How can I set the disk partition alignment using linux tools?

I took this from the Netapp best practices guide for aligning partitions on iscsi volumes but it should hold true since your goal is to set the starting sector to the appropriate value. In your case, the 64 can be changed to whatever is applicable per the SQL best practices guide.

Enter expert mode in fdisk and change the starting LBA of the partition to a value that is evenly divisible by 8. In the following example, the default starting sector is 63 and we will change it to 64 because 64 is evenly divisible by 8. The default starting sector chosen by fdisk is based on the size of the LUN. fdisk uses the LUN size to calculate a pseudo geometry which can vary between different versions of fdisk.

Command (m for help): x

Expert command (m for help): b
Partition number (1-4): 1
New beginning of data (63-62926604, default 63): 64

Due to 4 KiB sector issues, most of the tools will be updated:

• ATA 4 KiB sector issues
• The 4 KiB Sector Performance Issue