Error database or disk is full

sqlite3.OperationalError: database or disk is full while over 150 GB free on the drive #16

Hi, I’ve encountered another error — megalodon complained about lack of space on the disk, however there is over 150 GB free on my SSD.
I’ve noticed at times (especially toward the end of the run) megalodon uses way over 40-50GB of RAM, although most of the time it’s fine with just 3GB of RAM. Could that be an issue? Are you creating any databases in memory?

I’ve noticed some indices are created in memory:
./megalodon/mods.py:87: mod_index_in_memory=True, uuid_index_in_memory=True):

Could that be the problem?
This seems to be done toward the end of the run and some of my few days runs crashed toward the end and unfortunately nothing was stored in the per_read_modified_base_calls.db .

I guess this is related to megalodon/megalodon_helper.py — maybe do that a parameters specified by the user? 64GB for mapping in-memory sqlite3 db is crazy amount of RAM. Also another question, this is 64GB per process or overall?

Full stack below.

The text was updated successfully, but these errors were encountered:

For the first set of questions concerning in-memory databases and RAM usage. The databases held in memory are not actually stored in sqlite, but simple python dictionaries. Sqlite does not enable holding specific tables in memory, so this is a bit of a hack around this. This is necessary as other wise a sqlite index must be maintained on these databases during writing and this gets very expensive for even reasonably small runs. Looking at the code, the read_ids dictionary probably could be removed, but this is almost certainly not causing the RAM spike you are seeing as these are filled continuously throughout a run.

For the question regarding the memory mapped limit, this actually has to do with memory mapping (linking memory slots directly to the processor for faster access). This should not increase the RAM by this amount, but instead sets the size of the database to map in this fashion. For more details concerning memory mapping in sqlite see this help page.

Finally to what I believe is the core issue here. This error is coming after the message that the mods database index is being created. This database essentially copies the largest table from the database, but sorted by the reference position for access at aggregation time. Without this index the aggregation step would take much longer. Thus what I believe is happening is that the entire size of this index is likely requested at one time and this may in fact be larger than the 150 GB available on this storage device. This indexing step is also quite likely why the RAM is spiking as there should not be any large memory consumption within the megalodon internals at this stage of processing.

It is odd that the per-read mods database does not contain any data though. With the default settings, the database should retain all inserted data with an application failure. Have you set the —database-safety 0 flag by any chance? With the default setting even with this type of failure the results should be stored and a post-processing step could be made to add the index once the data were moved to a location with more storage.

Источник

Knowledge Base

41151: Acronis Backup Advanced 11.5: Exchange Backup Fails with Error “a SQLite Library Error: ‘Database or Disk Is Full’”

use Google Translate

Applies to:

Operating Systems:

Last update: 13-07-2017

You need to free up additional disk space or change location of temporary files

Symptoms

• You are backing up Microsoft Exchange Information Store to a centralized managed vault;
• The backup fails with the following error:

A SQLite library error: ‘database or disk is full’.

See the full sample message:

Error:
———————
Log Entry Details
———————
Type: Error
Date and time: 4/4/2013 12:23:50 PM
Backup plan: NEW Exch Data Store backup
Task: Transaction log backup
Managed entity type: Exchange server
Managed entity: MAIL
Machine: mail.johnsonpipe.com
Code: 20,250,685(0x135003D)
Module: 309
Owner:
Message:
Command ‘Backing up’ has failed.
Additional info:
———————
Error code: 61
Module: 309
LineInfo: 4a8728dc8a1c950f
Fields: $module : service_process_vs_32308
Message: Command ‘Backing up’ has failed.
———————
Error code: 1602
Module: 91
LineInfo: 9d08bc3c61bce3c9
Fields: IsReturnCode : 1, $module : arx_agent_fork_vs_32308
Message: A generic error of Microsoft Exchange Backuper.
———————
Error code: 17
Module: 91
LineInfo: 7edade4ed07d5271
Fields: IsReturnCode : 1, $module : arx_agent_fork_vs_32308
Message: Failed to back up the information store.
———————
Error code: 284
Module: 91
LineInfo: 3b69d552573c3a21
Fields: $module : arx_agent_fork_vs_32308
Message: Nothing is backed up. See the log for details. Last error:
———————
Error code: 4
Module: 355
LineInfo: a72228d344bcc5a9
Fields: $module : arx_asn_vsa64_32308
Message: Volume ‘C:’ on which metadata is temporarily stored is full.
———————
Error code: 1
Module: 351
LineInfo: 2041f19daa895a44
Fields: code : 13, extended_code : 13, $module : arx_asn_vsa64_32308
Message: A SQLite library error: ‘database or disk is full’.
———————
Acronis Knowledge Base: http://kb.acronis.com/errorcode/
Event code: 0x0135003D+0x005B0642+0x005B0011+0x005B011C+0x01630004+0x015F0001+0x0000000D

Cause

By default, during an operation, Acronis Agent for Exchange will save its temporary files to the ProgramDataAcronisTemp folder.

You may want to change this if the capacity of the disk with the ProgramData folder is an issue.

If the Acronis Storage Node is low on space in primary partition then the backup will fail with the error.

Solution

You can fix this issue with one of the following steps:

1. Free the disk space on the system partition of the Acronis Storage Node machine. If this is not possible, proceed with the next step.
2. Change location of temporary files of the Acronis Storage Node machine. See Acronis Backup Advanced 11.5 for Exchange: Changing Temp Files and Folder Location.

Источник

db failure: database or disk is full:stoppped #6

Hello my friend.
I use this image as a server for the Dude. Today I encountered such a problem while trying connect to server.
I freed up a couple megabytes of space on routeros but still can’t connect to the dude. How can fix it? May be is it possible to create a volume for a specific folder, or what may be the options?

The text was updated successfully, but these errors were encountered:

As you probably know the RouterOS is not support dockerization process, so i’ve used VDI image in combination with qemu virtual machine.

That mean if you see «not enough space» error then space is ended inside VDI image.

I can suggest to look at this article and resize the VDI of your RouterOS.

Another idea is to make automatic resizing of the disk at the time of assembly of the docker container.

Yet another article which may be helpful:

You can mount —bind any folder from your root system inside docker container, but for this will need update entrypoint.sh scripts with required parameters.

Thank you for your suggest. I will try this articles.

This topic about sharing host filesystem in qemu

I think better way is

1. create docker-compose with volume which is some folder on your host machine and mountpoint inside container is some folder like /share
2. update entrypont.sh, need to add binding from /share of container to somewhere in virtual machine (i guess it should be folder with the dude database files, you can login to RouteOS in debug mode as root and check file system tree)
3. restart composition with new settings

For right now i don’t know how exactly (only in general) make this but hope you can find the answer and explain to me 🙂

Just got to the case. So i added vdi file to vmware, expand disk to the required size, convert to vdi from vhdx and add it into the volume. Restarted container and that is all.
Thanks for the help)

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«Database or disk is full» Error #122

I occasionally get this exception:

My disk is definitely not full and my headphones.db file is just 1600k in size. this happens completely at random while adding or updating artists. When this exception occurs, scanning stops and I have to start all over again.

I’m using Windows 7 32 bit and python 2.6

28-Jul-2011 12:20:37 — INFO :: MainThread : Checking to see if the database has all tables.
28-Jul-2011 12:20:38 — INFO :: MainThread : Headphones is already up-to-date.
28-Jul-2011 12:20:39 — INFO :: MainThread : Starting Headphones on port: 8181
28-Jul-2011 12:21:02 — INFO :: Thread-12 : Now adding/updating: David Bowie
28-Jul-2011 12:21:11 — INFO :: Thread-12 : Now adding/updating album: David Bowie
28-Jul-2011 12:21:35 — INFO :: Thread-12 : Now adding/updating album: Space Oddity
28-Jul-2011 12:21:35 — WARNING :: Thread-12 : Database Error: unable to open database file
28-Jul-2011 12:21:56 — INFO :: Thread-12 : Now adding/updating album: The Man Who Sold the World
28-Jul-2011 12:22:19 — INFO :: Thread-12 : Now adding/updating album: Hunky Dory
28-Jul-2011 12:22:56 — INFO :: Thread-12 : Now adding/updating album: The Rise and Fall of Ziggy Stardust and the Spiders From Mars
28-Jul-2011 12:23:14 — INFO :: Thread-12 : Now adding/updating album: Aladdin Sane
28-Jul-2011 12:23:31 — INFO :: Thread-12 : Now adding/updating album: Pin Ups
28-Jul-2011 12:23:31 — WARNING :: Thread-12 : Database Error: unable to open database file
28-Jul-2011 12:23:32 — WARNING :: Thread-12 : Database Error: unable to open database file
28-Jul-2011 12:23:33 — WARNING :: Thread-12 : Database Error: unable to open database file
28-Jul-2011 12:23:57 — INFO :: Thread-12 : Now adding/updating album: Diamond Dogs
28-Jul-2011 12:24:12 — INFO :: Thread-12 : Now adding/updating album: Young Americans
28-Jul-2011 12:24:13 — ERROR :: Thread-12 : Database error: database or disk is full

The text was updated successfully, but these errors were encountered:

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Error database or disk is full

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I can not connect to the firewall 1400, in the logs error: «SQL error: database or disk is full»

How do I clean it?

Is there any description of the checkpoint’s file system, what is stored, what files are system, which ones can be deleted, etc.

[Expert@CPGW]# df -h
Filesystem Size Used Available Use% Mounted on
tmpfs 20.0M 1.1M 18.9M 5% /tmp
tmpfs 40.0M 40.0M 0 100% /fwtmp
ubi2_0 65.6M 1.1M 61.1M 2% /logs
ubi3_0 259.8M 149.9M 105.2M 59% /storage
ubi0_0 159.4M 105.0M 54.4M 66% /pfrm2.0
tmpfs 14.0M 0 14.0M 0% /tmp/log/local

[Expert@CPGW]# du -h /fwtmp/ | sort -n -r
776.0k /fwtmp/writers
88.0k /fwtmp/resources
52.0k /fwtmp/opt/CPInstLog
29.4M /fwtmp
26.9M /fwtmp/opt
26.8M /fwtmp/opt/fw1
25.2M /fwtmp/opt/fw1/cpeps
16.0k /fwtmp/opt/fw1/CPlogos
8.0k /fwtmp/opt/fw1/tmp/SessionCache_1
8.0k /fwtmp/opt/fw1/monitoring
8.0k /fwtmp/UserCheckLogs
8.0k /fwtmp/HotspotLogs
4.0k /fwtmp/opt/fw1/state
1.6M /fwtmp/opt/fw1/tmp
0 /fwtmp/opt/fw1/tmp/email_tmp/updates
0 /fwtmp/opt/fw1/tmp/email_tmp/aspam_sfw
0 /fwtmp/opt/fw1/tmp/email_tmp/aspam_engine
0 /fwtmp/opt/fw1/tmp/email_tmp
0 /fwtmp/opt/fw1/policies
0 /fwtmp/opt/fw1/monitoring/cpwd_monitor/new
0 /fwtmp/opt/fw1/monitoring/cpwd_monitor/monitor
0 /fwtmp/opt/fw1/monitoring/cpwd_monitor/finish
0 /fwtmp/opt/fw1/monitoring/cpwd_monitor
0 /fwtmp/opt/fw1/global_mutexes
0 /fwtmp/cprid
0 /fwtmp/UserCheckSession
0 /fwtmp/NACSession
0 /fwtmp/NACLogs
0 /fwtmp/HotspotSession

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Hello there,

A few weeks ago my hard drive was full and got an error from Dropbox. However there is more than enough space now but the app is still returning the same error every time, it says it can’t start. I’m using Ubuntu 16.04. Here’s the info on the text file generated:

bn.BUILD_KEY: Dropbox
bn.VERSION: 109.4.517
bn.constants.WINDOWS_SHELL_EXT_VERSION: 46
bn.is_frozen: True
machine_id: 6adf1293-ca20-4cbd-b61b-b2e21f7e0380
pid: 4125
ppid: 1845
ppid exe: ‘/sbin/upstart’
uid: 1000
user_info: pwd.struct_passwd(pw_name=’gorremu’, pw_passwd=’x’, pw_uid=1000, pw_gid=1000, pw_gecos=’gorremu,,,’, pw_dir=’/home/gorremu’, pw_shell=’/bin/bash’)
effective_user_info: pwd.struct_passwd(pw_name=’gorremu’, pw_passwd=’x’, pw_uid=1000, pw_gid=1000, pw_gecos=’gorremu,,,’, pw_dir=’/home/gorremu’, pw_shell=’/bin/bash’)
euid: 1000
gid: 1000
egid: 1000
group_info: grp.struct_group(gr_name=’gorremu’, gr_passwd=’x’, gr_gid=1000, gr_mem=[])
effective_group_info: grp.struct_group(gr_name=’gorremu’, gr_passwd=’x’, gr_gid=1000, gr_mem=[])
LD_LIBRARY_PATH: None
cwd: ‘/home/gorremu’
real_path=’/home/gorremu’
mode=0o40755 uid=1000 gid=1000
parent mode=0o40755 uid=0 gid=0
HOME: ‘/home/gorremu’
appdata: ‘/home/gorremu/.dropbox/instance1’
real_path=’/home/gorremu/.dropbox/instance1′
mode=0o40700 uid=1000 gid=1000
parent mode=0o40700 uid=1000 gid=1000
dropbox_path: ‘/home/gorremu/Dropbox’
real_path=’/home/gorremu/Dropbox’
mode=0o40700 uid=1000 gid=1000
parent mode=0o40755 uid=1000 gid=1000
sys_executable: ‘/home/gorremu/.dropbox-dist/dropbox-lnx.x86_64-109.4.517/dropbox’
real_path=’/home/gorremu/.dropbox-dist/dropbox-lnx.x86_64-109.4.517/dropbox’
mode=0o100755 uid=1000 gid=1000
parent mode=0o40755 uid=1000 gid=1000
trace.__file__: ‘/home/gorremu/.dropbox-dist/dropbox-lnx.x86_64-109.4.517/python-packages.zip/dropbox/client/ui/common/boot_error.pyc’
real_path=’/home/gorremu/.dropbox-dist/dropbox-lnx.x86_64-109.4.517/python-packages.zip/dropbox/client/ui/common/boot_error.pyc’
not found
parent not found
tempdir: ‘/tmp’
real_path=’/tmp’
mode=0o41777 uid=0 gid=0
parent mode=0o40755 uid=0 gid=0
Traceback (most recent call last):
File «dropbox/sqlite3_helpers.pyc», line 295, in execute
sqlite3.OperationalError: database or disk is full

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File «dropbox/client/main.pyc», line 7731, in main_startup
File «dropbox/client/main.pyc», line 3138, in run
File «dropbox/client/configuration/local_configuration.pyc», line 207, in load_config
File «dropbox/client/config.pyc», line 85, in __getitem__
File «dropbox/sqlite3_helpers.pyc», line 300, in execute
File «dropbox/sqlite3_helpers.pyc», line 266, in _raise_better_operational_exception
File «six.pyc», line 695, in reraise
File «dropbox/sqlite3_helpers.pyc», line 295, in execute
dropbox.sqlite3_exceptions.DatabaseOrDiskFullError

Any help would be greatly appreciated.