Difference between revisions of "Using Adastra"
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For people on the "Atmosphères Planétaires" GENCI project who need to open an account on Adastra, here is the procedure: | For people on the "Atmosphères Planétaires" GENCI project who need to open an account on Adastra, here is the procedure: | ||
| − | + | # Go to https://www.edari.fr/utilisateur and log in via Janus or create an account if you don't have a Janus login | |
| − | + | # Click on "se rattacher à un dossier ayant obtenu des ressources" | |
| − | + | # Project number to provide: A0140110391 | |
| − | + | # Ehouarn then receives an email to allow you to join the project. Once he has validated it, you receive a confirmation mail. | |
| − | + | # Once approved, you have to request for an account, click on "CINES: créer une demande d'ouverture de compte" | |
| − | + | # fill in the forms: name, contract end date, CINES, your lab information (LMD is the default) | |
| − | + | # Access IP address 134.157.47.46 , FQDN (Fully Qualified Domain Name): ssh-out.lmd.jussieu.fr | |
| − | + | # Add a second adress : 134.157.176.129 , FQDN: ciclad.ipsl.upmc.fr | |
| − | + | # click on option to have access to CCFR (only important if you have access to other GENCI machines) | |
| − | + | # Security person is Julien Lenseigne (it's all pre-filled, except phone: +33169335172) | |
| − | + | # YOU MUST THEN VALIDATE THE REQUEST: click on the "Valider la saisie des informations" | |
| − | + | # You then receive an automatic mail. You must now download the pre-filled form from e-dari: find "télécharger la demande" and download the pdf. Sign it, and upload it on e-dari "déposer la demande de création de compte" | |
| + | # Wait for your application to be preprocessed by the system... | ||
== A couple of pointers == | == A couple of pointers == | ||
Revision as of 11:47, 13 June 2023
This page provides a summary of examples and tools designed to help you get used with the Adastra environment.
Contents
Getting access to the cluster
For people on the "Atmosphères Planétaires" GENCI project who need to open an account on Adastra, here is the procedure:
- Go to https://www.edari.fr/utilisateur and log in via Janus or create an account if you don't have a Janus login
- Click on "se rattacher à un dossier ayant obtenu des ressources"
- Project number to provide: A0140110391
- Ehouarn then receives an email to allow you to join the project. Once he has validated it, you receive a confirmation mail.
- Once approved, you have to request for an account, click on "CINES: créer une demande d'ouverture de compte"
- fill in the forms: name, contract end date, CINES, your lab information (LMD is the default)
- Access IP address 134.157.47.46 , FQDN (Fully Qualified Domain Name): ssh-out.lmd.jussieu.fr
- Add a second adress : 134.157.176.129 , FQDN: ciclad.ipsl.upmc.fr
- click on option to have access to CCFR (only important if you have access to other GENCI machines)
- Security person is Julien Lenseigne (it's all pre-filled, except phone: +33169335172)
- YOU MUST THEN VALIDATE THE REQUEST: click on the "Valider la saisie des informations"
- You then receive an automatic mail. You must now download the pre-filled form from e-dari: find "télécharger la demande" and download the pdf. Sign it, and upload it on e-dari "déposer la demande de création de compte"
- Wait for your application to be preprocessed by the system...
A couple of pointers
- Connecting to Adastra: For those who had an account on Occigen, we have retained group and login credentials from then; To connect to Adastra you need first go through the LMD gateway (hakim) or the IPSL (Ciclad/Spirit) gateway and then
ssh your_cines_login@adastra.cines.fr
And then you will probably want to switch project using the myproject command, e.g. to switch to "lmd1167" (the old "Atmosphères Planétaires" GENCI project)
myproject -a lmd1167
and to switch to "cin0391" (the 2023-2024 "Atmosphères Planétaires" GENCI project)
myproject -a cin0391
WARNING: when you switch projects, you also switch HOME directory etc.
To get all the info about dedicated environment variables (e.g. paths to SCRATCH, STORE, etc.) you can use
myproject -c
- Changing the password of your CINES account
When your password is close to expiring, CINES asks you to change it on this website : https://rosetta.cines.fr
Please note that you can access this website only if you are on a machine that you declared as a gateway for Adastra. At LMD, we have generally declared hakim.lmd.jussieu.fr (aka ssh-out) and ciclad.ipsl.jussieu.fr as gateway machines. Hakim doesn't have any browser installed, but you can launch firefox on Ciclad and connect to the rosetta website.
If that doesn't work, you will have to mail svp@cines.fr
- Link to the Adastra technical documentation: https://dci.dci-gitlab.cines.fr/webextranet/
Submitting jobs
It's done using SLURM; you need to write up a job script and submit it using sbatch
sbatch myjob
You must specify in the header of the job which project ressources you are using ("cin0391" in our case):
#SBATCH --account=cin0391
Example of an MPI job to launch a simulation
#!/bin/bash
#SBATCH --job-name=job_mpi
#SBATCH --account=cin0391
### GENOA nodes accommodate 96 cores
#SBATCH --constraint=GENOA
### Number of Nodes to use
#SBATCH --nodes=1
### Number of MPI tasks per node
#SBATCH --ntasks-per-node=48
### Number of OpenMP threads per MPI task
#SBATCH --cpus-per-task=1
#SBATCH --threads-per-core=1
###SBATCH --exclusive
#SBATCH --output=job_mpi_%A.out
#SBATCH --time=00:45:00
#source env modules:
source ../trunk/LMDZ.COMMON/arch.env
ulimit -s unlimited
srun --cpu-bind=threads --label gcm_96x96x78_phyvenus_para.e > gcm.out 2>&1
Example of a mixed MPI/OpenMP job to launch a simulation
#!/bin/bash
#SBATCH --job-name=job_mpi_omp
#SBATCH --account=cin0391
### GENOA nodes accommodate 96 cores
#SBATCH --constraint=GENOA
### Number of Nodes to use
#SBATCH --nodes=1
### Number of MPI tasks per node
#SBATCH --ntasks-per-node=24
### Number of OpenMP threads per MPI task
#SBATCH --cpus-per-task=4
#SBATCH --threads-per-core=1
###SBATCH --exclusive
#SBATCH --output=job_mpi_omp_%A.out
#SBATCH --time=00:30:00
#source env modules:
source ../trunk/LMDZ.COMMON/arch.env
ulimit -s unlimited
### OMP_NUM_THREADS value must match "#SBATCH --cpus-per-task"
export OMP_NUM_THREADS=4
export OMP_STACKSIZE=400M
srun --cpu-bind=threads --label gcm_64x48x54_phymars_para.e > gcm.out 2>&1
