ISC, RIKEN

Q3. I want to transfer data to another project member free of charge.
A3. If the data is shared between project members, it can be transferred free of charge using the temporary directory /tmp_work.
Although /tmp_work is excluded from usage fees, data that has not been modified for over a week will be automatically deleted.

Below are the steps for user1 to transfer data to user2, who belongs to the same project RBXXXXXX, using /tmp_work:

1. user1 creates a directory under /tmp_work
   user1 logs into HBW2
   [user1@hokusai1 ~]$ cd /tmp_work

2. user1 changes the group owner of the created directory to RBXXXXXX (which user2 belongs to)
   [user1@hokusai1 tmp_work]$ mkdir dir1
   [user1@hokusai1 tmp_work]$ chgrp RBXXXXXX dir1

3. user1 copies the file to the created directory and changes the group owner of the file
   [user1@hokusai1 tmp_work]$ cd dir1
   [user1@hokusai1 dir1]$ cp ~/file1 .
   [user1@hokusai1 dir1]$ chgrp RBXXXXXX file1

4. user2 copies the transferred file to their own directory
   user2 logs into HBW2
   [user2@hokusai1 ~]$ cd /tmp_work/dir1
   [user2@hokusai1 dir1]$ cp file1 ~/

A1. Please follow the steps below to set up the Jupyter environment.

• Miniconda Installation
  This example installs Miniconda into a conda directory under the home directory. Adjust the path as needed.

[username@hokusai1 ~]$ wget -q -P . https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
[username@hokusai1 ~]$ ulimit -u 256
[username@hokusai1 ~]$ bash ./Miniconda3-latest-Linux-x86_64.sh -b -p ./conda
[username@hokusai1 ~]$ vi ~/.bashrc
(snip)
. ~/conda/etc/profile.d/conda.sh

[username@hokusai1 ~]$ conda update -n base conda
[username@hokusai1 ~]$ conda update –all
[username@hokusai1 ~]$ conda list

[username@hokusai1 ~]$ conda activate
[username@hokusai1 ~]$ conda config –append channels conda-forge
[username@hokusai1 ~]$ conda config –append channels bioconda
[username@hokusai1 ~]$ conda config –get

• Jupyter Notebook Installation

[username@hokusai1 ~]$ conda env list
[username@hokusai1 ~]$ conda create -n jupyter python=3.9
[username@hokusai1 ~]$ conda env list

[username@hokusai1 ~]$ conda activate jupyter
(jupyter) [username@hokusai1 ~]$ conda list
(jupyter) [username@hokusai1 ~]$ conda install jupyter matplotlib

• Run an Interactive Job

(jupyter) [username@hokusai1 ~]$ vi jupyter.sh
#!/bin/bash
hostname
. ~/conda/etc/profile.d/conda.sh
conda activate jupyter
export XDG_RUNTIME_DIR=””
jupyter-notebook –no-browser –port=8889 –ip=0.0.0.0
*Specify an unused port for –port*

(jupyter) [username@hokusai1 ~]$ salloc –partition=mpc –account=RB999999 –nodes=1 –ntasks=1 –time=1-00:00:00
[username@hokusai1 ~]$ srun jupyter.sh
bwmpcXXX
(snip)
To access the server, open this file in a browser:
file:///lustre/home/username/.local/share/jupyter/runtime/jpserver-904033-open.html
Or copy and paste one of these URLs:
http://bwmpcXXX:8889/～
http://127.0.0.1:8889/～

• Access Jupyter Notebook

From your PC, set up port forwarding and access the login node:
$ ssh -L 8889:bwmpcXXX:8889 username@hokusai.riken.jp

Then, open the URL such as http://127.0.0.1:8889/~ that was shown when running srun jupyter.sh in your browser.