Advanced Kadeploy

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Note.png Note

This tutorial is actively maintained by the Grid'5000 team. If you encounter problems, please report them (see the Support page). Additionally, as it is a wiki page, you are free to make minor corrections yourself if needed. If you would like to suggest a more fundamental change, please contact the Grid'5000 team.

What you need to know before starting

The first thing to understand is that by using kadeploy3, you will be running a command that attempts to remotely reboot many nodes at the same time, and boot them using configuration files hosted on a server. On some clusters, there is a failure rate associated with this operation that is not null. You might therefore experience failures on some operations during this tutorial. In this case, retry. The system doesn't retry for you as this implies waiting for long timeouts in all cases, even those where a 90% success rate is sufficient.

What is an Environment?

Where we describe what exactly is image, kernel, initrd and postinstall

An environment in kadeploy3 is a set of file describing a fully functional Operating System. To be able to setup a Operating System, kadeploy3 needs at least 4 files in the most common cases

  1. An image
    • An image is a file containing all the Operating System files. It can be a compressed archive (ie tgz file) or a dump of a device (ie dd file). In this tutorial, you will learn to build new images for Kadeploy3
  2. A kernel file
    • For the Unix based environment, the kernel file specifies which kernel to boot. It is the full path of the kernel file.
  3. initrd file (optional)
    • For the Linux based environment, the optional initrd file allows to use an initial ramdisk which will be used as the root filesytem at the boot sequence. More information: Initrd on Wikipedia
  4. A postinstall file (optional)
    • The postinstall file allows you to correctly configure all specificity on each cluster. It is not mandatory to specify it for Kadeploy3 environment but if you know what you are doing, feel free to define it.

Once you have this set of files, you can describe your environment to kadeploy3. This description represents an environment in the kadeploy3 sense.

How can I make my own environment?

To create our own environment there are two main ways. One way is to deploy an existing environment and the other way is to create an environment from scratch from a classical ISO installation. In both situations you can customize and save your environment in order to use it again later.

Search and deploy an existing environment

Search an environment

Grid'5000 maintains several reference environments directly available on any site. These environments are based on various versions of debian. And for each debian version you will find different variants of reference environments.
They are called reference environments because they can be used to generate customized environments. You will find different variants of reference environments, depending on which version of debian they are based on.

The description of the reference environments can be found here :

An environment library is maintained on each site in the /grid5000 directory of the frontend node. So all environments available on each site are stored in that directory.

To deploy a registered environment, you must know its name as registered in the Kadeploy database. It is the first information on the environment description page. This tutorial uses the debian9-x64-base environment.

You can also list all available environment in a site by using the kaenv3 command :

Terminal.png frontend:
kaenv3 -l

This command lists all public as well as your private environments.

We distinguish three levels of visibility for an environment :

  • public: All users can see those environments. Only administrators can tag them this way.
  • shared: Every users can see the environment provided they use the -u option to specify the user the environment belongs to.
  • private: The environment is only visible by the user the environment belongs to.

For example, a shared environment added by user user is listed this way :

Terminal.png frontend:
kaenv3 -l -u user

You can also look for a specific version with the --env-version option. All the versions of the environments can be found in /grid5000/images. The version number is the last part of the tgz file.

For example : jessie-x64-min-2016060814.tgz => it's the min Jessie-x64 reference environment version 2016060814

Being able to reproduce the experiments that are done is a desirable feature. Therefore, you should always try to control as much as possible the environment the experiment is done in. Therefore, we will attempt to check that the environment that was chosen in the environment directory is the one available on a given cluster. On the cluster you would like to deploy, type the following command to print information about an environment :

Terminal.png frontend:
kaenv3 -p debian9-x64-base -u deploy

You must specify the user option. In our case, all public environments belong to user deploy.

In theory, you should also check the post-install script. A post-install script adapts an environment to the site it is deployed on.

If everything seems ok, please proceed to the next step.

Make a job on a deployable node

By default, Grid'5000 nodes are running on the production environment, which already contains most of the important features and can be used to run experiments. But you will not have administrative privileges (root privileges) on these nodes. So you will not be able to customize these environments at will. In fact, only reference environments can be customized at will. But to have the right to deploy a reference environment on a node, you must supply the option -t deploy when submitting your job.

For this part of the tutorial, job made will be interactive (-I), of the deploy type (-t deploy), on only one machine (-l nodes=1) to do environment customization (we will give ourselves 3 hours with -l walltime=3), which gives us the following command, that will open a new shell session on the frontend node:

Terminal.png frontend:
oarsub -I -t deploy -l nodes=1,walltime=3

Since all Grid'5000 nodes do not necessary have console access, it is recommended in the context of this tutorial to add the option rconsole="YES" to your reservation command.

Terminal.png frontend:
oarsub -I -t deploy -l {"rconsole='YES'"}/nodes=1,walltime=3

Indeed, when you submit a job of the deploy type, a new shell is opened on the frontend node and not on the first machine of the job as for standard jobs. When you exit from this shell, the job ends. The shell is populated with OAR_* environment variables. You should look at the list of available variables to get an idea of the information you can use to script deployment later. As usual, if the job is successfull, you will get the name of the machine allocated to your job with:

Terminal.png frontend:
cat $OAR_FILE_NODES
Warning.png Warning

At the end of a reservation with the options -t deploy, the reserved nodes will be restarted to boot on the standard environment and thus be available to any other user. So you should only use this option -t deploy when you actually intend to deploy a reference environment on the reserved nodes.

Deploy a reference environment

To deploy your environment, you must discover the nodes you were allocated by OAR. The simplest way of doing this is to look at the content of the file whose name is stored in $OAR_FILE_NODES (this variable is labelled $OAR_NODE_FILE too) or the messages displayed when the job was made. This variable $OAR_NODE_FILE simply stores the url of the file containing the FQDN of all your reserved nodes. Deployment happens when you run the following command:

Terminal.png frontend:
kadeploy3 -e debian9-x64-base -m node.site.grid5000.fr

You can automate this to deploy on all nodes of your job with the -f option:

Terminal.png frontend:
kadeploy3 -e debian9-x64-base -f $OAR_FILE_NODES


In order to be able to connect to the node (as root), you must use the -k option and proceed by two ways :

  • You can either specify the public key that will be copied in /root/.ssh/authorized_keys on the deployed nodes :
Terminal.png frontend:
kadeploy3 -e debian9-x64-base -f $OAR_FILE_NODES -k ~/.ssh/my_special_key.pub
  • Or you can supply the -k option without argument. This will automatically copy your ~/.ssh/authorized_keys and replace the /root/.ssh/authorized_keys file on the deployed nodes.
Terminal.png frontend:
kadeploy3 -e debian9-x64-base -f $OAR_FILE_NODES -k

The second case is actually the simplest way. One of its advantages is that after deployments, you will be able to connect directly from your local computer to the deployed nodes, the same way you connect to the frontend of the site were those nodes are.
Once kadeploy has run successfully, the allocated node is deployed under debian9-x64-base environment. It will then be possible to tune this environment according to your needs.

Note.png Note

It is not necessary here, but you can specify destination partition with the -p option. You can find on the Grid5000:Node storage page all informations about the partitions table used on G5K

Connect to the deployed environment and customize it

1. Connection

On reference environments managed by the staff, you can use root account for login through ssh (kadeploy checks that sshd is running before declaring a deployment successful). To connect to the node type :

Terminal.png frontend:
ssh root@node.site.grid5000.fr

In case this doesn't work, please take a look at the kadeploy section of the Sidebar > FAQ

2. Adding software to an environment

Where you learn to install software using the package repository of your distribution on Grid'5000

You can therefore update your environment (to add missing libraries that you need, or remove packages that you don't so that sizes down the image and speeds up the deployment process, etc.) using:

Terminal.png node:
apt-get update
apt-get upgrade
apt-get install list of desired packages and libraries
apt-get --purge remove list of unwanted packages
apt-get clean

Create a new environment from a customized environment

We now need to save this customized environment, where you have a user account, to be able to use this account again each time you deploy it.
The first step to create an environment is to create an archive of the node you just customized. Because of the various implementations of the /dev filesystem tree, this can be a more or less complex operation.

1. Use the provided tools

You can use tgz-g5k to extract a Grid'5000 environment tarball from a running node.

Terminal.png frontend:
tgz-g5k -m node -f ~/path_to_myimage.tgz

This will create a file path_to_image.tgz into your home directory on frontend.

Note.png Note

Please consider the following:

  • If you want to extract a tarball from the Grid'5000 standard environment (i.e., a non-deployed job), you will need to add the option -o to use oarsh/oarcp instead of ssh/scp
  • If you want tgz-g5k to access the node with a custom user id, you can use the option -u myCustomeId (default is root)
  • You can find more information on tgz-g5k (e.g., available options, command line examples) by executing tgz-g5k -h. Some implementation details are also available on the man page (man tgz-g5k).

2. Describe the newly created environment for deployments

Kadeploy3 works using an environment description. The easiest way to create a description for your new environment is to change the description of the environment it is based on. We have based this tutorial on the debian9-x64-base environment of user deploy. We therefore print its description to a file that will be used as a good basis:

Terminal.png frontend:
kaenv3 -p debian9-x64-base -u deploy > mydebian9-x64-base.env

It should be edited to change the name, description, author lines, as well as the tarball line. Since the tarball is local, the path should be a simple absolute path (without a leading server://). The visibility line should be removed, or changed to shared or private. Once this is done, the newly created environment can be deployed using:

Terminal.png frontend:
kadeploy3 -f $OAR_NODEFILE -a mydebian9-x64-base.env

This kind of deployment is called anonymous deployment because the description is not recorded into the Kadeploy3 database. It is particularly useful when you perform the tuning of your environment if you have to update the environment tarball several times.

Once your customized environment is successfully tuned, you can save it to Kadeploy3 database so that you can directly deploy it with kadeploy3, by specifying its name:

Terminal.png frontend:
kaenv3 -a mydebian9-x64-base.env

and then (if your environment is named "mydebian9-base"):

Terminal.png frontend:
kadeploy3 -f $OAR_NODEFILE -e mydebian9-base

With kaenv3 command, you can manage your environments at your ease. Please refer to its documentation for an overview of its features.

Deploy an environment from a classical ISO installation

First of all, this method is OS independant, so you can create Kadeploy3 tgz (linux based systems) or ddgz (other systems) images for any kind of OS from a CD/DVD ISO.

This procedure is based on the usage of virtualization (KVM) mechanism to boot the CD/DVD iso of the OS installer. The system will be installed on a physical partition of a node and then copied as a Kadeploy3 system image.

To be sure the installed system will be bootable, we will make the OS installer install the system on the Grid'5000 deployment partition (sda3).

To make this possible, we will deploy the hypervisor's system on the temporary partition and then install the system on the deployment partition.

Preparation

  • Download your the CD/DVD ISO of your OS installer (say OS_ISO) and upload it on the frontend of the target site help here
Terminal.png local:
scp OS_ISO USERNAME@access.grid5000.fr:SITE/
  • Make a reservation with 1 node, with the deployment mode and the destructive mode (to be able to deploy on the temporary partition), two hours should be enough.
Terminal.png frontend:
oarsub -I -t deploy -t destructive -l nodes=1,walltime=2
  • Deploy a minimal system on the node's temporary partition, use your ssh key (since Grid'5000 is more Debian friendly, let's say Debian/debian9)
Terminal.png frontend:
kadeploy3 -e debian9-x64-min -p 5 -k -f $OAR_NODEFILE
  • Connect to the node and install the needed packages
Terminal.png frontend:
ssh root@NODE

Run the CD/DVD OS installer using KVM/VNC

  • Preparation
    Copy the OS's ISO to the node
Terminal.png frontend:
scp OS_ISO root@NODE:
  • Connect to the node and install tigervnc-viewer, parted and kvm on the system.

First update the packages definition

Terminal.png NODE:
apt-get -y update

Then install the needed packages

Terminal.png NODE:
apt-get install -y tigervnc-viewer parted kvm
  • Clean the old system's partition /dev/sda3
Terminal.png NODE:
echo -e 'd\n3\nn\np\n\n\nt\n3\n0\nw\n' | fdisk /dev/sda && sync && partprobe /dev/sda
  • Launch the virtual machine, booting on the OS's ISO, using VNC output
Terminal.png NODE:
kvm -drive file=/dev/sda -cpu host -m 1024 -net nic,model=e1000 -net user -k fr -vnc :1 -boot d -cdrom OS_ISO
Note.png Note

This is currently hard to build an image from KVM for nodes that network devices need specific drivers (bnx2, ...)

To be sure your node network device is compatible with the e1000e driver you can check the API using:

Terminal.png frontend:
curl -s -k https://api.grid5000.fr/stable/grid5000/sites/SITE/clusters/CLUSTERS/nodes/NODE

(The node has to be specified by basename: griffon-42.nancy.grid5000.frgriffon-42)

  • Connect to the frontend using SSH X11 forwarding and get the screen of our virtual machine using VNC
Terminal.png laptop:
ssh -Y root@NODE.SITE.g5k 'vncviewer :1'
Note.png Note

If your OS installer is changing the screen resolution, your vncviewer will be closed, you'll just have to relaunch the command to get the screen back

Warning.png Warning

Installation process IMPORTANT instructions:

  • You MUST not format the /dev/sda disk. When you are asked about partitioning the disk, select manual (and not guided).
  • You MUST install your system on /dev/sda3. Create the partition, if it does not exist. The mount point of this partition should be "/"
  • The system size of this partition should be limited to Grid'5000's deployment partition default size (16GiB)
  • You must install an SSH server
  • A bootloader should be installed on the partition /dev/sda3 and not on the MBR

  • Install the system
Note.png Note

after the installation process, the virtual machine will fail to boot, it's normal. You can close vncviewer and kvm

Customize the OS

  • Create the mounting point directory
Terminal.png frontend:
ssh root@NODE 'mkdir -p /mnt/myos'
  • Mount the partition
Terminal.png frontend:
ssh root@NODE 'partprobe'
Terminal.png frontend:
ssh root@NODE 'mount /dev/sda3 /mnt/myos'
Note.png Note

If this command fails, you can try to use this command first: partprobe /dev/sda

  • If you want to :
    • add a custom script that dynamically setup your node's hostname, you can take a look at /mnt/myos/etc/dhcp/dhclient-enter-hooks.d/.
    • disable selinux: example for Centos, put "SELINUX=disable" in /mnt/myos/etc/selinux/config
    • modifying the DNS by editing /etc/resolv.conf
  • Unmount the partition
Terminal.png frontend:
ssh root@NODE 'umount /mnt/myos'

Create a Kadeploy3 image of the filesystem of our OS

  • Save the filesystem in a tgz archive with tgz-g5k (tgz-g5k documentation is available here)
Terminal.png frontend:
tgz-g5k -m NODE -r /dev/sda3 -f IMAGE_FILE.tgz
  • Create an environment description file IMAGE_DESC_FILE such as:
---
name: IMAGE_NAME
version: 1
description: My OS Image
author: me@domain.tld
visibility: private
destructive: false
os: linux
image: 
  kind: tar
  compression: gzip
  file: /path/to/IMAGE_FILE.tgz
postinstalls: 
- archive: server:///grid5000/postinstalls/g5k-postinstall.tgz
  compression: gzip
  script: g5k-postinstall --net debian
boot: 
  kernel: /path/to/the/kernel/in/the/image
  initrd: /path/to/the/initrd/in/the/image
multipart: false
filesystem: ext4
partition_type: 0x83
Note.png Note

You can use Grid'5000 files for the postinstall

Note.png Note

For linux systems, most of times the path to the kernel file is /vmlinuz and the path to the initrd is /initrd.img. You can locate those files by connecting to NODE (like in the previous section using mount) and checking the /mnt/myos directory.

  • Test it !
Terminal.png frontend:
kadeploy3 -a IMAGE_DESC_FILE -m NODE -k
  • Add it to kadeploy (so that you can use the parameter -e IMAGE_NAME like the default g5k environments)
Terminal.png frontend:
kaenv3 -a IMAGE_DESC_FILE

Use disk(s) as I want

In some cases, kadeploy default handling of partitions is too limited and we need to use disks as we want (e.g. to deploy our environment in an optimal way). To do that there are two main ways:

  • simply deploy on another existing partition (sda2 or sda5)
  • repartition disks entirely and/or use several disks (such as sdb or sdc on hercule cluster)

Deploy on sda2 or sda5

First, as this kind of deployment will break node standard operation, you must tell to OAR that it should be redeployed entirely after the reservation with the -t destructive option:

Terminal.png frontend:
oarsub -t deploy -t destructive -l nodes=1,walltime=1 -p "cluster='hercule'" -I

Then you can deploy on sda2 or sda5 with the -p [2,5] option:

Terminal.png frontend:
kadeploy3 -e debian9-x64-nfs -f $OAR_NODEFILE -p 2 -k

Deploy on additional disks

First, as this kind of deployment will break node standard operation, you must tell to OAR that it should be redeployed entirely after the reservation with the -t destructive option:

Terminal.png frontend:
oarsub -t deploy -t destructive -l nodes=1,walltime=1 -p "cluster='hercule'" -I

Then you can deploy on an additional disk such as sdb with the -b sdb option:

Terminal.png frontend:
kadeploy3 -e debian9-x64-base -f $OAR_NODEFILE -b sdb -k

Format additional disks

In Kadeploy3, we can easily customize the deployment's automata. It's possible to add custom pre, post or substitute operations to each steps. In a custom operation it's possible to: send a file, execute a command or run a script.

This feature is explained in Kadeploy3's documentation (available on Kadeploy3's website) in the section 4.2.2, Use Case 10 and 4.7.

In this example, we will add some custom operations to the deployment workflow: our nodes have two additional hard disks and we want them to be formated during the deployment process.

We want to a new partition scheme such as:

  • classical grid5000 partitioning on sda
  • data1 ext4 on sdb1
  • data2 ext2 on sdc1

The three following sections describe how to perform such an operation.

1. Make the reservation in destructive mode

First of all, when you do your reservation, you must tell to OAR that it should redeploy the node entirely after the reservation with the -t destructive parameter:

Terminal.png frontend:
oarsub -t deploy -t destructive -l nodes=1,walltime=2 -p "cluster='hercule'" -I

2. Describe the custom operations

After that you have to create a file that describe the custom operations you want to be performed during the deployment. In our example we will first repartition the additional disks (using parted) and then format them (using the script format.sh).

  • The operation description file (let's say custom-partitioning.yml) should look like something like this:
---
# Our custom steps should be performed during the SetDeploymentEnv macro-step
SetDeploymentEnvUntrusted:
  # Custom partitioning step, done after the create_partition_table micro-step
  # In the sample this step is exploded in 4 steps but it can be done in 1 using a single parted command
  create_partition_table:
      post-ops:
        # We send a file on the node
        - action: send
          file: sdb.parted
          # The variable $KADEPLOY_TMP_DIR will be substitued by kadeploy
          destination: $KADEPLOY_TMP_DIR 
          name: send_partition_map_sdb
        # Then we execute the parted command using the previously sent file
        - action: exec
          name: partitioning_sdb
          # The variable $KADEPLOY_TMP_DIR will be substitued by kadeploy
          command: parted -a optimal /dev/sdb --script $(cat $KADEPLOY_TMP_DIR/sdb.parted)
        # Same operation for the second disk
        - action: send
          file: sdc.parted
          destination: $KADEPLOY_TMP_DIR 
          name: send_partition_map_sdc
        - action: exec
          name: partitioning_sdc
          command: parted -a optimal /dev/sdc --script $(cat $KADEPLOY_TMP_DIR/sdc.parted)
  # Custom format step, done after the format_deploy_part micro-step
  format_deploy_part:
      post-ops:
        # We run the script contained in the file 'format.sh'
        - action: run 
          name: format_disks
          file: format.sh
  • The file sdb.parted will look like something like this:
mklabel msdos
u GB mkpart primary ext4 0% 100%
align-check optimal 1
  • The file sdc.parted will look like something like this:
mklabel msdos
u GB mkpart primary ext2 0% 100%
align-check optimal 1
  • The file format.sh will look like something like this:
#!/bin/sh
set -e
# formating /dev/sdb
mkfs -t ext4 -b 4096 -O sparse_super,filetype,resize_inode,dir_index -q /dev/sdb1
# formating /dev/sdc
mkfs -t ext2 -b 4096 -O sparse_super,filetype,resize_inode,dir_index -q /dev/sdc1

3. Run the deployment

Now you can deploy you environment with this custom operation:

Terminal.png frontend:
kadeploy3 -e debian9-x64-min -f $OAR_NODE_FILE -k --custom-steps ./custom-partitioning.yml
Warning.png Warning

In some cases you should increase the step's timeout (for some long formatting for example) see Advanced_Kadeploy#Adjusting timeout for some environments for details.

Note: Both partitions are not mounted on boot. To mount those partitions you should do:

Terminal.png NODE:
mkdir -p /media/data1
Terminal.png NODE:
mkdir /media/data2
Terminal.png NODE:
mount /dev/sdb1 /media/data1
Terminal.png NODE:
mount /dev/sdc1 /media/data2

Use a custom partitioning scheme

In Kadeploy3, we can easily customize the deployment's automata. It's possible to add custom pre, post or substitute operations to each steps. In a custom operation it's possible to: send a file, execute a command or run a script.

This feature in explained in Kadeploy3's documentation (available on Kadeploy3's website) in the section 4.2.2, Use Case 10 and 4.7.


In this example, we will modify the deployment workflow: a different partition will be used for each of the /, /usr, /var, /tmp and /home directories.

Imagine that you want to make your own partitioning scheme like that:

  • swap 2G on primary partition sda1
  • root 18G on primary partition sda2
  • usr 30G on primary partition sda3
  • var 20G on extended partition sda5
  • home 20G on extended partition sda6
  • tmp everything else on extended partition sda7


The four following sections describe how to perform such an operation.

1. Make the reservation in destructive mode

First of all, when you do your reservation, you must tell to OAR that it should redeploy the node entirely after the reservation with the -t destructive parameter:

Terminal.png frontend:
oarsub -t deploy -t destructive -l nodes=1,walltime=2 -I

2. Describe the custom operations

After that you have to create a file that describe the custom operations you want to be performed during the deployment. In our example we will first create apply our custom partitioning scheme, format the partition and the mount them.

  • The operation description file (let's say custom-partitioning.yml) should look like something like this:
---
# Our custom steps should be performed during the SetDeploymentEnv macro-step
SetDeploymentEnvUntrusted:
  # Custom partitioning step that is substitued to the create_partition_table micro-step
  create_partition_table:
    substitute:
      # We send a file on the node
      - action: send
        file: map.parted
        # The variable $KADEPLOY_TMP_DIR will be substitued by kadeploy
        destination: $KADEPLOY_TMP_DIR 
        name: send_partition_map
      # Then we execute the parted command using the previously sent file
      - action: exec
        name: partitioning
        # The variable $KADEPLOY_TMP_DIR will be substitued by kadeploy
        command: parted -a optimal /dev/sda --script $(cat $KADEPLOY_TMP_DIR/map.parted)
  # Custom format step, done after the format_deploy_part micro-step
  format_deploy_part:
    post-ops:
      # We run the script contained in the file 'format.sh'
      - action: run 
        name: format_partitions
        file: format.sh
  # Custom mount step, done after thefmount_deploy_part micro-step
  mount_deploy_part:
    post-ops:
      # We run the script contained in the file 'format.sh'
      - action: run 
        name: mount_partitions
        file: mount.sh
# Hack to disable useless steps
  format_tmp_part:
    substitute:
      - action: exec
        name: remove_format_tmp_part_step
        command: /bin/true
  format_swap_part:
    substitute:
      - action: exec
        name: remove_format_swap_part_step
        command: /bin/true
Note.png Note

In order for Kadeploy to be able to perform the installation correctly, every partitions have to be mounted before the installation process which is done in the macro-step BroadcastEnv

  • The file map.parted will look like something like this:
mklabel msdos
u GB mkpart primary linux-swap 0% 2
u GB mkpart primary ext4 2 20
u GB mkpart primary ext4 20 50
u GB mkpart extended 50 100%
u GB mkpart logical ext4 50 70
u GB mkpart logical ext4 70 90
u GB mkpart logical ext4 90 100%
toggle 2 boot
align-check optimal 1
align-check optimal 2
align-check optimal 3
align-check optimal 4
align-check optimal 5
align-check optimal 6
align-check optimal 7
  • The file format.sh will look like something like this:
#!/bin/sh
set -e

mkfs_opts="sparse_super,filetype,resize_inode,dir_index"

mkswap ${KADEPLOY_BLOCK_DEVICE}1
# / will be formated by Kadeploy since we will precise the -p 2 option
# formating /usr/
mkfs -t ext4 -b 4096 -O $mkfs_opts -q ${KADEPLOY_BLOCK_DEVICE}3
# formating /var/
mkfs -t ext4 -b 4096 -O $mkfs_opts -q ${KADEPLOY_BLOCK_DEVICE}5
# formating /home/
mkfs -t ext4 -b 4096 -O $mkfs_opts -q ${KADEPLOY_BLOCK_DEVICE}6
# formating /tmp/
mkfs -t ext4 -b 4096 -O $mkfs_opts -q ${KADEPLOY_BLOCK_DEVICE}7
Note.png Note

When running a custom script, Kadeploy will export different variables, you can get a list of them by running "kadeploy -i".
A description of each of this variables is available in Kadeploy3's documentation (on Kadeploy3 website) in the section 4.4

  • The file mount.sh will look like something like this:
#!/bin/sh
set -e

# / will be mounted in ${KADEPLOY_ENV_EXTRACTION_DIR} by Kadeploy
# mount /usr
mkdir ${KADEPLOY_ENV_EXTRACTION_DIR}/usr
mount ${KADEPLOY_BLOCK_DEVICE}3 ${KADEPLOY_ENV_EXTRACTION_DIR}/usr/ 
# mount /var
mkdir ${KADEPLOY_ENV_EXTRACTION_DIR}/var
mount ${KADEPLOY_BLOCK_DEVICE}5 ${KADEPLOY_ENV_EXTRACTION_DIR}/var/
# mount /home
mkdir ${KADEPLOY_ENV_EXTRACTION_DIR}/home
mount ${KADEPLOY_BLOCK_DEVICE}6 ${KADEPLOY_ENV_EXTRACTION_DIR}/home/
# mount /tmp
mkdir ${KADEPLOY_ENV_EXTRACTION_DIR}/tmp
mount ${KADEPLOY_BLOCK_DEVICE}7 ${KADEPLOY_ENV_EXTRACTION_DIR}/tmp/

3. Customize the environment's postinstall

In order for our new partitions to be mounted at boot time we can modify the Grid'5000 postinstall files (this customization can also be done by adding another custom operation).

  • First of all we need to know where the postinstall of our environment is located (the field postinstalls/[archive]):
Terminal.png frontend:
kaenv3 -p debian9-x64-base -u deploy
  • Then we decompress it in a temporary directory:
Terminal.png frontend:
tmpdir=$(mktemp -d) && export tmpdir && pushd $tmpdir
Terminal.png frontend:
tar xzf /grid5000/postinstalls/debian-x64-base-2.5-post.tgz
Note.png Note

We asume that the current shell is BASH, if not please replace the "export" instruction

  • Modify the /etc/fstab file:
Terminal.png frontend:
cat dest/etc/fstab
# /etc/fstab: static file system information.
#
# <file system> <mount point>   <type> <options>  <dump>  <pass>
proc            /proc           proc   defaults   0       0
sysfs           /sys            sysfs  defaults   0       0
devpts          /dev/pts        devpts gid=5,mode=620 0   0
tmpfs           /dev/shm        tmpfs  defaults   0       0
<[SWAP_PART]>   none            swap   sw         0       0
<[ROOT_PART]>   /               <[ROOT_FSTYPE]>   errors=remount-ro  0  0
/dev/sda3       /usr            ext4   defaults   1       2
/dev/sda5       /var            ext4   defaults   1       2
/dev/sda6       /home           ext4   defaults   1       2
/dev/sda7       /tmp            ext4   defaults   1       2
  • Regenerate the postinstall archive:
Terminal.png frontend:
tar -czvf ~/custom-post.tgz *
  • Make some cleanup:
Terminal.png frontend:
popd && rm -R $tmpdir
  • Create the environment's description file (let's say custom-env.yml) based on the reference one:
Terminal.png frontend:
kaenv3 -p debian9-x64-base -u deploy | sed -e "s/archive:.*$/archive: \/home\/${USER}\/custom-post.tgz/" -e 's/public/shared/' > custom-env.yml

or

Terminal.png frontend:
kaenv3 -p debian9-x64-base -u deploy > custom-env.yml
Terminal.png frontend:
cat custom-env.yml
--- 
name: custom-env
version: 1
description: Custom env based on Debian 9
author: me@domain.tld
visibility: shared
destructive: false
os: linux
image: 
  kind: tar
  compression: gzip
  file: server:///grid5000/images/debian9-x64-std-2017122808.tgz
postinstalls: 
- script: traitement.ash /rambin
  archive: /home/me/custom-post.tgz
  compression: gzip
boot: 
  kernel: /vmlinuz
  initrd: /initrd.img
multipart: false
filesystem: ext4
partition_type: 131

4. Run the deployment

Finally, we deploy our custom environment with your custom operations:

Terminal.png frontend:
kadeploy3 -a custom-env.yml -f $OAR_NODE_FILE -p 2 -k --custom-steps custom-partitioning.yml
Warning.png Warning

In some case you should increase the step's timeout (for some long formatting for example) see Advanced_Kadeploy#Adjusting timeout for some environments for details.

Tuning the Kadeploy3 deployment workflow

kadeploy3 allows to fully modify the deployment workflow.

First of all you have to understand the different steps of a deployment. There are 3 macro-steps:

  1. SetDeploymentEnv: this step aims at setting up the deployment environment that contains all the required tools to perform a deployment ;
  2. BroadcastEnv: this step aims at broadcasting the new environment to the nodes and writing it to disk;
  3. BootNewEnv: this step aims at rebooting the nodes on their new environment.

kadeploy3 provides several implementations for each of those 3 macro-steps. You can consult that list in the kadeploy3 page. In Grid'5000, we use the following steps by default in all our clusters :

  • SetDeploymentEnv -> SetDeploymentEnvUntrusted : use an embedded deployment environment
  • BroadcastEnv -> BroadcastEnvKascade : use the Kascade tool to broadcast the environment
  • BootNewEnv -> BootNewEnvKexec : the nodes use kexec to reboot (if it fails, a BootNewEnvClassical, classical reboot, will be performed)

Each one of these implementations is divided in micro steps. You can can see the name of those micro-steps if you use the kadeploy3 option --verbose-level 4. And to see what is actually executed during those micro-steps you can add the debug option of kadeploy3 -d

Terminal.png frontend:
kadeploy3 -f $OAR_FILE_NODES -k -e debian9-x64-base --verbose-level 4 -d > ~/kadeploy3_steps

This command will store the kadeploy3 standard output in the file ~/kadeploy3_steps. Lets analyse its content:

Terminal.png frontend:
grep "Time in" ~/kadeploy3_steps

This command will print on the terminal all the micro-steps executed during the deployment process, and the time spent for each execution. Here are the micro-steps that you should see:

  1. SetDeploymentEnvUntrusted-switch_pxe: Configures the PXE server so that this node will boot on an environment that contains all the required tools to perform the deployment,
  2. SetDeploymentEnvUntrusted-reboot: Sends a reboot signal to the node
  3. SetDeploymentEnvUntrusted-wait_reboot: Waits for the node to restart.
  4. SetDeploymentEnvUntrusted-send_key_in_deploy_env: Sends kadeploy's user's ssh public key into the node's authorized_keys to ease the following ssh connections,
  5. SetDeploymentEnvUntrusted-create_partition_table: Creates the partition table
  6. SetDeploymentEnvUntrusted-format_deploy_part: Format the partition where your environment will be installed. This partition is by default /dev/sda3
  7. SetDeploymentEnvUntrusted-mount_deploy_part: Mounts the deployment partition in a local directory.
  8. SetDeploymentEnvUntrusted-format_tmp_part: Format the partition defined as tmp (by default, /dev/sda5)
  9. SetDeploymentEnvUntrusted-format_swap_part: Format the swap partition
  10. BroadcastEnvKascade-send_environment: Sends your environments into the node and untar it into the deployment partition.
  11. BroadcastEnvKascade-manage_admin_post_install: Execute post installation instructions defined by the site admins, in general to adapt to the specificities of the cluster: console baud rate, Infiniband,...
  12. BroadcastEnvKascade-manage_user_post_install: Execute user defined post installation instructions to automatically configure its node depending on its cluster, site, network capabilities, disk capabilities,...
  13. BroadcastEnvKascade-send_key: Sends the user public ssh key(s) to the node (if the user specified it with the option -k).
  14. BroadcastEnvKascade-install_bootloader: Properly configures the bootloader
  15. BootNewEnvKexec-switch_pxe: Configure the PXE server so that this node will boot on the partition where your environment has been installed
  16. BootNewEnvKexec-umount_deploy_part : Umount the deployment partition from the directory where it has been mounted during the step 7.
  17. BootNewEnvKexec-mount_deploy_part : ReMount the deployment partition
  18. BootNewEnvKexec-kexec: Perform a kexec reboot on the node
  19. BootNewEnvKexec-set_vlan: Properly configure the node's VLAN
  20. BootNewEnvKexec-wait_reboot: Wait for the node to be up.

That is it. You now know all the default micro-steps used to deploy your environments.

Note.png Note

It is recommended to consult the Grid5000:Node storage page to understand which partition is used at which step.

Adjusting timeout for some environments

Since kadeploy3 provides multiple macro-steps and micro-steps, its is important to detect when a step in failing its execution. This error detection is done by using timeout on each step. When a timeout is reached, the nodes that have not completed the given step are discarded from the deployment process.
The value of those timeouts varies from one cluster to another since they depend on the hardware configuration (network speed, hard disk speed, reboot speed, ...). All defaults timeouts are entered in the configurations files on the kadeploy3 server. But you can consult the default timeouts of each macro-steps by using the command kastat3

Terminal.png frontend:
kastat3 -I
 Kadeploy server configuration:
 Custom PXE boot method: PXElinux
 Automata configuration:
   hercule:
     SetDeploymentEnv: SetDeploymentEnvUntrusted,1,600
     BroadcastEnv: BroadcastEnvKascade,0,1000
     BootNewEnv: BootNewEnvKexec,0,180; BootNewEnvHardReboot,0,900
   nova:
     SetDeploymentEnv: SetDeploymentEnvUntrusted,1,600
     BroadcastEnv: BroadcastEnvKascade,0,1000
     BootNewEnv: BootNewEnvKexec,0,150; BootNewEnvHardReboot,0,600
 ...


kadeploy3 allow users to change timeouts in the command line. In some cases, when you try to deploy an environment with a large tarball or with a post-install that lasts too long, you may get discarded nodes. This false positive behavior can be avoided by manually modifying the timeouts for each step at the deployment time.

For instance, in our previous example, the timeout of each steps are:

  • SetDeploymentEnvUntrusted: 143
  • BroadcastEnvKascade: 111
  • BootNewEnvKexec: 33

You can increase the timeout of the second step to 1200 seconds with the following command :

Terminal.png frontend:
kadeploy3 -e my_big_env -f $OAR_FILE_NODES -k --force-steps "SetDeploymentEnv|SetDeploymentEnvUntrusted:1:450&BroadcastEnv|BroadcastEnvKascade:1:1200&BootNewEnv|BootNewEnvClassical:1:400"

Set Break-Point during deployment

As mentioned in the section above, a deployment is a succession of micro steps that can be consulted and modified.
Moreover, kadeploy3 allows user to set a break-point during deployment.

Terminal.png frontend:
kadeploy3 -f $OAR_FILE_NODES -k -e debian9-x64-base --verbose-level 4 -d --breakpoint BroadcastEnvKascade:manage_user_post_install

This command can be used for debugging purpose. It performs a deployment with the maximum verbose level and it asks to stop the deployment workflow just before executing the manage_user_post_install micro-step of the BroadcastEnvKascade macro-step. Thus you will be able to connect in the deployment environment and to manually run the user post install script to debug it.

Warning.png Warning

At the current state of kadeploy3, it is not possible to resume the deployment from the break-point step. Thus you will have to redeploy you environment from the first step. This feature will be implemented in future version of kadeploy3.

Modify the deployment workflow with custom operations

In Kadeploy3, we can easily customize the deployment's automata. It's possible to add custom pre, post or substitute operations to each steps. In a custom operation it's possible to: send a file, execute a command or run a script.

This feature in explained in Kadeploy3's documentation (available on Kadeploy3's website) in the section 4.2.2, Use Case 10 and 4.7.

You can find examples of deployment workflow tuning in the following sections:

Note.png Note

When running a custom script, Kadeploy will export different variables, you can get a list of them by running kadeploy3 -I.
A description of each of this variables is available in Kadeploy3's documentation (on Kadeploy3 website) in the section 4.4

Customizing the postinstalls

In Kadeploy3, postinstalls are scripts that are executed after the copy of the image file in order to customize site-specific or cluster-specific aspects. Since the beginning on 2018, on Grid'5000 the same postinstall script (called g5k-postinstall) is used for all reference environments (and is thus compatible with all supported Debian versions and distributions). That script takes parameters in order to define its behaviour (for example, to choose the style of network configuration to use).

The source code for g5k-postinstall is available on gitlab.inria.fr. Its parameters at the time of writing are:

g5k-postinstall [options]
    -d, --debug                      Run in debug mode, with output to terminal
    -n, --net t1,t2,t3               Network configuration specification
Valid tags for network specification:
  debian - write config in /etc/network/interfaces
  debian-bridged - write config in /etc/network/interfaces, with a bridge setup (for the std env)
  netplan - write config in /etc/netplan/01-netcfg.yaml (https://wiki.ubuntu.com/Netplan)
  redhat - write config in /etc/sysconfig/network-scripts/*
  traditional-names - use traditional NIC naming (e.g. eth0) instead of predictable
  force-ref-api-names - force the use of the name provided in the reference API
                        (by default, the predictable name determined by the kernel is used)
  hpc - add support for HPC (eg InfiniBand) interfaces
Example: --net debian-bridged,traditional-names,hpc

    -f, --fstab t1,t2,t3             Filesystems configuration specification
Valid tags for filesystems configuration in fstab:
  nfs - include generic NFS mounts (/home, /grid5000)
  site-specific - include site-specific NFS mounts (e.g. /softs)
Example: --fstab nfs,site-specific

    -r, --restrict-user MODE         User restriction mode
Valid modes for user restriction:
  std - if deployed on production partition, restrict to root,oar. else, restrict to the current user (see below)
  current - restrict to root and the user having currently reserved the node
  login:jdoe - restrict to a specific login (e.g. jdoe)
  none - no restriction (DEFAULT)

        --inittab PATTERN
                                     Configure console in inittab.
This is needed for non-systemd systems. Parameters in /proc/cmdline are used.
Example pattern: s0:12345:respawn:/sbin/agetty -L SPEED TTYSX vt100
SPEED and TTYSX are replaced by g5k-postinstall.

        --no-ref-api
                                     Do not use the Reference API
This is useful during initial configuration of new clusters.

        --disable-hacks h1,h2,h3
                                     Hacks to disable
g5k-postinstall includes a number of dirty hacks that can optionally be disabled.
  yeti-megaraid - install the megaraid_sas driver on yeti
Example: --disable-hacks yeti-megaraid

An example environment description using g5k-postinstall is:

$ kaenv3 -p debian9-x64-min
---
name: debian9-x64-min
version: 2018041820
description: Debian Debian9 (min)
author: support-staff@lists.grid5000.fr
visibility: public
destructive: false
os: linux
image:
  file: server:///grid5000/images/debian9-x64-min-2018041820.tgz
  kind: tar
  compression: gzip
postinstalls:
- archive: server:///grid5000/postinstalls/g5k-postinstall.tgz
  compression: gzip
  script: g5k-postinstall --net debian --net traditional-names
boot:
  kernel: "/vmlinuz"
  initrd: "/initrd.img"
  kernel_params: net.ifnames=0 biosdevname=0 modprobe.blacklist=myri10ge
filesystem: ext4
partition_type: 131
multipart: false

Things that you can do are:

  • Use a customized postinstall script: just point the postinstalls/archive/ field to another tar archive. (see README.md and TechTeam:Postinstalls for details)
  • Use different parameters to change the behaviour of the postinstall. Example parameters for various situations are:
    • Debian min environment with traditional NIC naming: g5k-postinstall --net debian --net traditional-names
    • Debian min environment with predictable NIC naming: g5k-postinstall --net debian
    • Debian NFS environment (mount /home, setup LDAP, restrict login to user who reserved the node): g5k-postinstall --net debian --fstab nfs --restrict-user current
    • Debian big environment (NFS + setup HPC networks and mount site-specific directories): g5k-postinstall --net debian --net traditional-names --net hpc --fstab nfs --fstab site-specific
    • RHEL/Centos style for network configuration: g5k-postinstall --net redhat --net traditional-names
    • Ubuntu 1710 or later: NetPlan for network configuration: g5k-postinstall --net netplan
    • Do not do any network configuration (useful for Gentoo), but force serial console settings: g5k-postinstall --net=none --inittab='s0:12345:respawn:/sbin/agetty -L SPEED TTYSX vt100'

Multisite deployment

In order to do a deployment on nodes from differents sites you just have to use the multiserver option of kadeploy : -M So to do a deployment:

kadeploy -M -f file_with_all_nodes -e debian9-x64-std