How to Fix: “warning: device is not properly aligned” with Parted

Because you are on this page I assume you have received the same warning I did. “warning: device is not properly aligned”. I allocated a new 1 TB iSCSI drive and I attached it to the initiating server. After the iSCSI device was connected I partitioned it to use 100% of the disk. Then I attempted to format the partition with the XFS file system using the following command.

mkfs.xfs /dev/sdb1 

I immediately got the following response:

warning: device is not properly aligned /dev/sdb1
Use -f to force usage of a misaligned device 

Finding the fix for “device is not properly aligned”

So I did some digging and came across this article about how to properly align the partition. I followed the post to grab the following values from the device.

[root@server ~]# cat /sys/block/sdb/queue/optimal_io_size
1048576
[root@server ~]# cat /sys/block/sdb/queue/minimum_io_size
131072
[root@server ~]# cat /sys/block/sdb/alignment_offset
0
[root@server ~]# cat /sys/block/sdb/queue/physical_block_size
131072 

Following the formula that was outlined (optimal_io_size + alignment_offset) / physical_block_size. And got the following results: (1048576 + 0) / 131072 = 8. I plugged that information into parted, which resulted in mixed results.

(parted) mklabel gpt                                                      
Warning: The existing disk label on /dev/sdb will be destroyed and all data on this disk will be lost. Do you want to continue?
Yes/No? Yes 
                                                              
(parted) mkpart primary 8s 100%
Warning: You requested a partition from 4096B to 1074GB.                  
The closest location we can manage is 17.4kB to 1074GB.
Is this still acceptable to you?
Yes/No? Yes     
                                                          
Warning: The resulting partition is not properly aligned for best performance.
Ignore/Cancel? Ignore 
                                                    
(parted) align-check optimal 1                                            
1 not aligned

Making Sense of the Parted Alignment Response

So my drive was still not properly aligned, but I had some better info which would help me fix the problem. So let’s break down the Parted commands

(parted) mklabel gpt 

Destroyed the existing partition table and cleared things out to start fresh.

(parted) mkpart primary 8s 100%

This command told Parted to create a new primary partition starting at sector 8 and use the rest of the drive. The response that came from this command gave me the clue that I needed to fix the alignment.

Warning: You requested a partition from 4096B to 1074GB.
The closest location we can manage is 17.4kB to 1074GB.

The warning output indicated that 8 sectors of 512B would only come to 4096B or 4kB. But Parted could only adjust the alignment to 17.4kB, so this was still out of alignment as the rest of the output indicated. That gave me the clue I needed to fix it though.

Alignment Fixed

Knowing now that Parted could only get within 17.4kB of the start of my drive I adjusted the sectors to match that. Since 8 sectors was 4096B, I adjusted it to be an even number of sectors beyond the 17.4kB point. Choosing 32768kB, or 64 sectors. This change yielded the following results.

(parted) mklabel gpt
Warning: The existing disk label on /dev/sdb will be destroyed and all data on this disk will be lost. Do you want to continue?
Yes/No? Yes                                                               

(parted) mkpart primary 64s 100%

(parted) align-check optimal 1
1 aligned

(parted) quit                                                             
Information: You may need to update /etc/fstab.

The partitioning was successful, using the 64 sector starting point pushed it beyond the 17.4kB point. Then it was properly aligned. I formatted the partition with XFS and all went swimmingly.

[root@server ~]# mkfs.xfs /dev/sdb1
 specified blocksize 4096 is less than device physical sector size 131072
 switching to logical sector size 512
 meta-data=/dev/sdb1              isize=256    agcount=32, agsize=8191872 blks
          =                       sectsz=512   attr=2, projid32bit=0
 data     =                       bsize=4096   blocks=262139648, imaxpct=25
          =                       sunit=32     swidth=256 blks
 naming   =version 2              bsize=4096   ascii-ci=0
 log      =internal log           bsize=4096   blocks=128000, version=2
          =                       sectsz=512   sunit=32 blks, lazy-count=1
 realtime =none                   extsz=4096   blocks=0, rtextents=0

Now the device is formatted, mounted, and working like a champ. Who would have known that a simple offset of 32kB could make such a problem.

If you are working with iSCSI then you may find you need to force disconnect and reconnect iSCSI on from time to time. Check out my post on how I handle that.

Rename a file that starts with a hyphen/dash

While working on your *nix based system you may run into this issue from time to time. The file may have a hyphen (-) at the start of the filename because of user error. Or it may have been added by a malicious bit of software. However the hyphen got there it can be a pain to deal with. In this post we will answer how to rename a file that starts with a hyphen.

The first time I encountered a filename like this was while searching the files of a compromised website. The offending malware had created several different new files on the site. And one had been created with a starting hyphen in the filename. This causes issues when you run ‘rm’ to remove the file.

rm -filename.php

The hyphen typically tells a command line utility to anticipate an execution option. So in this case the ‘rm’ command attempts to interpret -filename.php as an option. This would just cause ‘rm’ to return the following on a linux based machine.

rm: invalid option -- 'l'
Try `rm --help' for more information.

Both -f and -i are options for the command so when it gets to ‘l’ it assumes it is just an invalid option. So this becomes an issue when you try to remove or otherwise edit/manipulate a file with a hyphen in the name.

Dealing with the hyphenated filename

Fortunately there is a relatively easy method to deal with a file that starts with a hyphen/dash. Adding a double dash (–) before the filename will fix it.

 rm -- -filename.php

This behavior should be universal for GNU/Linux commands. The double dash/double hyphen tells the command that no more command line options will be given. As a result your favorite command will ignore any further dashes and allow you to mv/cp/rm the file.

So now you know how to rename a file that starts with a hyphen on the command line. Hopefully that makes your life a little better.

I originally learned of this technique from this helpful post on superuser.com.

Want to learn how to recursively delete specific files, check out this post to find out how.

Recursive Find and Replace on the Command Line

The Problem

Recently I moved a website that used a ton of legacy php code from the clients production server to a development location. After the move was complete I found that the previous developers had been extremely sloppy. Rather than having a single location/file for DB credentials, they had it in 4 places.

After I figured out where all the locations for DB credentials were I started getting Open_Basedir errors. The original developer had hard coded the web root location hundreds of times in hundreds of files. For just a moment I felt just a bit overwhelmed, then I remembered that I have the terminal to solve problems like this.

The Solution: Recursive Find and Replace on the Command Line

After a bit of research I came up with the following command to recursively search through the entire codebase. When an instance the old web root is detected it replaces it with the correct one.

grep -rl [search for string] . | xargs sed -i s@[search for string]@[replace with string]@g

Or another example with actual search/replace strings

grep -rl /var/www/vhosts/example.com/httpdocs . | xargs sed -i s@/var/www/vhosts/example.com/httpdocs@/var/www/vhosts/newdomain.com/subdomain/dev@g

That command breaks down in the following manner.

“grep -rl” searches recursively for the string you specified “/var/www/vhosts/example.com/httpdocs” starting in the current directory “.”, the “-r” option specifies the recursive search, and “-l” specifies that the system should return only the filenames that contain the string.

those results are then piped “| ” into “sed”, the “-i” option specifies that it should make the changes in place. Then the find replace sequence in this case “s@[search for string]@[replace with string]@g”. The “@” signs could be almost any other value, typically they are a “/” but in this case the strings to find and replace both had “/” in each one so it wouldn’t work as the bordering character. So replacing the “/” with “@” helps SED keep on track. It could easily have been a “#” or “$”, just use what you need to depending on your string.

And with that I was home free no more Open_Basedir issues. Thanks to the command line recursive find and replace all those entries didn’t have to be done by hand.

Thanks Linux Shell

Here are some of the resources that I used when researching this topic:

Find and Replace string in all files recursive using grep and sed

Now you’ve learned to perform a command line recursive find and replace, why not read this post. Learn how to recursively delete specific files using the command line.