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computing [2025/12/11 17:26] – 130.190.59.47computing [2025/12/19 15:34] (current) – admin
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 #### QuantumESPRESSO #### QuantumESPRESSO
  
-To run QE at the moment, use:+First you need to set up the DIAMOND GUIX channel by following the instructions here: https://gricad-gitlab.univ-grenoble-alpes.fr/diamond/guix/guix-channel 
 + 
 +Next, you can install QE using:
  
 ```bash ```bash
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 mpirun -np 192 pw.x -npool 8 -in < pwscf.in > pwscf.out mpirun -np 192 pw.x -npool 8 -in < pwscf.in > pwscf.out
 ``` ```
 +
 +
 +### Shared conda environments
 +
 +You can get access to the natively installed `conda` using:
 +
 +```
 +source /applis/environments/conda.sh
 +```
 +
 +then we store shared environments in `/bettik/uhrinm/camml/envs`, so for example you can access the shared `allegro` environment by using:
 +
 +```
 +conda activate /bettik/uhrinm/camml/envs/allegro
 +```
 +
 +be careful when `pip install`ing to make sure whatever you install does not conflict with what is already there, or you make break the environment for everyone else.
 +
  
 ## National resources ## National resources
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 At this point you are ready for accessing to IDRIS: At this point you are ready for accessing to IDRIS:
  
-1. Open a terminal and type ''ssh agalan@rotule.univ-grenoble-alpes.fr'', where, instead of ''agalan'' you should type your agalan username. Usually it corresponds to the surname followed by the first letter of your name (so John Smith becomes ''ssh smithj@rotule.univ-grenoble-alpes.fr'').+1. Open a terminal and type ''ssh <agalan>@rotule.univ-grenoble-alpes.fr'', where, instead of ''<agalan>'' you should type your agalan username. Usually it corresponds to the surname followed by the first letter of your name (so John Smith becomes ''ssh smithj@rotule.univ-grenoble-alpes.fr'').
 2. It asks you for the password: it's your agalan password (not the IDRIS one). 2. It asks you for the password: it's your agalan password (not the IDRIS one).
-3. Now you should be in agalan@rotule. Type ''ssh login_idris@jean-zay.idris.fr'', where the ''login_idris'' is your user login for IDRIS received by e-mail.+3. Now you should be in agalan@rotule. Type ''ssh <login_idris>@jean-zay.idris.fr'', where the ''<login_idris>'' is your user login for IDRIS received by e-mail.
 4. Now you are asked for the password, which is the concatenation of the two parts explained above. At the first login, you will be asked to change it with a new one and to repeat it twice. More details about the procedure and about the requirements of the password are in the Section "Passwords" of [this page](http://www.idris.fr/static/intro/doc_nouvel_utilisateur-eng.html). 4. Now you are asked for the password, which is the concatenation of the two parts explained above. At the first login, you will be asked to change it with a new one and to repeat it twice. More details about the procedure and about the requirements of the password are in the Section "Passwords" of [this page](http://www.idris.fr/static/intro/doc_nouvel_utilisateur-eng.html).
  
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 You are in IDRIS.  You are in IDRIS. 
- 
- 
  
 #### From IDRIS to camml-codes #### From IDRIS to camml-codes
  
-Now that you are in IDRIS, you may need to run our Python libraries under the [''camml-codes''](https://github.com/camml-lab/camml-codes). If this is the case, you will need to set up a proper conda environment and then to clone the repo in that environment. +Now that you are in IDRIS, you may need to run our Python libraries under the [''camml-codes''](https://github.com/camml-lab/camml-codes). If this is the case, you will need to set up a proper Conda environment and then to clone the repo in that environment. 
  
-To this end, you will not need to install Conda, since miniforge is already available on the cluster. However, you will need to follow some best practices. In particular, when a new Conda environment is created, all files are stored by default in ''$HOME/.conda''. This is far from ideal, as ''$HOME'' is limited in both space and inodes. It is therefore preferable to store everything in ''$WORK/.conda'' and create a symbolic link in ''$HOME'' that points to the target directory. So, if ''$HOME/.conda'' exists already, type +To this end, you will not need to install Conda, since miniforge is already available on the cluster. However, you will need to follow some good practices. In particular, when a new Conda environment is created, all files are stored by default in ''$HOME/.conda''. This is far from ideal, as ''$HOME'' is limited in both space and inodes. It is therefore preferable to store everything in ''$WORK/.conda'' and create a symbolic link in ''$HOME'' that points to the target directory. So, if ''$HOME/.conda'' exists already, type 
  
 ```bash ```bash
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 Further details are [here](http://www.idris.fr/eng/jean-zay/gpu/jean-zay-gpu-python-env-eng.html). Further details are [here](http://www.idris.fr/eng/jean-zay/gpu/jean-zay-gpu-python-env-eng.html).
  
-Now list the available miniforge versions +To list the available miniforge versions, type ''module avail miniforge'', and load miniforge with a command like 
- +
-```bash +
-module avail miniforge +
-``` +
- +
-and load the most recent, like+
  
 ```bash ```bash
 module load miniforge/25.9.1 module load miniforge/25.9.1
 ``` ```
 +
  
 At this point, on the left of your user login, it should have appeared a ''(base)'', similar to the following: At this point, on the left of your user login, it should have appeared a ''(base)'', similar to the following:
  
 ```bash ```bash
-(base) [<user_login>@jean-zay1: ~]$+(base) [<login_idris>@jean-zay1: ~]$
 ``` ```
  
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-Once the new environment is created and you are in thanks to ''conda activate <env_name>'', you need to git clone the ''camml-codes'' on it. However, some of the repos listed therein may be private. On a local machine, this would be solved by generating a key and linking it to your GitHub account. Unfortunately, this will not work here, as IDRIS cannot be ssh'ed on GitHub; indeed, the command ''ssh -T git@github.com'' would give ''ssh: connect to host github.com port 22: Connection timed out''.+Once the new environment is created and activated via ''conda activate <env_name>'', you need to git clone the ''camml-codes'' on it. However, some of the repos listed therein may be private. On a local machine, this would be solved by generating a key and linking it to your GitHub account. Unfortunately, this will not work here, as IDRIS cannot be ssh'ed on GitHub; indeed, the command ''ssh -T git@github.com'' would give ''ssh: connect to host github.com port 22: Connection timed out''.
  
-A workaround for this is the creation of a classic token on GitHub. In particular, access to your GitHub account in your browser. By clicking on your profile image (the small one at the top right of the screen), click then on Settings -> Developer settings -> Personal access tokens -> Tokens (classic) and generate a new classic token. You will be asked to give a short description in the ''Note'' field, choose an expiration date, and select the scopes; for this last purpose, select only ''repo'' and generate the token. Now you should see the token itself: this is the last time you will see it, so copy it somewhere else. +A workaround for this is the creation of a classic token on GitHub. In particular, access to your GitHub account in your browser. By clicking on your profile image (the small one at the top right of the screen), click then on ''Settings'' -> ''Developer settings'' -> ''Personal access tokens'' -> ''Tokens (classic)'' and generate a new classic token. You will be asked to give a short description in the ''Note'' field, choose an expiration date, and select the scopes; for this last purpose, select only ''repo'' and generate the token. Now you should see the token itself: this is the last time you will see it, so copy it somewhere else. 
  
 Now that you have your token, you can use it as the password when cloning private repositories. Now that you have your token, you can use it as the password when cloning private repositories.
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 ``` ```
  
-Remember that, every time you access to IDRIS, you will need to load ''miniforge'', as the ''conda'' command does not exist by default; after that, you'll be able to ''conda activate <env_name>''.+Remember that, every time you access to IDRIS, you will need to load ''miniforge'', as the ''conda'' command does not exist by default; after that, you'll be able to ''conda activate <env_name>''. Please, notice that you cannot use the ''Remote-SSH'' feature from VSCode on IDRIS because of some security restrictions; however, you can use [JupyterHub](http://www.idris.fr/eng/jean-zay/pre-post/jean-zay-jupyterhub-eng.html).
  
  
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 +#### Jean-Zay
  
 +To get an interactive session on Jean-Zay on the A100 partition you can use something like:
 +
 +```
 +salloc --nodes=1 --ntasks-per-node=1 --cpus-per-task=1 --gres=gpu:1 --hint=nomultithread -A iop@a100 -C a100 --time=00:30:00 bash
 +```
  
 +This will give you 1 GPU on 1 node with 1 associated CPU for 30 minutes.  You can change these if you need something different.  Also, make sure that the account (`-A`) is correct, as you may be on a different project.
  
  
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