From 81096e0684c853de9381289ffb54fc25c5d757d9 Mon Sep 17 00:00:00 2001 From: Danielle Pinto Date: Tue, 24 Jun 2025 22:10:17 -0400 Subject: [PATCH 1/6] add information about setting up HPC account --- protocols/onboarding.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/protocols/onboarding.md b/protocols/onboarding.md index 726a254..e50be88 100644 --- a/protocols/onboarding.md +++ b/protocols/onboarding.md @@ -69,6 +69,22 @@ Be assured that Kevin has aggressively curated his notifications πŸ˜‰. [zulip]: https://bonhamlab.zulipchat.com/ +## Getting access to the Tufts HPC +You will get an email from ` +Aff-account@tufts.edu` asking you to set up your Tufts account. Following the instructions in this email, you should + +- [ ] Reset password +- [ ] Follow instructions to set up duo security +- [ ] Set up VPN with Cisco AnyConnect + +Once all of these steps have been completed, you can connect to the HPC through the terminal with your new tufts username: +`ssh TUFTS_USERNAME@login.pax.tufts.edu`. You must be connected to the Tufts VPN for this to work. + +- Enter β€˜yes’ when you are asked if you want to add `login.pax.tufts.edu` to the list of known hosts + + +Troubleshooting: +- Some other lab members received a Tufts username and email, but an HPC account was not created for them. This could possibly happen to other lab members. If your newly created Tufts password does not allow you to connect to the HPC, this could be a possibility

From a8c9004a71b747d28ffd68b7c084271c6465976e Mon Sep 17 00:00:00 2001 From: Danielle Pinto Date: Tue, 1 Jul 2025 20:45:16 -0400 Subject: [PATCH 2/6] add information about hpc access --- protocols/onboarding.md | 42 +++++++++++++++++++++++++++++++++++------ 1 file changed, 36 insertions(+), 6 deletions(-) diff --git a/protocols/onboarding.md b/protocols/onboarding.md index e50be88..1fafb59 100644 --- a/protocols/onboarding.md +++ b/protocols/onboarding.md @@ -71,20 +71,50 @@ Be assured that Kevin has aggressively curated his notifications πŸ˜‰. ## Getting access to the Tufts HPC You will get an email from ` -Aff-account@tufts.edu` asking you to set up your Tufts account. Following the instructions in this email, you should +aff-account@tufts.edu` asking you to set up your Tufts account. Following the instructions in this email, you should -- [ ] Reset password -- [ ] Follow instructions to set up duo security -- [ ] Set up VPN with Cisco AnyConnect +- [ ] Reset your Tufts password +- [ ] Follow instructions to set up Duo Security +- [ ] Set up your VPN connection with Cisco AnyConnect Once all of these steps have been completed, you can connect to the HPC through the terminal with your new tufts username: `ssh TUFTS_USERNAME@login.pax.tufts.edu`. You must be connected to the Tufts VPN for this to work. -- Enter β€˜yes’ when you are asked if you want to add `login.pax.tufts.edu` to the list of known hosts +You will get a message saying: +``` +The authenticity of host 'login.pax.tufts.edu (XX.XXX.XXX.XX)' can't be established. +ED25519 key fingerprint is SHA256:someLongFingerprint. +This key is not known by any other names. +Are you sure you want to continue connecting (yes/no/[fingerprint])? +``` + +- Enter β€˜yes’ when you are asked if you want to keep connecting. This will trust the server from now on and add `login.pax.tufts.edu` to the list of known hosts in `~/.ssh/known_hosts/`. You won't get this prompt again. + +#### Setting up passwordless HPC connection +Set up a SSH key-based authentication so you don't need to enter your Tufts password each time you connect to the Tufts HPC + +1. Generate an SSH key pair: +- `ssh-keygen -t ed25519 -C tufts_email@tufts.edu` +- Press "enter" to save the key at `/Users/local_username/.ssh/id_ed25519` +- This creates: + - `~/.ssh/id_ed25519` (private key β€” keep safe) + - `~/.ssh/id_ed25519.pub` (public key β€” to be shared with servers) + +2. Copy your public key to the HPC login node +- `ssh-copy-id tufts_username@login.pax.tufts.edu` +- After entering your password again, this will append your public key to the file `~/.ssh/authorized_keys` on the HPC server +
+
+ +You can test if this works by entering `ssh tufts_username@login.pax.tufts.edu` +#### Helpful directories on the cluster +Once you have access to the Tufts HPC, you can access your personal directory within the Bonham Lab folder at `/cluster/tufts/bonhamlab`. This is a good plae to store data/results for personal projects. +- The shared bin (`/cluster/tufts/bonhamlab/shared/`) also contains helpful directories with conda environments, apptainer containers, bioinformatics tools (`bin`) and biobakery databases ( `databases`) + Troubleshooting: -- Some other lab members received a Tufts username and email, but an HPC account was not created for them. This could possibly happen to other lab members. If your newly created Tufts password does not allow you to connect to the HPC, this could be a possibility +- Some other lab members received a Tufts username and email, but an HPC account was not created for them. If your newly created Tufts password does not allow you to connect to the HPC, this could be something to check.

From eb974ada63ac30665e696a6f07d834fbe169a40d Mon Sep 17 00:00:00 2001 From: Danielle Pinto <108756057+danielle-pinto@users.noreply.github.com> Date: Tue, 1 Jul 2025 20:53:14 -0400 Subject: [PATCH 3/6] Update onboarding.md --- protocols/onboarding.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/protocols/onboarding.md b/protocols/onboarding.md index 1fafb59..eb77cb1 100644 --- a/protocols/onboarding.md +++ b/protocols/onboarding.md @@ -110,7 +110,7 @@ Set up a SSH key-based authentication so you don't need to enter your Tufts pas You can test if this works by entering `ssh tufts_username@login.pax.tufts.edu` #### Helpful directories on the cluster -Once you have access to the Tufts HPC, you can access your personal directory within the Bonham Lab folder at `/cluster/tufts/bonhamlab`. This is a good plae to store data/results for personal projects. +Once you have access to the Tufts HPC, you can access your personal directory within the Bonham Lab folder at `/cluster/tufts/bonhamlab`. This is a good place to store data/results for personal projects. - The shared bin (`/cluster/tufts/bonhamlab/shared/`) also contains helpful directories with conda environments, apptainer containers, bioinformatics tools (`bin`) and biobakery databases ( `databases`) Troubleshooting: From 44214e01acb110fa051f573c745e1c6e8fd6f7cf Mon Sep 17 00:00:00 2001 From: Danielle Pinto <108756057+danielle-pinto@users.noreply.github.com> Date: Wed, 2 Jul 2025 20:46:55 -0400 Subject: [PATCH 4/6] Update protocols/onboarding.md Co-authored-by: Kevin Bonham --- protocols/onboarding.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/protocols/onboarding.md b/protocols/onboarding.md index eb77cb1..1325585 100644 --- a/protocols/onboarding.md +++ b/protocols/onboarding.md @@ -70,8 +70,8 @@ Be assured that Kevin has aggressively curated his notifications πŸ˜‰. [zulip]: https://bonhamlab.zulipchat.com/ ## Getting access to the Tufts HPC -You will get an email from ` -aff-account@tufts.edu` asking you to set up your Tufts account. Following the instructions in this email, you should +You will get an email from `aff-account@tufts.edu` +asking you to set up your Tufts account. Following the instructions in this email, you should - [ ] Reset your Tufts password - [ ] Follow instructions to set up Duo Security From 5f292bc337eb2d166d6298121761399aea7b8d2b Mon Sep 17 00:00:00 2001 From: Danielle Pinto <108756057+danielle-pinto@users.noreply.github.com> Date: Wed, 2 Jul 2025 20:47:09 -0400 Subject: [PATCH 5/6] Update protocols/onboarding.md Co-authored-by: Kevin Bonham --- protocols/onboarding.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/protocols/onboarding.md b/protocols/onboarding.md index 1325585..f270e82 100644 --- a/protocols/onboarding.md +++ b/protocols/onboarding.md @@ -102,6 +102,10 @@ Set up a SSH key-based authentication so you don't need to enter your Tufts pas - `~/.ssh/id_ed25519` (private key β€” keep safe) - `~/.ssh/id_ed25519.pub` (public key β€” to be shared with servers) +> [!WARNING] +> Anyone with access to your private key can sign in as you with all of your privileges. +> Do not share with anyone, or upload the key to anywhere that others have access to. + 2. Copy your public key to the HPC login node - `ssh-copy-id tufts_username@login.pax.tufts.edu` - After entering your password again, this will append your public key to the file `~/.ssh/authorized_keys` on the HPC server From 486214f336efc1ba4f820ee2598b36e2c8fee3b6 Mon Sep 17 00:00:00 2001 From: Danielle Pinto Date: Sat, 5 Jul 2025 21:14:41 -0400 Subject: [PATCH 6/6] add information about ssh config --- protocols/onboarding.md | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/protocols/onboarding.md b/protocols/onboarding.md index f270e82..9244b02 100644 --- a/protocols/onboarding.md +++ b/protocols/onboarding.md @@ -113,6 +113,25 @@ Set up a SSH key-based authentication so you don't need to enter your Tufts pas
You can test if this works by entering `ssh tufts_username@login.pax.tufts.edu` + +#### Setting up `~/.ssh/config` +To simplify things even further, you can set up a `~/.ssh/config` file so that you can use access the Tufts HPC by simply typing `ssh tufts-hpc`. + +1. If you don't already have a `~/.ssh/config` file, create one by typing `nano ~/.ssh/config`. Then, add the following information into the file. +``` +Host tufts-hpc + HostName login.pax.tufts.edu + User tufts_username + IdentityFile ~/.ssh/id_ed25519 + Port 22 +``` +2. To make sure that no one can access this file except for you, run `chmod 600 ~/.ssh/config`. + +3. Once the file has been saved, you can type `ssh tufts-hpc` + +4. To exit the cluster, type `exit`. + + #### Helpful directories on the cluster Once you have access to the Tufts HPC, you can access your personal directory within the Bonham Lab folder at `/cluster/tufts/bonhamlab`. This is a good place to store data/results for personal projects. - The shared bin (`/cluster/tufts/bonhamlab/shared/`) also contains helpful directories with conda environments, apptainer containers, bioinformatics tools (`bin`) and biobakery databases ( `databases`)