl.so.2", "elfType" : 3, "buildId" : "1E42EBFB272D37B726F457D6FE3C33D2B094BB69" }, { "b" : "2AC870AFB000", "path" : "/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/bin/../lib/libstdc++.so.6", "elfType" : 3 }, { "b" : "2AC870C6F000", "path" : "/lib64/libm.so.6", "elfType" : 3, "buildId" : "808BD35686C193F218A5AAAC6194C49214CFF379" }, { "b" : "2AC86FFF5000", "path" : "/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/bin/../lib/libgcc_s.so.1", "elfType" : 3 }, { "b" : "2AC870F71000", "path" : "/lib64/libpthread.so.0", "elfType" : 3, "buildId" : "A48D21B2578A8381FBD8857802EAA660504248DC" }, { "b" : "2AC87118D000", "path" : "/lib64/libc.so.6", "elfType" : 3, "buildId" : "95FF02A4BEBABC573C7827A66D447F7BABDDAA44" }, { "b" : "2AC871550000", "path" : "/lib64/libutil.so.1", "elfType" : 3, "buildId" : "C1CAEB92FAB92F5D9AFBA13867535EFD4BB55055" }, { "b" : "2AC86FDF0000", "path" : "/lib64/ld-linux-x86-64.so.2", "elfType" : 3, "buildId" : "22FA66DA7D14C88BF36C69454A357E5F1DEFAE4E" } ] }}
 mongod(_ZN5mongo15printStackTraceERSo+0x3B) [0x55c81c8b5d6b]
 mongod(+0x141FFE6) [0x55c81c8b4fe6]
 mongod(+0x14204C3) [0x55c81c8b54c3]
 libpthread.so.0(+0xF5E0) [0x2ac870f805e0]
 libc.so.6(gsignal+0x37) [0x2ac8711c21f7]
 libc.so.6(abort+0x148) [0x2ac8711c38e8]
 mongod(_ZN5mongo32fassertFailedNoTraceWithLocationEiPKcj+0x0) [0x55c81bad4887]
 mongod(+0x1117597) [0x55c81c5ac597]
 mongod(__wt_eventv+0x3E4) [0x55c81badee75]
 mongod(__wt_err+0xA0) [0x55c81badf08c]
 mongod(__wt_panic+0x2F) [0x55c81badf2f5]
 mongod(__wt_turtle_read+0x227) [0x55c81d2ac9d7]
 mongod(__wt_metadata_search+0x99) [0x55c81d2ab1d9]
 mongod(__wt_conn_btree_open+0x73) [0x55c81d260893]
 mongod(__wt_session_get_btree+0xE4) [0x55c81d2eb974]
 mongod(__wt_session_get_btree+0x68F) [0x55c81d2ebf1f]
 mongod(__wt_session_get_btree_ckpt+0x14C) [0x55c81d2ec1cc]
 mongod(__wt_curfile_open+0x169) [0x55c81d26e8a9]
 mongod(+0x1E4C618) [0x55c81d2e1618]
 mongod(__wt_metadata_cursor_open+0x6E) [0x55c81d2aa8fe]
 mongod(__wt_metadata_cursor+0x4B) [0x55c81d2aa9eb]
 mongod(wiredtiger_open+0x183A) [0x55c81d25ce6a]
 mongod(_ZN5mongo18WiredTigerKVEngineC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_PNS_11ClockSourceES8_mbbbb+0x815) [0x55c81c591685]
 mongod(+0x10F49CA) [0x55c81c5899ca]
 mongod(_ZN5mongo20ServiceContextMongoD29initializeGlobalStorageEngineEv+0x69A) [0x55c81c46f50a]
 mongod(main+0xE9B) [0x55c81bae0bab]
 libc.so.6(__libc_start_main+0xF5) [0x2ac8711aec05]
 mongod(+0x6AFCFF) [0x55c81bb44cff]
-----  END BACKTRACE  -----

Thanks

updata…

I have try to do “cryosparcm update --overrid” to see if it fix the problem the install was successful but on restart I still got database: ERROR (spawn error)
Then I try to rename the cryosparc2_database to cryosparc2_database.old
Now the restart IS successful but I can’t login and I don’t have all my db.

Hi @Elad,

Do you have any recent database backups?
This error is usually caused by a disk fault that causes corruption.

Can you try the following:

  1. make a complete copy of your cryosparc2_database.old directory as a backup and keep it safe
  2. stop all cryosparc processes and remove the new cryosparc2_database directory that you created that has an empty database (no users and no data)
  3. rename the cryosparc2_database.old directory back to cryosparc2_database
  4. cd into the cryosparc2_database directory that has all your original database files
  5. run the following bash commands
eval $(cryosparcm env)
mongod --dbpath ./ --repair

This should attempt to repair your database. If the process completes successfully you should be able to start cryosparc normally again.

Please let us know what happens.

By the way, as a plan B, you can always start a new cryosparc instance/database and then import your projects from your old instance using the import project functionality. This does not require your old database to be operational, but you do need all the intact project directories from the old instance.

Hi,
Thanks you for your reply.
I have done all the steps but when I run the commands on step 5 from within the cryosparc2_database directory I get this:

bash-4.2$ eval $(cryosparcm status)
bash: eval: --: invalid option
eval: usage: eval [arg …]

Sorry! that was a typo. Should be
eval $(cryosparcm env)

Thanks, So I have try the first option and it wasn’t successful :frowning:
this is the output:

bash-4.2$ eval $(cryosparcm env)
bash-4.2$ mongod --dbpath ./ --repair
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] MongoDB starting : pid=38942 port=27017 dbpath=./ 64-bit host=cryogpu2.csb.vanderbilt.edu
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] allocator: tcmalloc
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] modules: none
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] build environment:
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] distarch: x86_64
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] target_arch: x86_64
2020-01-07T09:40:51.590-0600 I CONTROL [initandlisten] options: { repair: true, storage: { dbPath: “./” } }
2020-01-07T09:40:51.595-0600 W - [initandlisten] Detected unclean shutdown - ./mongod.lock is not empty.
2020-01-07T09:40:51.630-0600 I - [initandlisten] Detected data files in ./ created by the ‘wiredTiger’ storage engine, so setting the active storage engine to ‘wiredTiger’.
2020-01-07T09:40:51.631-0600 W STORAGE [initandlisten] Recovering data from the last clean checkpoint.
2020-01-07T09:40:51.632-0600 I STORAGE [initandlisten] wiredtiger_open config: create,cache_size=257430M,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),
2020-01-07T09:40:51.651-0600 E STORAGE [initandlisten] WiredTiger error (0) [1578411651:651363][38942:0x2b680d844e00], file:WiredTiger.wt, connection: WiredTiger.turtle: encountered an illegal file format or internal value
2020-01-07T09:40:51.651-0600 E STORAGE [initandlisten] WiredTiger error (-31804) [1578411651:651445][38942:0x2b680d844e00], file:WiredTiger.wt, connection: the process must exit and restart: WT_PANIC: WiredTiger library panic
2020-01-07T09:40:51.651-0600 I - [initandlisten] Fatal Assertion 28558 at src/mongo/db/storage/wiredtiger/wiredtiger_util.cpp 361
2020-01-07T09:40:51.651-0600 I - [initandlisten]

***aborting after fassert() failure

2020-01-07T09:40:51.660-0600 F - [initandlisten] Got signal: 6 (Aborted).

0x55cd815a6d6b 0x55cd815a5fe6 0x55cd815a64c3 0x2b680e7b95e0 0x2b680e9fb1f7 0x2b680e9fc8e8 0x55cd807c5887 0x55cd8129d597 0x55cd807cfe75 0x55cd807d008c 0x55cd807d02f5 0x55cd81f9d9d7 0x55cd81f9c1d9 0x55cd81f51893 0x55cd81fdc974 0x55cd81fdcf1f 0x55cd81fdd1cc 0x55cd81f5f8a9 0x55cd81fd2618 0x55cd81f9b8fe 0x55cd81f9b9eb 0x55cd81f4de6a 0x55cd81282685 0x55cd8127a9ca 0x55cd8116050a 0x55cd807d1bab 0x2b680e9e7c05 0x55cd80835cff
----- BEGIN BACKTRACE -----
{“backtrace”:[{“b”:“55CD80186000”,“o”:“1420D6B”,“s”:"_ZN5mongo15printStackTraceERSo"},{“b”:“55CD80186000”,“o”:“141FFE6”},{“b”:“55CD80186000”,“o”:“14204C3”},{“b”:“2B680E7AA000”,“o”:“F5E0”},{“b”:“2B680E9C6000”,“o”:“351F7”,“s”:“gsignal”},{“b”:“2B680E9C6000”,“o”:“368E8”,“s”:“abort”},{“b”:“55CD80186000”,“o”:“63F887”,“s”:"_ZN5mongo32fassertFailedNoTraceWithLocationEiPKcj"},{“b”:“55CD80186000”,“o”:“1117597”},{“b”:“55CD80186000”,“o”:“649E75”,“s”:"__wt_eventv"},{“b”:“55CD80186000”,“o”:“64A08C”,“s”:"__wt_err"},{“b”:“55CD80186000”,“o”:“64A2F5”,“s”:"__wt_panic"},{“b”:“55CD80186000”,“o”:“1E179D7”,“s”:"__wt_turtle_read"},{“b”:“55CD80186000”,“o”:“1E161D9”,“s”:"__wt_metadata_search"},{“b”:“55CD80186000”,“o”:“1DCB893”,“s”:"__wt_conn_btree_open"},{“b”:“55CD80186000”,“o”:“1E56974”,“s”:"__wt_session_get_btree"},{“b”:“55CD80186000”,“o”:“1E56F1F”,“s”:"__wt_session_get_btree"},{“b”:“55CD80186000”,“o”:“1E571CC”,“s”:"__wt_session_get_btree_ckpt"},{“b”:“55CD80186000”,“o”:“1DD98A9”,“s”:"__wt_curfile_open"},{“b”:“55CD80186000”,“o”:“1E4C618”},{“b”:“55CD80186000”,“o”:“1E158FE”,“s”:"__wt_metadata_cursor_open"},{“b”:“55CD80186000”,“o”:“1E159EB”,“s”:"__wt_metadata_cursor"},{“b”:“55CD80186000”,“o”:“1DC7E6A”,“s”:“wiredtiger_open”},{“b”:“55CD80186000”,“o”:“10FC685”,“s”:"_ZN5mongo18WiredTigerKVEngineC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_PNS_11ClockSourceES8_mbbbb"},{“b”:“55CD80186000”,“o”:“10F49CA”},{“b”:“55CD80186000”,“o”:“FDA50A”,“s”:"_ZN5mongo20ServiceContextMongoD29initializeGlobalStorageEngineEv"},{“b”:“55CD80186000”,“o”:“64BBAB”,“s”:“main”},{“b”:“2B680E9C6000”,“o”:“21C05”,“s”:"__libc_start_main"},{“b”:“55CD80186000”,“o”:“6AFCFF”}],“processInfo”:{ “mongodbVersion” : “3.4.10-4-g67ee356c6b”, “gitVersion” : “67ee356c6be377cda547d16423daef5beb4e8377”, “compiledModules” : [], “uname” : { “sysname” : “Linux”, “release” : “3.10.0-957.27.2.el7.x86_64”, “version” : “#1 SMP Mon Jul 29 17:46:05 UTC 2019”, “machine” : “x86_64” }, “somap” : [ { “b” : “55CD80186000”, “elfType” : 3, “buildId” : “A14732EAAA95508462633A5030B501E08B1B106F” }, { “b” : “7FFC34CA6000”, “elfType” : 3, “buildId” : “88212B24946DE81A7B05A4F4422F5A8B37CBD908” }, { “b” : “2B680D64B000”, “path” : “/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/lib/libpython2.7.so.1.0”, “elfType” : 3 }, { “b” : “2B680D84D000”, “path” : “/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/bin/…/lib/libssl.so.1.0.0”, “elfType” : 3 }, { “b” : “2B680DAC3000”, “path” : “/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/bin/…/lib/libcrypto.so.1.0.0”, “elfType” : 3 }, { “b” : “2B680DF28000”, “path” : “/lib64/librt.so.1”, “elfType” : 3, “buildId” : “6D322588B36D2617C03C0F3B93677E62FCFFDA81” }, { “b” : “2B680E130000”, “path” : “/lib64/libdl.so.2”, “elfType” : 3, “buildId” : “1E42EBFB272D37B726F457D6FE3C33D2B094BB69” }, { “b” : “2B680E334000”, “path” : “/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/bin/…/lib/libstdc++.so.6”, “elfType” : 3 }, { “b” : “2B680E4A8000”, “path” : “/lib64/libm.so.6”, “elfType” : 3, “buildId” : “808BD35686C193F218A5AAAC6194C49214CFF379” }, { “b” : “2B680D82E000”, “path” : “/home/binshtem/software/cryosparc/cryosparc2_master/deps/anaconda/bin/…/lib/libgcc_s.so.1”, “elfType” : 3 }, { “b” : “2B680E7AA000”, “path” : “/lib64/libpthread.so.0”, “elfType” : 3, “buildId” : “A48D21B2578A8381FBD8857802EAA660504248DC” }, { “b” : “2B680E9C6000”, “path” : “/lib64/libc.so.6”, “elfType” : 3, “buildId” : “95FF02A4BEBABC573C7827A66D447F7BABDDAA44” }, { “b” : “2B680ED89000”, “path” : “/lib64/libutil.so.1”, “elfType” : 3, “buildId” : “C1CAEB92FAB92F5D9AFBA13867535EFD4BB55055” }, { “b” : “2B680D629000”, “path” : “/lib64/ld-linux-x86-64.so.2”, “elfType” : 3, “buildId” : “22FA66DA7D14C88BF36C69454A357E5F1DEFAE4E” } ] }}
mongod(_ZN5mongo15printStackTraceERSo+0x3B) [0x55cd815a6d6b]
mongod(+0x141FFE6) [0x55cd815a5fe6]
mongod(+0x14204C3) [0x55cd815a64c3]
libpthread.so.0(+0xF5E0) [0x2b680e7b95e0]
libc.so.6(gsignal+0x37) [0x2b680e9fb1f7]
libc.so.6(abort+0x148) [0x2b680e9fc8e8]
mongod(_ZN5mongo32fassertFailedNoTraceWithLocationEiPKcj+0x0) [0x55cd807c5887]
mongod(+0x1117597) [0x55cd8129d597]
mongod(__wt_eventv+0x3E4) [0x55cd807cfe75]
mongod(__wt_err+0xA0) [0x55cd807d008c]
mongod(__wt_panic+0x2F) [0x55cd807d02f5]
mongod(__wt_turtle_read+0x227) [0x55cd81f9d9d7]
mongod(__wt_metadata_search+0x99) [0x55cd81f9c1d9]
mongod(__wt_conn_btree_open+0x73) [0x55cd81f51893]
mongod(__wt_session_get_btree+0xE4) [0x55cd81fdc974]
mongod(__wt_session_get_btree+0x68F) [0x55cd81fdcf1f]
mongod(__wt_session_get_btree_ckpt+0x14C) [0x55cd81fdd1cc]
mongod(__wt_curfile_open+0x169) [0x55cd81f5f8a9]
mongod(+0x1E4C618) [0x55cd81fd2618]
mongod(__wt_metadata_cursor_open+0x6E) [0x55cd81f9b8fe]
mongod(__wt_metadata_cursor+0x4B) [0x55cd81f9b9eb]
mongod(wiredtiger_open+0x183A) [0x55cd81f4de6a]
mongod(_ZN5mongo18WiredTigerKVEngineC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_PNS_11ClockSourceES8_mbbbb+0x815) [0x55cd81282685]
mongod(+0x10F49CA) [0x55cd8127a9ca]
mongod(_ZN5mongo20ServiceContextMongoD29initializeGlobalStorageEngineEv+0x69A) [0x55cd8116050a]
mongod(main+0xE9B) [0x55cd807d1bab]
libc.so.6(__libc_start_main+0xF5) [0x2b680e9e7c05]
mongod(+0x6AFCFF) [0x55cd80835cff]
----- END BACKTRACE -----
Aborted (core dumped)
I’ll try the plan B.

Thanks,

In the end I went to plan B and re-install a new cryosparc and import the project and now all working.

Thanks for the help.

I ran into a similar problem, but ended up restoring a backup from a few weeks ago. The database is now missing a few jobs from one of my projects, but all of the job directories are still in tact. I tried importing the project but got the following error

Unable to import project: exported project directory /[…]/P9 is already being used by P9

If I try importing just the jobs it gives this error:

Import Job Error in P9: Job is not located inside project directory. Please move the job folder into /[…]/P9/imports

Any suggestions for how to restore this project?

Thanks

Hi @Ablakely,

First, I’d suggest making a copy of the project you want to re-import into cryoSPARC. Move this copy to a different location. Then, use that directory to import your project again. You shouldn’t see the error message about the project directory path being used by another project, and it should import as a new project at that point.