15.2. Using Terminal access

• Using Terminal access
• Example: using of Environment Modules for the Cloud Pipeline runs
• Example: using of Slurm for the Cloud Pipeline's clusters

Terminal access is available to the OWNER of the running job and users with ADMIN role. With sufficient permissions, Terminal access can be achieved to any running job.
For more information see 13. Permissions.

Also you can get a terminal access to the running job using the pipe CLI. For more details see here.

All software in the Cloud Pipeline is located in Docker containers, and we can use Terminal access to the Docker container via the Interactive services.
This can be useful when:

• usage of a new bioinformatics tool shall be tested;
• batch job scripts shall be tested within a real execution environment;
• docker image shall be extended and saved (install more packages/bioinformatics tools) - see 10.4. Edit a Tool.

Using Terminal access

Both Pipelines and Tools can be run as interactive services. The example below shows launching tool scenario:

1. Navigate to the list of registered Tools and search for the Tool required (e.g. "base-generic-centos7").
   
2. Go to the Tool page and click the arrow near the Run button → Select "Custom Settings".
   
3. Launch Tool page form will load (it's the same form that is used to configure a batch run). The following fields shall be filled:
   • Node type
   • Disk size
   • Cloud Region
   • "Start idle" box should be chosen. Click the Launch button when all above parameters are set.
     
4. Once a run is scheduled and configured SSH hyperlink will appear in the "Run Log" form in the right upper corner of the form.
   Note: This link is only visible to the owner of the run and users with ROLE_ADMIN role assigned.
   
   Note: Also you can find this link at the Active Runs panel of the main Dashboard:
   
5. Clicking the SSH link will load a new browser tab with an authenticated Terminal.
   Note: If an unauthorized user will load a direct link, "Permission denied" error will be returned.
   

Example: using of Environment Modules for the Cloud Pipeline runs

Configure of Environment Modules using is available only for users with ADMIN role.

The Environment Modules package provides for the dynamic modification of a user's environment via modulefiles.

In the example below, we will use Modules to switch between two versions of Java Development Kit.

1. At the beginning we will create a storage for all JDK versions files and modulefiles. For that: open the Library, click Create + → Storages → Create new object storage
2. While creating - specify a storage name and mount point, e.g. /opt/software:
   
   Click the Create button.
3. Open the created storage and create two folders in it:
   • app - here we will upload JDK files
   • modulefiles - here we will create modulefiles for each JDK version
     
4. Open the modulefiles folder, create the jdk folder in it.
5. Open the jdk folder, create modulefile for the JDK ver. 9.0.4 - name it 9.0.4:
   
6. Click the file name, click the Fullscreen button at the file content panel:
   
7. At the popup click the EDIT button and input the modulefile content, e.g. for the JDK ver. 9.0.4:
   
   Save it.
8. Repeat steps 5-7 for the JDK ver. 11.0.2. At the end you will have two modulefiles in the jdk folder:
   
9. Open System Settings popup, click the Preferences tab, select Launch section.
   Into the launch.env.properties field add a new variable - CP_CAP_MODULES_FILES_DIR. That variable specify path to the source modulefiles.
   
   As you can see - during the run, when the storage created at step 2 will be mounted to the node in the specified mount-point (/opt/software), created above JDK modulefiles will be available in the modulefiles folder created at step 3 - by the path /opt/software/modulefiles.
   Save and close the Settings popup.
10. Go to the Tool page, open the tool page you want to use the Environment Modules with and click the arrow near the Run button → Select "Custom Settings".
    
11. At the Launch page expand Advanced section.
12. In the Limit mounts field select the storage created at step 2 (see more details here).
13. Click the Add system parameter button
14. In the popup select the CP_CAP_MODULES item and click the OK button:
    
    CP_CAP_MODULES parameter enables installation and using the Modules for the current run. While installing, Modules will be configured to the source modulefiles path from the CP_CAP_MODULES_FILES_DIR launch environment variable (that was set at step 9). If CP_CAP_MODULES_FILES_DIR is not set - default modulefiles location will be used.
    
15. Launch the tool.
16. Open Run logs page, wait until InstallEnvironmentModules task will appear and check that the Modules was installed successfully:
    
17. Wait until SSH hyperlink will appear in the right upper corner. Click it.
18. In the terminal run the command module use to check the ource path to the modulefiles:
    
19. Now, we will install JDK. For the ver. 9.0.4 run the following commands:

# Download "jdk 9.0.4" archive
wget https://download.java.net/java/GA/jdk9/9.0.4/binaries/openjdk-9.0.4_linux-x64_bin.tar.gz
# Extract archive content
tar -zxf openjdk-9.0.4_linux-x64_bin.tar.gz
# Copy "jdk 9.0.4" files into the mounted data storage
cp -r jdk-9.0.4 /opt/software/app/jdk-9.0.4

For the ver. 11.0.2 run the following commands:

# Download "jdk 11.0.2" archive
wget https://download.java.net/java/GA/jdk11/9/GPL/openjdk-11.0.2_linux-x64_bin.tar.gz
# Extract archive content
tar -zxf openjdk-11.0.2_linux-x64_bin.tar.gz
# Copy "jdk 11.0.2" files into the mounted data storage
cp -r jdk-11.0.2 /opt/software/app/jdk-11.0.2

Now, you can check the facilities of the Environment Modules package.
Load the available modulefiles list:

Load the JDK ver. 11.0.2:

Switch to the JDK ver. 9.0.4:

Unload all JDK versions:

Example: using of Slurm for the Cloud Pipeline's clusters

Slurm is an open source, highly scalable cluster management and job scheduling system for large and small Linux clusters.

In the example below, we will use Slurm for performing the simplest batch job.

1. Open the Tools page, select a tool and its version (Note: in our example we will use Ubuntu 18.04). Hover over the v button near the Run button and click the "Custom settings" item in the dropdown list.
2. At the Launch page expand "Exec environment" section and click the "Configure cluster" button:
   
3. In the appeared popup click the Cluster tab. Set the count of "child" nodes, tick the "Enable Slurm" checkbox and click the OK button to confirm:
   
4. Launch the tool:
   
5. Open the main Dashboard and wait until the SSH hyperlink will appear at the Active Runs panel for the just-launched tool, then click it:
   
6. The terminal web GUI will appear.
7. At the beginning, let's check general system state, view existing partitions in the system and the list of available nodes. For that, perform the sinfo command:
   
   Only main.q partition is created. All cluster nodes are attached to this partition.
8. To report more detailed information about partition - the scontrol command can be used:
   
   And to display detailed information about one of the nodes, e.g.:
   
9. Now, we'll parallely execute /bin/hostname on all three nodes (-N3 option) and include task numbers in the output (-l option) via the srun command.
   The default partition will be used. One task per node will be used by default:
   
10. For the batch job, create the following script:
    
    This script contains a timelimit for the job embedded within itself (via the --time option after the #SBATCH prefix).
    Script contains the command /bin/hostname that will be executed on the first node in the allocation (where the script runs) plus two job steps initiated using the srun command and executed sequentially.
    To submit a job script for execution over all three nodes use the sbatch command, result will be written to the file (-o option):
    
11. During the script execution you can check the queue of running jobs in priority order via the squeue command:
    
12. The result of the sbatch command performing: