Deploying Polarity Server Virtual Machine on Azure

• Setup the Virtual Machine

  • Basics

  • Disk

  • Networking

  • Management, Advanced

  • Tags

  • SSH Access

• Configuring Disks

  • Get Disk Names

  • Partition Disks

  • Format Disks

  • Mount the Partitions

• Install Polarity Server

  • Install the Polarity License

  • Update FQDN in Polarity Config

  • Tune PostgreSQL

    • Polarity Server with 16 GB of RAM

  • Polarity Server with 32 GB of RAM

  • Polarity Server with 64 GB of RAM

Setup the Virtual Machine

The following guide walks through setting up a Polarity Server within the Azure Virtual Machine environment using Polarity provided CentOS 7 RPMs. Within Azure, navigate to Virtual Machines and add a new one.

Basics

Option	Value
Virtual Machine Name	polarity-server
Region	Please pick appropriate region for your users
Availability options	No infrastructure redundancy required
Image	RedHat Enterprise Linux 8.6+
Size	Standard_D4s_v4 - 4 vcpus, 16 GiB memory (Pilot Deployment) Standard_D8s_v4 - 8 vcpus, 32 GiB memory (10-50 users) Standard_D16_v4 - 16 vcpus, 64 GiB memory (50+ users) Please contact [e-mail] for additional sizing information.
Authentication type	SSH public key
Username	azureuser
Inbound port rules	Allow selected ports
Inbound Port Rules	SSH (22), HTTP (80), HTTPS (443) *HTTP inbound access (port 80) is required for LetsEncrypt SSL certificate. Port 80 is redirected to Port 443 by the server and is not required to be open.

Disk

Option	Value
OS disk type	Premium SSD
Encryption type	(Default) encryption at-rest with a platform-managed key
Data disks	Add two additional disks (Create and attach a new disk) Disk 1: Name: polarity-server_DataDiskVar_0 Size: 128 GiB Premium SSD Disk 2: Name: polarity-server_DataDiskApp_0 Size: 64 GiB Premium SSD *Note that while the Polarity server can be run off a single partition (we’d recommend a minimum of 128 GiB for the partition), better performance can be achieved if the PostgreSQL database runs on its own partition (polarity-server_DataDiskVar_0).

Networking

Option	Value
Virtual Network	*Use default
Subnet	*Use default
Public IP	*Use default
NIC network security group	Basic
Select inbound ports	SSH (22), HTTP (80), HTTPS (443) *HTTP inbound access (port 80) is required for LetsEncrypt SSL certificate. Port 80 is redirected to Port 443 by the server and is not required to be open.
Accelerated Networking	On
Load balancing	No

Management, Advanced

Use default settings for both Management, and Advanced configuration unless otherwise required by your organization.

Tags

Apply system tags as required by your organization.

SSH Access

When creating the Virtual Machine, you will be given the option to download the private key in PEM format. Download the key and keep it in a safe place. If you are using the pem key with Putty you will need to convert it into the ppk format using the PuttyGen application https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html

Configuring Disks

Most command will need to be run as root either via sudo or changing to the root user.

The following instructions provide information on how to setup two partitions on your Polarity Server. If you have other tools for partitioning your disks you can skip the below instructions. You will want to have /var on one partition for the database (128+ GiB recommended), and /app on another partition (64+ GiB recommended).

Once the VM is up and running SSH into the server to begin the configuration process. To start we will configure the two additional disks we added when creating the server.

We added two additional disks when setting up the VM. The first 128 GiB disk is will be used to mount /var onto. The /var directory contains our PostgreSQL database and other system logs.

The second 64 GiB disk will be used to mount /app which contains the Polarity server code, Polarity server logs, integrations, and integration logs.

To set up the disks we will need to do the following:

1. Get the names of the disks

2. Create partitions using fdisk

3. Format the disks to XFS using mkfs.xfs

4. Move /var to the new 128 GiB disk and mount the disk

5. Mount the new 64 GiB disk to /app

Get Disk Names

To check the names of the disk use the command lsblk

[azureuser@polarity-server ~]$ lsblk
NAME   MAJ:MIN RM  SIZE RO TYPE MOUNTPOINT
fd0      2:0    1    4K  0 disk
sda      8:0    0   30G  0 disk
├─sda1   8:1    0  500M  0 part /boot
└─sda2   8:2    0 29.5G  0 part /
sdb      8:16   0   32G  0 disk
└─sdb1   8:17   0   32G  0 part /mnt/resource
sdc      8:32   0  128G  0 disk
sdd      8:48   0   64G  0 disk
sr0     11:0    1 1024M  0 rom

In the output above you can see that our 128 GiB disk meant for /var is named sdc and our 64 GiB disk meant for /app is named sdd. The disks should also be represented as files in the /dev directory.

The disk names may be flipped depending on the order you added the disks to the Virtual Machine. If the disk names are different, ensure /var is mapped to the 128 GiB disk, and that /app is mapped to the 64 GiB disk.

Partition Disks

Now that we have the disk names we will create partitions on both disks. We’ll start with sdc:

fdisk /dev/sdc

Type n to create a new partition and then p for a primary partition.

Command (m for help): n
Partition type:
   p   primary (0 primary, 0 extended, 4 free)
   e   extended
Select (default p):

Use the default partition settings which will create a single primary partition across the entire disk.

Finally, you will need to write the partition to the disk by typing w.

Command (m for help): w
The partition table has been altered!

Calling ioctl() to re-read partition table.
Syncing disks.

Repeat the same process for /dev/sdd

fdisk /dev/sdd

When running lsblk you will now see the partitions sdc1 and sdd1

[azureuser@polarity-server ~]$ lsblk
NAME   MAJ:MIN RM  SIZE RO TYPE MOUNTPOINT
fd0      2:0    1    4K  0 disk
sda      8:0    0   30G  0 disk
├─sda1   8:1    0  500M  0 part /boot
└─sda2   8:2    0 29.5G  0 part /
sdb      8:16   0   32G  0 disk
└─sdb1   8:17   0   32G  0 part /mnt/resource
sdc      8:32   0  128G  0 disk
└─sdc1   8:33   0  128G  0 part 
sdd      8:48   0   64G  0 disk
└─sdd1   8:49   0   64G  0 part 
sr0     11:0    1 1024M  0 rom

Format Disks

Now that the disks are partitioned we can format them with xfs using the utility mkfs.xfs

mkfs.xfs /dev/sdc1
mkfs.xfs /dev/sdd1

Mount the Partitions

The final step is to mount the new partitions we created. We’ll start with sdc1 which is the 128 GiB disk as we will need to first transfer the current /var contents.

mkdir /mnt/newvar
mount /dev/sdc1 /mnt/newvar

Next we will copy the current contents of /var to the new location

rsync -aqxPX /var/* /mnt/newvar

The flags on rsync are very important. In particular the X flag will ensure selinux contexts are copied.

Now that the contents of /var have been copied we can unmount /mnt/newvar

umount /mnt/newvar/

Next, we’ll mount our /app directory onto sdd1. Since this directory does not currently exist we do not need to copy any contents into it:

mount /dev/sdd1 /app

Next we’ll want to get the UUID values for our two disks so we can permanently add the mount points to our /etc/fstab file. We can use the blkid command to get the UUIDs of the disks:

[azureuser@polarity-server ~]$ blkid
/dev/sdb1: UUID="025f92de-eae0-4443-b815-59b670e17e9d" TYPE="ext4"
/dev/sdc1: UUID="a868cbc7-20cb-430d-820f-1b602164d07d" TYPE="xfs"
/dev/sdd1: UUID="13ea2266-14db-4159-8544-5a53abe8347a" TYPE="xfs"
/dev/sda1: UUID="fa2f8157-21c9-43b6-85e3-ff04422dfa00" TYPE="xfs"
/dev/sda2: UUID="12907c8a-6b2f-4981-b94c-f3cd772270a7" TYPE="xfs"

Copy down the UUID value for /dev/sdc1 and /dev/sdd1. Next, open the /etc/fstab file for editing and add the following two lines to the bottom. Make sure the UUID for /app maps to the 64 GiB drive, and that the UUID for /var maps to the 128 GiB drive.

vi /etc/fstab

Then add the following two lines to the bottom of the file and save the changes.

UUID=13ea2266-14db-4159-8544-5a53abe8347a /app                    xfs     defaults        0 2
UUID=a868cbc7-20cb-430d-820f-1b602164d07d /var                    xfs     defaults        0 3

Your UUID values will be different than those above

Restart the virtual machine to finish (can be done from the Azure web interface).

When the virtual machine restarts, SSH in and check to make sure all your partitions were mounted correctly.

[azureuser@polarity-server ~]$ lsblk
NAME   MAJ:MIN RM  SIZE RO TYPE MOUNTPOINT
fd0      2:0    1    4K  0 disk
sda      8:0    0   30G  0 disk
├─sda1   8:1    0  500M  0 part /boot
└─sda2   8:2    0 29.5G  0 part /
sdb      8:16   0   32G  0 disk
└─sdb1   8:17   0   32G  0 part /mnt/resource
sdc      8:32   0  128G  0 disk
└─sdc1   8:33   0  128G  0 part /var
sdd      8:48   0   64G  0 disk
└─sdd1   8:49   0   64G  0 part /app
sr0     11:0    1 1024M  0 rom

You should see the sdc1 partition (128 GiB) with a mountpoint of /var and the sdd1 partition (64 GiB) with a mount point of /app.

Install Polarity Server

Now that our disks are configured we’re ready to install the Polarity Server.

Please contact your Polarity customer success representative for the latest installation instructions on your preferred Operating System.

[e-mail]

Supported operating systems are RHEL 7, Amazon Linux 2, RHEL 8 and Oracle Linux 8.

Once the Polarity Software is installed you can continue with the below steps.

Install the Polarity License

At this point you will need to install your Polarity License provided to you by your Polarity support or customer success team. The license file will be named polarity.lic. Upload the polarity.lic license file to the Polarity Server.

Copy the polarity.lic file to the license directory

cp polarity.lic /app/polarity-server/license/polarity.lic

Ensure the license file is owned by the polarityd user

chown polarityd:polarityd /app/polarity-server/license/polarity.lic

Finally restart your server so the license is loaded

systemctl restart polarityd

You can now navigate to the polarity web interface by opening a browser (Chrome is recommended) and navigating to https://<your-polarity-server>

You can login with the default user admin and the password PolarityServer2015!

Update FQDN in Polarity Config

By default the Polarity server will assume the FQDN for your server matches the server hostname. If this is not the case, you will need to modify the Polarity Server config file to set the appropriate config.

To modify the Polarity server config begin by opening the config file in an editor.

vi /app/polarity-server/config/config.js

Find the setting rest.fullyQualifiedDomainName and set it to your FQDN

"rest": {
   "fullyQualifiedDomainName": "your.fqdn.com"
}

Save the change and restart the server:

systemctl restart polarityd

Tune PostgreSQL

The following parameters were changed from their default values on the PostgreSQL database. To edit the settings open the postgresql.conf file located at /var/lib/pgsql/13/data/postgresql.conf.

vi /var/lib/pgsql/13/data/postgresql.conf

Adjust settings per the table below and then restart PostgreSQL and the Polarity Server

systemctl restart postgresql-13
systemctl restart polarityd

Polarity Server with 16 GB of RAM

Setting	Value
max_connections	100
shared_buffers	1843MB
work_mem	18MB
maintenance_work_mem	896MB
random_page_cost	1.5 *If using SSDs, otherwise leave unchanged
max_wal_size	4GB
effective_cache_size	5500MB
cpu_tuple_cost = 0.0030	0.0030
cpu_index_tuple_cost	0.0010
cpu_operator_cost	0.0005

Polarity Server with 32 GB of RAM

Setting	Value
max_connections	100
shared_buffers	4700MB
work_mem	47MB
maintenance_work_mem	2355MB
random_page_cost	1.5 *If using SSDs, otherwise leave unchanged
max_wal_size	4GB
effective_cache_size	14GB
cpu_tuple_cost = 0.0030	0.0030
cpu_index_tuple_cost	0.0010
cpu_operator_cost	0.0005

Polarity Server with 64 GB of RAM

Setting	Value
max_connections	100
shared_buffers	10GB
work_mem	100MB
maintenance_work_mem	5GB
random_page_cost	1.5 *If using SSDs, otherwise leave unchanged
max_wal_size	4GB
effective_cache_size	30GB
cpu_tuple_cost = 0.0030	0.0030
cpu_index_tuple_cost	0.0010
cpu_operator_cost	0.0005