mshahriarinia / neondsr Goto Github PK
View Code? Open in Web Editor NEWBig data analytics on dataset on hyperspectral images.
License: Apache License 2.0
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SciDB Startall Stopall Fail
After restarting my machine. When trying to start SciDB I get:
scidb@dsr01:~$ scidb.py startall SingleInstance
checking (server 0 (localhost) local instance 0) Welcome scidb to dsr01. Mon, 14 Oct 2013 - 17:52 PM
EDT Operating system: CentOS release 6.4 (Final) eth0 IP address: 128.227.170.232 Free memory: 43.3
140% Disk usage: /dev/mapper/vg_dsr01-lv_root 46% /dev/sda1 21% /dev/mapper/vg_dsr01-lv_home 9% ...
Found 13 scidb processes
SciDB is still running. Try the stopall command before starting.
When trying to stop them:
scidb@dsr01:~$ scidb.py stopall SingleInstance [23/168]
stop(server 0 (localhost) local instance 0)
checking (server 0 (localhost) local instance 0) Welcome scidb to dsr01. Mon, 14 Oct 2013 - 17:52 PM
EDT Operating system: CentOS release 6.4 (Final) eth0 IP address: 128.227.170.232 Free memory: 43.2
871% Disk usage: /dev/mapper/vg_dsr01-lv_root 46% /dev/sda1 21% /dev/mapper/vg_dsr01-lv_home 9% ...
Found 13 scidb processes
checking (server 0 (localhost) local instance 0) Welcome scidb to dsr01. Mon, 14 Oct 2013 - 17:52 PM
EDT Operating system: CentOS release 6.4 (Final) eth0 IP address: 128.227.170.232 Free memory: 43.2
897% Disk usage: /dev/mapper/vg_dsr01-lv_root 46% /dev/sda1 21% /dev/mapper/vg_dsr01-lv_home 9% ...
Found 13 scidb processes
checking (server 0 (localhost) local instance 0) Welcome scidb to dsr01. Mon, 14 Oct 2013 - 17:52 PM
EDT Operating system: CentOS release 6.4 (Final) eth0 IP address: 128.227.170.232 Free memory: 43.2
790% Disk usage: /dev/mapper/vg_dsr01-lv_root 46% /dev/sda1 21% /dev/mapper/vg_dsr01-lv_home 9% ...
Found 13 scidb processes
checking (server 0 (localhost) local instance 0) Welcome scidb to dsr01. Mon, 14 Oct 2013 - 17:52 PM
EDT Operating system: CentOS release 6.4 (Final) eth0 IP address: 128.227.170.232 Free memory: 43.2
790% Disk usage: /dev/mapper/vg_dsr01-lv_root 46% /dev/sda1 21% /dev/mapper/vg_dsr01-lv_home 9% ...
Found 13 scidb processes
checking (server 0 (localhost) local instance 0) Welcome scidb to dsr01. Mon, 14 Oct 2013 - 17:52 PM
EDT Operating system: CentOS release 6.4 (Final) eth0 IP address: 128.227.170.232 Free memory: 43.2
735% Disk usage: /dev/mapper/vg_dsr01-lv_root 46% /dev/sda1 21% /dev/mapper/vg_dsr01-lv_home 9% ...
Found 13 scidb processes
checking (server 0 (localhost) local instance 0) Welcome scidb to dsr01. Mon, 14 Oct 2013 - 17:52 PM
EDT Operating system: CentOS release 6.4 (Final) eth0 IP address: 128.227.170.232 Free memory: 43.2
690% Disk usage: /dev/mapper/vg_dsr01-lv_root 46% /dev/sda1 21% /dev/mapper/vg_dsr01-lv_home 9% ...
Found 13 scidb processes
checking (server 0 (localhost) local instance 0) Welcome scidb to dsr01. Mon, 14 Oct 2013 - 17:52 PM
EDT Operating system: CentOS release 6.4 (Final) eth0 IP address: 128.227.170.232 Free memory: 43.2
627% Disk usage: /dev/mapper/vg_dsr01-lv_root 46% /dev/sda1 21% /dev/mapper/vg_dsr01-lv_home 9% ...
Found 13 scidb processes
checking (server 0 (localhost) local instance 0) Welcome scidb to dsr01. Mon, 14 Oct 2013 - 17:52 PM
EDT Operating system: CentOS release 6.4 (Final) eth0 IP address: 128.227.170.232 Free memory: 43.2
770% Disk usage: /dev/mapper/vg_dsr01-lv_root 46% /dev/sda1 21% /dev/mapper/vg_dsr01-lv_home 9% ...
Found 13 scidb processes
checking (server 0 (localhost) local instance 0) Welcome scidb to dsr01. Mon, 14 Oct 2013 - 17:52 PM
EDT Operating system: CentOS release 6.4 (Final) eth0 IP address: 128.227.170.232 Free memory: 43.3
015% Disk usage: /dev/mapper/vg_dsr01-lv_root 46% /dev/sda1 21% /dev/mapper/vg_dsr01-lv_home 9% ...
Found 13 scidb processes
checking (server 0 (localhost) local instance 0) Welcome scidb to dsr01. Mon, 14 Oct 2013 - 17:52 PM
EDT Operating system: CentOS release 6.4 (Final) eth0 IP address: 128.227.170.232 Free memory: 43.2
957% Disk usage: /dev/mapper/vg_dsr01-lv_root 46% /dev/sda1 21% /dev/mapper/vg_dsr01-lv_home 9% ...
Found 13 scidb processes
checking (server 0 (localhost) local instance 0) Welcome scidb to dsr01. Mon, 14 Oct 2013 - 17:52 PM
EDT Operating system: CentOS release 6.4 (Final) eth0 IP address: 128.227.170.232 Free memory: 43.2
966% Disk usage: /dev/mapper/vg_dsr01-lv_root 46% /dev/sda1 21% /dev/mapper/vg_dsr01-lv_home 9% ...
Found 13 scidb processes
Failed to stop SciDB!
Check processes:
scidb@dsr01:~$ scidb.py check-pids SingleInstance
checking (server 0 (localhost) local instance 0) Welcome scidb to dsr01. Mon, 14 Oct 2013 - 17:55 PM
EDT Operating system: CentOS release 6.4 (Final) eth0 IP address: 128.227.170.232 Free memory: 43.0
446% Disk usage: /dev/mapper/vg_dsr01-lv_root 46% /dev/sda1 21% /dev/mapper/vg_dsr01-lv_home 9% ...
Found 13 scidb processes
SciDB Memory Error Halt
SciDB halts after a memory error and does not release memory.
Total memory: 2696164B Used: 2603516B, free: 92648B. Only 600 is used by non-SciDB softwares.
2013-10-19 18:45:39,429 [0x7fc3225ec700] [INFO ]: Executing query(1102219090553): redimension_store(hsi_img_flat, hsi_img); from program: 127.0.0.1:56429/opt/scidb/13.6/bin/iquery -a ;
2013-10-19 18:45:39,430 [0x7fc3225ec700] [DEBUG]: Request shared lock of array hsi_img_flat@1 for query 1102219090553
2013-10-19 18:45:39,430 [0x7fc3225ec700] [DEBUG]: Granted shared lock of array hsi_img_flat@1 for query 1102219090553
2013-10-19 18:45:39,454 [0x7fc3225ec700] [DEBUG]: Request exclusive lock of array hsi_img for query 1102219090553
2013-10-19 18:45:39,454 [0x7fc3225ec700] [DEBUG]: Granted exclusive lock of array hsi_img for query 1102219090553
2013-10-19 18:45:39,473 [0x7fc3225ec700] [DEBUG]: Request shared lock of array hsi_img@1 for query 1102219090553
2013-10-19 18:45:39,473 [0x7fc3225ec700] [DEBUG]: Granted shared lock of array hsi_img@1 for query 1102219090553
2013-10-19 18:45:39,487 [0x7fc3225ec700] [DEBUG]: [RedimStore] Begins.
2013-10-19 18:48:11,688 [0x7fc3225ec700] [DEBUG]: Create array NID_213@1:x(223) in query 1102219090553
2013-10-19 18:48:11,690 [0x7fc3225ec700] [DEBUG]: Request shared lock of array NID_213@1:x for query 1102219090553
2013-10-19 18:48:11,690 [0x7fc3225ec700] [DEBUG]: Granted shared lock of array NID_213@1:x for query 1102219090553
2013-10-19 18:49:58,725 [0x7fc3225ec700] [DEBUG]: Create array NID_213@1:y(224) in query 1102219090553
2013-10-19 18:49:58,726 [0x7fc3225ec700] [DEBUG]: Request shared lock of array NID_213@1:y for query 1102219090553
2013-10-19 18:49:58,726 [0x7fc3225ec700] [DEBUG]: Granted shared lock of array NID_213@1:y for query 1102219090553
2013-10-19 18:49:58,752 [0x7fc3225ec700] [DEBUG]: [RedimStore] build mapping index took 259264 ms, or 4 minutes 19 seconds 264 milliseconds
2013-10-19 19:10:03,048 [0x7fc3225ec700] [DEBUG]: [RedimStore] inputArray --> RowCollection took 1204062 ms, or 20 minutes 4 seconds 62 milliseconds
2013-10-19 19:10:40,538 [0x7fc3225ec700] [DEBUG]: Query::done: queryID=1102219090553, _commitState=0, erorCode=67
2013-10-19 19:10:40,564 [0x7fc3225ec700] [ERROR]: executeClientQuery failed to complete: SystemException in file: src/query/executor/SciDBExecutor.cpp function: executeQuery line: 233
Error id: scidb::SCIDB_SE_NO_MEMORY::SCIDB_LE_MEMORY_ALLOCATION_ERROR
Error description: Not enough memory. Error 'std::bad_alloc' during memory allocation.
Failed query id: 1102219090553
2013-10-19 19:10:40,610 [0x7fc3225ec700] [DEBUG]: Query (1102219090553) is being aborted
2013-10-19 19:10:40,610 [0x7fc3225ec700] [ERROR]: Query (1102219090553) error handlers (2) are being executed
2013-10-19 19:10:40,610 [0x7fc3225ec700] [DEBUG]: Update error handler is invoked for query (1102219090553)
2013-10-19 19:10:41,379 [0x7fc3224eb700] [DEBUG]: Query (1102219090553) is being aborted
2013-10-19 19:10:41,379 [0x7fc3224eb700] [DEBUG]: Deallocating query (1102219090553)
2013-10-19 19:10:41,493 [0x7fc3225ec700] [DEBUG]: UpdateErrorHandler::handleErrorOnCoordinator: the new version 1 of array hsi_img is being rolled back for query (1102219090553)
2013-10-19 19:10:41,502 [0x7fc3225ec700] [DEBUG]: Performing rollback
2013-10-19 19:10:41,565 [0x7fc3225ec700] [DEBUG]: End of log at position 224 rc=112
2013-10-19 19:10:41,565 [0x7fc3225ec700] [DEBUG]: End of log at position 0 rc=0
2013-10-19 19:10:41,691 [0x7fc3225ec700] [DEBUG]: Rollback complete
2013-10-19 19:10:42,320 [0x7fc3225ec700] [DEBUG]: Broadcast ABORT message to all instances for query 1102219090553
2013-10-19 19:10:42,320 [0x7fc3225ec700] [DEBUG]: Releasing locks for query 1102219090553
2013-10-19 19:10:42,320 [0x7fc3225ec700] [DEBUG]: SystemCatalog::deleteArrayLocks instanceId = 0 queryId = 1102219090553
2013-10-19 19:10:42,422 [0x7fc3225ec700] [DEBUG]: Release lock of array NID_213@1:x for query 1102219090553
2013-10-19 19:10:42,432 [0x7fc3225ec700] [DEBUG]: Release lock of array NID_213@1:y for query 1102219090553
2013-10-19 19:10:42,433 [0x7fc3225ec700] [DEBUG]: Release lock of array hsi_img for query 1102219090553
2013-10-19 19:10:42,433 [0x7fc3225ec700] [DEBUG]: Release lock of array hsi_img@1 for query 1102219090553
2013-10-19 19:10:42,433 [0x7fc3225ec700] [DEBUG]: Release lock of array hsi_img_flat@1 for query 1102219090553
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