Tutorials – HowTos i-Trop cluster

Howtos cluster i-Trop

Description HowTos for i-Trop Cluster
Author Ndomassi TANDO (
Creation date 08/11/19
Modification date 01/02/2024



Architecture of the i-Trop cluster :

The i-Trop computing cluster is made up of a set of computing servers accessible via a front-end machine. Connections to these compute servers are made via this master machine, which ensures the distribution of the different analyses between the machines available at any given moment.

The computing cluster is composed of :

  • 1 master machine
  • 1 san bay for temporary storage of project data up to 800TB
  • 32 CPU computing nodes with a total capacity of 1148 cores and 6329GB of RAM and a GPU server with 8 RTX 2080 graphics cards..

Here is the architecture:

Connecting to a server in ssh from a Windows machine
System Softwares Description url
mobaXterm an advanced terminal for Windows with an X11 server and an SSH client Download
putty Putty allows to connect to a Linux server from a Windows machine . Télécharger
Transfer files from your computer to Linux servers with SFTP
Systems Softwares Description url
filezilla FTP and SFTP client Download
View and edit files locally or on a remote server
Type url
Distant, console mode nano Tutorial
Distant, console mode vi Tutorial
Distant, graphic mode komodo edit Télécharger
Linux & windows éditeur Notepad++ Télécharger

How to : Add ssh keys to connect to the cluster

Follow the instructions here:

How to : Transfer files with filezilla sftp

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

  1. Put the Logon Type to "key File" and choose the id_rsa.ppk key retreived before
  2. 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:
    • 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 then press OKs

From a MAC or Linux:

Open terminal application and type the following command:


with login: your cluster account

How to : Reserve one or several cores of a node

Cluster uses Slurm ( 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, 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.

Features Description Nodes
512 allows to select 512 GB RAM memory nodes in highmem partition node5, node28,node29,node30
avx allows to select nodes with avx processors node0, node1, node4, node5, node7, node17, node18, node20, node21, node22, node23, node24, node25, node26, node27, node28, node29, node31
BEAST allows to select nodes to use BEAST with beagle node4, node7, node28, node29, node30
dell allows to select dell nodes node28,node29,node30
geforce allows to choose gpu nodes with geforce graphical card node26
infiniband allows to select infiniband nodes to speed up your data transfer node0, node1, node4, node5, node7, node8, node11, node17, node20, node21, node22, node24, node25, node26, node27
rtx2080 allows to select nodes with rtx2080 gpu cards node26
xeon allows to select nodes with intel xeon processors node0, node1, node5,node8, node10, node11, node12, node13, node14, node15, node16, node17, node18, node20, node21, node22, node23, node24, node25, node27
xeon-gold allows to select nodes with intel xeon-gold processors node4, node7, node26, node28, node29, node30, node31

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:

srun constraint=avx --pty bash -i

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

srun -p highmem --constraint=512,infiniband --pty bash -i

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

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

Be careful:On and the nodes, the /users and the /home partitions contain the same data . This is not the case for : /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:

The infiniband network (  allows users to have access to an high speed network to transfer their data from the san to the nodes or between infiniband nodes.

Only certain nodes are equiped with infiniband for now :  node0, node1, node4, node5, node7, node8, node9, node11, node17, node20, node21, node22, node23, node24, node25, node26, node27

To use the infiniband network, we have to add the "-ib" siffix to the alias of the machine, for example san will become san-ib, node0 will become node0-ib etc...

Use the options    -p partition ( with partition being the node partition) --constraint=infiniband to reserve one or several cores on a infiniband node:

For example, we want to reserve an infiniband node on highmem partition in a interactive mode, type the following command:

srun -p highmem --constraint=infiniband --pty bash -i

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, 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


        $ 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:

## 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 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.

partition role nodes list Number of cores Ram
short short jobs < 1 day (high priority,interactive jobs) node2,node13,node14,node15,node16,node18,node19 12 cores 48 à 64 Gb
normal jobs < 7 days node0,node1,node17,node20,node21,node22,node23,node24 20 to 48 cores 64 to 144Gb
long <7 dayss< long jobs< 45 days node3,node8,node9,node10,node11,node12 12 to 24 cores 48 to 96 Gb
highmem jobs with memory needs node4,node5, node7,node27,node28,node29,node30 24 to 112 cores 144 to 512 Gb
global partition for the GLOBAL project node31 112 cores 512 Gb
supermem jobs with important memory needs node25 40 coeurs 1 To
gpu analyses on GPU cores node26 24 cpus and 8 GPUS cores 192 Go

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/

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/

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


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.



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