df -h giving fake data? - linux

when i'm writing df -h in my instance i'm getting this data:
Filesystem Size Used Avail Use% Mounted on
devtmpfs 7.7G 0 7.7G 0% /dev
tmpfs 7.7G 0 7.7G 0% /dev/shm
tmpfs 7.7G 408K 7.7G 1% /run
tmpfs 7.7G 0 7.7G 0% /sys/fs/cgroup
/dev/nvme0n1p1 32G 24G 8.5G 74% /
tmpfs 1.6G 0 1.6G 0% /run/user/1000
but when i'm clicking sudo du -sh / i'm getting:
11G /
So in df -h, / size is 24G but in du -sh same directory the size is 11G.
I'm trying to get some free space on my instance and can't find the files that cause that.
What i'm missing?
did df -h is really giving fake data?

This question comes up quite often. The file system allocates disk blocks in the file system to record its data. This data is referred to as metadata which is not visible to most user-level programs (such as du). Examples of metadata are inodes, disk maps, indirect blocks, and superblocks.
The du command is a user-level program that isn't aware of filesystem metadata, while df looks at the filesystem disk allocation maps and is aware of file system metadata. df obtains true filesystem statistics, whereas du sees only a partial picture.
There are many causes on why the disk space used or available when running the du or df commands differs.
Perhaps the most common is deleted files. Files that have been deleted may still be open by at least one process. The entry for such files is removed from the associated directory, which makes the file inaccessible. Therefore the command du which only counts files does not take these files into account and comes up with a smaller value. As long as a process still has the deleted file in use, however, the associated blocks are not yet released in the file system, so df which works at the kernel level correctly displays these as occupied. You can find out if this is the case by running the following:
lsof | grep '(deleted)'
The fix for this issue would be to restart the services that still have those deleted files open.
The second most common cause is if you have a partition or drive mounted on top of a directory with the same name. For example, if you have a directory under / called backup which contains data and then you mount a new drive on top of that directory and label it /backup but it contains no data then the space used will show up with the df command even though the du command shows no files.
To determine if there are any files or directories hidden under an active mount point, you can try using a bind-mount to mount your / filesystem which will enable me to inspect underneath other mount points. Note, this is recommended only for experienced system administrators.
mkdir /tmp/tmpmnt
mount -o bind //tmp/tmpmnt
du /tmp/tmpmnt
After you have confirmed that this is the issue, the bind mount can be removed by running:
umount /tmp/tmpmnt/
rmdir /tmp/tmpmnt
Another possible cause might be filesystem corruption. If this is suspected, please make sure you have good backups, and at your convenience, please unmount the filesystem and run fsck.
Again, this should be done by experienced system administrators.
You can also check the calculation by running:
strace -e statfs df /
This will give you output similar to:
statfs("/", {f_type=XFS_SB_MAGIC, f_bsize=4096, f_blocks=20968699, f_bfree=17420469,
f_bavail=17420469, f_files=41942464, f_ffree=41509188, f_fsid={val=[64769, 0]},
f_namelen=255, f_frsize=4096, f_flags=ST_VALID|ST_RELATIME}) = 0
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/vda1 83874796 14192920 69681876 17% /
+++ exited with 0 +++
Notice the difference between f_bfree and f_bavail? These are the free blocks in the filesystem vs free blocks available to an unprivileged user. The used column is merely a calculation between the two.
Hope this will make your idea clear. Let me know if you still have any doubts.

Related

Different sizes for /var/lib/docker

I don't know actually if this is more a "classic" linux or a docker question but:
On an VM where some of my docker containers are running I've a strange thing. /var/lib/docker is an own partitionwith 20GB. When I look over the partition with df -h I see this:
eti-gwl1v-dockerapp1 root# df -h
Filesystem Size Used Avail Use% Mounted on
devtmpfs 7.8G 0 7.8G 0% /dev
tmpfs 7.8G 0 7.8G 0% /dev/shm
tmpfs 7.8G 815M 7.0G 11% /run
tmpfs 7.8G 0 7.8G 0% /sys/fs/cgroup
/dev/sda2 12G 3.2G 8.0G 29% /
/dev/sda7 3.9G 17M 3.7G 1% /tmp
/dev/sda5 7.8G 6.8G 649M 92% /var
/dev/sdb2 20G 47M 19G 1% /usr2
/dev/sdb1 20G 2.9G 16G 16% /var/lib/docker
So usage is at 16%. But when I now navigate to /var/lib and do a du -sch docker I see this:
eti-gwl1v-dockerapp1 root# cd /var/lib
eti-gwl1v-dockerapp1 root# du -sch docker
19G docker
19G total
eti-gwl1v-dockerapp1 root#
So same directory/partition but two sizes? How is that going?
This is really a question for unix.stackexchange.com, but there is filesystem overhead that makes the partition larger than the total size of the individual files within it.
du and df show you two different metrics:
du shows you the (estimated) file space usage, i.e. the sum of all file sizes
df shows you the disk space usage, i.e. how much space on the disk is actually used
These are distinct values and can often diverge:
disk usage may be bigger than the mere sum of file sizes due to additional meta data: e.g. the disk usage of 1000 empty files (file size = 0) is >0 since their file names and permissions need to be stored
the space used by one or multiple files may be smaller than their reported file size due to:
holes in the file - block consisting of only null bytes are not actually written to disk, see sparse files
automatic file system compression
deduplication through hard links or copy-on-write
Since docker uses the image layers as a means of deduplication the latter is most probably the cause of your observation - i.e. the sum of the files is much bigger because most of them are shared/deduplicated through hard links.
du estimates filesystem usage through summing the size of all files in it. This does not deal well with the usage of overlay2: there will be many directories which contain the same files as contained in another, but overlaid with additional layers using overlay2. As such, du will show a very inflated number.
I have not tested this since my Docker daemon is not using overlay2, but using du -x to avoid going into overlays could give the right amount. However, this wouldn't work for other Docker drivers, like btrfs, for example.

Filesystems, and quota for the home directory and /usr/local on the Google Cloud VM

I created a Debian VM on google cloud. Below is information from "df -h". What are those filesystems, such as tmpfs or /dev/sda1, mean? Any beginner-friendly reference for them? In particular, how much space can I use at my working directory "~", and how much space can I use in /usr/local (for installing software). Any idea?
zell#instance-1:~$ df -h
Filesystem Size Used Avail Use% Mounted on
udev 1.8G 0 1.8G 0% /dev
tmpfs 371M 6.4M 365M 2% /run
/dev/sda1 9.8G 1.4G 7.9G 15% /
tmpfs 1.9G 0 1.9G 0% /dev/shm
tmpfs 5.0M 0 5.0M 0% /run/lock
tmpfs 1.9G 0 1.9G 0% /sys/fs/cgroup
df -h
shows the amount of disk space used and available on Linux file systems. The command df stands for Disk Free and -h means human-readable form.
You can also see information about a specific filesystem, as follows:
df /dev/sda1
From Documentation:
Tmpfs is a file system which keeps all files in virtual memory.
Everything in tmpfs is temporary in the sense that no files will be
created on your hard drive. If you unmount a tmpfs instance,
everything stored therein is lost.
They can be mounted on different directories. For example, a tmpfs filesystem mounted at /dev/shm is used for the implementation of POSIX shared memory, an inter-process communication (IPC) where two or more processes may read from and write to the shared memory region, and POSIX semaphores, which allows processes and threads to sync their actions.
From What does /dev/sda mean?:
/dev/ is the part in the unix directory tree that contains all "device" files -- unix traditionally treats just about everything you can access as a file to read from or write to. Therefore, /dev/sda1 means the first partition on the first drive, and /dev/sda9 will mean the ninth partition on the first drive.
Check out the link for more information.
To display the amount of disk space used by the specified files and for each subdirectory, you can run the following command:
du -h
WHERE du stands for Disk Usage and -h means human-readable form.
Optionally you can use the following command to display the amount of disk space used by a certain directory:
du -h usr/local

Options for storing many small images for fast batch access on Google Cloud?

We have a few datasets of small images, where each image is about 100KB, and there about 50K images per dataset (around 5GB each dataset). We typically use these datasets to batch-load each image incrementally into a memory of a Google VM instance in order to perform machine learning studies. This is done several times a day.
Currently, a few of us each have our own Google Persistent Disk attached to the VM with the datasets replicated on each. This is not ideal since they are pricey, however, data access is very fast which allows us to iterate on our studies fairly rapidly. We don't share one disk because of the inconvenience of having to manage read/write settings with Google disks when sharing.
Is there an alternative Google Cloud option to handle this use case? Google Buckets are too slow since it is reading many small files.
If your main interest is having rapid I/O your best bet is using an SSD for obvious reasons. Why I don't understand is why you don't want to share one disk. You can have one SSD attached to one of your instances as R/W for loading and modifying your datasets and mounting it read-only to the instances that need to fetch the data.
I'm not sure how faster will be this solution compared to using a bucket, though. I guess you are aware that gsutil has an option for multithreading transfers, which exponentially increases the data transfer speed, specially when transfering a lot of small files? The flag is -m
-m Causes supported operations (acl ch, acl set, cp, mv, rm, rsync,
and setmeta) to run in parallel. This can significantly improve
performance if you are performing operations on a large number of
files over a reasonably fast network connection.
gsutil performs the specified operation using a combination of
multi-threading and multi-processing, using a number of threads
and processors determined by the parallel_thread_count and
parallel_process_count values set in the boto configuration
file. You might want to experiment with these values, as the
best values can vary based on a number of factors, including
network speed, number of CPUs, and available memory.
Using the -m option may make your performance worse if you
are using a slower network, such as the typical network speeds
offered by non-business home network plans. It can also make
your performance worse for cases that perform all operations
locally (e.g., gsutil rsync, where both source and destination
URLs are on the local disk), because it can "thrash" your local
disk.
If a download or upload operation using parallel transfer fails
before the entire transfer is complete (e.g. failing after 300 of
1000 files have been transferred), you will need to restart the
entire transfer.
Also, although most commands will normally fail upon encountering
an error when the -m flag is disabled, all commands will
continue to try all operations when -m is enabled with multiple
threads or processes, and the number of failed operations (if any)
will be reported at the end of the command's execution.
If you want to go with the instance with R/W SSD and multiple read only clients see below:
One option is to set up an NFS on your SSD, one instance will act as the NFS server with R/W rights and the rest will have only read permissions. I will be using Ubuntu 16.04 but the process is similar in all distros:
1 - Install the required packages on both server and clients:
Server: sudo apt install nfs-kernel-server
Client: sudo apt install nfs-common
2 - Mount the disk SSD disk on the server (after formatting it to the filesystem you want to use):
Server:
jordim#instance-5:~$ lsblk
NAME MAJ:MIN RM SIZE RO TYPE MOUNTPOINT
sdb 8:16 0 50G 0 disk <--- My extra SSD disk
sda 8:0 0 10G 0 disk
└─sda1 8:1 0 10G 0 part /
jordim#instance-5:~$ sudo fdisk /dev/sdb
(I will create a single primary ext4 partition)
jordim#instance-5:~$ sudo fdisk /dev/sdb
(create partition)
jordim#instance-5:~$ lsblk
NAME MAJ:MIN RM SIZE RO TYPE MOUNTPOINT
sdb 8:16 0 50G 0 disk
└─sdb1 8:17 0 50G 0 part <- Newly created partition
sda 8:0 0 10G 0 disk
└─sda1 8:1 0 10G 0 part /
jordim#instance-5:~$ sudo mkfs.ext4 /dev/sdb1
(...)
jordim#instance-5:~$ sudo mkdir /mount
jordim#instance-5:~$ sudo mount /dev/sdb1 /mount/
Make a dir for your NFS share folder:
jordim#instance-5:/mount$ sudo mkdir shared
Now configure the exports on your server. Add the folder to share and the private IPs of the clients. Also you can tweak permissions here, use "ro" for "read only" or "rw" for read-write permissions.
jordim#instance-5:/mount$ sudo vim /etc/exports
(inside the exports file, note the IP is the private IP of the client instance):
/mount/share 10.142.0.5(ro,sync,no_subtree_check)
Now start the nfs service on the server:
root#instance-5:/mount# systemctl start nfs-server
Now to create the mountpoint on the client:
jordim#instance-4:~$ sudo mkdir -p /nfs/share
And mount the folder:
jordim#instance-4:~$ sudo mount 10.142.0.6:/mount/share /nfs/share
Now let's test it:
Server:
jordim#instance-5:/mount/share$ touch test
Client:
jordim#instance-4:/nfs/share$ ls
test
Also, see the mounts:
jordim#instance-4:/nfs/share$ df -h
Filesystem Size Used Avail Use% Mounted on
udev 1.8G 0 1.8G 0% /dev
tmpfs 370M 9.9M 360M 3% /run
/dev/sda1 9.7G 1.5G 8.2G 16% /
tmpfs 1.9G 0 1.9G 0% /dev/shm
tmpfs 5.0M 0 5.0M 0% /run/lock
tmpfs 1.9G 0 1.9G 0% /sys/fs/cgroup
tmpfs 370M 0 370M 0% /run/user/1001
10.142.0.6:/mount/share 50G 52M 47G 1% /nfs/share
There you go, now you have only one instance with a r/w disk and as many clients as you want with read only permissions.

Hudson: returned status code 141: fatal: write error: No space left on device

I copied one of the existing project and created a new project in Hudson. While running build it says "returned status code 141: fatal: write error: No space left on device"
Like suggested in other forums I checked free space and inode used in file system and nothing seems problematic here. Hudson is running as service and Hudons user has been given sudo privilege. Older job can be run so nothing different in new cloned job.
Disk Space
bash-4.1$ df -h
Filesystem Size Used Avail Use% Mounted on
/dev/mapper/vg_dev-lv_root
20G 19G 28K 100% /
tmpfs 1.9G 192K 1.9G 1% /dev/shm
/dev/sda1 485M 83M 377M 19% /boot
/dev/mapper/vg_dev-lv_home
73G 26G 44G 38% /home
i-nodes used
bash-4.1$ df -i
Filesystem Inodes IUsed IFree IUse% Mounted on
/dev/mapper/vg_dev-lv_root
1310720 309294 1001426 24% /
tmpfs 490645 4 490641 1% /dev/shm
/dev/sda1 128016 46 127970 1% /boot
/dev/mapper/vg_dev-lv_home
4833280 117851 4715429 3% /home
Hudson build log
bash-4.1$ cat log
Started by user anonymous
Checkout:workspace / /var/lib/hudson/jobs/Demo/workspace - hudson.remoting.LocalChannel#1d4ab266
Using strategy: Default
Checkout:workspace / /var/lib/hudson/jobs/Demo/workspace - hudson.remoting.LocalChannel#1d4ab266
Fetching changes from the remote Git repository
Fetching upstream changes from ssh://demouser#10.10.10.10:20/home/git-repos/proj.git
ERROR: Problem fetching from origin / origin - could be unavailable. Continuing anyway
ha:AAAAWB+LCAAAAAAAAABb85aBtbiIQSmjNKU4P08vOT+vOD8nVc8DzHWtSE4tKMnMz/PLL0ldFVf2c+b/lb5MDAwVRQxSaBqcITRIIQMEMIIUFgAAckCEiWAAAAA=ERROR: (Underlying report) : Error performing command: git fetch -t ssh://demouser#10.10.10.10:20/home/git-repos/proj.git +refs/heads/*:refs/remotes/origin/*
Command "git fetch -t ssh://demouser#10.10.10.10:20/home/git-repos/proj.git +refs/heads/*:refs/remotes/origin/*" returned status code 141: fatal: write error: No space left on device
ha:AAAAWB+LCAAAAAAAAABb85aBtbiIQSmjNKU4P08vOT+vOD8nVc8DzHWtSE4tKMnMz/PLL0ldFVf2c+b/lb5MDAwVRQxSaBqcITRIIQMEMIIUFgAAckCEiWAAAAA=ERROR: Could not fetch from any repository
ha:AAAAWB+LCAAAAAAAAABb85aBtbiIQSmjNKU4P08vOT+vOD8nVc8DzHWtSE4tKMnMz/PLL0ldFVf2c+b/lb5MDAwVRQxSaBqcITRIIQMEMIIUFgAAckCEiWAAAAA=FATAL: Could not fetch from any repository
ha:AAAAWB+LCAAAAAAAAABb85aBtbiIQSmjNKU4P08vOT+vOD8nVc8DzHWtSE4tKMnMz/PLL0ldFVf2c+b/lb5MDAwVRQxSaBqcITRIIQMEMIIUFgAAckCEiWAAAAA=hudson.plugins.git.GitException: Could not fetch from any repository
at hudson.plugins.git.GitSCM$3.invoke(GitSCM.java:887)
at hudson.plugins.git.GitSCM$3.invoke(GitSCM.java:845)
at hudson.FilePath.act(FilePath.java:758)
at hudson.FilePath.act(FilePath.java:740)
at hudson.plugins.git.GitSCM.gerRevisionToBuild(GitSCM.java:845)
at hudson.plugins.git.GitSCM.checkout(GitSCM.java:622)
at hudson.model.AbstractProject.checkout(AbstractProject.java:1483)
at hudson.model.AbstractBuild$AbstractRunner.checkout(AbstractBuild.java:507)
at hudson.model.AbstractBuild$AbstractRunner.run(AbstractBuild.java:424)
at hudson.model.Run.run(Run.java:1366)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:46)
at hudson.model.ResourceController.execute(ResourceController.java:88)
at hudson.model.Executor.run(Executor.java:145)
Your error message is quite clear: There is no space left on device.
This is verified by your df output:
Filesystem Size Used Avail Use% Mounted on
/dev/mapper/vg_dev-lv_root 20G 19G 28K 100% /
This tells you, you have a root partition / with a total size of 20GB which is use by 100%.
20GB is probably a bit small in your case. As this "partition" is managed by LVM (/dev/mapper/vg...) it is possible to extend it to create more space for your data.
Otherwise you have to check, if there is some "garbage" laying around which can be removed.
You can use something like xdiskusage / to find out, what is occupying your precious disk space.
But if you don't understand the concept of a file system, maybe it is easier to find someone else to do it for you.
I had a very similar issue, it turned out to be a 40 gig log file from a "neverending" build which had been running for 8 hours

Understanding Linux partitions with Amazon EC2

I am relatively new to Linux. In one of our projects, we use amazon's EC2 instance for processing of some files. We upload files to S3 server after processing. EC2 instance is booted using an existing AMI
Recently I got an error no space left on disk, hence processing of files was halted. I cleaned up some older files and the processing continued.
Now when I look at available space using df -h
Filesystem Size Used Avail Use% Mounted on
/dev/xvda1 9.9G 5.7G 3.7G 61% /
none 3.7G 0 3.7G 0% /dev/shm
/dev/xvdb 414G 199M 393G 1% /mnt
/dev/xvdc 414G 199M 393G 1% /data
I can see my files are effecting only /dev/xvda1.
I have following queries
What is the use of other partitions when I can see my files only effecting /dev/xvda1
It looks like we are only using 10 GB of space effectively and other is being wasted. How can I use other space? Can I move some disk space to /dev/xvda1 or directly store files in other areas?
As you can see from the output of df -h, there are two large partitions mouted on /mnt and /data respectively. I suggest that you use those partitions by processing the files in one of those directories. If you cannot move where the processing happens for some reason, you can remount the partitions in the appropriate place.
If for example your files are processed in the directory /var/mydir and you cannot change that, do the following (as root):
umount /mnt
mount /dev/xvdb /var/mydir
You can use the other partition as well of course if you prefer that.

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