update hostname to CSD3

materials/02-ssh.md

@@ -106,7 +106,7 @@ After registering for a HPC account, you were sent the following information by
 > 
 > - Username: emailed separately
 > - Password: emailed separately
-> - Host: `train.bio`
+> - Host: `login.hpc.cam.ac.uk`
 > 
 > You were automatically allocated 40GB in `/home/USERNAME/` (backed storage) and 1TB in `/home/USERNAME/rds/hpc-work` (non-backed high-performance "scratch" space for computations). 
 
@@ -122,10 +122,10 @@ Can you identify and navigate to your high-performance compute directory?
 To login to the HPC we run the following from the terminal:
 
 ```bash
-ssh USERNAME@train.bio
+ssh USERNAME@HOSTNAME
 ```
 
-Replacing "USERNAME" by your HPC username. 
+Replacing "USERNAME" by your HPC username and "HOSTNAME" with the name of the server you are accessing. 
 After typing it, you will be prompted for your password. 
 Note that as you type the password nothing shows on the screen - that's normal! 
 The password is still being input. 

materials/05-arrays.md

@@ -289,7 +289,7 @@ Our objective is to automate running these models in parallel on the HPC.
     - Fix the `#SBATCH -a` option - this array should have as many jobs as we have parameter combinations in our CSV file.
     - Fix the `head` command further down the script. This command intends to fetch each line from the CSV parameters file, using the `$SLURM_ARRAY_TASK_ID` variable.
 2. Launch the job with `sbatch` and monitor its progress (`squeue`), whether it runs successfully (`scontrol show job JOBID` or `seff JOBID`), and examine the SLURM output log files. 
-3. Examine the output files in the `results/turing/` folder. Note: to view image files on the HPC, you have to enable X11 forwarding. You can do this by loging in to the HPC using `ssh -Y username@train.bio` (note the `-Y` option). Then, you can preview a PNG file using the `eog` program (for example: `eog results/turing/f0.03_k0.055.png`).
+3. Examine the output files in the `results/turing/` folder. Note: to view image files on the HPC, you have to enable X11 forwarding. You can do this by loging in to the HPC using `ssh -Y username@login.hpc.cam.ac.uk` (note the `-Y` option). Then, you can preview a PNG file using the `eog` program (for example: `eog results/turing/f0.03_k0.055.png`).
 
 :::{.callout-hint}
 The array should have as many numbers as there are lines in our CSV file. However, make sure the array number starts at 2 because the CSV file has a header with column names.

materials/07-files.md

@@ -31,7 +31,7 @@ This program has a graphical interface, for those that prefer it and its use is
 To connect to the remote server (see Figure 3): 
 
 1. Fill in the following information on the top panel:
-  - Host: train.bio
+  - Host: login.hpc.cam.ac.uk
   - Username: your HPC username
   - Password: your HPC password
   - Port: 22
@@ -51,10 +51,10 @@ The syntax is as follows:
 
 ```bash
 # copy files from the local computer to the HPC
-scp -r path/to/source_folder <user>@train.bio:path/to/target_folder
+scp -r path/to/source_folder <user>@login.hpc.cam.ac.uk:path/to/target_folder
 
 # copy files from the HPC to a local directory
-scp -r <user>@train.bio:path/to/source_folder path/to/target_folder
+scp -r <user>@login.hpc.cam.ac.uk:path/to/source_folder path/to/target_folder
 ```
 
 The option `-r` ensures that all sub-directories are copied (instead of just files, which is the default).
@@ -69,10 +69,10 @@ The most common usage is:
 
 ```bash
 # copy files from the local computer to the HPC
-rsync -auvh --progress path/to/source_folder <user>@train.bio:path/to/target_folder
+rsync -auvh --progress path/to/source_folder <user>@login.hpc.cam.ac.uk:path/to/target_folder
 
 # copy files from the HPC to a local directory
-rsync -auvh --progress <user>@train.bio:path/to/source_folder path/to/target_folder
+rsync -auvh --progress <user>@login.hpc.cam.ac.uk:path/to/source_folder path/to/target_folder
 ```
 
 - the options `-au` ensure that only files that have changed _and_ are newer on the source folder are transferred
@@ -112,10 +112,10 @@ Notice that these commands are **run from your local terminal**:
 
 ```bash
 # with scp
-scp -r ~/Desktop/hpc_workshop_files.zip username@train.bio:rds/hpc-work/hpc_workshop/
+scp -r ~/Desktop/hpc_workshop_files.zip username@login.hpc.cam.ac.uk:rds/hpc-work/hpc_workshop/
 
 # with rsync
-rsync -avhu ~/Desktop/hpc_workshop_files.zip username@train.bio:rds/hpc-work/hpc_workshop/
+rsync -avhu ~/Desktop/hpc_workshop_files.zip username@login.hpc.cam.ac.uk:rds/hpc-work/hpc_workshop/
 ```
 
 Once we finish transfering the files we can go ahead and decompress the data folder.