HPC / CFD Final Exam Revision Guide¶

One-page summary per chapter. Use this on the morning of the exam.

Top Strategy¶

Read each one-pager once.
Read HPC_Final_Cheat_Sheets.pdf once.
Walk through the four practice sets in HPC_Written_Exam_Preparation.pdf solving by hand.
Drink water. Sleep 8 hours.

In the exam:

Read every question fully before starting.
Allocate time = (marks/total marks) × duration.
Start with the biggest question you know best — quick wins build confidence.
For commands always quote the variable: "${VAR}".
For diagrams use a small text Venn / arrow diagram even if hand-drawn.
For C++ remember the compile command at the top.

Chapter 1 — Course Introduction & HPC Overview¶

HPC = aggregating many cores so calculations finish in hours not years.
CFD discretises Navier–Stokes on $10^{9}$ cells × $10^{5}$ steps → $10^{15}$+ ops → needs HPC.
Top500 = LINPACK-ranked list; #1 El Capitan (1.7 EF), #2 Frontier, #3 Aurora.
All Top500 run Linux.
Why Linux? open, stable, scriptable, POSIX, modular.
Key term: SAF (Sustainable Aviation Fuel), Cluster of Excellence SE²A (Hannover/Braunschweig).
Likely question: Why HPC for CFD? Define + 1 example + 1 limitation.

Chapter 2 — Unix / Linux Basics¶

Unix = 1970 AT&T proprietary OS family.
POSIX = IEEE standard for portability.
GNU = free Unix-like userland (bash, gcc, coreutils).
Linux = the kernel; "GNU/Linux" = the OS.
Distributions = kernel + userland + init + package mgr (Ubuntu, Rocky, SLES).
User vs kernel mode → system calls (syscall instr).
Likely question: Define Unix/POSIX/GNU/Linux + Venn.

Chapter 3 — Linux Commands & File Permissions¶

ls -lh, cd, mkdir -p, cp -r, rm -rf, mv, touch, wc -l, cat/less/head/tail, chmod, chown.
Permissions: r=4 w=2 x=1. 755=rwxr-xr-x, 644=rw-r--r--, 600=rw-------.
Special: setuid 4, setgid 2, sticky 1 → chmod 4755, chmod 1777 /tmp.
Redirection: > >> 2> 2>&1 < <<EOF. Pipe: |.
FHS: /, /home, /etc, /var, /usr, /tmp, /dev, /proc.
Likely question: Translate ls -l to chmod numeric. Explain > vs >> vs 2>&1.

Chapter 4 — bashrc, SSH, Remote Workflows¶

.bashrc for aliases/functions/prompt. .bash_profile for login.
Env: export VAR=value. PATH/HOME/USER/SHELL/EDITOR/LD_LIBRARY_PATH.
Symmetric (AES) one key fast; asymmetric (Ed25519/RSA) pub+priv slow.
SSH: 1) ECDH key exchange, 2) AES session, 3) public-key auth.
Passwordless: ssh-keygen -t ed25519 -b 4096 -f ~/.ssh/k, ssh-copy-id, ~/.ssh/config, chmod 600/700.
Compare: scp (one-shot) / rsync -avzP --delete (incremental) / sftp (interactive) / sshfs (mount).
nohup ./run > log 2>&1 &; disown. tmux new -s sim; detach Ctrl-b d.
ssh -L 8080:host:80 local fwd; -R reverse; -D SOCKS.
Likely question: passwordless setup steps; scp vs rsync.

Chapter 5 — Vim & Command-Line Editing¶

Modes: Normal, Insert (i a o I A O), Visual (v V Ctrl-v), Cmd-line (:).
Grammar: [count][verb][motion]. Verbs: d c y > gU. Motions: w b e 0 $ gg G %.
dd 5dd yy y2j p P u Ctrl-r .. Search /pat n N *.
Replace: :%s/old/new/gc. Whole-word \<word\>. Multifile :bufdo … | update.
Macros: qa…q, @a, 5@a, :reg a.
Buffers/windows/tabs: :e :sp :vsp :tabnew gt :ls.
.vimrc: set number expandtab hlsearch incsearch.
Lecture macro (Task 3): qa /[<Enter> v /]<Enter> d 0 /><Enter> p 0 q then @a.
Likely question: keystrokes to transform "before" into "after"; record macro.

Chapter 6 — Regex & Globbing¶

Glob: * ? [abc] {a,b}. Brace expansion {a..e}, dir-{1,3}/*[0-9].h.
Regex flavours: BRE (grep, sed default), ERE (-E), PCRE (-P).
Atoms: . *(0+) +(1+) ?(0/1) {n,m} (in ERE). Anchors ^ $ \< \> \b.
Char class: [abc], [^abc], [[:alpha:]], [[:digit:]]. Backref \1.
E04 solutions:
Phone: \+[0-9]+ [0-9]{3}-[0-9]{3}-[0-9]{4}
Email: ^[[:alnum:]_.]+@[[:alpha:]]+\.[[:alpha:]]{2,}$
Glob dir-{1,3}/*[0-9].h, dir-3/*[A-Z]*.h
Likely question: Phone/email/IP regex; predict matches.

Chapter 7 — Linux Text Tools¶

find <path> -name -type f -size +N -mtime -N -exec cmd {} +
grep -EinrlA 2 -B 1 flags.
sed -E -i.bak 's/pat/repl/g'. Print only matching sed -n '/p/p'.
awk 'BEGIN{FS=",";OFS="\t"} /pat/ {print $1,$3}' file.
column -t -s ':' /etc/passwd.
E05 solutions: find -regex -exec chmod, awk salary filter, sed grouping \1-\5.
Likely question: write awk/sed/grep for CSV; predict output.

Chapter 8 — Shell Scripting¶

Shebang #!/bin/bash; strict set -euo pipefail.
Vars $1 $# $@ $? $$ $!. Quote "${VAR}".
Tests [ -f f ], [[ "$x" =~ pat ]], (( a+b )).
if/elif/else, case (pat) cmds ;;), for/while/until.
Arrays A=(a b c); "${A[@]}"; ${#A[@]}.
getopts: OPTSTRING=":a:b:v", while-getopts case + shift $((OPTIND-1)).
Function fn(){ local x=$1; ... }. Capture r=$(fn).
backup-data.sh: getopts -v / extended -s for rsync.
Likely question: walk through backup-data.sh; write parameter-sweep script.

Chapter 9 — Gnuplot Postprocessing¶

Plot plot 'd' using 1:2 with linespoints lt 1 lw 2 pt 7 lc rgb "red" title 'X'.
Customisations: set title/xlabel/ylabel/grid/xrange/yrange/logscale y/key/xtics.
Linestyle: set style line N lt 1 lw 2 pt 7 ps 1.5 lc rgb "...".
Multiplot: set multiplot layout R,C ... unset multiplot.
Fit: f(x)=a*x**2+b*x+c; fit f(x) 'd' via a,b,c.
Errorbars: using 1:2:3 with yerrorbars.
PNG: set terminal png; set output 'x.png'; replot. Heredoc: gnuplot <<EOF…EOF.
Bash automation: for f in *.txt; do gnuplot <<EOF...EOF; done.
Likely question: customise plot; fit quadratic; multiplot 2×2; PNG export.

Chapter 10 — Git Version Control¶

Zones: working dir → staging (index) → local repo → remote.
Setup: git config --global user.{name,email}.
Cycle: status add commit log diff. Modify+stage+commit pattern.
Branch: switch -c x, merge x, branch -d x.
Remote: remote add origin url, push -u origin main, pull --rebase.
GitLab TU-BS: PAT (api/read/write scopes) or SSH key.
Conflicts: edit markers, add, commit.
Likely question: setup + first commit + branch + merge; PAT setup.

Chapter 11 — C++ Basics¶

Compile g++ -O2 -std=c++17 -Wall src.cpp -o exe.
Types int 4B, char 1B, float 4B, double 8B, bool 1B.
Pointer int *p=&a; *p=7;. Reference int& r=a; r=7;.
Pass by value (copy) / pointer (int*) / reference (int&).
Class: class C{private:…;public:…;}; + C::method outside.
Complex class with add (a+c)+(b+d)i, multiply (ac-bd)+(ad+bc)i, modulus sqrt(a²+b²).
Likely question: predict example10.cpp output; complete Complex; swap by pointer.

Chapter 12 — Build Process¶

Stages: .cpp→-E→.i→-S→.s→-c→.o→link→.exe.
Header guard #ifndef X #define X #endif.
Static lib ar rcs lib.a *.o. Shared lib g++ -fPIC -shared -o lib.so *.cpp.
Link -L path -l name. Run-time LD_LIBRARY_PATH.
Make rule: target: deps\n\trecipe. Auto vars $@ $< $^. .PHONY: clean.
CMake: cmake_minimum_required, project, add_library, add_executable, target_link_libraries; cmake -B build.
Likely question: pipeline diagram; write Makefile splitting Complex; CMake equivalent.

Chapter 13 — Debugging¶

Build for debug: g++ -O0 -g.
gdb: break run next step print backtrace watch continue list quit.
Watchpoint: watch i.
Common bugs: off-by-one (i<=5), NULL deref, infinite loop, leak (debug06), logical (debug05).
valgrind: valgrind --leak-check=full --track-origins=yes ./prog.
Sanitizers: -fsanitize=address,undefined (~2× slower).
Mapper2D bug: xyToPos should be x + sx*y (lecture's (sx-1)*y is wrong).
Likely question: find bug with gdb step-by-step; explain leak detection.

Chapter 14 — Parallelization¶

Shared memory ↔ OpenMP. Distributed memory ↔ MPI. Hybrid common.
Amdahl S(N)=1/(f+(1-f)/N). Strong vs weak scaling.
OpenMP: #pragma omp parallel for reduction(+:sum) schedule(dynamic,k).
MPI 6 calls: Init / Comm_rank / Comm_size / Send / Recv / Finalize.
Send args: buf, count, type, dest, tag, comm.
Domain decomposition + halo cells for CFD.
Compile mpic++ -O2. Run mpirun -n N.
Likely question: OpenMP vs MPI; MPI hello; race condition fix.

Chapter 15 — HPC Cluster Usage¶

Nodes: login (don't compute) / compute / GPU / fat / vis / storage / managing.
Modules: module purge, module load gcc/12 openmpi/4.1, module list, module spider.
SLURM: sbatch run.sbatch, squeue -u $USER, scancel ID, sinfo, srun --pty bash, salloc.
Job script: #SBATCH --nodes=N --ntasks-per-node=M --cpus-per-task=K --time=HH:MM:SS --partition=name --output=...
Env vars in script: $SLURM_NTASKS, $SLURM_CPUS_PER_TASK, $SLURM_NODELIST, $SLURM_JOB_ID, $SLURM_SUBMIT_DIR.
OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK; mpirun -n $SLURM_NTASKS ./solver.
Storage: $HOME slow / $WORK fast / $ARCHIVE tape.
Likely question: write a SBATCH script; explain sbatch vs srun vs salloc.

Last-Minute Checklist¶

[ ] I can convert -rwxr-xr-- ↔ 754.
[ ] I can write a regex for email + IP + phone.
[ ] I can write awk -F, 'NR>1 && $4>1000'.
[ ] I can sketch the SSH passwordless flow.
[ ] I can record + apply a Vim macro.
[ ] I can write backup-data.sh (verbose + sync).
[ ] I can write a multi-curve gnuplot with PNG export.
[ ] I can git init → branch → merge → push.
[ ] I can compile and run a C++ program with pointers.
[ ] I can explain pipeline .cpp → .i → .s → .o → exe with flags.
[ ] I can run gdb to find a NULL deref.
[ ] I can write MPI hello and an OpenMP reduction.
[ ] I can write a SBATCH file for an MPI job.

High-Probability Long-Answer Topics¶

"Discuss why HPC clusters use Linux."
"Compare experiments and CFD simulations in research."
"Walk through SSH passwordless authentication step by step."
"Explain the build pipeline of a C++ program with all four stages."
"Compare OpenMP and MPI; explain hybrid parallelism for CFD."
"Describe the architecture of an HPC cluster and how a job traverses it."

Common Traps¶

Trap	Fix
`chmode` typo	`chmod`
`[ $a==$b ]` (no spaces)	`[ "$a" = "$b" ]`
forgot `git add` before commit	`git add` first
`*` in regex vs glob	different meaning
forgot `-E` for ERE	`grep -E`, `sed -E`
Missing `$` brace in `${VAR}`	always `${...}`
TAB vs spaces in Makefile	always TAB
Forgot `nohup` + `disown`	job dies on logout
Permission `644` on private SSH key	must be `600`
Forgot `MPI_Finalize`	always close

Good luck — viel Erfolg!

End of revision guide.