Posts Tagged ‘filesystem’

What is inode and how to find out which directory is eating up all your filesystem inodes on Linux, Increase inode count on a ext3 ext4 and ufs filesystems

Tuesday, August 20th, 2019

what-is-inode-find-out-which-filesystem-or-directory-eating-up-all-your-system-inodes-linux_inode_diagram

If you're a system administrator of multiple Linux servers used for Web serving delivery / Mail server sysadmin, Database admin or any High amount of Drives Data Storage used for backup servers infra, Data Repository administrator such as Linux hosted Samba / CIFS shares, etc. or using some Linux Hosting Provider to host your website or any other UNIX like Infrastructure servers that demands a storage of high number of files under a Directory  you might end up with the common filesystem inode depletion issues ( Maximum Inode number for a filesystem is predefined, limited and depending on the filesystem configured size).

In case a directory stored files end up exceding the amount of possible addressable inodes could prevent any data to be further assiged and stored on the Filesystem.

When a device runs out of inodes, new files cannot be created on the device, even though there may be plenty free space available and the first time it happened to me very long time ago I was completely puzzled how this is possible as I was not aware of Inodes existence  …

Reaching maximum inodes number (e.g. inode depletion), often happens on Busy Mail servers (receivng tons of SPAM email messages) or Content Delivery Network (CDN – Website Image caching servers) which contain many small files on EXT3 or EXT4 Journalled filesystems. File systems (such as Btrfs, JFS or XFS) escape this limitation with extents or dynamic inode allocation, which can 'grow' the file system or increase the number of inodes.

 

Hence ending being out of inodes could cause various oddities on how stored data behaves or communicated to other connected microservices and could lead to random application disruptions and odd results costing you many hours of various debugging to find the root cause of inodes (index nodes) being out of order.

In below article, I will try to give an overall explanation on what is an I-Node on a filesystem, how inodes of FS unit could be seen, how to diagnose a possible inode poblem – e.g.  see the maximum amount of inodes available per filesystem and how to prepare (format) a new filesystem with incrsed set of maximum inodes.

 

What are filesystem i-nodes?

 

This is a data structure in a Unix-style file system that describes a file-system object such as a file or a directory.
The data structure described in the inodes might vary slightly depending on the filesystem but usually on EXT3 / EXT4 Linux filesystems each inode stores the index to block that contains attributes and disk block location(s) of the object's data.
– Yes for those who are not aware on how a filesystem is structured on *nix it does allocate all stored data in logical separeted structures called data blocks. Each file stored on a local filesystem has a file descriptor, there are virtual unit structures file tables and each of the inodes that are a reference number has a own data structure (inode table).

Inodes / "Index" are slightly unusual on file system structure that stored the access information of files as a flat array on the disk, with all the hierarchical directory information living aside from this as explained by Unix creator and pioneer- Dennis Ritchie (passed away few years ago).

what-is-inode-very-simplified-explanation-diagram-data

Simplified explanation on file descriptors, file table and inode, table on a common Linux filesystem

Here is another description on what is I-node, given by Ken Thompson (another Unix pioneer and father of Unix) and Denis Ritchie, described in their paper published in 1978:

"    As mentioned in Section 3.2 above, a directory entry contains only a name for the associated file and a pointer to the file itself. This pointer is an integer called the i-number (for index number) of the file. When the file is accessed, its i-number is used as an index into a system table (the i-list) stored in a known part of the device on which the directory resides. The entry found thereby (the file's i-node) contains the description of the file:…
    — The UNIX Time-Sharing System, The Bell System Technical Journal, 1978  "


 

What is typical content of inode and how I-nodes play with rest of Filesystem units?


The inode is just a reference index to a data block (unit) that contains File-system object attributes. It may include metadata information such as (times of last change, access, modification), as well as owner and permission data.

 

On a Linux / Unix filesystem, directories are lists of names assigned to inodes. A directory contains an entry for itself, its parent, and each of its children.

Structure-of-inode-table-on-Linux-Filesystem-diagram

 

Structure of inode table-on Linux Filesystem diagram (picture source GeeksForGeeks.org)

  • Information about files(data) are sometimes called metadata. So you can even say it in another way, "An inode is metadata of the data."
  •  Inode : Its a complex data-structure that contains all the necessary information to specify a file. It includes the memory layout of the file on disk, file permissions, access time, number of different links to the file etc.
  •  Global File table : It contains information that is global to the kernel e.g. the byte offset in the file where the user's next read/write will start and the access rights allowed to the opening process.
  • Process file descriptor table : maintained by the kernel, that in turn indexes into a system-wide table of files opened by all processes, called the file table .

The inode number indexes a table of inodes in a known location on the device. From the inode number, the kernel's file system driver can access the inode contents, including the location of the file – thus allowing access to the file.

  •     Inodes do not contain its hardlink names, only other file metadata.
  •     Unix directories are lists of association structures, each of which contains one filename and one inode number.
  •     The file system driver must search a directory looking for a particular filename and then convert the filename to the correct corresponding inode number.

The operating system kernel's in-memory representation of this data is called struct inode in Linux. Systems derived from BSD use the term vnode, with the v of vnode referring to the kernel's virtual file system layer.


But enough technical specifics, lets get into some practical experience on managing Filesystem inodes.
 

Listing inodes on a Fileystem


Lets say we wan to to list an inode number reference ID for the Linux kernel (files):

 

root@linux: # ls -i /boot/vmlinuz-*
 3055760 /boot/vmlinuz-3.2.0-4-amd64   26091901 /boot/vmlinuz-4.9.0-7-amd64
 3055719 /boot/vmlinuz-4.19.0-5-amd64  26095807 /boot/vmlinuz-4.9.0-8-amd64


To list an inode of all files in the kernel specific boot directory /boot:

 

root@linux: # ls -id /boot/
26091521 /boot/


Listing inodes for all files stored in a directory is also done by adding the -i ls command flag:

Note the the '-1' flag was added to to show files in 1 column without info for ownership permissions

 

root@linux:/# ls -1i /boot/
26091782 config-3.2.0-4-amd64
 3055716 config-4.19.0-5-amd64
26091900 config-4.9.0-7-amd64
26095806 config-4.9.0-8-amd64
26091525 grub/
 3055848 initrd.img-3.2.0-4-amd64
 3055644 initrd.img-4.19.0-5-amd64
26091902 initrd.img-4.9.0-7-amd64
 3055657 initrd.img-4.9.0-8-amd64
26091756 System.map-3.2.0-4-amd64
 3055703 System.map-4.19.0-5-amd64
26091899 System.map-4.9.0-7-amd64
26095805 System.map-4.9.0-8-amd64
 3055760 vmlinuz-3.2.0-4-amd64
 3055719 vmlinuz-4.19.0-5-amd64
26091901 vmlinuz-4.9.0-7-amd64
26095807 vmlinuz-4.9.0-8-amd64

 

To get more information about Linux directory, file, such as blocks used by file-unit, Last Access, Modify and Change times, current External Symbolic or Static links for filesystem object:
 

root@linux:/ # stat /etc/
  File: /etc/
  Size: 16384         Blocks: 32         IO Block: 4096   catalog
Device: 801h/2049d    Inode: 6365185     Links: 231
Access: (0755/drwxr-xr-x)  Uid: (    0/    root)   Gid: (    0/    root)
Access: 2019-08-20 06:29:39.946498435 +0300
Modify: 2019-08-14 13:53:51.382564330 +0300
Change: 2019-08-14 13:53:51.382564330 +0300
 Birth: –

 

Within a POSIX system (Linux-es) and *BSD are more or less such, a file has the following attributes[9] which may be retrieved by the stat system call:

   – Device ID (this identifies the device containing the file; that is, the scope of uniqueness of the serial number).
    File serial numbers.
    – The file mode which determines the file type and how the file's owner, its group, and others can access the file.
    – A link count telling how many hard links point to the inode.
    – The User ID of the file's owner.
    – The Group ID of the file.
    – The device ID of the file if it is a device file.
    – The size of the file in bytes.
    – Timestamps telling when the inode itself was last modified (ctime, inode change time), the file content last modified (mtime, modification time), and last accessed (atime, access time).
    – The preferred I/O block size.
    – The number of blocks allocated to this file.

 

Getting more extensive information on a mounted filesystem


Most Linuxes have the tune2fs installed by default (in debian Linux this is through e2fsprogs) package, with it one can get a very good indepth information on a mounted filesystem, lets say about the ( / ) root FS.
 

root@linux:~# tune2fs -l /dev/sda1
tune2fs 1.44.5 (15-Dec-2018)
Filesystem volume name:   <none>
Last mounted on:          /
Filesystem UUID:          abe6f5b9-42cb-48b6-ae0a-5dda350bc322
Filesystem magic number:  0xEF53
Filesystem revision #:    1 (dynamic)
Filesystem features:      has_journal ext_attr resize_inode dir_index filetype needs_recovery sparse_super large_file
Filesystem flags:         signed_directory_hash
Default mount options:    (none)
Filesystem state:         clean
Errors behavior:          Continue
Filesystem OS type:       Linux
Inode count:              30162944
Block count:              120648960
Reserved block count:     6032448
Free blocks:              13830683
Free inodes:              26575654
First block:              0
Block size:               4096
Fragment size:            4096
Reserved GDT blocks:      995
Blocks per group:         32768
Fragments per group:      32768
Inodes per group:         8192
Inode blocks per group:   512
Filesystem created:       Thu Sep  6 21:44:22 2012
Last mount time:          Sat Jul 20 11:33:38 2019
Last write time:          Sat Jul 20 11:33:28 2019
Mount count:              6
Maximum mount count:      22
Last checked:             Fri May 10 18:32:27 2019
Check interval:           15552000 (6 months)
Next check after:         Wed Nov  6 17:32:27 2019
Lifetime writes:          338 GB
Reserved blocks uid:      0 (user root)
Reserved blocks gid:      0 (group root)
First inode:              11
Inode size:              256
Required extra isize:     28
Desired extra isize:      28
Journal inode:            8
First orphan inode:       21554129
Default directory hash:   half_md4
Directory Hash Seed:      d54c5a90-bc2d-4e22-8889-568d3fd8d54f
Journal backup:           inode blocks


Important note to make here is file's inode number stays the same when it is moved to another directory on the same device, or when the disk is defragmented which may change its physical location. This also implies that completely conforming inode behavior is impossible to implement with many non-Unix file systems, such as FAT and its descendants, which don't have a way of storing this invariance when both a file's directory entry and its data are moved around. Also one inode could point to a file and a copy of the file or even a file and a symlink could point to the same inode, below is example:

$ ls -l -i /usr/bin/perl*
266327 -rwxr-xr-x 2 root root 10376 Mar 18  2013 /usr/bin/perl
266327 -rwxr-xr-x 2 root root 10376 Mar 18  2013 /usr/bin/perl5.14.2

A good to know is inodes are always unique values, so you can't have the same inode number duplicated. If a directory is damaged, only the names of the things are lost and the inodes become the so called “orphan”, e.g.  inodes without names but luckily this is recoverable. As the theory behind inodes is quite complicated and is complicated to explain here, I warmly recommend you read Ian Dallen's Unix / Linux / Filesystems – directories inodes hardlinks tutorial – which is among the best academic Tutorials explaining various specifics about inodes online.

 

How to Get inodes per mounted filesystem

 

root@linux:/home/hipo# df -i
Filesystem       Inodes  IUsed   IFree IUse% Mounted on

 

dev             2041439     481   2040958   1% /dev
tmpfs            2046359     976   2045383   1% /run
tmpfs            2046359       4   2046355   1% /dev/shm
tmpfs            2046359       6   2046353   1% /run/lock
tmpfs            2046359      17   2046342   1% /sys/fs/cgroup
/dev/sdb5        1221600    2562   1219038   1% /usr/var/lib/mysql
/dev/sdb6        6111232  747460   5363772  13% /var/www/htdocs
/dev/sdc1      122093568 3083005 119010563   3% /mnt/backups
tmpfs            2046359      13   2046346   1% /run/user/1000


As you see in above output Inodes reported for each of mounted filesystems has a specific number. In above output IFree on every mounted FS locally on Physical installed OS Linux is good.


Here is an example on how to recognize a depleted Inodes on a OpenXen Virtual Machine with attached Virtual Hard disks.

linux:~# df -i
Filesystem         Inodes     IUsed      IFree     IUse%   Mounted on
/dev/xvda         2080768    2080768     0      100%    /
tmpfs             92187      3          92184   1%     /lib/init/rw
varrun            92187      38          92149   1%    /var/run
varlock            92187      4          92183   1%    /var/lock
udev              92187     4404        87783   5%    /dev
tmpfs             92187       1         92186   1%    /dev/shm

 

Finding files with a certain inode


At some cases if you want to check all the copy files of a certain file that have the same i-node pointer it is useful to find them all by their shared inode this is possible with simple find (below example is for /usr/bin/perl binary sharing same inode as perl5.28.1:

 

ls -i /usr/bin/perl
23798851 /usr/bin/perl*

 

 find /usr/bin -inum 435308 -print
/usr/bin/perl5.28.1
/usr/bin/perl

 

Find directory that has a large number of files in it?

To get an overall number of inodes allocated by a certain directory, lets say /usr /var

 

root@linux:/var# du -s –inodes /usr /var
566931    /usr
56020    /var/

To get a list of directories use by inode for a directory with its main contained sub-directories sorted from 1 till highest number use:
 

du -s –inodes * 2>/dev/null |sort -g

 

Usually running out of inodes means there is a directory / fs mounts that has too many (small files) that are depleting the max count of possible inodes.

The most simple way to list directories and number of files in them on the server root directory is with a small bash shell loop like so:
 

for i in /*; do echo $i; find $i |wc -l; done


Another way to identify the exact directory that is most likely the bottleneck for the inode depletion in a sorted by file count, human readable form:
 

find / -xdev -printf '%h\n' | sort | uniq -c | sort -k 1 -n


This will dump a list of every directory on the root (/) filesystem prefixed with the number of files (and subdirectories) in that directory. Thus the directory with the largest number of files will be at the bottom.

 

The -xdev switch is used to instruct find to narrow it's search to only the device where you're initiating the search (any other sub-mounted NAS / NFS filesystems from a different device will be omited).

 

Print top 10 subdirectories with Highest Inode Usage

 

Once identifed the largest number of files directories that is perhaps the issue, to further get a list of Top subdirectories in it with highest amount of inodes used, use below cmd:

 

for i in `ls -1A`; do echo "`find $i | sort -u | wc -l` $i"; done | sort -rn | head -10

 

To list more than 10 of the top inodes used dirs change the head -10 to whatever num needed.

N.B. ! Be very cautious when running above 2 find commands on a very large filesystems as it will be I/O Excessive and in filesystems that has some failing blocks this could create further problems.

To omit putting a high I/O load on a production filesystem, it is possible to also use du + very complex regular expression:
 

cd /backup
du –inodes -S | sort -rh | sed -n         '1,50{/^.\{71\}/s/^\(.\{30\}\).*\(.\{37\}\)$/\1…\2/;p}'


Results returned are from top to bottom.

 

How to Increase the amount of Inodes count on a new created volume EXT4 filesystem

Some FS-es XFS, JFS do have an auto-increase inode feature in case if their is physical space, whether otheres such as reiserfs does not have inodes at all but still have a field reported when queried for errors. But the classical Linux ext3 / ext4 does not have a way to increase the inode number on a live filesystem. Instead the way to do it there is to prepare a brand new filesystem on a Disk / NAS / attached storage.

The number of inodes at format-time of the block storage can be as high as 4 billion inodes. Before you create the new FS, you have to partition the new the block storage as ext4 with lets say parted command (or nullify the content of an with dd to clean up any previous existing data on a volume if there was already existing data:
 

parted /dev/sda


dd if=/dev/zero of=/dev/path/to/volume


  then format it with this additional parameter:

 

mkfs.ext4 -N 3000000000 /dev/path/to/volume

 

Here in above example the newly created filesystem of EXT4 type will be created with 3 Billion inodes !, for setting a higher number on older ext3 filesystem max inode count mkfs.ext3 could be used instead.

Bear in mind that 3 Billion number is a too high number and if you plan to have some large number of files / directories / links structures just raise it up to your pre-planning requirements for FS. In most cases it will be rarely anyone that want to have this number higher than 1 or 2 billion of inodes.

On FreeBSD / NetBSD / OpenBSD setting inode maximum number for a UFS / UFS2 (which is current default FreeBSD FS), this could be done via newfs filesystem creation command after the disk has been labeled with disklabel:

 

freebsd# newfs -i 1024 /dev/ada0s1d

 

Increase the Max Count of Inodes for a /tmp filesystem

 

Sometimes on some machines it is necessery to have ability to store very high number of small files (e.g. have a very large number of inodes) on a temporary filesystem kept in memory. For example some web applications served by Web Server Apache + PHP, Nginx + Perl-FastCGI are written in a bad manner so they kept tons of temporary files in /tmp, leading to issues with exceeded amount of inodes.
If that's the case to temporary work around you can increase the count of Inodes for /tmp to a very high number like 2 billions using:

 

mount -o remount,nr_inodes=<bignum> /tmp

To make the change permanent on next boot if needed don't forget to put the nr_inodes=whatever_bignum as a mount option for the temporary fs to /etc/fstab

Eventually, if you face this issues it is best to immediately track which application produced the mess and ask the developer to fix his messed up programs architecture.

 

Conclusion

 

It was explained on the very common issue of having maximum amount of inodes on a filesystem depleted and the unpleasent consequences of inability to create new files on living FS.
Then a general overview was given on what is inode on a Linux / Unix filesystem, what is typical content of inode, how inode addressing is handled on a FS. Further was explained how to get basic information about available inodes on a filesystem, how to get a filename/s based on inode number (with find), the well known way to determine inode number of a directory or file (with ls) and get more extensive information on a FS on inodes with tune2fs.
Also was explained how to identify directories containing multitudes of files in order to determine a sub-directories that is consuming most of the inodes on a filesystem. Finally it was explained very raughly how to prepare an ext4 filesystem from scratch with predefined number to inodes to much higher than the usual defaults by mkfs.ext3 / mkfs.ext4 and *bsds newfs as well as how to raise the number of inodes of /tmp tmpfs temporary RAM filesystem.

Why du and df reporting different on a filesystem / How to fix inconsistency between used space on FS and disk showing full strangeness

Wednesday, July 24th, 2019

linux-why-du-and-df-shows-different-result-inconsincy-explained-filesystem-full-oddity

If you're a sysadmin on a large server environment such as a couple of hundred of Virtual Machines running Linux OS on either physical host or OpenXen / VmWare hosted guest Virtual Machine, you might end up sometimes at an odd case where some mounted partition mount point reports its file use different when checked with
df
cmd than when checked with du command, like for example:
 

root@sqlserver:~# df -hT /var/lib/mysql
Filesystem   Type  Size Used Avail Use% Mounted On
/dev/sdb5      ext4    19G  3,4G    14G  20% /var/lib/mysql

Here the '-T' argument is used to show us the filesystem.

root@sqlserver:~# du -hsc /var/lib/mysql
0K    /var/lib/mysql/
0K    total

 

1. Simple debug on what might be the root cause for df / du inconsistency reporting

 

Of course the basic thing to do when in that weird situation is to be totally shocked how this is possible and to investigate a bit what is the biggest first level sub-directories that eat up the space on the mounted location, with du:

 

# du -hkx –max-depth=1 /var/lib/mysql/|uniq|sort -n
4       /var/lib/mysql/test
8       /var/lib/mysql/ezmlm
8       /var/lib/mysql/micropcfreak
8       /var/lib/mysql/performance_schema
12      /var/lib/mysql/mysqltmp
24      /var/lib/mysql/speedtest
64      /var/lib/mysql/yourls
144     /var/lib/mysql/narf
320     /var/lib/mysql/webchat_plus
424     /var/lib/mysql/goodfaithair
528     /var/lib/mysql/moonman
648     /var/lib/mysql/daniel
852     /var/lib/mysql/lessn
1292    /var/lib/mysql/gallery

The given output is in Kilobytes so it is a little bit hard to read, if you're used to Mbytes instead, do

 

 # du -hmx –max-depth=1 /var/lib/mysql/|uniq|sort -n|less

 

I've also investigated on the complete /var directory contents sorted by size with:

 

 # du -akx ./ | sort -n
5152564    ./cache/rsnapshot/hourly.2/localhost
5255788    ./cache/rsnapshot/hourly.2
5287912    ./cache/rsnapshot
7192152    ./cache


Even after finding out the bottleneck dirs and trying to clear up a bit, continued facing that inconsistently shown in two commands and if you're likely to be stunned like me and try … to move some files to a different filesystem to free up space or assigned inodes with a hope that shown inconsitency output will be fixed as it might be caused  due to some kernel / FS caching ?? and this will eventually make the mounted FS to refresh …

But unfortunately, if you try it you'll figure out clearing up a couple of Megas or Gigas will make no difference in cmd output.

In my exact case /var/lib/mysql is a separate mounted ext4 filesystem, however same issue was present also on a Network Filesystem (NFS) and thus, my first thought that this is caused by a network failure problem or NFS bug turned to be wrong.

After further short investigation on the inodes on the Filesystem, it was clear enough inodes are available:
 

# df -i /var/lib/mysql
Filesystem       Inodes  IUsed   IFree IUse% Mounted on
/dev/sdb5      1221600  2562 1219038   1% /var/lib/mysql

 

So the filled inodes count assumed issue also has been rejected.
P.S. (if you're not well familiar with them read manual, i.e. – man 7 inode).
 

– Remounting the mounted filesystem

To make sure the filesystem shown inconsistency between du and df is not due to some hanging network mount or bug, first logical thing I did is to remount the filesytem showing different in size, in my case this was done with:
 

# mount -o remount,rw -t ext4 /var/lib/mysql

For machines with NFS remote mounted storage locations, used:

# mount -o remount,rw -t nfs /var/www


FS remount did not solved it so I continued to ponder what oddity and of course I thought of a workaround (in case if this issues are caused by kernel bug or OS lib issue) reboot might be the solution, however unfortunately restarting the VMs was not a wanted easy to do solution, thus I continued investigating what is wrong …

Next check of course was to check, what kind of network connections are opened to the affected hosts with:
 

# netstat -tupanl


Did not found anything that might point me to the reported different Megabytes issue, so next step was to check what is the situation with currently opened files by running processes on the weird df / du reported systems with lsof, and boom there I observed oddity such as multiple files

 

# lsof -nP | grep '(deleted)'

COMMAND   PID   USER   FD   TYPE DEVICE    SIZE NLINK  NODE NAME
mysqld   2588  mysql    4u   REG 253,17      52     0  1495 /var/lib/mysql/tmp/ibY0cXCd (deleted)
mysqld   2588  mysql    5u   REG 253,17    1048     0  1496 /var/lib/mysql/tmp/ibOrELhG (deleted)
mysqld   2588  mysql    6u   REG 253,17       777884290     0  1497 /var/lib/mysql/tmp/ibmDFAW8 (deleted)
mysqld   2588  mysql    7u   REG 253,17       123667875     0 11387 /var/lib/mysql/tmp/ib2CSACB (deleted)
mysqld   2588  mysql   11u   REG 253,17       123852406     0 11388 /var/lib/mysql/tmp/ibQpoZ94 (deleted)

 

Notice that There were plenty of '(deleted)' STATE files shown in memory an overall of 438:

 

# lsof -nP | grep '(deleted)' |wc -l
438


As I've learned a bit online about the problem, I found it is also possible to find deleted unlinked files only without any greps (to list all deleted files in memory files with lsof args only):

 

# lsof +L1|less


The SIZE field (fourth column)  shows a number of files that are really hard in size and that are kept in open on filesystem and in memory, totally messing up with the filesystem. In my case this is temp files created by MYSQLD daemon but depending on the server provided service this might be apache's www-data, some custom perl / bash script executed via a cron job, stalled rsync jobs etc.
 

2. Check all the list open files with the mysql / root user as part of the the server filesystem inconsistency debugging with:

 

– Grep opened files on server by user

# lsof |grep mysql
mysqld    1312                       mysql  cwd       DIR               8,21       4096          2 /var/lib/mysql
mysqld    1312                       mysql  rtd       DIR                8,1       4096          2 /
mysqld    1312                       mysql  txt       REG                8,1   20336792   23805048 /usr/sbin/mysqld
mysqld    1312                       mysql  mem       REG               8,21      24576         20 /var/lib/mysql/tc.log
mysqld    1312                       mysql  DEL       REG               0,16                 29467 /[aio]
mysqld    1312                       mysql  mem       REG                8,1      55792   14886933 /lib/x86_64-linux-gnu/libnss_files-2.28.so

 

# lsof | grep root
COMMAND    PID   TID TASKCMD          USER   FD      TYPE             DEVICE   SIZE/OFF       NODE NAME
systemd      1                        root  cwd       DIR                8,1       4096          2 /
systemd      1                        root  rtd       DIR                8,1       4096          2 /
systemd      1                        root  txt       REG                8,1    1489208   14928891 /lib/systemd/systemd
systemd      1                        root  mem       REG                8,1    1579448   14886924 /lib/x86_64-linux-gnu/libm-2.28.so

Other command that helped to track the discrepancy between df and du different file usage on FS is:
 

# du -hxa  / | egrep '^[[:digit:]]{1,1}G[[:space:]]*'
 

 

3. Fixing large files kept in memory filesystem problem


What is the real reason for ending up with this file handlers opened by running backgrounded programs on the Linux OS?
It could be multiple  but most likely it is due to exceeded server / client interactions or breaking up RAM or HDD drive with writing plenty of logs on the FS without ending keeping space occupied or Programming library bugs used by hanged service leaving the FH opened on storage.

What is the solution to file system files left in memory problem?

The best solution is to first fix custom script or hanged service and then if possible to simply restart the server to make the kernel / services reload or if this is not possible just restart the problem creation processes.

Once the process is identified like in my case this was MySQL on systemd enabled newer OS distros, just do:

 

 

# systemctl restart mysqld.service


or on older init.d system V ones:

# /etc/init.d/service restart


For custom hanged scripts being listed in ps axuwef you can grep the pid and do a kill -HUP (if the script is written in a good way to recognize -HUP and restart the sub-running process properly – BE EXTRA CAREFUL IF YOU'RE RESTARTING BROKEN SCRIPTS as this might cause your running service disruptions …).

# pgrep -l script.sh
7977 script.sh


# kill -HUP PID

 

Now finally this should either mitigate or at best case completely solve the reported disagreement between df and du, after which the calculated / reported disk space should be back to normal and show up approximately the same (note that size changes a bit as mysql service is writting data) constantly extending the size between the two checks.

 

# df -hk /var/lib/mysql; du -hskc /var/lib/mysql
Filesystem       Inodes  IUsed   IFree IUse% Mounted on
/dev/sdb5        19097172 3472744 14631296  20% /var/lib/mysql
3427772    /var/lib/mysql
3427772    total

 

What we learned?

What I've explained in this article is why and how it comes that 'zoombie' files reside on a filesystem
appearing to be eating disk space on a mounted local or network partition, giving strange inconsistent
reports, leading to system service disruptions and impossibility to have correctly shown information on used
disk space on mounted drive.

I went through with some standard logic on debugging service / filesystem / inode issues up explainat, that led me to the finding about deleted files being kept in filesystem and producing the filesystem strange sized / showing not correct / filled even after it was extended with tune2fs and was supposed to have extra 50GBs.

Finally it was explained shortly how to HUP / restart hanging script / service to fix it.

Some few good readings that helped to fix the issue:

What to do when du and df report different usage is here
df in linux not showing correct free space after file removal is here
Why do “df” and “du” commands show different disk usage?
 

How to check Linux OS install date / How long ago was Linux installed

Sunday, October 22nd, 2017

If you're sysadmin who inherited a few hundreds of Linux machines from a previous admin and you're in process of investigating how things were configured by the previous administrator one of the crucial things to find out might be

How Long ago was Linux installed?

Here is how to check the Linux OS install date.

The universal way nomatter the Linux distribution is to use fullowing command:

 

root@pcfreak:~# tune2fs -l /dev/sda1 | grep 'Filesystem created:'
Filesystem created:       Thu Sep  6 21:44:22 2012

 

 

Above command assumes the Linux's root partition / is installed on /dev/sda1 however if your case is different, e.g. the primary root partition is installed on /dev/sda2 or /dev/sdb1 / dev/sdb2 etc. just place the right first partition into the command.

If primary install root partition is /dev/sdb1 for example:
 

root@pcfreak:~# tune2fs -l /dev/sdb1 | grep 'Filesystem created:'

 


To find out what is the root partition of the Linux server installed use fdisk command:

 

 

 

root@pcfreak:~# fdisk -l

 

Disk /dev/sda: 465,8 GiB, 500107862016 bytes, 976773168 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0x00051eda

Device     Boot     Start       End   Sectors   Size Id Type
/dev/sda1  *         2048 965193727 965191680 460,2G 83 Linux
/dev/sda2       965195774 976771071  11575298   5,5G  5 Extended
/dev/sda5       965195776 976771071  11575296   5,5G 82 Linux swap / Solaris

Disk /dev/sdb: 111,8 GiB, 120034123776 bytes, 234441648 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0x00000000

 


Other ways to check the Linux OS install date on Debian / Ubuntu / Mint etc. deb. based GNU / Linux

 


Deban based Linux distributions do create an initial /var/log/installer directory containing various install information such as hardware-summary, partition, initial installed deb packages, exact version of Linux distribution, and the way it was installed either it was installed from an ISO image, or it was network install etc.

 

root@pcfreak:~# ls -al /var/log/installer/
total 1228
drwxr-xr-x  3 root root   4096 sep  6  2012 ./
drwxr-xr-x 72 root root  12288 окт 22 06:26 ../
drwxr-xr-x  2 root root   4096 sep  6  2012 cdebconf/
-rw-r–r–  1 root root  17691 sep  6  2012 hardware-summary
-rw-r–r–  1 root root    163 sep  6  2012 lsb-release
-rw——-  1 root root 779983 sep  6  2012 partman
-rw-r–r–  1 root root  51640 sep  6  2012 status
-rw——-  1 root root 363674 sep  6  2012 syslog

 

If those directory is missing was wiped out by the previous administrator, to clear up traces of his previous work before he left job another possible way to find out exact install date is to check timestamp of /lost+found directory;
 

root@pcfreak:~# ls -ld /lost+found/
drwx—— 2 root root 16384 sep  6  2012 /lost+found//

 

Check OS Linux install date on (Fedora, CentOS, Scientific Linux, Oracle and other Redhat RPM based Distros)

 

[root@centos: ~]# rpm -qi basesystem
Name        : basesystem
Version     : 10.0
Release     : 7.el7
Architecture: noarch
Install Date: Mon 02 May 2016 19:20:58 BST
Group       : System Environment/Base
Size        : 0
License     : Public Domain
Signature   : RSA/SHA256, Tue 01 Apr 2014 14:23:16 BST, Key ID     199e2f91fd431d51
Source RPM  : basesystem-10.0-7.el7.src.rpm
Build Date  : Fri 27 Dec 2013 17:22:15 GMT
Build Host  : ppc-015.build.eng.bos.redhat.com
Relocations : (not relocatable)
Packager    : Red Hat, Inc. <http://bugzilla.redhat.com/bugzilla>
Vendor      : Red Hat, Inc.
Summary     : The skeleton package which defines a simple Red Hat Enterprise Linux system
Description :
Basesystem defines the components of a basic Red Hat Enterprise Linux
system (for example, the package installation order to use during
bootstrapping). Basesystem should be in every installation of a system,
and it should never be removed.

 

How to mount NFS network filesystem to remote server via /etc/fstab on Linux

Friday, January 29th, 2016

mount-nfs-in-linux-via--etc-fstab-howto-mount-remote-partitions-from-application-server-to-storage-server
If you have a server topology part of a project where 3 (A, B, C) servers need to be used to deliver a service (one with application server such as Jboss / Tomcat / Apache, second just as a Storage Server holding a dozens of LVM-ed SSD hard drives and an Oracle database backend to provide data about the project) and you need to access server A (application server) to server B (the Storage "monster") one common solution is to use NFS (Network FileSystem) Mount. 
NFS mount is considered already a bit of obsoleted technology as it is generally considered unsecre, however if SSHFS mount is not required due to initial design decision or because both servers A and B are staying in a serious firewalled (DMZ) dedicated networ then NTS should be a good choice.
Of course to use NFS mount should always be a carefully selected Environment Architect decision so remote NFS mount, imply  that both servers are connected via a high-speed gigabyte network, e.g. network performance is calculated to be enough for application A <-> to network storage B two sides communication not to cause delays for systems end Users.

To test whether the NFS server B mount is possible on the application server A, type something like:

 

mount -t nfs -o soft,timeo=900,retrans=3,vers=3, proto=tcp remotenfsserver-host:/home/nfs-mount-data /mnt/nfs-mount-point


If the mount is fine to make the mount permanent on application server host A (in case of server reboot), add to /etc/fstab end of file, following:

1.2.3.4:/application/local-application-dir-to-mount /application/remote-application-dir-to-mount nfs   rw,bg,nolock,vers=3,tcp,timeo=600,rsize=32768,wsize=32768,hard,intr 1 2


If the NTFS server has a hostname you can also type hostname instead of above example sample IP 1.2.3.4, this is however not recommended as this might cause in case of DNS or Domain problems.
If you want to mount with hostname (in case if storage server IP is being commonly changed due to auto-selection from a DHCP server):

server-hostA:/application/local-application-dir-to-mount /application/remote-application-dir-to-mount nfs   rw,bg,nolock,vers=3,tcp,timeo=600,rsize=32768,wsize=32768,hard,intr 1 2

In above example you need to have the /application/local-application-dir-to-mount (dir where remote NFS folder will be mounted on server A) as well as the /application/remote-application-dir-to-mount
Also on server Storage B server, you have to have running NFS server with firewall accessibility from server A working.

The timeou=600 (is defined in) order to make the timeout for remote NFS accessibility 1 hour in order to escape mount failures if there is some minutes network failure between server A and server B, the rsize and wsize
should be fine tuned according to the files that are being red from remote NFS server and the network speed between the two in the example are due to environment architecture (e.g. to reflect the type of files that are being transferred by the 2)
and the remote NFS server running version and the Linux kernel versions, these settings are for Linux kernel branch 2.6.18.x which as of time of writting this article is obsolete, so if you want to use the settings check for your kernel version and
NTFS and google and experiment.

Anyways, if you're not sure about wsize and and rise, its perfectly safe to omit these 2 values if you're not familiar to it.

To finally check the NFS mount is fine,  grep it:

 

# mount|grep -i nfs
sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw)
server-hostA:/application/remote-application-dir-to-mount on /application/remote-application-dir-to-mount type nfs (rw,bg,nolock,nfsvers=3,tcp,timeo=600,rsize=32768,wsize=32768,hard,intr,addr=1.2.3.4)


That's all enjoy 🙂

 

 

Fix MySQL ibdata file size – ibdata1 file growing too large, preventing ibdata1 from eating all your server disk space

Thursday, April 2nd, 2015

fix-solve-mysql-ibdata-file-size-ibdata1-file-growing-too-large-and-preventing-ibdata1-from-eating-all-your-disk-space-innodb-vs-myisam

If you're a webhosting company hosting dozens of various websites that use MySQL with InnoDB  engine as a backend you've probably already experienced the annoying problem of MySQL's ibdata1 growing too large / eating all server's disk space and triggering disk space low alerts. The ibdata1 file, taking up hundreds of gigabytes is likely to be encountered on virtually all Linux distributions which run default MySQL server <= MySQL 5.6 (with default distro shipped my.cnf). The excremental ibdata1 raise appears usually due to a application software bug on how it queries the database. In theory there are no limitation for ibdata1 except maximum file size limitation set for the filesystem (and there is no limitation option set in my.cnf) meaning it is quite possible that under certain conditions ibdata1 grow over time can happily fill up your server LVM (Storage) drive partitions.

Unfortunately there is no way to shrink the ibdata1 file and only known work around (I found) is to set innodb_file_per_table option in my.cnf to force the MySQL server create separate *.ibd files under datadir (my.cnf variable) for each freshly created InnoDB table.
 

1. Checking size of ibdata1 file

On Debian / Ubuntu and other deb based Linux servers datadir is /var/lib/mysql/ibdata1

server:~# du -hsc /var/lib/mysql/ibdata1
45G     /var/lib/mysql/ibdata1
45G     total


2. Checking info about Databases and Innodb storage Engine

server:~# mysql -u root -p
password:

mysql> SHOW DATABASES;
+——————–+
| Database           |
+——————–+
| information_schema |
| bible              |
| blog               |
| blog-sezoni        |
| blogmonastery      |
| daniel             |
| ezmlm              |
| flash-games        |


Next step is to get some understanding about how many existing InnoDB tables are present within Database server:

 

mysql> SELECT COUNT(1) EngineCount,engine FROM information_schema.tables WHERE table_schema NOT IN ('information_schema','performance_schema','mysql') GROUP BY engine;
+————-+——–+
| EngineCount | engine |
+————-+——–+
|         131 | InnoDB |
|           5 | MEMORY |
|         584 | MyISAM |
+————-+——–+
3 rows in set (0.02 sec)

To get some more statistics related to InnoDb variables set on the SQL server:
 

mysqladmin -u root -p'Your-Server-Password' var | grep innodb


Here is also how to find which tables use InnoDb Engine

mysql> SELECT table_schema, table_name
    -> FROM INFORMATION_SCHEMA.TABLES
    -> WHERE engine = 'innodb';

+————–+————————–+
| table_schema | table_name               |
+————–+————————–+
| blog         | wp_blc_filters           |
| blog         | wp_blc_instances         |
| blog         | wp_blc_links             |
| blog         | wp_blc_synch             |
| blog         | wp_likes                 |
| blog         | wp_wpx_logs              |
| blog-sezoni  | wp_likes                 |
| icanga_web   | cronk                    |
| icanga_web   | cronk_category           |
| icanga_web   | cronk_category_cronk     |
| icanga_web   | cronk_principal_category |
| icanga_web   | cronk_principal_cronk    |


3. Check and Stop any Web / Mail / DNS service using MySQL

server:~# ps -efl |grep -E 'apache|nginx|dovecot|bind|radius|postfix'

Below cmd should return empty output, (e.g. Apache / Nginx / Postfix / Radius / Dovecot / DNS etc. services are properly stopped on server).

4. Create Backup dump all MySQL tables with mysqldump

Next step is to create full backup dump of all current MySQL databases (with mysqladmin):

server:~# mysqldump –opt –allow-keywords –add-drop-table –all-databases –events -u root -p > dump.sql
server:~# du -hsc /root/dump.sql
940M    dump.sql
940M    total

 

If you have free space on an external backup server or remotely mounted attached (NFS or SAN Storage) it is a good idea to make a full binary copy of MySQL data (just in case something wents wrong with above binary dump), copy respective directory depending on the Linux distro and install location of SQL binary files set (in my.cnf).
To check where are MySQL binary stored database data (check in my.cnf):

server:~# grep -i datadir /etc/mysql/my.cnf
datadir         = /var/lib/mysql

If server is CentOS / RHEL Fedora RPM based substitute in above grep cmd line /etc/mysql/my.cnf with /etc/my.cnf

if you're on Debian / Ubuntu:

server:~# /etc/init.d/mysql stop
server:~# cp -rpfv /var/lib/mysql /root/mysql-data-backup

Once above copy completes, DROP all all databases except, mysql, information_schema (which store MySQL existing user / passwords and Access Grants and Host Permissions)

5. Drop All databases except mysql and information_schema

server:~# mysql -u root -p
password:

 

mysql> SHOW DATABASES;

DROP DATABASE blog;
DROP DATABASE sessions;
DROP DATABASE wordpress;
DROP DATABASE micropcfreak;
DROP DATABASE statusnet;

          etc. etc.

ACHTUNG !!! DON'T execute!DROP database mysql; DROP database information_schema; !!! – cause this might damage your User permissions to databases

6. Stop MySQL server and add innodb_file_per_table and few more settings to prevent ibdata1 to grow infinitely in future

server:~# /etc/init.d/mysql stop

server:~# vim /etc/mysql/my.cnf
[mysqld]
innodb_file_per_table
innodb_flush_method=O_DIRECT
innodb_log_file_size=1G
innodb_buffer_pool_size=4G

Delete files taking up too much space – ibdata1 ib_logfile0 and ib_logfile1

server:~# cd /var/lib/mysql/
server:~#  rm -f ibdata1 ib_logfile0 ib_logfile1
server:~# /etc/init.d/mysql start
server:~# /etc/init.d/mysql stop
server:~# /etc/init.d/mysql start
server:~# ps ax |grep -i mysql

 

You should get no running MySQL instance (processes), so above ps command should return blank.
 

7. Re-Import previously dumped SQL databases with mysql cli client

server:~# cd /root/
server:~# mysql -u root -p < dump.sql

Hopefully import should went fine, and if no errors experienced new data should be in.

Altearnatively if your database is too big and you want to import it in less time to mitigate SQL downtime, instead import the database with:

server:~# mysql -u root -p
password:
mysql>  SET FOREIGN_KEY_CHECKS=0;
mysql> SOURCE /root/dump.sql;
mysql> SET FOREIGN_KEY_CHECKS=1;

 

If something goes wrong with the import for some reason, you can always copy over sql binary files from /root/mysql-data-backup/ to /var/lib/mysql/
 

8. Connect to mysql and check whether databases are listable and re-check ibdata file size

Once imported login with mysql cli and check whther databases are there with:

server:~# mysql -u root -p
SHOW DATABASES;

Next lets see what is currently the size of ibdata1, ib_logfile0 and ib_logfile1
 

server:~# du -hsc /var/lib/mysql/{ibdata1,ib_logfile0,ib_logfile1}
19M     /var/lib/mysql/ibdata1
1,1G    /var/lib/mysql/ib_logfile0
1,1G    /var/lib/mysql/ib_logfile1
2,1G    total

Now ibdata1 will grow, but only contain table metadata. Each InnoDB table will exist outside of ibdata1.
To better understand what I mean, lets say you have InnoDB table named blogdb.mytable.
If you go into /var/lib/mysql/blogdb, you will see two files
representing the table:

  •     mytable.frm (Storage Engine Header)
  •     mytable.ibd (Home of Table Data and Table Indexes for blogdb.mytable)

Now construction will be like that for each of MySQL stored databases instead of everything to go to ibdata1.
MySQL 5.6+ admins could relax as innodb_file_per_table is enabled by default in newer SQL releases.


Now to make sure your websites are working take few of the hosted websites URLs that use any of the imported databases and just browse.
In my case ibdata1 was 45GB after clearing it up I managed to save 43 GB of disk space!!!

Enjoy the disk saving! 🙂

How to find and Delete Duplicate files in directory on Linux server with find and fdupes command

Monday, March 16th, 2015

search-duplcate-files-linux-command-and-graphical-tools-how-to-find-duplicate-files-on-linux-mac-and-windows-os

Linux / UNIX find command is very helpful to do a lot of tasks to us admins such as Deleting empty directories to free up occupied inodes or finding and printing only empty files within a root file system within all sub-directories
There is too much of uses of find, however one that is probably rarely used known by sysadmins find command use is how to search for duplicate files on a Linux server:
 

find -not -empty -type f -printf “%s\n” | sort -rn | uniq -d | xargs -I{} -n1 find -type f -size {}c -print0 | xargs -0 md5sum | sort | uniq -w32 –all-repeated=separate

If you're curious how does duplicate files finding works, they are found by comparing file sizes and MD5 signatures, followed by a byte-by-byte comparison.

Most common application of below command is when you want to search and get rid of some old obsolete files which you forgot to delete such as old /etc/ configurations, old SQL backups and PHP / Java / Python programming code files etc.

If you have to do a regular duplicate file find on multiple servers Linux servers perhaps you should install and use  fdupes command.
On Debian Linux to install it:

root@pcfreak:/# apt-cache show fdupes|grep -i descr -A 4
Description: identifies duplicate files within given directories
 FDupes uses md5sums and then a byte by byte comparison to find
 duplicate files within a set of directories. It has several useful
 options including recursion.
Homepage: http://code.google.com/p/fdupes/

 

root@pc-freak.net:/# apt-get install –yes fdupes

To search for duplicate files with fdupes in lets /etc/ just run fdupes without arguments:

 

root@pcfreak:/# fdupes /etc/
/etc/magic
/etc/magic.mime

/etc/odbc.ini
/etc/.pwd.lock
/etc/environment
/etc/odbcinst.ini

/etc/shadow-
/etc/shadow


If you want to look up for all duplicate files within root directory:
 

root@pcfreak:/# fdupes -r /etc/
Building file list /

 

You can also find duplicate files for multiple directories by just passing all directories as arguments to fdupes

 

root@pcfreak:/# fdupes -r /etc/ /usr/ /root /disk /nfs_mount /nas


The -r argument (makes a recursive subdirectory search for duplicates), if you want to also see what is the size of duplicate files found add -S option

 

fdupes -r -S /etc/ /usr/ /root /disk /nfs_mount /nas

 


If you want to delete all duplicate files within lets say /etc/

 

root@pcfreak:/# fdupes -d /etc/

fdupes is also available and installable also on RPM based Linux distros Fedora / RHEL / CentOS etc., install on CentOS with:
 

[root@centos~ ]# yum -y install fdupes


There is also a port available for those who want to run it on FreeBSD on BSD install it from ports:

 

freebsd# cd /usr/ports/sysutils/fdupes
freebsd# make install clean


If you have a GUI environment installed on the server and you don't want to bother with command line to search for all duplicate files under main filesystem and other lint (junk) files take a look at FSlint

FSlint-2.02-search-for-duplicate-and-lint-files-linux-gui-tool

If you're looking for a GUI cross platform duplicate file finder tool that runs on all major used Operating Systems Mac OS X / Windows / Linux take a look at dupeGuru

 

Windows how to check which process locks file command – A M$ Windows equivalent of lsof command

Monday, February 23rd, 2015

windows-how-to-check-which-process-locks-file-command-a-ms-windows-equivalent-of-lsof-command

I've had a task today to deploy a new WAR (Web Application Archive) Tomcat file on Apache Tomcat server running  on Windows server 2008 R2 UAT environment.
The client Tomcat application within war is providing a frontend to an proprietary Risk Analysis application called Risiko Management (developed by a German vendor called Schleupen).
The update of WAR file was part of a version upgrade of application so, both "Risk Analysis" desktop standalone server RiskKit and the Web frontend was developed by Schleupen had to be updated.
In order to update I followed the usual .WAR Tomcat Javafile upadate Tomcat process.

1. Stopped Tomcat running service Instance via services.msc command e.g.
 

Start (menu) -> Run
 

services.msc

 

stopping-tomcat-application-howto-stop-service-ms-windows-screenshot
 


2. Move (by Renaming) old risk-analysis.war to risk-analysis_backup_2015.war

and also rename the automatically Tomcat extracted folder (named same name as the WAR archive file directory – D:\web\Apache-Tomcat-7.0.33\webapps\Risiko-Analysis\ to :\web\Apache-Tomcat-7.0.33\webapps\Risiko-Analysis_backup_2015, i.e. run:
 

C:\Users\risk-analysis> D:
D:\>
D:\> CD \Web\Apache-Tomcat-7.0.33\webapps\

D:\Web\Apache-Tomcat-7.0.33\webapps> move risk-analysis.war risk-analysis_2015.war
D:\Web\Apache-Tomcat-7.0.33\webapps> move  
Risiko-Analysis\  Risiko-Analysis_backup_2015\


But unfortunately I couldn't rename it and I got below error:

move-windows-command-access-is-denied-tiny-screenshot

Also I tried copying it using Windows Explorer Copy / Paste but this didn't worked either, and I got below error :

cant-move-risk-analysis-tomcat-java-application-error-ms-windows-screenshot

3. Finding what Locks a directory or File on M$ Windows


Obviously, the reason for unable to copy the directory was something was locking it. Actually there are plenty of locked files many running applications like Explorer do. A good example for all time locked file is Windows (swap file) pagefile.sys – this is Windows Linux equivalent of swap filesystem (enabled / disabled with spapon / swapoff commands)

Having the directory locked was a strange problem, because the Tomcat process was not running as I checked closely both in Windows taskmgr GUI interface and manually grepped for the process with tasklist command like so:

 

d:\>tasklist /m|find /i "tomcat"


tomcat7.exe                   4396 ntdll.dll, kernel32.dll, KERNELBASE.dll,

For people like me who use primary Linux , above command shows you very precious debugging information, it shows which Windows libraries (DLL) are loaded in memory and used by the process 

 

(Note that when Tomcat is running, it is visible with command)
 

D:\> wmic.exe process list brief | find /i "tomcat"
526          tomcat7.exe          8         4396       49           156569600


Just for those wondering the 156569600 number is number of bytes loaded in Windows memory used by Tomcat.

After tomcat was stopped above command returned empty string meaning obviously that tomcat is stopped ..

BTW, wmic command is very useful to get a list of process names (to list all running processes):

 D:> wmic.exe process list brief

get-all-process-names-in-command-line-with-windows-wmic-command-screenshot

Well obviously something was locking this directory (some of its subdirectories or a file name within the directory / folder), so I couldn't rename it just like that.
In Linux finding which daemon (service) is locking a file is pretty easy with lsof command (for those new to lsof check my previous article how to how to check what process listens on network port in Linux), however it was unknown to me how I can check which running service is locking a file and did a quick google search which pointed me to the famous handle part of SysInternals tools.
The command tool Handle.exe was exactly what I was looking for. 

handle-sysinternals-tool-to-windows-see-all-locked-files-and-what-is-locking-them-ms-windows-screenshot

To get list of all opened (locked) files and see which application has opened it just exec command without arguments, you will get
plenty of useful info which will help you to better understand what Windows OS is doing invisible in the background and what app uses what.

handle-command-part-of-sysinternals-witout-any-arguments-display-opened-locked-files-in-windows

handle is pretty much Windows equivalent command of Linux lsof

To get which file was locked by Tomcat I used handle in conjuntion with find /i command which is pretty much like Linux's grep equivalent

 

C:\TEMP> Handle.exe | FIND /I "Tomcat"
   1C: File  (RW-)   D:\Web\Apache-Tomcat-7.0.33\webapps\Risk-Analysis\images\app


Alternatively if you have sysinternals and prefer GUI environment you can use SysInternals Process Explorer (press CTRL + F) and look for a string:

process-explorer-toolbar-find-what-is-locking-a-file-or-directory-windows

Next to handle I found also another GUI program (Internet Explorer extension) WhoLockMe, that can be used to show you all running programs and locked files by this programs.
WhoLockMe is pretty straight forward to use, though it shows GUI output you have to run the command from cmd line. Below is sample output screenshot of wholockme.


who-lock-me-windows-screenshot-see-which-files-running-programs-are-locking-on-ms-windows

 

To Install Wholockme 


Unzip "WhoLockMe.zip" in a directory (for exemple : "C:\Program Files\WhoLockMe")
Launch "Install.bat" or execute this Windows registry modification command :
 

regsvr32 "C:\Program Files\WhoLockMe\WhoLockMe.dll"


To Uninstall WhoLockMe – if you need to later:

 

Execute command :
 

regsvr32 /u "C:\Program Files\WhoLockMe\WhoLockMe.dll"


Reboot (Or Kill Explorer.exe).

Removes the "C:\Program Files\WhoLockMe" directory and its contents.

Probably there are other ways to find out what is locking a file or direcotry using powershell scripts or .bat (batch) scripting. If you know of other way using default Windows embedded commands, please share in comments.

 

Configure Linux users to see only their own user processes with Hidepid – Stop users to see what others are doing

Tuesday, December 23rd, 2014

configure-Linux-users-to-see-only-ther-own-processes-with-hidepid-ps-aux-stop-system-users-to-see-what-others-are-doing
If you administer a university shared free shell Linux server, have a small community of *NIX users offering free accounts for them, or responsible for Linux software company with development servers, where programmers login and use daily to program software / websites its necessery to have tightened security rules with a major goal to keep the different user accounts processes separate one from other (hide all system and user processes from single logged in user).

Preventing users to see other users processes is essential for Linux servers which are at high risk to be hacked. At earlier times to achieve hiding all processes besides own ones from a logged in user was possible by using A kernel security module Grsecurity.
In latest currenlt Linux kernel version 3.2+ (on both Debian (unstable) / Ubuntu 14.04 / RHEL/CentOS v6.5+ above) you can hide process from other user so only root (useruser) can see all running process with (ps auxwwf) with a native kernel option hidepid. 

Configuring Hidepid

To enable hidepid option you have to remount the /proc filesystem with the Linux kernel hardening hidepid option, to make it one time setting on already running server issue:
 

 mount -o remount,rw,hidepid=2 /proc


To make the hidepid setting permanently active its necessery to modify /proc filesystem settings in /etc/fstab


 

vim /etc/fstab

proc    /proc    proc    defaults,hidepid=2     0     0
 

  • hidepid=0 – Anybody may read all world-readable /proc/PID/* files (default).
  • hidepid=1 – Means users may not access any /proc/ / directories, but only ones owned by them.Important  files like cmdline, sched*, status are now protected to read from other other users.
  • hidepid=2 – Means hidepid=1 plus all /proc/PID/ will be invisible to other users besides logged in. Using this options stops Cracker's from gathering info about running processes, indication of daemon (services) which runs with elevated privileges, other user running processes (some might contain password) passed as argument or some sensitive data. Revealing such data is frequently used to get versions of local / remote running services that can be exploited.
     

Below is output of htop of a logged in user on hidepid activated server:

:htop_screenshot_on_hideid_showing-only-own-user-credentials-gnu-linux-debian

Make Apache webserver fix spelling mistyped URL errors and serve files case insensitive with mod_speling

Wednesday, July 16th, 2014

make_apache_fix_mistyped_spelling_urls_errors_and_serve_files_case_insensitive_mod_speling_logo
On most if not all modern GNU / Linux distributions, Apache webserver comes preinstalled with mod_speling.

What mod_speling does is it tries to find and serve files and directories for non-existing  (404 return code) urls with a similar name to passed URL. Other thing mod_speling does is it serves files case-insensitive, even though the UNIX / Linux filesystems are built to understand files case-sensitive.

mod_speling is a very useful module especially when files are being pushed (synchronized) to Apache visible from web document folder from operating systems like Windows whose filesystem doesn't store files case sensitive.

Let me give you a small example on M$ Windows a create file NewFile.html, NEWFILE.HTML, NeWfIlE.Html etc. are one and the same file newfile.html and not 3 different files like it is usually on UNIX / Linux filesystems.

If you happen to migrate old static Websites from Microsoft Internet Information Services (IIS) to UNIX / Linux based hosting. Often Html coders which create websites on Windows platform doesn't respect in website hyperlinks case-sensitive, because anyways Windows FS is case-insetive, thus moving the website to Linux host with Apache the website/s will end up with many 404 error pages, whose fixing for big static websites will be a real pain in the ass.

Also there might be need for mod_speling module enabled, for PHP / Python / Perl websites developed on MS Windows platform and tested on Windows host and then officially to be deployed on Linux.

Note that mod_speling name as a funny thing as actually the module is also converting mis-pelled / mis-typed Apache URLs:

If for example, someone tried to link to your website from a forum mistyping the URL address with mod_speling the mistyped URL could still be handled to open the real existing URL:

Lets say you have URL:
 

http://your-domain.com/files/what-Ever-fle.php


and the actual URL is:

http://your-domain.com/files/what-Ever-file.php

 

mod_speling will make Apache scan in /files/ for any files with similar name to what-Ever-fle.php and will open any similar matched file name, preventing you from the normal 404 error and therefore often serving exactly what it has to. Of course such a behavior could be unwanted in same cases for CMSes, which depend on 404 error code for proper operating, so be very sure when configuring mod_speling that this is exactly what you need.

mod_speling can be also useful sometimes for Search Engine Optimization – SEO, as it will show less 404 pages to Crawler search engine bots.

1. Enable mod_speling module on Debian GNU / Linux and Ubuntu

Enabling mod_speling in Apache in Debian / Ubuntu etc. debian based Linuxes is done with either creating symlink from /etc/apache2/mods-available/speling.load to /etc/apache2/mods-enabled/speling.load :
 

ln -sf /etc/apache2/mods-available/speling.load /etc/apache2/mods-enabled/speling.load

Or by using a2enmodDebian apache module enabling script:
 

a2ensite sitename


To enable mod_speling mis-speling resolve feature config directive is:

 

CheckSpelling on


To disable case sensitivity – as I said earlier helpful for migrations from Microsoft Windows hosts to Linux, use directive:

CheckCaseOnly on


To enable both use:

<IfModule mod_speling.c>
    CheckCaseOnly on
    CheckSpelling on
</IfModule>

Enabling mod_speling case-insensitivity and fixing mistypes in URL could be done from .htaccess, for any <Directory> (vhost) with enabled .htaccess with

AllowOverride All

To enable it for default set host in new Apache install place it in /etc/apache2/apache2.conf and /etc/apache2/sites-enabled/000-default

Then as usual to make the configuration changes take affect, restart Apache:
 

/etc/init.d/apache2 restart


2. Enablig mod_speling on CentOS, RHEL and Fedora Linux

 

Most of RPM based Linux distributions have already mod_speling by default in Apache, so there will be no need to explicitly enable the module within HTTPD.

To check whether mod_speling is already enabled in httpd issue:
 

/usr/sbin/httpd -M |grep -i mod_speling


If you don't get no output from command this means the module is not enabled. This is the case with CentOS Linux 6.5 for example …

To enable mod_speling on Apache level add in /etc/httpd/conf/httpd.conf

LoadModule speling_module modules/mod_speling.so

and restart webserver
 

/etc/init.d/httpd restart


If you get instead
 

/usr/sbin/httpd -M |grep -i mod_speling
speling_module (shared)

 

Then it is already loaded in HTTPD to enable the module for default domain add to /etc/httpd/conf/httpd.conf – within (<Directory "/var/www/html">),

<IfModule mod_speling.c>
    CheckCaseOnly on
    CheckSpelling on
</IfModule>

Or if you want to make it active for specific directories within /var/www/html/whatever-dir use either new <Directory ..> directive within Apache config, or enable .htaccess processing with AllowOverride All and place them in .htaccess . For complete mod_speling reference check on Apache's official website