wrote a guide for linking jupyter to a cluster compute node

Manifest.toml

@@ -1,8 +1,13 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.11.4"
+julia_version = "1.11.6"
 manifest_format = "2.0"
-project_hash = "466211ef6f405feebed0a653388154f8873df086"
+project_hash = "a45f85a71e35bf3e1235da274041a3eb67efb1ad"
+
+[[deps.ANSIColoredPrinters]]
+git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c"
+uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9"
+version = "0.0.1"
 
 [[deps.ArgTools]]
 uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
@@ -21,6 +26,10 @@ git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d"
 uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35"
 version = "0.1.9"
 
+[[deps.CRC32c]]
+uuid = "8bf52ea8-c179-5cab-976a-9e18b702a9bc"
+version = "1.11.0"
+
 [[deps.CodecZlib]]
 deps = ["TranscodingStreams", "Zlib_jll"]
 git-tree-sha1 = "962834c22b66e32aa10f7611c08c8ca4e20749a9"
@@ -51,17 +60,6 @@ deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 version = "1.11.0"
 
-[[deps.DelimitedFiles]]
-deps = ["Mmap"]
-git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae"
-uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
-version = "1.9.1"
-
-[[deps.DocStringExtensions]]
-git-tree-sha1 = "e7b7e6f178525d17c720ab9c081e4ef04429f860"
-uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
-version = "0.9.4"
-
 [[deps.Downloads]]
 deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
@@ -88,17 +86,11 @@ version = "0.1.10"
 uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
 version = "1.11.0"
 
-[[deps.Franklin]]
-deps = ["Dates", "DelimitedFiles", "DocStringExtensions", "ExprTools", "FranklinTemplates", "HTTP", "Literate", "LiveServer", "Logging", "Markdown", "NodeJS", "OrderedCollections", "Pkg", "REPL", "Random", "TOML"]
-git-tree-sha1 = "31e70717e0640d6576fe04d611a33df1c9c312d6"
-uuid = "713c75ef-9fc9-4b05-94a9-213340da978e"
-version = "0.10.95"
-
-[[deps.FranklinTemplates]]
-deps = ["LiveServer"]
-git-tree-sha1 = "c01813a615149ddb3b3d133f33de29d642fbe57b"
-uuid = "3a985190-f512-4703-8d38-2a7944ed5916"
-version = "0.10.2"
+[[deps.FranklinParser]]
+deps = ["PrecompileTools", "REPL"]
+git-tree-sha1 = "7daf95d2334d4c0f73353e110c9396e9d5258afb"
+uuid = "796511e7-1510-466f-ad0c-1823c64bcafa"
+version = "0.7.1"
 
 [[deps.Git]]
 deps = ["Git_jll"]
@@ -114,9 +106,9 @@ version = "2.49.0+0"
 
 [[deps.HTTP]]
 deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "PrecompileTools", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"]
-git-tree-sha1 = "f93655dc73d7a0b4a368e3c0bce296ae035ad76e"
+git-tree-sha1 = "ed5e9c58612c4e081aecdb6e1a479e18462e041e"
 uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
-version = "1.10.16"
+version = "1.10.17"
 
 [[deps.Hyperscript]]
 deps = ["Test"]
@@ -264,9 +256,9 @@ version = "2.0.0"
 
 [[deps.OpenSSL]]
 deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"]
-git-tree-sha1 = "38cb508d080d21dc1128f7fb04f20387ed4c0af4"
+git-tree-sha1 = "f1a7e086c677df53e064e0fdd2c9d0b0833e3f6e"
 uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c"
-version = "1.4.3"
+version = "1.5.0"
 
 [[deps.OpenSSL_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -275,9 +267,9 @@ uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95"
 version = "3.0.16+0"
 
 [[deps.OrderedCollections]]
-git-tree-sha1 = "cc4054e898b852042d7b503313f7ad03de99c3dd"
+git-tree-sha1 = "05868e21324cede2207c6f0f466b4bfef6d5e7ee"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-version = "1.8.0"
+version = "1.8.1"
 
 [[deps.PCRE2_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -326,6 +318,11 @@ deps = ["SHA"]
 uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 version = "1.11.0"
 
+[[deps.Reexport]]
+git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b"
+uuid = "189a3867-3050-52da-a836-e630ba90ab69"
+version = "1.2.2"
+
 [[deps.SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 version = "0.7.0"
@@ -392,9 +389,9 @@ uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 version = "0.11.3"
 
 [[deps.URIs]]
-git-tree-sha1 = "cbbebadbcc76c5ca1cc4b4f3b0614b3e603b5000"
+git-tree-sha1 = "bef26fb046d031353ef97a82e3fdb6afe7f21b1a"
 uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
-version = "1.5.2"
+version = "1.6.1"
 
 [[deps.UUIDs]]
 deps = ["Random", "SHA"]
@@ -405,6 +402,14 @@ version = "1.11.0"
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 version = "1.11.0"
 
+[[deps.Xranklin]]
+deps = ["ANSIColoredPrinters", "CRC32c", "Dates", "FranklinParser", "IOCapture", "LiveServer", "Logging", "Markdown", "OrderedCollections", "Pkg", "REPL", "Reexport", "Serialization", "TOML", "URIs"]
+git-tree-sha1 = "00c83bd65338e9cf1ca1b8a183bd27f5df60767e"
+repo-rev = "main"
+repo-url = "git@github.com:tlienart/Xranklin.jl.git"
+uuid = "558449b0-171e-4e1f-900f-d076a5ddf486"
+version = "0.1.0"
+
 [[deps.Zlib_jll]]
 deps = ["Libdl"]
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"

Project.toml

@@ -1,8 +1,8 @@
 [deps]
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
-Franklin = "713c75ef-9fc9-4b05-94a9-213340da978e"
 Git = "d7ba0133-e1db-5d97-8f8c-041e4b3a1eb2"
 Hyperscript = "47d2ed2b-36de-50cf-bf87-49c2cf4b8b91"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 NodeJS = "2bd173c7-0d6d-553b-b6af-13a54713934c"
 TimeZones = "f269a46b-ccf7-5d73-abea-4c690281aa53"
+Xranklin = "558449b0-171e-4e1f-900f-d076a5ddf486"

protocols/code.md

@@ -201,4 +201,86 @@ host presentations, etc.
 
 Each software or analysis project should have its own repo or repos
 
-##  
+##  Using Tufts high-performance computing (HPC) cluster
+
+For detailed guidelines regarding Tufts HPC usage please visit [the dedicated website](https://it.tufts.edu/high-performance-computing)
+
+## "Linking" your Jupyter notebook to a cluster's compute node
+
+1. ssh into the cluster:
+
+   ```bash
+   ssh your_name@login.cluster.edu
+   ```
+
+2. Request access to an interactive compute node and its resources:
+
+   CPU:
+
+   ```bash
+   srun -t 0-02:00 --mem 2000 -p interactive --pty bash
+   ```
+
+   GPU:
+
+   ```bash
+     srun -t 0-02:00 --mem 2000 -p gpu --gres gpu --pty bash
+   ```
+
+This gives a 2-hour time limit interactive session with a bash terminal, with 2GB of memory.
+You can adjust the -t or the -mem requests as needed.
+
+### Requesting specific types of gpus:
+
+Use the `--gres` option for either srun or sbatch commands
+
+General syntax: `--gres=gpu[:type][:number]`. Specifying either type or number is optional.
+
+For example:
+
+- A100 gpu: `--gres gpu:a100`
+- V100 gpu: `--gres gpu:v100`
+- T4 gpu: `--gres gpu:t4`
+- RTX 6000 gpu: `--gres gpu:rtx_6000`
+- RTX A6000 gpu: `--gres gpu:rtx_a6000`
+
+See [GPU Hardware List](https://www.cs.tufts.edu/cs/152L3D/2024f/tufts_hpc_setup.html#gpu-hardware-list)
+
+3. Activating your conda environment and launching Jupyter notebook on a specific port:
+
+   ```bash
+   conda activate <ENV>
+   jupyter notebook --no-browser --port=<PORT>
+   ```
+
+   >[!NOTE]
+   after you've launched Jupyter, in the output you will see something like:
+   `.../localhost:6789/tree?token=<TOKEN>`
+   You need to copy the <TOKEN> for this session; you will need it later.
+
+4. Tunneling the remote HPC port to your local machine port:
+   After you have entered the "srun" command, you will be allocated a certain node.
+   Now, go to the terminal on your local machine and enter the following:
+
+
+   First, tunnel the port you bound Jupyter to (f.e. 6789) to some port on your local machine:
+
+   ```bash
+   ssh your_name@login.cluster.edu -L <JUPYTER-PORT>:localhost:<PORT>
+   # for example
+   # ssh yehor@login.cluster.edu -L 6789:localhost:6789
+   ```
+
+   Now, do the same for the compute node you were allocated (f.e. i2cmp003):
+   ```bash
+   ssh <NODE> -L <JUPYTER-PORT>:localhost:<PORT>
+   # for example
+   # ssh i2cmp003 -L 6789:localhost:6789
+   ```
+
+5. Opening Jupyter in the browser
+   Go to an internet browser on your machine and look up the following address:
+   `http://localhost:<PORT>` (again, you may use 6789 as the port number throughout the process)
+   Now, enter the token you copied in the cluster terminal
+   as well as some password you need to come up with for this session only.
+   Done. Now do science.