Tag Archives: BASH

CLI

Use BASH to append an incremental suffix to directories

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In migrating Splunk indexes I came across the need to add an incrementing suffix of _(numbers) to a bunch of directories. For example, renaming directories

test
test1
test2
test3

to

test_100
test1_101
test2_102
test3_103

After a bunch of searching I settled on this approach of using a simple bash loop to accomplish this:

I=100; for F in db_*; do mv $F $F\_$I; I=$((I+1)); done

There is an initial variable, I, which is set to 100. The for loop goes through each file beginning with db_ and then renames it adding the proper suffix in the iteration (_###). The last step is to increment the value of I.

Replace I for whatever you want you suffix to begin with and change db_* with whatever the criteria for the files you want to rename are. Simple, but it works.

CLI

Using screen to run interactive programs at startup

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Oftentimes I will encounter programs that weren’t necessarily designed to be automatically run that I want to run on startup. Sometimes that program will have interactive information that you will want to see later, but you still want it to run on startup.

The solution to this particular problem is using screen in combination with su and bash. In my situation, I want to run the HDSurfer plugin on bootup as a different user. The solution I came up is as follows (thanks to superuser.com and stackoverflow.com for the guidance I needed to set this up.)

Install screen

Screen is like having a separate X window session to keep a program running, except it is for console programs. You can attach and detach to this screen whenever you’d like and not worry about the program terminating.

sudo apt-get install screen

Create a script to run your program with all required arguments

In my case I needed to execute the command “python /usr/bin/HDSurferWave/hdsurferwave.py start” as a different user in a screen session (so it wouldn’t terminate when the terminal session did.) To do this,

  • invoke screen with the -dm command (to begin the program in detached mode)
  • issue the bash -c argument afterward to invoke bash
  • Include your desired command after that

My one line script looks like this:

screen -dm bash -c "python /usr/bin/HDSurferWave/hdsurferwave.py start"

Run your script

I use the su command with the -c argument to change the user that will be running the script, as the startup script launches things as root by default (with pre-systemd systems, anyway.) The -s command initiates a shell to launch, and the last argument is the user you want to run as. My launch argument is:

su -c "/usr/bin/HDSurferWave/start.sh" -s /bin/sh nicholas

Configure the script to run on startup

Edit /etc/rc.local and add your script command from above, then mark that file as executable by running chmod +x /etc/rc.local. Note: This will not work with systems using systemd.

 

 

CLI

Manipulate dd output with sed, tr, and awk

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While improving a backup script I came across a need to modify the information output by the dd command. FreeNAS, the system the script runs on, does not have a version of dd that has the human readable option. My quest: make the output from dd human readable.

I’ve only partially fulfilled this quest at this point, but the basic functionality is there. The first step is to redirect all output of the dd command (both stdout and stderr) to a variable (this particular syntax is for bash)

DD_OUTPUT=$(dd if=/dev/zero of=test.img bs=1000000 count=1000 2>&1)

The 2>&1 redirects all output to the variable instead of the console.

The next step is to use sed to remove unwanted information (number records in and out)

sed -r '/.*records /d'

Next, remove any parenthesis. This is due to the parenthesis from dd output messing up the math that’s going to be done later.

tr -d '()'

-d ‘()’ simply tells tr to remove any instance of the characters between the single quotes.

And now, for awk. Awk allows you to manipulate certain pieces of a text file. Each section, separated by a space, is known as a record. Awk lets us edit some parts of text while keeping others intact. My expertise with awk is that of a n00b so I’m sure there is a more efficient way of doing this; nevertheless here is my solution:

awk '{print ($1/1024)/1024 " MB" " " $3 " " $4 " " $5*60 " minutes"  " (" ($7/1024)/1024 " MB/sec)" }'

Since dd outputs its information in bytes I’m having it divide by 1024 twice so the resulting number is now in megabytes. I also have it divide the seconds by 60 to return the number of minutes dd took. Additionally I’m re-inserting the parenthesis removed by the tr command now that the math is correctly done.

The last step is to pipe all of this together:

DD_OUTPUT=$(dd if=/dev/zero of=test.img bs=1000000 count=10000 2>&1)
DD_HUMANIZED=$(echo "$DD_OUTPUT" | sed -r '/.*records /d' | tr -d '()' | awk '{print ($1/1024)/1024 " MB" " " $3 " " $4 " " $5/60 " minutes"  " (" ($7/1024)/1024 " MB/sec)" }')

After running the above here are the results:

Original output:

echo "$DD_OUTPUT"
10000+0 records in
10000+0 records out
10000000000 bytes transferred in 103.369538 secs (96740299 bytes/sec)

Humanized output:

echo "$DD_HUMANIZED"
9536.74 MB transferred in 1.72283 minutes (92.2587 MB/sec)

The printf function of awk would allow us to round the calculations but I couldn’t quite get the syntax to work and have abandoned the effort for now.

Of course all this is not necessary if you have the correct dd version. The GNU version of dd defaults to human readability; certain BSD versions have the option of passing the msgfmt=human argument per here.

Update: I discovered that the awk method above will only print the one line it finds and ignore all other lines, which is less than ideal for scripting. I updated the awk syntax to do a search and replace (sub) instead so that it will print all other lines as well:

awk '{sub(/.*bytes /, $1/1024/1024" MB "); sub(/in .* secs/, "in "$5/60" mins "); sub(/mins .*/, "mins (" $7/1024/1024" MB/sec)"); printf}')

My new all in one line is:

DD_HUMANIZED=$(echo "$DD_OUTPUT" | sed -r '/.*records /d' | tr -d '()' | awk '{sub(/.*bytes /, $1/1024/1024" MB "); sub(/in .* secs/, "in "$5/60" mins "); sub(/mins .*/, "mins (" $7/1024/1024" MB/sec)"); printf}')
CLI

ZFS remote replication script with reporting

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In my experimentation with FreeNAS one thing I found lacking was the quality of reports it generated. I suppose one philosophy is that the smaller the e-mail the better, but my philosophy is that the e-mail should still be legible. Some of the e-mails I get from FreeNAS are simply bizarre and cryptic.

FreeNAS has an option to replicate your ZFS volumes to a remote source for backup. As far as I can tell there is no report e-mail when the replication is done, although there may be a cryptic e-mail if anything failed. I have grown used to daily status e-mails from my previous NAS solution (Debian with homegrown scripts.) I set out to do this with FreeNAS and added a few added features along the way.

My script requires that you have already created an appropriate user and private/public key pair for both the source and destination machines (to allow for passwordless logins.) Instructions on how to do this are detailed below. You can download the script here.

Notes and observations

I learned quite a bit when creating this script. The end result is a script that e-mails me a beautiful report telling me anything that was added or removed since the last backup.

  • I used dd for greater speed as suggested here
  • I learned from here that the -R switch for ZFS send sends the entire snapshot tree.
  • The ZFS diff command currently has a bug where it does not always report deleted files / folders. It was opened two years ago, closed, and then recently re-opened as it is still an issue. It is the reason my script uses both ZFS dff and rsync – so I can continually see the bug in action.
  • When dealing with rsync, remember the / at the end!
  • In bash you can pipe output from a command to a variable.
  • When echoing above variable, make sure you enclose it in quotes to preserve formatting.
  • Use the -r flag in sed -r for extended regex functions
  • In my testing the built in freeNAS replication script didn’t appear to replicated the latest snapshot. Interesting…

Below are the preliminary steps that are needed in order for the script to run properly.

Configure a user for replication

Create users

Either manually or through the FreeNAS UI, create a user that will run the backup script. Create that same user on the remote box (backup server.)

Generate RSA keys

Log into local host and generate RSA keys to allow for passwordless login to the system

cd .ssh
ssh-keygen

Make note of the filenames you gave it (the default is id-rsa and id-rsa.pub)

Authorize the resulting public key

Log into remote host and add the public key of local host in ~/username/.ssh/authorized_keys where username is the user you created above. One way to accomplish this is to copy the public key on the main server and paste it into the authorized keys file of the backup server.

On the main server

(assuming the keyfile name is id-rsa)

cd .ssh
less id-rsa.pub

Copy the output on the screen in its entirety

On the backup server

Paste that public key into the authorized_keys file of the backup user

cd .ssh
vi authorized_keys

Allow the new user to mount filesystems

FreeNAS requires you to specifically allow regular users to mount filesystems as described here.

  1. In the web interface under System > Sysctls > Add sysctl:
    Variable: vfs.usermount
    Value: 1
    Enabled: yes

Grant ZFS permissions to the new user

In order for the dataset creation (full backup) feature to work the user we’ve created needs to have specific ZFS permissions granted as outlined here.

Run this command on both the main and backup servers:

zfs allow backup create,destroy,snapshot,rollback,clone,promote,rename,mount,send,receive,quota,reservation,hold storage

where backup is the new user and storage is the dataset name. I’m pretty sure you can make those permissions a little more fine grained but I threw a bunch of them in there for simplicity’s sake.

Configure HP iLo (optional)

My current backup server is an old HP Proliant server equipped with HP iLo. I decided to add a section in my script that, when enabled in the variables section, would have the script use iLo to power the machine on. If you do not have / wish to use iLo to control your backup server you can skip this section.

First, create a user in ILo and grant it Virtual Power and Reset permissions (all the rest can be denied.)

Next, copy the .pub file you created earlier to your computer so you can go into iLo web interface and upload it. Make sure an iLo user exists and the last part  (the username) of the public key file matches exactly with the user you created in HP iLo.

When I first tried this no matter what I tried I couldn’t get passwordless login to work. After much weeping, wailing, and gnashing of teeth. I finally discovered from here that the -f and -C options of the ssh-keygen command are required for iLo to accept the key. I had to regenerate a private/public key pair via the following options, where backup is the user I created in iLo:

ssh-keygen -b 1024 -f backup -C backup

CLI

Compare two latest ZFS snapshots for differences

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In my previous post about ZFS snapshots I discussed how to get the latest snapshot name. I came across a need to get the name of the second to last snapshot and then compare that with the latest. A little CLI kung-fu is required for this but nothing too scary.

The command of the day is: zfs diff.

zfs diff storage/mythTV@auto-20141007.1248-2h storage/mythTV@auto-20141007.1323-2h

If you get an error using zfs diff, you aren’t running as root. You will need to delegate the diff ZFS permission to the account you’re using:

zfs allow backup diff storage

where backup is the account you want to grant permissions for and storage is the dataset you want to grant permissions to.

The next step is to grab the two latest snapshots using the following commands.

Obtain latest snapshot:

zfs list -t snapshot -o name -s creation -r storage/Documents | tail -1

Obtain the second to latest snapshot:

zfs list -t snapshot -o name -s creation -r storage/Documents | tail -2 | sort -r | tail -1

Putting it together in one line:

zfs diff `zfs list -t snapshot -o name -s creation -r storage/Documents | tail -2 | sort -r | tail -1` `zfs list -t snapshot -o name -s creation -r storage/Documents | tail -1`

While doing some testing I came across an unfortunate bug with the ZFS diff function. Sometimes it won’t show files that have been deleted! It indicates that the folder where the deleted files were in was modified but doesn’t specify any further. This bug appears to affect all ZFS implementations per here and here. As of this writing there has been no traction on this bug. The frustrating part is the bug is over two years old.

The workaround for this regrettable bug is to use rsync  with the -n parameter to compare snapshots. -n indicates to only do a dry run and not actually try to copy anything.

To use Rsync for comparison, you have to do a little more CLI-fu to massage the output from the zfs list command so it’s acceptable to rsync as well as include the full mountpoint of both snapshots. When working with rsync, don’t forget the trailing slash.

rsync -vahn --delete /mnt/storage/Documents/.zfs/snapshot/`zfs list -t snapshot -o name -s creation -r storage/Documents | tail -2 | sort -r | tail -1 | sed 's/.*@//g'`/ /mnt/storage/Documents/.zfs/snapshot/`zfs list -t snapshot -o name -s creation -r storage/Documents | tail -1 | sed 's/.*@//g'`/

Command breakdown:

Rsync arguments:
-v means verbose (lists files added/deleted)
-a means archive (preserve permissions)
-h means human readable numbers
-n means do a dry run only (no writing)
–delete will delete anything in the destination that’s not in the source (but not really since we’re doing -n – it will just print what it would delete on the screen)

Sed arguments
/s search and replace
/.*@ simple regex meaning anything up to and including the @ sign
/  What comes after this slash is what we would like to replace what was matched in the previous command. In this case, we choose nothing, and move directly to the last argument
/g tells sed to keep looking for other matches (not really necessary if we know there is only one in the stream)

All these backticks are pretty ugly, so for readability sake, save those commands into variables instead. The following is how you would do it in bash:

FIRST_SNAPSHOT="`zfs list -t snapshot -o name -s creation -r storage/Documents | tail -2 | sort -r | tail -1 | sed 's/.*@//g'/`"
SECOND_SNAPSHOT="`zfs list -t snapshot -o name -s creation -r storage/Documents | tail -1 | sed 's/.*@//g'/`"
rsync -vahn --delete /mnt/storage/Documents/.zfs/snapshot/$FIRST_SNAPSHOT /mnt/storage/Documents/.zfs/snapshot/$SECOND_SNAPSHOT

I think I’ll stop for now.

CLI

Blow away ZFS snapshots and watch the progress

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For the last month I have had a testing system (FreeNAS) take ZFS snapshots of sample datasets every five minutes. As you can imagine, the snapshot count has risen quite dramatically. I am currently at over 12,000 snapshots.

In testing a backup script I’m working on I’ve discovered that replicating 12,000 snapshots takes a while. The initial data transfer completes in a reasonable time frame but copying each subsequent snapshot takes more time than the original data. Consequently, I decided to blow away all my snapshots. It took a while! I devised this fun little way to watch the progress.

Open two terminal windows. In terminal #1, enter the following:

bash
while [ true ]; do zfs list -H -t snapshot | wc -l; sleep 6; done

The above loads BASH and the runs a simple loop to count the total number of snapshots on the system. The sleep command is only there because it takes a few seconds to return the results when you have more than 10,000 snapshots.

Alternatively you could make the output a little prettier by entering the following:

while [ true ]; do REMAINING="`zfs list -H -t snapshot | wc -l`"; echo "Snapshots remaining: $REMAINING" ; sleep 6; done

In terminal #2, enter the following (taken from here):

bash
for snapshot in `zfs list -H -t snapshot | cut -f 1`
do
zfs destroy $snapshot
done

You can now hide terminal#2 and observe terminal #1. It will show you how many snapshots are left, refreshing the number every 6 seconds. Neat.

CLI

Watch a zpool resilver in freeNAS

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In my experiments with freeNAS and RaidZ I have come to miss some functionality I enjoyed with Linux and mdadm. One such function was being able to watch an array rebuild, or in ZFS parlance, a pool resilvering.

My inability to watch the resilvering stems from the difference between what the watch command in Linux does and what it does in FreeBSD. Watch in BSD snoops on a tty line whereas watch in Linux executes a command repeatedly.

One option is to install a watch utility for BSD that behaves as the Linux watch command; however, freeNAS is a small read only image so installing things isn’t an option.

The way to do it in freeNAS is to use a while loop in the command line. After 20 minutes of googling I realized that there is no easy way to do this in one line like you can in bash (something about things requiring to be on a new line), so I had to settle for a quick script like one outlined here.

My familiarity with scripts comes from BASH, but I quickly found out freeNAS doesn’t ship with BASH.

echo $shell
/bin/csh

edit: It turns out freeNAS does indeed ship with bash! It’s just not the default shell. Simply execute “bash” in the shell and use your familiar bash shell syntax to your heart’s content. The BASH equivalent of the script below is:

while [ true ]; do clear; zpool status; sleep 1; done

I’ll leave the rest in for reference sake.

I did some digging on how to write CSH scripts and thanks to this website was able to write a simple CSH script to execute a given command at a given interval indefinitely.

Here is my C style watch script:

#!/bin/csh

#A simple script to replace the Linux watch functionality. The first input it takes is how many seconds to refresh; the second, the command to run. If the command has arguments (spaces), it must be passed in quotes.

set INTERVAL = "$1"
set COMMAND = "$2"

while ( 1 )
        clear
        $COMMAND
        sleep $INTERVAL
end

I placed this script in the /tmp directory, made it executable by running chmod +x, and then executing it by running ,/script.sh 1 “command”