Merge pull request #83 from ARTbio/google_vm

update deployment instruction on GCE

docs/AnalyseGenomes_2023/Google_cloud_Account.md

@@ -1,43 +1,144 @@
 # Get your ![googleCloud logo](images/googlecloud.png){width="200"} coupon and activate it.
-
-
-- We will send you in the Slack board a URL which you will need to access in order to request
+We will send you in the Slack board a URL which you will need to access in order to request
 a Google Cloud coupon.
-- Through this URL, you will be asked to provide your University email address (which must
-belong to either `sorbonne-university.fr` or `u-paris.fr domains`) and your name. An email
-will be sent to you to confirm these details before a coupon is sent to you.
-- Your coupon is valid through: 11/21/2023
-- You can **only request ONE coupon per unique** email address.
-
-# Access to your Google Cloud dashboard
-
-The coupon will drive you to a Google Cloud account (note that the Google Cloud account
-is different from your Gmail account if you have one).
-
-:warning: The coupon does not know by default whether you have already a Google Cloud
-account or not. We assume that most of you never used the Google Cloud resources and therefore
-do not have a Google Cloud account. If you actually have one, do not expect that the coupon
-will feed your account credits. It will activate, another separate account.
 
+Through this URL, you will be asked to provide your University email address and your name.
+This year, valid email addresses have the following domain names
 
+- sorbonne-university.fr
+- etu.sorbonne-universite.fr
+- u-paris.fr
+- univ-rouen.fr
+- etu.unicaen.fr
+- edu.bio.ens.psl.eu
+- u-psud.fr
 
-It is possible that the first thing you will be asked to do is to create a new "project",
-unless the coupon is automatically opening this project.
-
-Try immediately to access to your [Google Cloud dashboard](https://console.cloud.google.com/home/dashboard)
-Then to [Compute engine](https://console.cloud.google.com/compute/instances) and
-_CREATE AN INSTANCE_
+An email
+will be sent to you to confirm these details before a coupon is sent to you.
 
-Use the [documentation here](../bare-galaxy-google/#1-spin-off-a-virtual-machine-bare-galaxy-with-google-cloud-engine)
-or [here](../spin_off_VM) to fill the instance form before start.
+- Your coupon is valid through: 11/20/2024
+- You can **only request ONE coupon per unique** email address.
 
-As soon as you can see
+# Access to your Google Cloud Account
+
+- [x] The coupon will drive you to your newly created Google Cloud account.
+
+    *Note that the Google Cloud account is different from your Gmail account if you have one.*
+
+The logic of Google Cloud Engine accounts... is not that simple ! You should not have to
+dive in. However, we provide you below with a few explanations in case you feel lost.
+
+??? info "Your Google Cloud Account"
+    First, a GCE provides *services* (red line) to your GCE account. These services are
+    listed in the  **main menu** (red arrow).
+
+    Secondly, your GCE account is composed of 1 (your case by default) or multiple **projects**
+    (red ellipse).
+
+    Thirdly, within your GCE account, you have 1 (your case by default) or multiple **comptes de
+    facturation (billing accounts)**. Your active "compte de facturation" is probably named
+    "Compte de facturation des établissements d'enseignement" or something close.
+    It is noteworthy that 1 project is attached to 1 "compte de facturation", whereas 1 "compte
+    de facturation" may be attached to multiple projects.
+
+    Finally, when you use a service (purple rectangle) - in your case **Compute Engine** - you will
+    prompted the first time to activate the API (Application Programming Interface). This is
+    normal behavior.
+
+    ![](images/GCE_main_menu.png){width="400"}
+
+??? info "Your Google Cloud Dashboard"
+    Depending on your navigation, or if you click the upper left logo
+    ![](images/googlecloud.png){width="150"}, you will access the GCE account **dashboard**.
+
+    Basically, the same items as those discussed previously are available in this view. You
+    will find again
+
+    - The main service menu (red arrow)
+    - The project selector (red ellipse)
+    - A quick access to some selected services (red line)
+    - A direct access to the main service you are interested in: **Compute Engine** (purple
+      rectangle)
+
+    ![](images/GCE_dashboard.png){width="800"}
+
+- [x] Click the "Compute Engine" service.
+- [x] Since this is probably the first time you access this service, you have to activate its
+    Application Programming Interface (API)
+
+    ![](images/Google_Engine_API.png){width="300"}
+
+- [x] Then click **CREATE AN INSTANCE** (**CRÉER UNE INSTANCE**)
+    and use the following settings:
+
+??? info "VM settings"
+    - Name: `bare-galaxy`
+    - Region `europe-west6 (Zurich)` (or any region available with you Google coupon). ==As
+    it is unlikely that a single Google zone will be able to provide enough resources
+    to support 18 virtual machines at the same time, we will have to
+    distribute our instances to different zones in Europe and USA==.
+    - Zone: `europe-west6-a` (or `-b` or `-c`)
+    - **Configuration de la machine**
+        - `USAGE général`
+        - Série: `E2`
+        - Type de machine: `PRÉDEFINI` :arrow_forward: `Standard` :arrow_forward: `e2-standard-8`
+    - **Disque de démarrage (Modifier)**
+        - `IMAGES PUBLIQUES`
+        - Système d'exploitation: `Ubuntu`
+        - Version*: `Ubuntu 20.04 LTS`
+        - Type de disque de démarrage: `Disque persistant avec équilibrage`
+        - Taille (Go): ==`200`==
+        - ==SELECTIONNER==
+    - **Pare-feu**
+        - Check `Autoriser le trafic HTTP`
+
+    These settings should look like:
+
+    ![](images/GCE_spin.png){: style="width:600px"}
+    ![](images/GCE_OS.png){: style="width:450px"}
+    ![](images/GCE_firewall.png){: style="width:450px"}
+
+As soon as you can see the instance spot turning green,
 
 ![running instance](images/instance_check.png)
 
-==Please report in the Slack of Analyse des Génomes 2022.==
-
-:warning: **If you have troubles to get a running instance with a green spot, please,
-do not wait for the 29/11/2022 at 13:30 to say it because it may be to late**
-
-
+you can connect it using the ssh web console
+
+- [x] Connect to the VM using the ssh web console
+
+Roll down the `ssh` menu in the control pannel and select the first option
+`Ouvrir dans une fenêtre du navigateur`
+
+![Select ssh session in browser](images/select_ssh.png)
+
+**This opens a web ssh shell session to control your VM:**
+
+![](images/web_ssh_console.png)
+
+- [x] In this console, type:
+    ```
+    lsb_release -a && lscpu | grep 'CPU(s):' && free -h | grep 'Mem:' && df -h | grep '/$'
+    ```
+
+- [x] Copy the result of this command and paste it in the chanel `galaxy` of your Slack
+    `Analyse des Génomes 2023`
+    This should look like:
+??? info "Exemple of returned result"
+    ```
+    drosofff@bare-galaxy:~$ lsb_release -a && lscpu | grep 'CPU(s):' && free -h | grep 'Mem:' && df -h | grep '/$'
+    No LSB modules are available.
+    Distributor ID: Ubuntu
+    Description:    Ubuntu 20.04.6 LTS
+    Release:        20.04
+    Codename:       focal
+    CPU(s):                             8
+    NUMA node0 CPU(s):                  0-7
+    Mem:           31Gi       284Mi        30Gi       0.0Ki       509Mi        30Gi
+    /dev/root       194G  1.9G  192G   1% /
+    ```
+
+- [x] You can now close the console window
+- [x] :warning: Do not forget to stop (or even trash) your instance:
+    ![](images/stop_vm.png){width="500px"}
+
+---

docs/AnalyseGenomes_2023/bare-galaxy-google.md

@@ -3,7 +3,7 @@
 - [x] You have obtained and activated your Google Coupon for this training as described in
 [Appendix 1](../Google_cloud_Account)
 - [x] You have accessed to the Google dashboard and tested Starting and Stopping a virtual
-machine (VM) instance as described in [Appendix 2](../spin_off_VM)
+machine (VM) instance as described in [Appendix 1](../Google_cloud_Account)
 
 ### 1. Spin off a virtual Machine `bare-galaxy` with ![](images/google-padok.png){: style="width:30px"} Google Cloud Engine
 
@@ -16,14 +16,14 @@ machine (VM) instance as described in [Appendix 2](../spin_off_VM)
 !!! info "with the following settings"
     - Name: `bare-galaxy`
     - Region `europe-west6 (Zurich)` (or any region available with you Google coupon). ==As
-    it is very unlikely that a single Google zone will be able to provide enough resources
-    to support 18 virtual machines at the same time, we will have to coordinate to
+    it is unlikely that a single Google zone will be able to provide enough resources
+    to support 18 virtual machines at the same time, we will have to
     distribute our instances to different zones in Europe and USA==.
     - Zone: `europe-west6-a` (or `-b` or `-c`)
     - **Configuration de la machine**
-        - `OPTIMISEE POUR LE CALCUL` (or `COMPUTE-OPTIMISED`) ==:link:[in case of trouble](#trouble-shouting)==
-        - Série: `C2`
-        - Type de machine: `c2-standard-8 (8 processeurs virtuels, 32 Go de mémoire)`
+        - `USAGE général`
+        - Série: `E2`
+        - Type de machine: `PRÉDEFINI` :arrow_forward: `Standard` :arrow_forward: `e2-standard-8`
     - **Disque de démarrage (Modifier)**
         - `IMAGES PUBLIQUES`
         - Système d'exploitation: `Ubuntu`
@@ -34,9 +34,9 @@ machine (VM) instance as described in [Appendix 2](../spin_off_VM)
     - **Pare-feu**
         - Check `Autoriser le trafic HTTP`
 
-This settings should look like:
+These settings should look like:
 
-![](images/GCE_spin.png){: style="width:450px"}
+![](images/GCE_spin.png){: style="width:600px"}
 ![](images/GCE_OS.png){: style="width:450px"}
 ![](images/GCE_firewall.png){: style="width:450px"}
 
@@ -72,3 +72,5 @@ Roll down the `ssh` menu in the control pannel and select the first option
 **This opens a web ssh shell session to control your VM:**
 
 ![](images/web_ssh_console.png)
+
+---