Tutorials – HowTos i-Trop cluster

Open FileZilla and save the i-Trop cluster into the site manager

In the FileZilla menu, go to File > Site Manager. Then go through these 5 steps:

1. Click on New Site.
2. Add an explicit name.

3. Choose host bioinfo-san.ird.fr

4. Put the Logon Type to "key File" and choose the id_rsa.ppk key retreived before
5. Choose port 22 and press the "Connect" button.

Transferring files

1. From your computer to the cluster : click and drag an text file item from the left local column to the right remote column
2. From the cluster to your computer: click and drag an text file item from he right remote column to the left local column

How to : How to: Connect to the i-Trop cluster via ssh

From a windows computer :

with mobaXterm:

1. Click the session button and choose SSH.
   • In the remote host box, type: bioinfo-master1.ird.fr
   • Check the specify username box and enter your login
2. Choose Advanced SSH settings
3. Tick the « Use private key » box and provides your id_rsa.ppk from your ssh-login.zip then press OKs

From a MAC or Linux:

Open terminal application and type the following command:

ssh login@bioinfo-master1.ird.fr

with login: your cluster account

How to : Reserve one or several cores of a node

Cluster uses Slurm (https://slurm.schedmd.com/documentation.html) to deal with users analyses

It monitors available resources (CPU et RAM ) and allocate them to the users for job launching

When you are connected on bioinfo-master1.ird.fr, you have the possibily to reserve one or serveral cores among them of the 28 nodes available

Reserving one core

Type the following command:

srun -p short --pty bash -i

You will be randomly connected to one of the nodes of the short partition with one core reserved.

Reserving several cores at the same time

Typê the following command:

srun -p short -c X --pty bash -i

With X the number of cores between 2 and 12.

You will be randomly connected to one of the nodes of the short partition with X reserved cores

Reserving one core of a specific node:

type the following command

srun -p short --nodelist=nodeX --pty bash -i

With nodeX belonging to the short partition

Reserving one or several cores of a  node using  --constraint option:

Features/Constraints allow users to make very specific requests to the scheduler. On our cluster, with have different features depending on what you need.

To use one o several features, you have to use the --constraint option

For example, to choose a node with avx processors , you will type:

For example, to choose a node with infiniband and 512 GB of ram on highmem partition, you will type:

How to : Transfer my data from the san bay to nodes

On the cluster, every node has its own local partition called /scratch.

/scratch is used to receive data to analyse, perform analyses on them and produces data results temporarly.
Data on /scratch is hosted for 30 days max expect for the nodes from the long partition until 45 day
It is mandatory to transfer its data to the /scratch of the reserved node before launching its analyses.

The /scratch volumes range from 1TB to 14TB depending on the chosen node.

When the analyses are finished, consider recovering your data.

scp command:

To transfer data between 2 remote servers, we use the command scp

scp -r source destination

There are 2 possible syntaxes:

Retrieve data from the san:

scp -r san:path_to_files/file local_destination

Transfer data to the san:

scp -r /local_path_to_files/file san:remote_destination

Description of the partitions:

User data

Each user has a 100GB personal volume to host data.

This personal folders are hosted into the /users partition of the bioinfo-san.ird.fr

For example for user test is personal folder will be /users/test

Be careful:On bioinfo-master1.ird.fr and the nodes, the /users and the /home partitions contain the same data . This is not the case for bioinfo-san.ird.fr : /home is different from /users

Projects partitions

• /projects/medium: hosts small or temporary projects up to 1000 GB
• /projects/large: hosts normal projects from 1 to 4,9TB
• /projects/xl: hosts big projects from 5 to 9,9TB

share partitions

the /share partition is used to hosts data such as banks or to make available temporary data

Use the infiniband nodes to transfer:

you now have access to the infiniband network, to use it just change the alias san to san-ib to do your transfers

There are 2 possible syntaxes:

Retrieve data from the san:

scp -r san-ib:path_to_files/file local_destination

Transfer data to the san:

scp -r /local_path_to_files/file san-ib:remote_destination

How to : Use module Environnement

Module Environment allows you to dynamically change your environment variable(PATH, LD_LIBRARY_PATH) and then choose your version software.
The nomenclature use for modules is package_name/package_version
Software are divided in 2 groups:

• bioinfo: list bioinformatics software
• system: list system softwares

Displaying the available software

module avail

Displaying the description of a sotfware

module whatis module_name/version

with module_name: the name of themodule.

For example : samtools version 1.7:

module whatis samtools/1.7

load a software:

module load module_name/version

with module_name: module name.

For example : samtools version 1.7:

module load samtools/1.7

unload a software

module unload module_name/version

with module_name: module name.

For example : samtools version 1.7:

module unload samtools/1.7

Displaying the loaded modules

module list

Unloading all the modules

module purge

How to : Launch a job with Slurm

Cluster uses Slurm to manage and prioritize users jobs .

It checks the ressources availables (CPU and RAM ) and allocate them to the users to perform their analyses.

Connected to bioinfo-master1.ird.fr, we can launch a command with srun or a script withsbatch.

Use srun with a command:

If you simply want to launch a command that will be executed on a node:.

        $ srun + command

Example:

        $ srun hostname

will launch the command hostname on the node choose by Slurm..

Use sbatch to launch a script:

Lthe batch mode allows to launch a analysis in several setps defined in a script.

Slurm allows to use several scripts languages
such as bash, perl or python.

Slurm allocates the desired resources and launches the analyses in background.

To be interpreted by Slurm, a script must contain a header with the Slurm options beginning by the keyword #BATCH.

Slurm example script:

#!/bin/bash
## Define the job name
#SBATCH --job-name=test
## Define the output file
#SBATCH --output=res.txt
## Define the number of tasks
#SBATCH --ntasks=1
## Define the execution limit
#SBATCH --time=10:00
## Define 100Mb of memory per cpu
#SBATCH --mem-per-cpu=100
sleep 180 #lance une pause de 180s

to launch a analysis via a script:

$ sbatch script.sh

Withscript.sh the script to use

More Slurm options here: Slurm options

Example of script :

template for a abyss script

How to: Choose a particular partition

Depending on the type of jobs (analyses) you want to run, you can choose between different partitions.

Partitions are analysis queues with specific priorities and constraints such as the size or time limit of a job, the users authorized to use it, etc...

Jobs are prioritized and processed using the resources (CPU and RAM) of the nodes making up these partitions.

The access to the gpu partition is restricted . A request can be made here: : request access to gpu

The partition can be chosen following this scheme:

By default, the chosen partition is the normal partition.

Warning, highmem and highmemplus should only be used for jobs requiring at least 35-40GB of memory..

The supermem partition should be used for large assemblies and jobs requiring more than 100GB of memory.

You can use the htop on a node to visualize the memory consumed by a process.

To choose a partition, use the -p option.

sbatch -p partition
srun -p partition

With partition the chosen partition.

How to : View and delete your data contained in the /scratch partition of the nodes

the 2 scripts are located here/opt/scripts/scratch-scripts/

To see your data contained in the /scratch of the nodes:

sh /opt/scripts/scratch-scripts/scratch_use.sh

and follow the instructions

To delete your data contained in the /scratch partition of the nodes: launch the following command:

sh /opt/scripts/scratch-scripts/clean_scratch.sh


and follow the instructions

How to : Use a singularity container

Singularity is installed on the Itrop Cluster with several versions

Containers are located in /usr/local/bioinfo/containers

You first need to load the environment with the command:

module load singularity or module load singularity/version_wanted

Get help:

Use the command:

singularity help /usr/local/bioinfo/containers/singularity_version/container.simg

with container.simg the container name .

Shell connection to a container:

singularity shell /usr/local/bioinfo/containers/singularity_version/container.simg

Launch a container with only one application:

singularity run /usr/local/bioinfo/containers/singularity_version/container.simg + arguments

Launch a container with several applications:

singularity exec /usr/local/bioinfo/containers/singularity_version/container.simg + tools + arguments

Bind a host folder to a singularity container.

Use the option --bind /host_partition:/container_partition

Example:

singularity exec --bind /toto2:/tmp /usr/local/bioinfo/containers/singularity_version/container.simg + tools + arguments

The container will have access to the file of the partition /toto2 of the host in its /tmp partition

By default, partitions /home, /opt,/scratch, /projects/medium, projects/large/projects/xl, /users and /share are already binded.

How to : Cite the Itrop platform in your publications

Please just copy the following sentence:

“The authors acknowledge the ISO 9001 certified IRD i-Trop HPC (South Green Platform) at IRD montpellier for providing HPC resources that have contributed to the research results reported within this paper.
URL: https://bioinfo.ird.fr/- http://www.southgreen.fr
”

Links

• Related courses : Linux for Dummies
• Related courses : HPC
• Tutorials : Linux Command-Line Cheat Sheet

License

The resource material is licensed under the Creative Commons Attribution 4.0 International License (here).
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