Train domain-specific language models from scratch with full pipeline transparency

🌍 nanoGPT-Seis

English | 中文 | 🎯 Post-Training (SFT & GRPO RL) | 🤗 Hugging Face Base Model

Train a small GPT for earthquake science - the entire LLM lifecycle, from a blank folder to a talking model, explained block by block.

Crawl → Clean → Tokenize → Model → Train → Infer, on 2× NVIDIA A30 (48 GB).

🚀 Phase II & Phase III Post-Training Available: Looking for Supervised Fine-Tuning (SFT) and Verifier Reinforcement Learning (GRPO RLVR)? Check out the post-training code repository: nanoGPT-Seis-Posttrain and fine-tuned model weights on Hugging Face.

nanoGPT-Seis is a teaching repository. It is not trying to be a great earthquake model - it is trying to make every stage of pretraining a language model legible: where the data comes from, how it is cleaned and deduplicated, how a tokenizer is built, why the Transformer looks the way it does, how it is trained across two GPUs, and how it is served. Every design decision is explained, and every number (perplexity, VRAM, tokens) is one we actually measured on this hardware.

The corpus mixes earthquake / seismology text (open-access papers via Crossref+Unpaywall, arXiv/EarthArXiv preprints, the "Earthquake Insights" Substack) with general text (Wikipedia + FineWeb-Edu) for plain-language fluency - about 24% domain / 76% general. A focused corpus lets a ~100M-param model become genuinely fluent on a single node, so you can see the whole loop close in a day, not a month. (Why the general mix? See §1.)

Status: the pretraining lifecycle is complete - crawl through inference.

Table of contents

1. Results at a glance
2. Quick start
3. Stage 1 - Data crawling
4. Stage 2 - Processing & dedup
5. Stage 3 - The BPE tokenizer
6. Stage 4 - The model (RoPE, GQA, …)
7. Stage 5 - Training (DDP, VRAM, LR)
8. Stage 6 - Inference
9. Repository layout
10. Scaling-law experiments

1. Results at a glance

Three findings worth pausing on:

• Longer context helped. A controlled A/B (data held fixed) - retraining at 4096 vs 1024 dropped perplexity ~11% (9.74 → 10.93 domain-only) for only ~26% more compute per step - papers have long-range structure a 1024-token window can't see across.
• The model uses that context. In a 4096-token window, loss on tokens at positions 2048-4096 is 25% lower than at 0-64 - it conditions on thousands of preceding tokens (see §8).
• A general-text mix restores fluency. Adding Wikipedia + FineWeb-Edu (~2.4:1 general:domain) cut bits/byte on general prose by 35% vs a paper-only base - see the data-mix comparison below.

Data mix: domain-only (v1) → general + domain (v2)

A paper-only base is fluent in paper-register but repetitive/incoherent in plain prose. Adding ~540M tokens of Wikipedia + FineWeb-Edu (→ ~823M train tokens, ~2.4:1 general:domain, ~3.8 epochs - within the ~4-epoch repeat budget shown to be near-lossless by Muennighoff et al., 2023) gives v2.

Measured with bits-per-byte (tokenizer-independent, so v1↔v2 is fair; src/compare_models.py):

v2 is far more fluent on general prose (−35% bits/byte) and generates coherent non-earthquake text where v1 emits gibberish, at the cost of some domain sharpness (+22%) - the classic fluency↔specialization trade-off. This fluent base is the right starting point for SFT; base pretraining alone never yields chat. Domain-only weights are kept as checkpoints/ckpt_v1_domain.pt.

2. Quick start

2.1 Try the pretrained model

The pretrained 113M checkpoint is hosted on the Hugging Face Hub: jiazhe868/nanogpt_seis.

# environment (a working CUDA-12.4 PyTorch; see the note below)
conda activate nanogpt_seis
pip install -r requirements.txt

# download the checkpoint, tokenizer, and model config into the paths expected by
# src/inference.py
huggingface-cli download jiazhe868/nanogpt_seis \
    checkpoints/ckpt.pt \
    data/tokenized/tokenizer.json \
    data/tokenized/meta.json \
    configs/gpt120m_ctx4k.yaml \
    --local-dir .

python -m src.inference --prompt "The 2011 Tohoku earthquake"

2.2 Reproduce pretraining from scratch

# environment (a working CUDA-12.4 PyTorch; see the note below)
conda activate nanogpt_seis
pip install -r requirements.txt

# --- run the whole pipeline ---
# earthquake-domain sources
python -m src.crawl.wikipedia        --max-pages 500                              # earthquake-titled pages
python -m src.crawl.fulltext         --per-journal 3000 --broad 30000 --workers 64
python -m src.crawl.preprints        --arxiv 3000 --eartharxiv 2000
python -m src.crawl.substack         --max 500
# general-text mix for fluency (~540M tokens: Wikipedia + FineWeb-Edu)
python -m src.crawl.general          --wiki-tokens 300000000 --fineweb-tokens 240000000

python -m src.process.build_corpus   --val-frac 0.005      # clean · dedup · split
python -m src.tokenizer.train_bpe    --vocab-size 16384    # train the tokenizer
python -m src.tokenizer.encode                             # → uint16 shards

torchrun --standalone --nproc_per_node=2 \
    -m src.train --config configs/gpt120m_ctx4k.yaml       # train on 2 GPUs

python -m src.inference --prompt "The 2011 Tohoku earthquake"   # streams live

⚠️ Environment gotcha. A PyTorch built for a newer CUDA than your driver will silently report cuda.is_available() == False and fall back to CPU. Verify with python -c "import torch; print(torch.cuda.is_available())" - it must print True. This project uses torch 2.6.0+cu124 to match a CUDA-12.5 driver.

3. Stage 1 - Data crawling

Goal: assemble a large, legal, full-text earthquake corpus from free sources. Code: src/crawl/.

3.1 The sources and how each is fetched

Why a general-text mix? A ~113M model trained only on research papers becomes fluent in paper-register but repetitive and incoherent in plain prose, and 240M tokens is far below compute-optimal (Hoffmann et al., 2022). So we add ~240M tokens of Wikipedia (encyclopedic) + FineWeb-Edu (Penedo et al., 2024; quality-filtered educational web) for a ~1:1 general:domain mix - a fluent base that the planned SFT stage can then make conversational. (Base pretraining alone never yields chat; that's SFT.)

Every document is normalized to one schema (src/crawl/common.py):

@dataclass
class Doc:
    source: str          # "fulltext" | "arxiv" | "wikipedia" | ...
    id: str              # stable per-source id (used for dedup)
    title: str
    text: str            # the cleaned body we will tokenize
    url: str = ""
    date: str = ""
    extra: dict = field(default_factory=dict)   # venue, cited_by, full_text, ...

3.2 How the web crawling actually works

Finding the papers (Crossref). Crossref indexes ~150M scholarly works with a free, generous API. We page through earthquake journal-articles with a deep cursor (no offset limit), filtered by journal ISSN:

# src/crawl/fulltext.py — iter_crossref()
params = {"rows": 1000, "cursor": cursor,
          "filter": "type:journal-article,issn:0094-8276",   # e.g. GRL
          "query.bibliographic": "earthquake", "mailto": EMAIL}

Finding the open PDF (Unpaywall). A DOI is not a PDF. Unpaywall (free, ~100k/day) maps a DOI to its legal open-access copies. We try repository (green OA) locations first - publisher links are frequently bot-blocked stubs:

# repository copies download far more reliably than publisher links
prio = 0 if loc.get("host_type") == "repository" else 1

Downloading in parallel, politely. PDFs come from many hosts, so we use a thread pool but throttle per host - different servers download concurrently while any single server stays rate-limited:

class HostThrottle:                 # src/crawl/fulltext.py
    def wait(self, host):
        with self._guard:                                  # get/create this host's lock
            host_lock = self._locks.setdefault(host, threading.Lock())
            self._last.setdefault(host, 0.0)
        with host_lock:                                    # serialize only this host
            delta = self.min - (time.monotonic() - self._last[host])
            if delta > 0: time.sleep(delta)
            self._last[host] = time.monotonic()

Validating every download. Not every "OA PDF" is real - many are 5 KB anti-bot landing pages. We accept a download only if it is a real PDF with enough text:

if not pdf_bytes.startswith(b"%PDF"): return None   # HTML / stub
if doc.page_count < 2:                return None    # cover page
if len(text) < min_chars:             return None    # too little extracted

Not wasting the budget. Some journals (Science, Nature) are almost entirely paywalled - scanning thousands of their DOIs would burn the Unpaywall budget for zero full text. A low-yield abort gate skips a journal once its hit-rate stays under a threshold:

if scanned >= abort_after and got_ft / max(1, scanned) < min_hit:
    break        # this venue isn't worth more API calls

Resumable. Output is appended line-by-line and already-fetched ids are skipped on restart, so a multi-hour crawl survives interruption:

done = _load_done_ids(out)          # ids already in the JSONL
...
if iid in done: continue            # skip work we already have

War story (why Crossref + Unpaywall). This project originally enumerated papers via OpenAlex, which changed to a paid credit model mid-build - the free daily budget ran out after ~100 requests. Crossref + Unpaywall is the free, robust replacement, and it is what the code ships with. The lesson - pin your data source assumptions and make the crawler resumable - is baked into the design.

Full-text yield varies a lot by source: arXiv ~99% (open by design), the broad OA pool ~15%, paywalled journals ~0% (abstract fallback). Net corpus: ~20k full-text papers + ~26k abstracts.

3.3 The general pattern - a thread-safe BFS crawler

The crawler above is API-driven, but the shape underneath is the classic one: a breadth-first traversal of a link graph, run across many threads. It is worth writing that general pattern out in full, because getting the concurrency right is the hard part. The crux is shared state that every worker touches at once - a frontier of URLs still to visit, and a set of URLs already seen.

Three rules make it correct:

• The frontier is a queue.Queue, which is internally synchronised: get() and put() are atomic, and get() blocks until work exists, so workers never busy-wait.
• The seen-set gets its own lock. "Is this URL new? if so, add it" is a read-modify-write; without the lock two threads can both judge the same URL new and enqueue it twice.
• Termination uses Queue.join() / task_done(). The hard question in a concurrent BFS is knowing when you are done: a worker finding the frontier momentarily empty does not mean the crawl is finished, because another worker may be one instruction away from enqueuing more links. join() counts outstanding tasks and only releases once every enqueued URL has been fully processed.

import re, threading, queue, requests
from urllib.parse import urljoin, urldefrag, urlparse

class BFSCrawler:
    """Breadth-first web crawler: one shared frontier, N worker threads."""

    def __init__(self, seeds, max_pages=5000, n_workers=16, min_interval=1.0):
        self.frontier   = queue.Queue()          # thread-safe BFS queue of (url, depth)
        self.seen       = set(seeds)             # every URL ever enqueued
        self.seen_lock  = threading.Lock()       # guards `seen` (check-then-add races)
        self.pages      = []                     # kept (url, html) pairs
        self.pages_lock = threading.Lock()       # guards `pages` + the page counter
        self.max_pages  = max_pages
        self.n_workers  = n_workers
        self.throttle   = HostThrottle(min_interval)   # §3.2 — politeness, per host
        for s in seeds:
            self.frontier.put((s, 0))            # seed the frontier at depth 0

    def _links(self, base, html):                # extract absolute, de-fragmented links
        for m in re.finditer(r'href=["\'](.*?)["\']', html):
            url, _ = urldefrag(urljoin(base, m.group(1)))   # relative → absolute, drop #frag
            if url.startswith(("http://", "https://")):
                yield url

    def _enqueue(self, url, depth):
        with self.seen_lock:              # the check AND the add are ONE critical section,
            if url in self.seen:          # else two threads both see `url` as new and
                return                    # enqueue it twice
            self.seen.add(url)
        self.frontier.put((url, depth))

    def _worker(self):
        while True:
            url, depth = self.frontier.get()      # blocks; (None, _) is the stop sentinel
            if url is None:
                self.frontier.task_done()
                return
            try:
                with self.pages_lock:
                    if len(self.pages) >= self.max_pages:
                        continue                  # budget spent — drain the rest quietly
                self.throttle.wait(urlparse(url).netloc)      # rate-limit this host
                html = requests.get(url, timeout=10).text
                with self.pages_lock:
                    if len(self.pages) >= self.max_pages:
                        continue
                    self.pages.append((url, html))
                for link in self._links(url, html):           # BFS: expand the frontier
                    self._enqueue(link, depth + 1)
            except Exception:
                pass                              # one dead link must not kill a worker
            finally:
                self.frontier.task_done()         # pairs with the get() above

    def run(self):
        workers = [threading.Thread(target=self._worker, daemon=True)
                   for _ in range(self.n_workers)]
        for t in workers:
            t.start()
        self.frontier.join()                      # wait until the frontier is truly drained
        for _ in workers:                         # then release the idle, blocked workers
            self.frontier.put((None, 0))
        for t in workers:
            t.join()
        return self.pages

ThreadPoolExecutor reaches the same result with less bookkeeping - submit _worker n_workers times and let the pool own the threads - but spelling out the Queue.join() handshake is what makes the termination logic visible.

This repo's fulltext.py is a one-hop specialisation of exactly this skeleton: the frontier is the list of DOIs Crossref returns, each is "expanded" not into page out-links but into its Unpaywall PDF locations, and the shared guarded state is the resume-set of already-fetched ids rather than a seen set of URLs. The thread pool and the per-host throttle are identical. A full multi-hop BFS would instead follow <a href> links, which is the version above.

4. Stage 2 - Processing & dedup

Code: src/process/. Turns messy data/raw/*.jsonl into clean train/val splits.

4.1 Cleaning (source-aware) - clean.py

def normalize(text):
    text = html.unescape(text)                 # 
 & → real chars
    text = unicodedata.normalize("NFKC", text) # fi ligatures, full-width, …
    text = _CTRL_RE.sub("", text)              # strip control bytes
    text = _MULTISPACE_RE.sub(" ", text)       # collapse whitespace
    ...

PDFs get extra care: line-break de-hyphenation (earth-\nquake → earthquake) and reference-section stripping (truncate at the last "References"/"Bibliography" heading - the bibliography is noise for a language model).

4.2 Quality filtering

Three cheap, effective filters (passes_filters):

• length - drop < 200 chars;
• English ratio - fraction of tokens that are common English stopwords; drops the Spanish-translated Substack posts without a language-ID dependency;
• alpha ratio - fraction of letters/spaces; drops garbled PDF tables and math dumps.

4.3 Deduplication - dedup.py

Duplicate training data measurably hurts language models (Lee et al., 2021) - repeated documents get over-memorised and waste the token budget. But comparing every document against every other is O(N²) and reads every byte, so good dedup is an exercise in doing the cheap test first: eliminate non-candidates with progressively more expensive checks, and pay the expensive one only on what survives.

The cascade, in its classic form. The same idea drives the textbook "find duplicate files on disk" problem. Two files can only be identical if they have the same size; of the same-size files, only those whose first kilobyte also matches can be identical; and only those earn a full-content hash. Each tier is strictly more expensive than the last and runs on strictly fewer inputs:

import os, hashlib
from collections import defaultdict

def find_duplicate_files(root: str) -> list[list[str]]:
    def file_hash(path: str, first_chunk_only=False, chunk=8192) -> str:
        h = hashlib.md5()
        try:
            with open(path, "rb") as f:
                if first_chunk_only:
                    h.update(f.read(1024))                    # cheap: one small read
                else:
                    for block in iter(lambda: f.read(chunk), b""):
                        h.update(block)                       # full read of the file
        except OSError:
            return ""
        return h.hexdigest()

    # Tier 1 — group by size. Just a stat() per file; no bytes are read.
    by_size: dict[int, list[str]] = defaultdict(list)
    for dirpath, _, names in os.walk(root):
        for name in names:
            path = os.path.join(dirpath, name)
            if os.path.islink(path):
                continue
            try:
                size = os.path.getsize(path)
            except OSError:
                continue
            if size > 0:
                by_size[size].append(path)

    # Tier 2 — within each size group, group by a partial (first-1KB) hash.
    by_partial: dict[str, list[str]] = defaultdict(list)
    for paths in by_size.values():
        if len(paths) > 1:                                    # a lone file can't be a dup
            for p in paths:
                if (ph := file_hash(p, first_chunk_only=True)):
                    by_partial[ph].append(p)

    # Tier 3 — only now pay for a full-content hash, on the few real candidates.
    by_full: dict[str, list[str]] = defaultdict(list)
    for paths in by_partial.values():
        if len(paths) > 1:
            for p in paths:
                if (fh := file_hash(p, first_chunk_only=False)):
                    by_full[fh].append(p)

    return [paths for paths in by_full.values() if len(paths) > 1]

Why it is fast: N files cost N cheap stat() calls; a partial read happens only for files that share a size; a full read happens only for files that also share a first kilobyte. Almost everything is filtered out before Tier 3, so the expensive full-content pass touches a tiny fraction of the data - the O(N²)-looking problem collapses to roughly O(N). The design rule generalises: cheapest discriminator first, narrow to candidates, confirm last.

Exact pass, applied to documents. Text documents are small enough that a single hash is the whole cascade - the trick is what you hash. We normalise first (lowercase, collapse whitespace) so copies that differ only in formatting collide, then key on one SHA-1. Normalisation is the moral equivalent of the size/partial tiers: it forces "same content, different wrapping" into the same bucket before the hash even runs.

def exact_key(text: str) -> str:                 # src/process/dedup.py
    normalized = " ".join(text.lower().split())  # canonicalise whitespace + case
    return hashlib.sha1(normalized.encode("utf-8")).hexdigest()

seen, unique = set(), []
for d in docs:
    k = exact_key(d["text"])
    if k in seen:            # O(1) set membership — the whole exact pass is O(N)
        continue
    seen.add(k); unique.append(d)

Near-duplicate pass (MinHash + LSH). Exact hashing misses documents that are almost identical - e.g. an abstract that also appears verbatim inside its full-text PDF, plus one extra sentence: one byte differs, so the SHA-1s diverge completely. For those we need a similarity measure, and LSH is the same cascade idea applied to fuzzy matching. Each document becomes a set of word 5-grams (shingles); a MinHash (Broder, 1997) signature (128 permutations) estimates the Jaccard similarity of two shingle sets in constant space; and an LSH index buckets signatures so only likely-similar documents are ever compared - the cheap candidate filter that replaces the O(N²) all-pairs comparison, exactly like Tier 1 above. Documents are processed longest-first, so when a near-dup is found we keep the fullest version:

m = MinHash(num_perm=128)
for shingle in word_5grams(text): m.update(shingle.encode())
if lsh.query(m):          # LSH returns only bucket-mates — the candidate set
    near_dups += 1        # a ≥70%-similar doc is already kept → drop this one
else:
    lsh.insert(id, m); kept.append(doc)

The MinHash step is the expensive tier (it reads every surviving document), so dedup.py computes signatures across a process pool - worker processes inherit the document list by copy-on-write and return just the signatures - while the stateful LSH insert/query stays serial but cheap (dict ops on precomputed signatures). On the real corpus this removed 1,126 exact + 304 near duplicates. Finally the docs are shuffled with a fixed seed and split into train / val, preserving each doc's metadata.

5. Stage 3 - The BPE tokenizer

Code: src/tokenizer/. We train our own tokenizer rather than reuse GPT-2's - owning this stage is the point, and a domain vocabulary encodes seismology text more efficiently.

5.1 Why byte-level BPE

BPE (Byte-Pair Encoding - Sennrich et al., 2015, adapting a 1994 compression scheme) starts from single characters and greedily merges the most frequent adjacent pair, over and over, until it reaches the target vocab size. Frequent sequences (earthquake, sub, duction) become single tokens; rare ones stay in pieces. Byte-level (Wang et al., 2019) means the base alphabet is the 256 raw bytes, so any input is representable - there are no <unk> tokens, ever.

# src/tokenizer/train_bpe.py
tokenizer = Tokenizer(BPE(unk_token=None))
tokenizer.pre_tokenizer = ByteLevel(add_prefix_space=False)
trainer = BpeTrainer(vocab_size=16384, special_tokens=["<|endoftext|>"],
                     initial_alphabet=ByteLevel.alphabet())   # all 256 bytes
tokenizer.train_from_iterator(_iter_texts(train_jsonl), trainer)

We use 16,384 tokens (vs GPT-2's 50,257): smaller vocab → smaller embedding matrix (a big fraction of a small model's params) and the domain is narrow. Measured compression on our corpus is ~3.9 chars/token - healthy. The single special token <|endoftext|> marks document boundaries.

5.2 How BPE works (from scratch)

tokenizers does this for us in fast Rust, but the algorithm is small enough to write by hand - and understanding it is the point. A BPE tokenizer is just a base alphabet plus an ordered list of merge rules, learned in two phases.

The whole thing fits in one small class - training learns the merges, encoding replays them, decoding concatenates the bytes back:

from collections import defaultdict

class BPETokenizer:
    def __init__(self, vocab_size: int):
        assert vocab_size >= 256
        self.vocab_size = vocab_size
        self.vocab = {}      # token id -> merged bytes
        self.merges = {}     # (id1, id2) -> new id

    def _get_stats(self, ids: list) -> dict:            # count adjacent id pairs
        count = defaultdict(int)
        for i in range(len(ids) - 1):
            count[(ids[i], ids[i + 1])] += 1
        return count

    def _merge(self, ids: list, pair: tuple, newidx: int) -> list:
        output, i = [], 0
        while i < len(ids):
            if i < len(ids) - 1 and pair == (ids[i], ids[i + 1]):
                output.append(newidx); i += 2
            else:
                output.append(ids[i]); i += 1
        return output

    def train(self, text: str):
        for i in range(256):                            # base vocab = the 256 bytes
            self.vocab[i] = bytes([i])
        ids = list(text.encode("utf-8"))
        for i in range(self.vocab_size - 256):          # each merge adds one token
            stats = self._get_stats(ids)
            if not stats:
                break
            top_pair = max(stats, key=stats.get)        # most frequent adjacent pair...
            newidx = 256 + i
            ids = self._merge(ids, top_pair, newidx)    # ...becomes one new token
            self.merges[top_pair] = newidx
            self.vocab[newidx] = self.vocab[top_pair[0]] + self.vocab[top_pair[1]]

    def encode(self, text: str) -> list:                # text -> BPE token ids
        ids = list(text.encode("utf-8"))
        while len(ids) >= 2:
            stats = self._get_stats(ids)
            # apply the pair whose merge was learned earliest (smallest new id)
            pair = min(stats, key=lambda p: self.merges.get(p, float("inf")))
            if pair not in self.merges:
                break
            ids = self._merge(ids, pair, self.merges[pair])
        return ids

    def decode(self, ids: list) -> str:                 # token ids -> text
        raw = b"".join(self.vocab[i] for i in ids)
        return raw.decode("utf-8", errors="replace")

train starts from the 256 byte values, then repeatedly counts adjacent id pairs, merges the most frequent pair into a fresh id (256 + i), and records both the merge rule and its byte expansion - one new token per iteration, so it stops after vocab_size − 256 merges. encode replays those merges greedily, always applying the one learned earliest (min by new id = highest priority) until no learned pair is left. decode concatenates each id's bytes and UTF-8-decodes. Because the base alphabet is all 256 bytes, nothing is ever out-of-vocabulary. (For a longer from-scratch treatment of this exact algorithm, see Karpathy's minbpe and the "Let's build the GPT Tokenizer" video.)

On our real 16k tokenizer (verified) the same mechanism gives earthquake and subduction one token each (they're common in the corpus), newest → [new, est], seismogram → [seism, ogram], and a genuinely rare word splits far more - antidisestablishmentarianism → [ant, id, is, establish, ment, arian, ism].

This minimal version merges over the raw byte stream; production tokenizers - including our tokenizers-based train_bpe.py - add a byte-level pre-tokenizer that first splits text into word-ish chunks so merges never cross word boundaries. But the core loop is exactly the above, just in fast Rust so it handles the 3 GB corpus.

5.3 Encoding to uint16 shards

encode.py streams the corpus through the tokenizer and writes one flat array of token ids per split, documents separated by the eot id:

for enc in tok.encode_batch(batch):
    buf.extend(enc.ids); buf.append(eot_id)       # eot between docs
    if len(buf) >= FLUSH_EVERY:
        np.asarray(buf, dtype=np.uint16).tofile(fout)   # 2 bytes/token

uint16 (0-65535) fits our 16k vocab in 2 bytes/token → 822.7M tokens ≈ 1.6 GB, and the training loader np.memmaps it (no RAM blow-up). Crucially, this file is context-length-agnostic - the window width is chosen at training time, which is why switching 1024→4096 needed no re-tokenization.

6. Stage 4 - The model

Code: src/model/gqa_gpt.py. A modern, Llama-style decoder-only Transformer.

6.1 Why these components

6.2 Attention - queries, keys, and values

Attention is the operation that lets tokens exchange information. Each token's vector is linearly projected into three roles:

• query q - what this token is looking for;
• key k - what this token offers to others;
• value v - the information it passes on when attended to.

For one head of width d_k, stack these over the sequence into Q, K, V of shape T × d_k (one row per token). Attention scores every query against every key, turns the scores into weights, and returns each query's weighted average of the values:

Attention(Q, K, V) = softmax( Q Kᵀ / √d_k + M ) · V

• Q Kᵀ is the T × T matrix of query·key dot products - how strongly token i's query matches token j's key. softmax over each row makes weights that sum to 1, and multiplying by V averages the values under those weights.
• M is the causal mask: 0 on and below the diagonal, −∞ above, so a token attends only to itself and earlier tokens - it can't peek at the future it is trained to predict.

Why divide by √d_k. q·k is a sum of d_k products; for roughly unit-variance, independent entries that sum has variance d_k, so raw scores grow like √d_k. Feed large scores into softmax and it saturates - one weight ≈ 1, the rest ≈ 0 - and its gradient vanishes, so learning stalls. Dividing by √d_k rescales scores back to ~unit variance and keeps softmax in a responsive range. (RoPE in §6.3 is applied to q and k just before this product; GQA in §6.4 shares K/V across heads.)

Why several heads, not one. Instead of one attention over the full d_model width, we split into h heads of d_k = d_model / h (here 12 × 64), attend independently, and concatenate. A single head must collapse every kind of relationship - local adjacency, syntax, long-range coreference - into one weight distribution; separate heads let each specialise in a different pattern and a different subspace at the same time. Total compute is unchanged (h · d_k = d_model), and the specialisation is visible in the trained model (§8.4: some heads are previous-token, some broad, some attention sinks).

Cost. Both Q Kᵀ and the weighting of V are T × T × d_k per head, so attention is O(T² · d_model) in time and O(T²) in memory for the score matrix - quadratic in sequence length T. That quadratic is why long context is expensive, and why the next two subsections matter: GQA shrinks the per-token state that has to be cached, and FlashAttention removes the O(T²) memory term entirely.

6.3 RoPE - Rotary Position Embeddings

A Transformer is permutation-invariant; it needs to be told token order. RoPE encodes position by rotating each query/key vector by an angle proportional to its position. The dot product of a rotated query at position m and key at position n then depends only on their relative distance m − n - which is exactly what attention should care about, and it lets the model handle positions it can partly extrapolate to.

The cleanest way to see it: treat each pair of channels as a complex number - rotating a 2-D vector by angle θ is just multiplying by the unit complex number e^{iθ}. Precompute e^{i·m·θ_j} for every position m and frequency θ_j, then encoding position is a single complex multiply:

def precompute_mtheta(dim: int, seqlen: int, base: float = 1e4) -> torch.Tensor:
    theta = 1 / (base ** (torch.arange(0, dim, 2) / dim))    # D/2 frequencies
    m = torch.arange(0, seqlen)                              # S positions
    mtheta = torch.outer(m, theta)                           # S × D/2 angles
    return torch.polar(torch.ones_like(mtheta), mtheta)      # unit complex e^{i·mθ}

def apply_rope(x: torch.Tensor, mtheta: torch.Tensor) -> torch.Tensor:
    # x: (B, S, H, D);  mtheta: (S, D/2)
    x_complex = torch.view_as_complex(x.float().unflatten(-1, (-1, 2)))   # B S H D/2
    mtheta = mtheta[:x.shape[1]].reshape(1, x.shape[1], 1, -1)            # 1 S 1 D/2
    x_rotated = torch.view_as_real(x_complex * mtheta).flatten(3)         # B S H D
    return x_rotated.type_as(x)

Each channel pair (x₂ⱼ, x₂ⱼ₊₁) becomes the complex number x₂ⱼ + i·x₂ⱼ₊₁ and is rotated by m·θ_j; low-index pairs use large θ_j (rotate fast), high-index pairs small θ_j (slow). There are no learned parameters, and the rotation preserves norm. The dot product of a rotated query at m and key at n then depends only on the relative offset m − n - the whole point.

Our repo implements the algebraically-equivalent real-valued rotate_half form (same rotation, no complex tensors - friendlier to the compiled / FlashAttention path); cos/sin are precomputed once and applied to Q and K just before attention:

def _apply_rope(x, cos, sin):          # x: (B, n_head, T, head_dim)
    return x * cos + _rotate_half(x) * sin

(One convention pairs adjacent channels, the other pairs channel j with j + D/2; both give the same relative-position behavior - just a different weight layout.)

Two consequences (both computed from this model's head_dim=64, θ=10000): the q·k score depends only on the relative distance - curves for queries at positions 200/800/2000 lie exactly on top of each other (left) - and the channel pairs rotate at a geometric spread of frequencies, fast to slow (right), so the model can resolve both nearby and far-apart positions.

6.4 GQA - Grouped-Query Attention

Standard multi-head attention gives every one of the 12 query heads its own key/value head - so at inference the KV cache (the stored keys/values for every past token) holds 12 heads' worth per token. GQA (Ainslie et al., 2023) lets several query heads share a KV head - interpolating between full MHA and multi-query attention (Shazeer, 2019). We use 12 query : 4 KV heads, so the KV cache is 3× smaller - cheaper long-context inference - at nearly no quality cost, because attention quality is dominated by the number of query heads (still 12).

# src/model/gqa_gpt.py — GroupedQueryAttention
# Per-head projection written as an einsum so the contraction is explicit:
#   out[b, h, t, i] = Σ_d  x[b, t, d] · W[h, i, d]
q = torch.einsum("btd,hid->bhti", x, self.wq.weight.view(n_head, hd, d))  # 12 heads
k = torch.einsum("btd,hid->bhti", x, self.wk.weight.view(n_kv,   hd, d))  #  4 heads  ← fewer
v = torch.einsum("btd,hid->bhti", x, self.wv.weight.view(n_kv,   hd, d))  #  4 heads
if n_kv != n_head:                       # broadcast KV heads to match Q for SDPA
    k = k.repeat_interleave(rep, dim=1)  # (the cache itself still stores only n_kv heads)
    v = v.repeat_interleave(rep, dim=1)
y = F.scaled_dot_product_attention(q, k, v, is_causal=True)   # FlashAttention kernel

That one scaled_dot_product_attention call is just the standard attention math - worth spelling out once. Here is the explicit, non-Flash equivalent (also how src/figures/attention_map.py recovers the weights, since the fused kernel doesn't expose them):

import math
# q, k, v: (B, n_head, T, head_dim) — KV already broadcast to n_head above
scores = torch.einsum("bhqd,bhkd->bhqk", q, k) / math.sqrt(head_dim)  # (B,n_head,T,T)
mask = torch.triu(torch.ones(T, T, dtype=torch.bool), diagonal=1)
scores = scores.masked_fill(mask, float("-inf"))                      # causal
attn = torch.softmax(scores, dim=-1)                                  # each row sums to 1
y = torch.einsum("bhqk,bhkd->bhqd", attn, v)                          # (B,n_head,T,head_dim)

The two einsums are the query·key similarity (bhqd,bhkd->bhqk) and the value-weighted sum (bhqk,bhkd->bhqd) - identical to q @ kᵀ and attn @ v, just with the contracted axis named.

Why FlashAttention (Dao et al., 2022; FlashAttention-2, 2023). F.scaled_dot_product_attention computes exactly the above (verified identical to ~1e-7), but attention written this way is memory-bandwidth bound, not compute bound: the naive version writes the T×T scores and attn matrices out to the GPU's large-but-slow main memory (HBM) and reads them back, and shuttling those O(T²) intermediates dominates the wall-clock. FlashAttention never builds them. It splits Q, K, V into blocks small enough to fit in on-chip SRAM - the fast per-SM scratchpad (tens of KB, ~10-20× the bandwidth of HBM) - and for each query block streams over the key/value blocks, accumulating the result tile by tile so the O(T²) intermediates never leave SRAM. Only the O(T) output is written back to HBM.

The online softmax, in code. The one hard part is the softmax. An ordinary softmax needs the whole row at once - subtract the row max for numerical stability, exponentiate, divide by the sum - but a query block only ever sees one key block at a time. The fix is an online softmax that keeps three running quantities per query row and updates them block by block: the running max m, the running normaliser l = Σ exp(·), and the running un-normalised output o. When a new block raises the max, the earlier accumulators are rescaled by exp(m_old − m_new) to rebase them onto the new max:

import torch, math

class FlashAttention:
    """Tiled attention with an online softmax — the FlashAttention forward pass in
    plain PyTorch. Never materialises the full S×S score matrix, only Br×Bc tiles."""

    def __init__(self, block_q: int, block_kv: int):
        self.Br = block_q        # query-block size (rows of the score matrix)
        self.Bc = block_kv       # key/value-block size (columns)

    def __call__(self, q, k, v):
        # q, k, v: (B, H, S, D)  ->  out: (B, H, S, D)
        B, H, S, D = q.shape
        scale = 1.0 / math.sqrt(D)
        out = torch.zeros_like(q)

        for i in range(0, S, self.Br):                    # outer loop: query blocks
            q_i = q[..., i:i + self.Br, :]                # (B,H,Br,D) — stays in SRAM
            o_i = torch.zeros_like(q_i)                   # running un-normalised output
            l_i = torch.zeros(*q_i.shape[:-1], 1, device=q.device, dtype=q.dtype)  # running Σexp
            m_i = torch.full_like(l_i, float("-inf"))     # running row-max

            for j in range(0, S, self.Bc):                # inner loop: stream K/V blocks
                k_j = k[..., j:j + self.Bc, :]
                v_j = v[..., j:j + self.Bc, :]

                s_ij  = torch.matmul(q_i, k_j.transpose(-2, -1)) * scale   # (B,H,Br,Bc) scores
                m_new = torch.maximum(m_i, s_ij.max(dim=-1, keepdim=True).values)   # new row-max
                p_ij  = torch.exp(s_ij - m_new)           # tile probabilities vs the new max
                corr  = torch.exp(m_i - m_new)            # rescale earlier accumulators (≤ 1)

                l_i = l_i * corr + p_ij.sum(dim=-1, keepdim=True)   # rebase Σexp, add this tile
                o_i = o_i * corr + torch.matmul(p_ij, v_j)          # rebase output, add p·V
                m_i = m_new                               # advance the running max

            out[..., i:i + self.Br, :] = o_i / l_i        # normalise once, write O(T) to HBM

        return out

One inner step reads a Br×Bc score tile s_ij, folds its row-max into the running max (m_new), forms that tile's probabilities p_ij = exp(s_ij − m_new) against the new max, and - before adding them in - multiplies the earlier l and o by the correction corr = exp(m_i − m_new) ≤ 1. That correction is the whole trick: it retroactively puts the running sum and output on the latest max's scale, so after the final block o / l is bit-for-bit a full softmax (max abs diff ~1e-15 vs scaled_dot_product_attention) while nothing larger than one Br×Bc tile is ever held. The production CUDA kernel is this exact recurrence with the tiles living in registers/SRAM. For a causal decoder like ours the inner loop simply skips future key blocks (j > i) and triangular-masks only the diagonal block, so causality roughly halves the work as well.

Far fewer HBM round-trips → both O(T) memory and a big speedup - which is exactly what makes 4096-token context affordable on a 24 GB card.

6.5 Normalization - RMSNorm, and pre-norm vs post-norm

Every sublayer is wrapped in normalisation. We use RMSNorm: scale each token vector to unit root-mean-square, then apply a learned per-channel gain g - no mean subtraction, no bias:

RMSNorm(x) = x / sqrt( mean(x²) + ε ) · g

LayerNorm additionally centres the vector ((x − μ)/σ · γ + β); RMSNorm drops the mean and the bias, which is cheaper and works as well in practice - the Llama default.

Where the norm sits matters as much as which one. The original Transformer is post-norm - normalise after the residual add; modern decoders (GPT-2, Llama, us) are pre-norm - normalise inside the residual branch, before the sublayer:

post-norm:  x  ←  Norm( x + Sublayer(x) )
pre-norm:   x  ←  x + Sublayer( Norm(x) )

Why pre-norm. In pre-norm the residual path x + … is an unbroken identity highway: gradients flow from the loss straight back to every layer without passing through a normaliser, so deep stacks train stably from scratch. Post-norm puts a norm on that main path, so the gradient is rescaled at every layer on the way down - deep post-norm Transformers need careful learning-rate warmup and initialisation just to converge. The price of pre-norm is that the residual stream's variance grows with depth (each block adds to it without renormalising the sum); we offset that in the weight init (§6.7).

6.6 SwiGLU - the gated feed-forward

Between attention layers, each token is transformed on its own by a feed-forward network. The classic version is W₂ · GELU(W₁ x): project up, apply a pointwise activation, project down. We use SwiGLU, a gated variant with three matrices:

SwiGLU(x) = W₂ ( SiLU(W₁ x) ⊙ (W₃ x) ),     SiLU(z) = z · sigmoid(z)

The up-projection W₃ x is multiplied element-wise (⊙) by a data-dependent gate SiLU(W₁ x): the network learns, per token and per hidden unit, how much signal to let through. That multiplicative interaction is more expressive than a single fixed activation and gives better quality per parameter. Because SwiGLU uses three matrices instead of two, its hidden width is set to ≈ 8/3 · d_model (rounded to a multiple of 256) rather than 4 · d_model, so the parameter count matches a plain MLP - the ⌈8/3·d⌉ rule. Code: src/model/gqa_gpt.py's SwiGLU (w1 gate, w3 up, w2 down).

6.7 Weight initialization

Initialisation decides whether the first steps are stable. Three rules:

• Linear and embedding weights: Normal(0, 0.02). A small standard deviation keeps activations and the initial logits in a sane range. At init the model should be maximally unsure, so the loss should be ln(vocab_size) = ln(16384) ≈ 9.70; ours starts at 9.85 ✓ - the quickest check that the model and loss are wired correctly.
• Residual output projections scaled by 1/√(2·n_layer) (the GPT-2 trick): the attention Wo and the SwiGLU W₂ - the two matrices that write back into the residual stream - are initialised with std = 0.02/√(2·n_layer). In a pre-norm net (§6.5) each of the 2·n_layer sublayers adds to the residual stream without renormalising the sum, so without this its variance would grow with depth and the logits would blow up; shrinking those writes keeps the residual variance roughly constant from the first block to the last.
• No biases anywhere, and RMSNorm gains start at 1.

(For the scaling experiments, muP rescales both this init and the learning rate by width; §10.2.)

6.8 Hyperparameters and why

configs/gpt120m_ctx4k.yaml:

n_layer: 16      d_model: 768      n_head: 12   n_kv_head: 4     # GQA 12:4
block_size: 4096   vocab_size: 16384   ffn hidden: 2048 (SwiGLU)

• d_model 768 / 12 heads / 16 layers ≈ GPT-2-small shape → ~113M params, a size that trains comfortably on one node and is big enough to be fluent.
• head_dim 64 (768/12) - the sweet spot FlashAttention is tuned for.
• SwiGLU hidden 2048 - the Llama ⌈8/3·d⌉ rule rounded to a multiple of 256.

7. Stage 5 - Training

Code: src/train.py. Data-parallel across both A30s.

7.1 DDP - how two GPUs train one model

We launch with torchrun --nproc_per_node=2, which starts one process per GPU. DistributedDataParallel keeps a replica of the model on each GPU; each processes a different micro-batch, and gradients are all-reduced (averaged) across GPUs before the optimizer step - so both replicas stay identical. The effective batch is the sum across GPUs.

init_process_group(backend="nccl")
model = torch.compile(model)                       # fuse kernels
model = DDP(model, device_ids=[local_rank])        # replicate + all-reduce grads

Gradient accumulation multiplies the batch further: we run several micro-batches before stepping, and - importantly - only sync gradients on the last one, so the in-between backward passes don't pay the all-reduce cost:

for micro in range(gra

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