From 32fbd8de4b52711be289d83e5fe12a9e94489af9 Mon Sep 17 00:00:00 2001 From: Thomas Gardos <3973626+trgardos@users.noreply.github.com> Date: Tue, 13 Aug 2024 17:18:14 -0400 Subject: [PATCH 1/2] initial commit for lectures qmds --- .vscode/settings.json | 4 + lectures/fa24/.gitignore | 3 + lectures/fa24/_quarto.yml | 32 +++++++ lectures/fa24/about.qmd | 5 ++ .../assets/images/macos_terminal_icon.jpeg | Bin 0 -> 4176 bytes lectures/fa24/command.sh | 18 ++++ lectures/fa24/command_shells.qmd | 81 ++++++++++++++++++ lectures/fa24/index.qmd | 62 ++++++++++++++ lectures/fa24/lecture02.qmd | 7 ++ lectures/fa24/lecture03.qmd | 12 +++ lectures/fa24/scc.qmd | 21 +++++ lectures/fa24/styles.css | 1 + 12 files changed, 246 insertions(+) create mode 100644 .vscode/settings.json create mode 100644 lectures/fa24/.gitignore create mode 100644 lectures/fa24/_quarto.yml create mode 100644 lectures/fa24/about.qmd create mode 100644 lectures/fa24/assets/images/macos_terminal_icon.jpeg create mode 100755 lectures/fa24/command.sh create mode 100644 lectures/fa24/command_shells.qmd create mode 100644 lectures/fa24/index.qmd create mode 100644 lectures/fa24/lecture02.qmd create mode 100644 lectures/fa24/lecture03.qmd create mode 100644 lectures/fa24/scc.qmd create mode 100644 lectures/fa24/styles.css diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..c5dba24 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,4 @@ +{ + "quarto.render.previewType": "internal", + "quarto.render.renderOnSave": true +} \ No newline at end of file diff --git a/lectures/fa24/.gitignore b/lectures/fa24/.gitignore new file mode 100644 index 0000000..8ebd73e --- /dev/null +++ b/lectures/fa24/.gitignore @@ -0,0 +1,3 @@ +/.quarto/ +_site/ +_revealjs/ diff --git a/lectures/fa24/_quarto.yml b/lectures/fa24/_quarto.yml new file mode 100644 index 0000000..f5f2752 --- /dev/null +++ b/lectures/fa24/_quarto.yml @@ -0,0 +1,32 @@ +project: + type: website + +website: + title: "CS/DS 549 Lectures" + back-to-top-navigation: true + sidebar: + style: "docked" + search: true + contents: + - href: index.qmd + text: Home + - section: "*nux Shell and Shared Computing Cluster" + contents: + - command_shells.qmd + - scc.qmd + - section: "Git" + contents: + - lecture02.qmd + - section: "VS Code" + contents: + - lecture03.qmd + - about.qmd + +format: + html: + theme: cosmo + css: styles.css + toc: true + + + diff --git a/lectures/fa24/about.qmd b/lectures/fa24/about.qmd new file mode 100644 index 0000000..07c5e7f --- /dev/null +++ b/lectures/fa24/about.qmd @@ -0,0 +1,5 @@ +--- +title: "About" +--- + +About this site diff --git a/lectures/fa24/assets/images/macos_terminal_icon.jpeg b/lectures/fa24/assets/images/macos_terminal_icon.jpeg new file mode 100644 index 0000000000000000000000000000000000000000..4a3754f530511826b1da9b0bd8a1402f20296726 GIT binary patch literal 4176 zcmbtW2{e@J8~?^gs3B#Sl#J}MOk^!tZj{Lw%M3=cWlOSTO{r9fi$T;_hRJTS?-W_b z5(W)rDf`kC#=iVV_ny1_@A;o|&-p*!ci#8+KF{;L&+IB4Fit=7N&zo+39qI{RjkdiD($@mIGBNPU>pn*1{gR%U=GmUd*C?TK?Vje-OE4dz(Gc41~AjU)bI$v00My- z*w~p4fEmI2Dj)_h;{gtOFvm{GT{J@2c---fE-d2Y5=uYi0IgH3za)62~hl0N=j zQR{|ngLW+5IHR}`ddZHy9}j4s{;>4>esqB#2MC}$0se~+#K3V;PRr<&{N507m@Z@B z0CNDEK+OdJ)a?28ZN95J0{WDk_|(xb2fZ*8SL*7#a^jeT!n5nu!;jHjwP`Mtg<0e) zYnmF;=Iw}T(_O#mx@tF69@0tghDnZL-kV`(70&SJ!;6{kW$U_jafZjH9qNa6t~wKO zTLb8RF~k>?Q(c*;RB?8IChgg6lxzJjLy11!t1de&G{K}jz+>mCm0wTo_S)_cX(dHt zMK)ODUZ?#g6PZ*NUW{4G-HhxE7)jqqs$NS8*jQc-knPo2rqXq~?KgGFq#ZYQ2Lm_% zs5!wz>C!pPtp3rO`QdKD!m4{l&@^TwNY=49==62E8qdE~BL$Fy6{rriR5KdPld7?{ zJiV}Low4eSS=WkZSsQ&fYYsJ>zG_!M4{CVnAG#!d|4))^?jdoiXqwYnQ$}i#< z2Dhx~I`x?&&MTgo0Yuuf?-bYi%dvW@<$2!oM%m3pJ$nFWC_T_y=lYAY?rIeUh*o`6 z`0NsuP=v}QE>>Zo-4O{DYn4hk)w&@v6k*CwWlX!-a5i@6xyh%^kB6U~>zQ=A!Q9SW z_NK+eje3-GPFz~+%8e$xA( zFCjeEzfGjHokuybC))|TP#!p`)mj)a-@d9_$E*rL4{E7{!7aB44G3olOrXOOr#$?k~%> zy?1)kE2DD4oEeV|A@9o3uKip-$T|XdGWyige@Q=bN+X9U^`bgK&r`?*BBAM-Wmm>znOd>c9K+xK%Ry#_5hWsT^LhZH+D zkKE5i&-n{{Ue+HM6#aqYs=|+y^Ps5e#x~zvhH(DKMNSEc0sq1tEsqwa(qu_1#lEZR z$UfavZtk1%wIB2KTTC$ros%L9N(Btw>Eegr2-y#-5bY)N(g4USg0XgFgTyJB=sx| z^R;4VB^{b#{pRK0v>ucVWn%L6`%i=sP+b`#pC*RgaX94I1lhFO_xP3J9NxBC0yVhI zrsuS7%p;^3VX?OOg}RT6Oc?htsc=y-&RM<)EfC&hBQiU#T$;-#g@L%mozUjKW#$lC z3*oY;Go zw-HxiVU8ymx$yBJhV=Lc-VOXR@_`&tVf$kv`n~A~hus~Y`6|-Q*ye&K`gybw9J~^n zyoKhwcY1^}9cDSn_rd~m&ccm-(|gur5Ab2r+%(8pOqR2*jrAPws*gR}1@O5&^wXH! zR6&T>Y{K_|$m0BJJ8PIkiu{+_K)soH;e_s2HLUIRJFQIov*mXw()c2O2W1ohCzvdWrekvfQYbHo*^SYS;Sb#R*+lV?Xo`l_EyUr(gW_b2mTf-ib2p#+IhQ1(Rb*&R-xM}q!NLP04eMIxvl`)^D@!UO-pp0i z@pD#*gW}@_;wmGT$Rl!ZClTqd2

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We'll get you familiar with command shells for +Windows and MacOS here. In the next section we'll cover the Shared Computing Cluster +at BU and its Linux operating system. + +Topics to cover: + +1. why important (the basic control language for machine learning) +2. MacOS (zsh) versus Windows (terminal and linux subsystem) versus linux distributions (e.g. SCC) + +## Getting to a command shell + +The types and how you start command shells varies by operating system. + +::: {.panel-tabset} + +### MacOS + +In MacOS, start the `terminal` app. ![MacoS Terminal](assets/images/macos_terminal_icon.jpeg){width="30px"} + +Starting with MacOS Catalina, the default shell is [`zsh`](https://zsh.org/). If +you've upgraded from an earlier version of Catalina, you might still be using `bash` +shell. If you are still using `bash`, there should be reminder everytime you +open Terminal instructing how you switch to `zsh`. + +The reason it is important to know which cell you are running is that the shell +startup configuration files are particular to the shell. There are some other +subtle differences in shell commands and syntax. + +You can see which shell you are running with the process status command `ps`. +One or more of the processes listed will include `bash` or `zsh`. + +### SCC + +The easiest way to get to a terminal session on the Shared Computing Cluster (SCC) +is to navigate to [SCC On Demand](https://scc-ondemand.bu.edu). + +You can also `ssh` to @scc1.bu.edu or @scc2.bu.edu or + @scc3.bu.edu, the login nodes. + + The first time you `ssh`, you might get the message a like this with `scc1`: + + ``` + The authenticity of host 'scc2.bu.edu (192.12.187.131)' can't be established. +ED25519 key fingerprint is SHA256:OmvL4FQ48QTpcXDpYE63rse1tM6pfKfSUgaVW1+mlIw. +This key is not known by any other names. +Are you sure you want to continue connecting (yes/no/[fingerprint])? +``` + +Just type yes and hit `return`. + + +### Windows + +sdfsd + +#### Windows terminal + +#### Windows GIT terminal + +#### Windows Subsystem for linux (WSL) + +::: + +Commands to cover: + +Directory commands: +```sh +pwd; cd; ls +``` + +File handling commands: +```sh +``` diff --git a/lectures/fa24/index.qmd b/lectures/fa24/index.qmd new file mode 100644 index 0000000..c69e74a --- /dev/null +++ b/lectures/fa24/index.qmd @@ -0,0 +1,62 @@ +--- +title: "CS/DS549 ML Practicum -- Fall 2024" +--- + +# Introduction + +Each lecture is ~30 minutes followed by either in class exercise in the early +part of the course or lab time. + +## Topics + +### Command Shells + +1. MacOS command shell +2. Windows command shell options + 1. Windows Command + 2. Git shell + 3. WSL + +Basic shell commands + +### Shared Computing Cluster + +1. SCC Overview +2. SCC group, changing default group +3. shell commands, user/group/world permissions +2. Login nodes vs compute nodes +3. Differences in compute nodes and options, CDS buy-in +3. Interactive sessions + 1. desktop + 2. vs code +4. Batch sessions + +### Git and Github + +1. git basics +2. github and git servers +3. exercise: forking, cloning, topic branch, push, create PR +3. github actions workflows +4. CI/CD + +### Tabular data + +1. pandas +2. scikit-learn + +### Pytorch + +### Tensorflow/Keras + +### Huggingface Transformers and Models + +### Huggingface Spaces + +### LLMs + +1. Chainlit/literal.ai +2. langchain +3. llamaindex +4. HF Transformers + + diff --git a/lectures/fa24/lecture02.qmd b/lectures/fa24/lecture02.qmd new file mode 100644 index 0000000..c30f31b --- /dev/null +++ b/lectures/fa24/lecture02.qmd @@ -0,0 +1,7 @@ +--- +title: "lecture 02" +--- + +# Intro + +blah blah diff --git a/lectures/fa24/lecture03.qmd b/lectures/fa24/lecture03.qmd new file mode 100644 index 0000000..caa2d16 --- /dev/null +++ b/lectures/fa24/lecture03.qmd @@ -0,0 +1,12 @@ +--- +title: "Lecture 03" +--- + +# Lecture Title + +Blah blah. + +## Next section + +More blah blah. + diff --git a/lectures/fa24/scc.qmd b/lectures/fa24/scc.qmd new file mode 100644 index 0000000..d9e5509 --- /dev/null +++ b/lectures/fa24/scc.qmd @@ -0,0 +1,21 @@ +--- +title: "Shared Computing Cluster" +--- + +# Topics to Cover + +Blah blah. + +## Next section + +More blah blah. + +```{python} +x = 5 +x +``` + +```{markdown} +Text $x = 5$. +``` + diff --git a/lectures/fa24/styles.css b/lectures/fa24/styles.css new file mode 100644 index 0000000..2ddf50c --- /dev/null +++ b/lectures/fa24/styles.css @@ -0,0 +1 @@ +/* css styles */ From fefaace6fcf15ee48f764674ed60f5b0c7c9c2b4 Mon Sep 17 00:00:00 2001 From: Thomas Gardos <3973626+trgardos@users.noreply.github.com> Date: Tue, 13 Aug 2024 18:18:32 -0400 Subject: [PATCH 2/2] updated placeholder files --- ...mmand_shells.qmd => 01_command_shells.qmd} | 0 lectures/fa24/{scc.qmd => 02_scc.qmd} | 0 lectures/fa24/03_git_and_github.qmd | 6 +++++ lectures/fa24/04_vscode.qmd | 5 ++++ lectures/fa24/05_tabular_data.qmd | 6 +++++ lectures/fa24/06_pytorch.qmd | 5 ++++ lectures/fa24/07_tensorflow_keras.qmd | 5 ++++ lectures/fa24/08_huggingface.qmd | 5 ++++ lectures/fa24/09_huggingface_spaces.qmd | 5 ++++ lectures/fa24/10_llms.qmd | 5 ++++ lectures/fa24/README.md | 25 +++++++++++++++++++ lectures/fa24/_quarto.yml | 21 ++++++++-------- lectures/fa24/about.qmd | 5 ---- lectures/fa24/index.qmd | 7 ++++++ lectures/fa24/lecture02.qmd | 7 ------ lectures/fa24/{lecture03.qmd => vscode.qmd} | 0 16 files changed, 84 insertions(+), 23 deletions(-) rename lectures/fa24/{command_shells.qmd => 01_command_shells.qmd} (100%) rename lectures/fa24/{scc.qmd => 02_scc.qmd} (100%) create mode 100644 lectures/fa24/03_git_and_github.qmd create mode 100644 lectures/fa24/04_vscode.qmd create mode 100644 lectures/fa24/05_tabular_data.qmd create mode 100644 lectures/fa24/06_pytorch.qmd create mode 100644 lectures/fa24/07_tensorflow_keras.qmd create mode 100644 lectures/fa24/08_huggingface.qmd create mode 100644 lectures/fa24/09_huggingface_spaces.qmd create mode 100644 lectures/fa24/10_llms.qmd create mode 100644 lectures/fa24/README.md delete mode 100644 lectures/fa24/about.qmd delete mode 100644 lectures/fa24/lecture02.qmd rename lectures/fa24/{lecture03.qmd => vscode.qmd} (100%) diff --git a/lectures/fa24/command_shells.qmd b/lectures/fa24/01_command_shells.qmd similarity index 100% rename from lectures/fa24/command_shells.qmd rename to lectures/fa24/01_command_shells.qmd diff --git a/lectures/fa24/scc.qmd b/lectures/fa24/02_scc.qmd similarity index 100% rename from lectures/fa24/scc.qmd rename to lectures/fa24/02_scc.qmd diff --git a/lectures/fa24/03_git_and_github.qmd b/lectures/fa24/03_git_and_github.qmd new file mode 100644 index 0000000..72214c5 --- /dev/null +++ b/lectures/fa24/03_git_and_github.qmd @@ -0,0 +1,6 @@ +--- +title: Git and Github +--- + +# Introduction + diff --git a/lectures/fa24/04_vscode.qmd b/lectures/fa24/04_vscode.qmd new file mode 100644 index 0000000..3318301 --- /dev/null +++ b/lectures/fa24/04_vscode.qmd @@ -0,0 +1,5 @@ +--- +title: VS Code +--- + +# Introduction diff --git a/lectures/fa24/05_tabular_data.qmd b/lectures/fa24/05_tabular_data.qmd new file mode 100644 index 0000000..1cb09440 --- /dev/null +++ b/lectures/fa24/05_tabular_data.qmd @@ -0,0 +1,6 @@ +--- +title: Tabular Data +--- + +# Introduction + diff --git a/lectures/fa24/06_pytorch.qmd b/lectures/fa24/06_pytorch.qmd new file mode 100644 index 0000000..a1686f9 --- /dev/null +++ b/lectures/fa24/06_pytorch.qmd @@ -0,0 +1,5 @@ +--- +title: Pytorch +--- + +# Intro diff --git a/lectures/fa24/07_tensorflow_keras.qmd b/lectures/fa24/07_tensorflow_keras.qmd new file mode 100644 index 0000000..9c793df --- /dev/null +++ b/lectures/fa24/07_tensorflow_keras.qmd @@ -0,0 +1,5 @@ +--- +title: Tensorflow Keras +--- + +# Intro diff --git a/lectures/fa24/08_huggingface.qmd b/lectures/fa24/08_huggingface.qmd new file mode 100644 index 0000000..4452556 --- /dev/null +++ b/lectures/fa24/08_huggingface.qmd @@ -0,0 +1,5 @@ +--- +title: Hugging Face Transformers and Models +--- + +# Intro diff --git a/lectures/fa24/09_huggingface_spaces.qmd b/lectures/fa24/09_huggingface_spaces.qmd new file mode 100644 index 0000000..54b5f90 --- /dev/null +++ b/lectures/fa24/09_huggingface_spaces.qmd @@ -0,0 +1,5 @@ +--- +title: Hugging Face Spaces +--- + +# Intro diff --git a/lectures/fa24/10_llms.qmd b/lectures/fa24/10_llms.qmd new file mode 100644 index 0000000..9734027 --- /dev/null +++ b/lectures/fa24/10_llms.qmd @@ -0,0 +1,5 @@ +--- +title: LLMs and Tools +--- + +# Intro diff --git a/lectures/fa24/README.md b/lectures/fa24/README.md new file mode 100644 index 0000000..964c85a --- /dev/null +++ b/lectures/fa24/README.md @@ -0,0 +1,25 @@ +# Fall 2024 Lecture Topics + +This folder (`lectures/fa24`) contains draft lectures for various introductory +practical machine tools. + +The topic list is in [index.qmd](./index.qmd). + +It is in [Quarto](https://quarto.org/) website format. + +To edit, preview and render you'll need to setup Quarto. + +1. Install Quarto as directed in Quarto + [Get Started](https://quarto.org/docs/get-started/). +2. We suggest you edit with VS Code and the +[Quarto Extension](https://marketplace.visualstudio.com/items?itemName=quarto.quarto). +3. From VS Code you can preview using + 1. the preview icon on the top right of one of the qmd edit panels, or + 2. run `quarto preview` from the integrated VS Code terminal from the + `lectures/fa24` directory. + +There are placeholder files for each of the major topics. If you add a new +file or change a file name, be sure to update it in [_quarto.yml](./_quarto.yml) +file too. + +**Coming Soon:** Instructions on how to render slides from quarto. diff --git a/lectures/fa24/_quarto.yml b/lectures/fa24/_quarto.yml index f5f2752..2edc61c 100644 --- a/lectures/fa24/_quarto.yml +++ b/lectures/fa24/_quarto.yml @@ -10,17 +10,16 @@ website: contents: - href: index.qmd text: Home - - section: "*nux Shell and Shared Computing Cluster" - contents: - - command_shells.qmd - - scc.qmd - - section: "Git" - contents: - - lecture02.qmd - - section: "VS Code" - contents: - - lecture03.qmd - - about.qmd + - 01_command_shells.qmd + - 02_scc.qmd + - 03_git_and_github.qmd + - 04_vscode.qmd + - 05_tabular_data.qmd + - 06_pytorch.qmd + - 07_tensorflow_keras.qmd + - 08_huggingface.qmd + - 09_huggingface_spaces.qmd + - 10_llms.qmd format: html: diff --git a/lectures/fa24/about.qmd b/lectures/fa24/about.qmd deleted file mode 100644 index 07c5e7f..0000000 --- a/lectures/fa24/about.qmd +++ /dev/null @@ -1,5 +0,0 @@ ---- -title: "About" ---- - -About this site diff --git a/lectures/fa24/index.qmd b/lectures/fa24/index.qmd index c69e74a..2f3be3c 100644 --- a/lectures/fa24/index.qmd +++ b/lectures/fa24/index.qmd @@ -39,6 +39,13 @@ Basic shell commands 3. github actions workflows 4. CI/CD +### VS Code + +1. Python extensions and support +2. Jupyter extensions and support (debugging) +2. Git/Github extensions and support + + ### Tabular data 1. pandas diff --git a/lectures/fa24/lecture02.qmd b/lectures/fa24/lecture02.qmd deleted file mode 100644 index c30f31b..0000000 --- a/lectures/fa24/lecture02.qmd +++ /dev/null @@ -1,7 +0,0 @@ ---- -title: "lecture 02" ---- - -# Intro - -blah blah diff --git a/lectures/fa24/lecture03.qmd b/lectures/fa24/vscode.qmd similarity index 100% rename from lectures/fa24/lecture03.qmd rename to lectures/fa24/vscode.qmd