Simplify pos handling, auto-increment output arg

- no longer multiply by num_queries
- remove unused interleaved prompts
- Rename to Queries*
- Rename batch_start/interleaved_pos/pos to queries_pos

PiperOrigin-RevId: 663331823

evals/benchmark_helper.cc

@@ -108,10 +108,9 @@ std::pair<std::string, size_t> GemmaEnv::QueryModel(
   std::string res;
   size_t total_tokens = 0;
 
-  const double time_start = hwy::platform::Now();
-  const BatchStreamFunc batch_stream_token =
-      [&res, &total_tokens, &time_start, this](
-          size_t query_index, size_t pos, int token, float) {
+  const BatchStreamFunc batch_stream_token = [&res, &total_tokens, this](
+                                                 size_t query_index, size_t pos,
+                                                 int token, float) {
     ++total_tokens;
     res += StringFromTokens(std::vector<int>{token});
     return true;
@@ -130,23 +129,19 @@ std::pair<std::string, size_t> GemmaEnv::QueryModel(
 }
 
 std::vector<std::pair<std::string, size_t>> GemmaEnv::BatchQueryModel2(
-    const MultiplePromptsTokens& prompts) {
-  const size_t num_queries = prompts.size();
+    const QueriesPromptTokens& queries_prompt) {
+  const size_t num_queries = queries_prompt.size();
   HWY_ASSERT(num_queries != 0);
   std::vector<std::pair<std::string, size_t>> res(num_queries);
   std::fill(res.begin(), res.end(), std::make_pair("", 0));
-  size_t total_tokens = 0;
-
-  const double time_start = hwy::platform::Now();
-  const BatchStreamFunc batch_stream_token =
-      [&res, &total_tokens, &time_start, this](
-          size_t query_index, size_t pos, int token, float) {
+  const BatchStreamFunc batch_stream_token = [&res, this](size_t query_index,
+                                                          size_t pos, int token,
+                                                          float) {
     std::string token_text;
     HWY_ASSERT(
         model_->Tokenizer().Decode(std::vector<int>{token}, &token_text));
     res[query_index].first.append(token_text);
     res[query_index].second += 1;
-    ++total_tokens;
     return true;
   };
   if (app_.verbosity >= 2) {
@@ -171,8 +166,9 @@ std::vector<std::pair<std::string, size_t>> GemmaEnv::BatchQueryModel2(
   gcpp::TimingInfo timing_info = {.verbosity = app_.verbosity};
   runtime_config_.batch_stream_token = batch_stream_token;
   inference_args_.CopyTo(runtime_config_);
-  model_->GenerateBatch(runtime_config_, prompts,
-                        std::vector<size_t>(num_queries, 0),
+  std::vector<size_t> queries_pos(num_queries, 0);
+  model_->GenerateBatch(runtime_config_, queries_prompt,
+                        QueriesPos(queries_pos.data(), num_queries),
                         KVCaches(&kv_caches_[0], num_queries), timing_info);
   return res;
 }
@@ -197,7 +193,7 @@ std::vector<std::pair<std::string, size_t>> GemmaEnv::BatchQueryModel(
   for (auto& prompt : prompts) {
     prompt_vector.push_back(PromptTokens(prompt.data(), prompt.size()));
   }
-  MultiplePromptsTokens prompt_span(prompt_vector.data(), prompt_vector.size());
+  QueriesPromptTokens prompt_span(prompt_vector.data(), prompt_vector.size());
   return BatchQueryModel2(prompt_span);
 }
 

evals/benchmark_helper.h

@@ -69,7 +69,7 @@ class GemmaEnv {
   // the number of tokens that were generated.
   std::pair<std::string, size_t> QueryModel(const std::vector<int>& tokens);
   std::vector<std::pair<std::string, size_t>> BatchQueryModel2(
-      const MultiplePromptsTokens& prompts);
+      const QueriesPromptTokens& queries_prompt);
   // Adds turn structure to input, tokenizes and calls the above overload.
   std::pair<std::string, size_t> QueryModel(std::string& input);
   std::vector<std::pair<std::string, size_t>> BatchQueryModel(

evals/gemma_test.cc

@@ -82,7 +82,7 @@ class GemmaTest : public ::testing::Test {
       for (const auto& prompt : prompts_vector) {
         prompt_spans.push_back(PromptTokens(prompt.data(), prompt.size()));
       }
-      MultiplePromptsTokens prompts(prompt_spans.data(), prompt_spans.size());
+      QueriesPromptTokens prompts(prompt_spans.data(), prompt_spans.size());
       for (auto [response, n] : s_env->BatchQueryModel2(prompts)) {
         replies.push_back(response);
       }

evals/run_mmlu.cc

@@ -110,13 +110,13 @@ void Run(GemmaEnv& env, JsonArgs& json) {
 
     std::vector<int> predicted_token_ids;
     predicted_token_ids.reserve(4096);
-    size_t current_pos = 0;
-    const StreamFunc stream_token = [&current_pos, prompt_size,
+    size_t generated = 0;
+    const StreamFunc stream_token = [&generated, prompt_size,
                                      &predicted_token_ids](int token,
                                                            float proba) {
       PROFILER_ZONE("Stream");
-      ++current_pos;
-      if (current_pos > prompt_size) {
+      ++generated;
+      if (generated > prompt_size) {
         predicted_token_ids.push_back(token);
       }
       return true;

examples/hello_world/run.cc

@@ -47,7 +47,7 @@ int main(int argc, char** argv) {
   gcpp::Gemma model = gcpp::CreateGemma(loader, pools);
   gcpp::KVCache kv_cache =
       gcpp::KVCache::Create(loader.Info().model, inference.prefill_tbatch_size);
-  size_t pos = 0;  // KV Cache position
+  size_t generated = 0;
 
   // Initialize random number generator
   std::mt19937 gen;
@@ -56,14 +56,14 @@ int main(int argc, char** argv) {
 
   // Tokenize instructions.
   std::string prompt = "Write a greeting to the world.";
-  const std::vector<int> tokens =
-      gcpp::WrapAndTokenize(model.Tokenizer(), loader.Info(), pos, prompt);
-  size_t ntokens = tokens.size();
+  const std::vector<int> tokens = gcpp::WrapAndTokenize(
+      model.Tokenizer(), loader.Info(), generated, prompt);
+  const size_t prompt_size = tokens.size();
 
   // This callback function gets invoked every time a token is generated
-  auto stream_token = [&pos, &ntokens, &model](int token, float) {
-    ++pos;
-    if (pos < ntokens) {
+  auto stream_token = [&generated, &prompt_size, &model](int token, float) {
+    ++generated;
+    if (generated < prompt_size) {
       // print feedback
     } else if (token != gcpp::EOS_ID) {
       std::string token_text;

gemma/gemma-inl.h

@@ -68,13 +68,13 @@ namespace HWY_NAMESPACE {
 // count `num_interleaved`. Functions that are query-dependent, such as
 // `Attention`, use separate `num_tokens` and `num_queries`.
 
+// TODO: add batch query support for Griffin (QueriesPos).
 template <class TConfig>
 HWY_NOINLINE void GriffinRecurrent(
-    size_t batch_start, size_t num_tokens, size_t num_queries, size_t layer,
+    size_t batch_start, size_t num_tokens, size_t layer,
     Activations& activations, const CompressedLayer<TConfig>* layer_weights,
     const KVCaches& kv_caches, hwy::ThreadPool& pool) {
   PROFILER_ZONE("Gen.Griffin");
-  HWY_ASSERT(num_queries == 1);  // TODO: add batch query support for Griffin.
   KVCache& kv_cache = kv_caches[0];
   namespace hn = hwy::HWY_NAMESPACE;
   using D = hn::ScalableTag<float>;
@@ -233,8 +233,7 @@ class GemmaAttention {
   // Fills activations.q and computes KV. For kIsMHA, a single MatMul suffices
   // and we later copy KV from q to KVCache. Otherwise, a second MatMul writes
   // KV directly to KVCache.
-  HWY_NOINLINE void ComputeQKV(const MultiplePositions& batch_start,
-                               const size_t num_interleaved) {
+  HWY_NOINLINE void ComputeQKV(const size_t num_interleaved) {
     PROFILER_ZONE("Gen.Attention.QKV");
     // For the computation of Q, K, and V, it is useful to remember that
     // qkv_einsum_w has shape [(kHeads + kKVHeads * 2), kKQVDim, kModelDim]
@@ -255,9 +254,9 @@ class GemmaAttention {
       // Single query and no wraparound means we can use a matmul and write
       // directly into the KV cache with a stride of kCachePosSize.
       if (num_queries_ == 1 &&
-          batch_start[0] + num_tokens_ <= div_seq_len_.GetDivisor()) {
+          queries_pos_[0] + num_tokens_ <= div_seq_len_.GetDivisor()) {
         const size_t kv_ofs =
-            batch_start[0] * kCachePosSize + layer_ * kCacheLayerSize;
+            queries_pos_[0] * kCachePosSize + layer_ * kCacheLayerSize;
         // KV structure is [k, v, k, v, ....] = kKVHeads pairs of (k, v).
         float* HWY_RESTRICT kv = kv_caches_[0].kv_cache.get() + kv_ofs;
         MatMul_4x4</*kAdd=*/false>(
@@ -275,7 +274,7 @@ class GemmaAttention {
           const size_t batch_idx = interleaved_idx / num_queries_;
           KVCache& kv_cache = kv_caches_[query_idx];
           const size_t cache_pos =
-              div_seq_len_.Remainder(batch_start[query_idx] + batch_idx);
+              div_seq_len_.Remainder(queries_pos_[query_idx] + batch_idx);
           const size_t kv_offset =
               cache_pos * kCachePosSize + layer_ * kCacheLayerSize;
           float* HWY_RESTRICT kv = kv_cache.kv_cache.get() + kv_offset;
@@ -295,7 +294,7 @@ class GemmaAttention {
           const size_t interleaved_idx = task / kKVHeads;
           const size_t query_idx = interleaved_idx % num_queries_;
           const size_t batch_idx = interleaved_idx / num_queries_;
-          const size_t pos = batch_start[query_idx] + batch_idx;
+          const size_t pos = queries_pos_[query_idx] + batch_idx;
           const size_t cache_pos = div_seq_len_.Remainder(pos);
           const size_t kv_offset = cache_pos * kCachePosSize +
                                    layer_ * kCacheLayerSize +
@@ -374,8 +373,7 @@ class GemmaAttention {
     }
   }
 
-  HWY_NOINLINE void DotSoftmaxWeightedSum(const MultiplePositions& batch_start,
-                                          const size_t num_interleaved) {
+  HWY_NOINLINE void DotSoftmaxWeightedSum(const size_t num_interleaved) {
     PROFILER_ZONE("Gen.Attention.DotSoftmax");
     GEMMA_CONSTEXPR_SQRT float kQueryScale = ChooseQueryScale<TConfig>();
 
@@ -398,7 +396,7 @@ class GemmaAttention {
                     activations_.q.Batch(interleaved_idx) + head * kQStride;
 
                 // Apply rope and scaling to Q.
-                const size_t pos = batch_start[query_idx] + batch_idx;
+                const size_t pos = queries_pos_[query_idx] + batch_idx;
                 PositionalEncodingQK(q, pos, layer_, kQueryScale, q);
 
                 const size_t start_pos = StartPos(pos, layer_);
@@ -440,45 +438,34 @@ class GemmaAttention {
   }
 
  public:
-  GemmaAttention(const MultiplePositions& interleaved_start, size_t num_tokens,
-                 size_t num_queries, size_t layer, Activations& activations,
+  GemmaAttention(const QueriesPos& queries_pos, size_t num_tokens, size_t layer,
+                 Activations& activations,
                  const CompressedLayer<TConfig>* layer_weights,
                  const hwy::Divisor& div_seq_len, const KVCaches& kv_caches,
                  hwy::ThreadPool& pool)
-      : num_tokens_(num_tokens),
-        num_queries_(num_queries),
+      : queries_pos_(queries_pos),
+        num_queries_(queries_pos.size()),
+        num_tokens_(num_tokens),
         layer_(layer),
         activations_(activations),
         layer_weights_(*layer_weights),
         div_seq_len_(div_seq_len),
         kv_caches_(kv_caches),
         pool_(pool) {
-    HWY_DASSERT(
-        std::all_of(interleaved_start.cbegin(), interleaved_start.cend(),
-                    [this](size_t pos) { return pos % num_queries_ == 0; }));
     HWY_DASSERT(num_queries_ <= kv_caches_.size());
-
-    batch_start_.reserve(interleaved_start.size());
-    for (auto i = interleaved_start.cbegin(); i != interleaved_start.cend();
-         ++i) {
-      batch_start_.emplace_back(*i / num_queries_);
-    }
   }
 
   HWY_INLINE void operator()() {
-    const MultiplePositions batch_start(batch_start_.data(),
-                                        batch_start_.size());
     const size_t num_interleaved = num_tokens_ * num_queries_;
-
-    ComputeQKV(batch_start, num_interleaved);
-    DotSoftmaxWeightedSum(batch_start, num_interleaved);
+    ComputeQKV(num_interleaved);
+    DotSoftmaxWeightedSum(num_interleaved);
     SumHeads(num_interleaved);
   }
 
  private:
-  std::vector<size_t> batch_start_;
-  const size_t num_tokens_;
+  const QueriesPos& queries_pos_;
   const size_t num_queries_;
+  const size_t num_tokens_;
   const size_t layer_;
   Activations& activations_;
   const CompressedLayer<TConfig>& layer_weights_;
@@ -489,24 +476,21 @@ class GemmaAttention {
 
 template <class TConfig>
 HWY_NOINLINE void Attention(LayerAttentionType type,
-                            const MultiplePositions& interleaved_start,
-                            size_t num_tokens, size_t num_queries, size_t layer,
-                            Activations& activations,
+                            const QueriesPos& queries_pos, size_t num_tokens,
+                            size_t layer, Activations& activations,
                             const CompressedLayer<TConfig>* layer_weights,
                             const hwy::Divisor& div_seq_len,
                             const KVCaches& kv_caches, hwy::ThreadPool& pool) {
   if (type == LayerAttentionType::kGemma) {
-    GemmaAttention<TConfig>(interleaved_start, num_tokens, num_queries, layer,
-                            activations, layer_weights, div_seq_len, kv_caches,
-                            pool)();
+    GemmaAttention<TConfig>(queries_pos, num_tokens, layer, activations,
+                            layer_weights, div_seq_len, kv_caches, pool)();
   } else {
     // Only reached if the model is Griffin. `if constexpr` prevents generating
     // this code for non-Griffin models.
     if constexpr (TConfig::kGriffinLayers > 0) {
-      HWY_ASSERT(num_queries == 1);
-      GriffinRecurrent<TConfig>(interleaved_start[0], num_tokens, num_queries,
-                                layer, activations, layer_weights, kv_caches,
-                                pool);
+      HWY_ASSERT(queries_pos.size() == 1);
+      GriffinRecurrent<TConfig>(queries_pos[0], num_tokens, layer, activations,
+                                layer_weights, kv_caches, pool);
     }
   }
 }
@@ -608,12 +592,12 @@ void PostNorm(size_t num_interleaved, const WeightT& weights, InOutT* inout) {
 
 template <class TConfig>
 HWY_NOINLINE void TransformerLayer(
-    size_t num_tokens, size_t num_queries, const MultiplePositions& pos,
-    size_t layer, const CompressedLayer<TConfig>* layer_weights,
-    Activations& activations, const hwy::Divisor& div_seq_len,
-    const KVCaches& kv_caches, hwy::ThreadPool& pool) {
+    const QueriesPos& queries_pos, size_t num_tokens, size_t layer,
+    const CompressedLayer<TConfig>* layer_weights, Activations& activations,
+    const hwy::Divisor& div_seq_len, const KVCaches& kv_caches,
+    hwy::ThreadPool& pool) {
   constexpr size_t kModelDim = TConfig::kModelDim;
-  const size_t num_interleaved = num_tokens * num_queries;
+  const size_t num_interleaved = num_tokens * queries_pos.size();
   auto type = TConfig::kLayerConfig[layer];
   size_t layer_of_type =
       NumLayersOfTypeBefore(TConfig::kLayerConfig, type, layer);
@@ -622,8 +606,8 @@ HWY_NOINLINE void TransformerLayer(
                  layer_weights->pre_attention_norm_scale.data_scale1(),
                  activations.pre_att_rms_out.All(), kModelDim);
 
-  Attention<TConfig>(type, pos, num_tokens, num_queries, layer_of_type,
-                     activations, layer_weights, div_seq_len, kv_caches, pool);
+  Attention<TConfig>(type, queries_pos, num_tokens, layer_of_type, activations,
+                     layer_weights, div_seq_len, kv_caches, pool);
 
   PostNorm<TConfig>(num_interleaved, layer_weights->post_attention_norm_scale,
                     activations.att_sums.All());
@@ -646,6 +630,9 @@ HWY_NOINLINE void TransformerLayer(
                               /*is_attention=*/false);
 }
 
+// Prefill and Transformer() advance positions in-place.
+using QueriesMutablePos = hwy::Span<size_t>;
+
 // Batches are important for amortizing loading weights over multiple tokens.
 // This is possible in prefill because we know all tokens beforehand, whereas
 // decode depends on the previous output token. However, each prefill batch of a
@@ -696,16 +683,16 @@ class PrefillState {
   }
 
   template <class TConfig>
-  HWY_NOINLINE void Prefill(const MultiplePromptsTokens& prompts,
+  HWY_NOINLINE void Prefill(const QueriesPromptTokens& queries_prompt,
                             const size_t prefill_per_query,
-                            const MultiplePositions& pos,
+                            const QueriesMutablePos& queries_pos,
                             const size_t query_idx_start,
                             const CompressedWeights<TConfig>& weights,
                             const RuntimeConfig& runtime_config,
                             const hwy::Divisor& div_seq_len,
                             const KVCaches& kv_caches, PerClusterPools& pools) {
     PROFILER_ZONE("Gen.Prefill");
-    const size_t num_queries = prompts.size();
+    const size_t num_queries = queries_prompt.size();
     HWY_ASSERT(kv_caches.size() == num_queries);
     const size_t max_tbatch_size = activations_[0].x.BatchSize();
 
@@ -716,10 +703,10 @@ class PrefillState {
           Activations& activations = activations_[qi];
           hwy::ThreadPool& inner_pool = pools.Inner(qthread);
 
-          // Single query at a time, so pass a slice of the KV cache because
-          // GemmaAttention will only access the first.
-          const size_t kPrefillQueries = 1;
-          KVCaches prefill_kv_caches(&kv_caches[qi], kPrefillQueries);
+          // Single query at a time, so pass slices of the spans because
+          // GemmaAttention will only access the first KV cache and position.
+          KVCaches single_kv_cache(&kv_caches[qi], 1);
+          QueriesPos single_query_pos(&queries_pos[qi], 1);
 
           // For each batch of tokens in the query:
           for (size_t tbatch_start = 0; tbatch_start < prefill_per_query;
@@ -728,30 +715,28 @@ class PrefillState {
             const size_t tbatch_size =
                 HWY_MIN(max_tbatch_size, prefill_per_query - tbatch_start);
             for (size_t ti = 0; ti < tbatch_size; ++ti) {
-              const int token = prompts[qi][tbatch_start + ti];
-              EmbedToken<TConfig>(token, ti, pos[qi] + ti, weights,
-                                  activations.x);
+              const int token = queries_prompt[qi][tbatch_start + ti];
+              const size_t pos = queries_pos[qi] + ti;
+              EmbedToken<TConfig>(token, ti, pos, weights, activations.x);
             }
 
-            const size_t tbatch_pos = pos[qi] + tbatch_start;
-            const MultiplePositions prefill_tbatch_pos(&tbatch_pos,
-                                                       kPrefillQueries);
-
             // Transformer with one batch of tokens from a single query.
             for (size_t layer = 0; layer < TConfig::kLayers; ++layer) {
               const auto* layer_weights = weights.GetLayer(layer);
-              TransformerLayer<TConfig>(tbatch_size, kPrefillQueries,
-                                        prefill_tbatch_pos, layer,
+              TransformerLayer<TConfig>(single_query_pos, tbatch_size, layer,
                                         layer_weights, activations, div_seq_len,
-                                        prefill_kv_caches, inner_pool);
+                                        single_kv_cache, inner_pool);
             }
 
             // NOTE: we unconditionally call StreamToken, even if EOS.
             for (size_t ti = 0; ti < tbatch_size; ++ti) {
-              const int token = prompts[qi][tbatch_start + ti];
-              runtime_config.StreamToken(query_idx_start + qi, tbatch_pos + ti,
-                                         token, 0.0f);
+              const size_t pos = queries_pos[qi] + ti;
+              const int token = queries_prompt[qi][pos];
+              runtime_config.StreamToken(query_idx_start + qi, pos, token,
+                                         0.0f);
             }
+
+            queries_pos[qi] += tbatch_size;
           }  // for tbatch_start
         });
   }
@@ -760,58 +745,60 @@ class PrefillState {
   std::vector<Activations> activations_;  // One per query, filled by Init.
 };
 
-// `tokens` is length `num_tokens * num_queries`. In autoregressive decode,
-// `num_tokens == 1`.
+// Generates one token for each query. `queries_token` is the previous token
+// from each query, and `queries_pos` are their position in the sequence.
 template <class TConfig>
-HWY_NOINLINE void Transformer(const int* tokens, size_t num_tokens,
-                              size_t num_queries, const MultiplePositions& pos,
+HWY_NOINLINE void Transformer(const QueriesToken& queries_token,
+                              const QueriesMutablePos& queries_pos,
                               const CompressedWeights<TConfig>& weights,
                               Activations& activations,
                               const hwy::Divisor& div_seq_len,
                               const KVCaches& kv_caches, hwy::ThreadPool& pool,
                               const LayersOutputFunc& layers_output) {
-  const size_t num_interleaved = num_tokens * num_queries;
-  if (layers_output) {
-    for (size_t token_idx = 0; token_idx < num_interleaved; ++token_idx) {
-      const size_t query_idx = token_idx % num_queries;
-      const size_t logical_pos = (pos[query_idx] + token_idx) / num_queries;
-      const float token_f = tokens[token_idx];
-      layers_output(query_idx, logical_pos, "tokens", -1, &token_f, 1);
-    }
-  }
   constexpr size_t kModelDim = TConfig::kModelDim;
-  for (size_t token_idx = 0; token_idx < num_interleaved; ++token_idx) {
-    const size_t query_idx = token_idx % num_queries;
-    EmbedToken<TConfig>(tokens[token_idx], token_idx, pos[query_idx], weights,
-                        activations.x);
+  const size_t num_queries = queries_token.size();
+  HWY_DASSERT(queries_pos.size() == num_queries);
+
+  if (layers_output) {
+    for (size_t query_idx = 0; query_idx < num_queries; ++query_idx) {
+      const float token_f = queries_token[query_idx];
+      layers_output(query_idx, queries_pos[query_idx], "tokens", -1, &token_f,
+                    1);
+    }
+  }
+
+  for (size_t query_idx = 0; query_idx < num_queries; ++query_idx) {
+    EmbedToken<TConfig>(queries_token[query_idx], query_idx,
+                        queries_pos[query_idx], weights, activations.x);
   }
 
   for (size_t layer = 0; layer < TConfig::kLayers; ++layer) {
     const CompressedLayer<TConfig>* layer_weights = weights.GetLayer(layer);
-    TransformerLayer<TConfig>(num_tokens, num_queries, pos, layer,
+    TransformerLayer<TConfig>(queries_pos, /*num_tokens=*/1, layer,
                               layer_weights, activations, div_seq_len,
                               kv_caches, pool);
 
     if (layers_output) {
-      for (size_t token_idx = 0; token_idx < num_interleaved; ++token_idx) {
-        const size_t query_idx = token_idx % num_queries;
-        const size_t logical_pos = (pos[query_idx] + token_idx) / num_queries;
-        layers_output(token_idx % num_queries, logical_pos, "blocks", layer,
-                      activations.x.Batch(token_idx), kModelDim);
+      for (size_t query_idx = 0; query_idx < num_queries; ++query_idx) {
+        layers_output(query_idx, queries_pos[query_idx], "blocks", layer,
+                      activations.x.Batch(0), kModelDim);
       }
     }
   }
 
-  RMSNormInplaceBatched(num_interleaved, weights.final_norm_scale.data_scale1(),
+  RMSNormInplaceBatched(num_queries, weights.final_norm_scale.data_scale1(),
                         activations.x.All(), kModelDim);
+
   if (layers_output) {
-    for (size_t token_idx = 0; token_idx < num_interleaved; ++token_idx) {
-      const size_t query_idx = token_idx % num_queries;
-      const size_t logical_pos = (pos[query_idx] + token_idx) / num_queries;
-      layers_output(query_idx, logical_pos, "final_norm", -1,
-                    activations.x.Batch(token_idx), kModelDim);
+    for (size_t query_idx = 0; query_idx < num_queries; ++query_idx) {
+      layers_output(query_idx, queries_pos[query_idx], "final_norm", -1,
+                    activations.x.Batch(0), kModelDim);
     }
   }
+
+  for (size_t query_idx = 0; query_idx < num_queries; ++query_idx) {
+    queries_pos[query_idx] += 1;
+  }
 }
 
 template <class TConfig>
@@ -848,32 +835,16 @@ void RangeChecks(size_t& max_tokens, size_t& max_generated_tokens,
 
 // Placeholder for internal test3, do not remove
 
-// Returns interleaved tokens: one from each query, followed by the second from
-// all queries, with EOS padding.
-static std::vector<int> InterleaveQueries(const MultiplePromptsTokens& queries,
-                                          const RuntimeConfig& runtime_config,
-                                          size_t& min_prompt_size,
-                                          size_t& max_prompt_size) {
-  const size_t num_queries = queries.size();
+// Returns the min and max number of tokens for all queries.
+static void ScanQueryLengths(const QueriesPromptTokens& queries_prompt,
+                             size_t& min_prompt_size, size_t& max_prompt_size) {
+  const size_t num_queries = queries_prompt.size();
   min_prompt_size = hwy::LimitsMax<size_t>();
   max_prompt_size = 0;
   for (size_t i = 0; i < num_queries; ++i) {
-    min_prompt_size = std::min(min_prompt_size, queries[i].size());
-    max_prompt_size = std::max(max_prompt_size, queries[i].size());
+    min_prompt_size = std::min(min_prompt_size, queries_prompt[i].size());
+    max_prompt_size = std::max(max_prompt_size, queries_prompt[i].size());
   }
-
-  std::vector<int> prompt;
-  prompt.reserve(max_prompt_size * num_queries);
-  for (size_t pos = 0; pos < max_prompt_size; ++pos) {
-    for (size_t q = 0; q < num_queries; ++q) {
-      if (pos < queries[q].size()) {
-        prompt.push_back(queries[q][pos]);
-      } else {
-        prompt.push_back(runtime_config.eos_id);
-      }
-    }
-  }
-  return prompt;
 }
 
 // Holds "is at end of stream" state for each query.
@@ -901,21 +872,22 @@ class TokenStreamer {
   hwy::BitSet4096<> is_eos_;
 };
 
-// Generates one token for each query in `prompts`, which is one qbatch whose
-// size is at most the `batch_size` passed to `activations.Allocate`.
+// Generates one continuation for each query in `queries_prompt`, which is one
+// qbatch whose size is at most the `batch_size` passed to
+// `activations.Allocate`.
 //
-// `pos` indexes the KV cache. In the first turn of a chat, pos = 0, and it
-// continues to increase by one for each prefilled/generated token per query.
+// `queries_pos` stores the KV cache position for each query. In the first turn
+// of a chat, pos = 0; we increment each query's position after each token.
 //
 // `query_idx_start` is the query_idx of the first query in the batch, so that
 // `StreamFunc` gets the global query index, not relative to the batch.
 //
-// `kv_caches` is for the batch, size must match `prompts`.
+// `kv_caches` is for the batch, size must match `queries_prompt`.
 template <class TConfig>
 void GenerateT(const ByteStorageT& weights_u8, Activations& activations,
                const RuntimeConfig& runtime_config,
-               const MultiplePromptsTokens& prompts,
-               const MultiplePositions& pos, const size_t query_idx_start,
+               const QueriesPromptTokens& queries_prompt,
+               const QueriesPos& queries_pos_in, const size_t query_idx_start,
                const KVCaches& kv_caches, PerClusterPools& pools,
                TimingInfo& timing_info) {
   constexpr size_t kModelDim = TConfig::kModelDim;
@@ -926,22 +898,28 @@ void GenerateT(const ByteStorageT& weights_u8, Activations& activations,
   // TODO: remove once all parallel sections support hierarchical parallelism.
   hwy::ThreadPool& pool = pools.Inner(0);
 
-  const size_t num_queries = prompts.size();
+  // Copy so we can increment without requiring users to pass in a mutable span.
+  std::vector<size_t> queries_pos_copy(queries_pos_in.cbegin(),
+                                       queries_pos_in.cend());
+  const QueriesMutablePos queries_mutable_pos(queries_pos_copy.data(),
+                                              queries_pos_copy.size());
+
+  const size_t num_queries = queries_prompt.size();
   HWY_ASSERT(num_queries <= 4096);  // TokenStreamer uses BitSet4096.
   HWY_ASSERT(num_queries <= activations.x.BatchSize());
+  HWY_ASSERT(queries_pos_in.size() == num_queries);
   HWY_ASSERT(kv_caches.size() == num_queries);
   const hwy::Divisor div_seq_len(static_cast<uint32_t>(kv_caches[0].seq_len));
 
   size_t min_prompt_size, max_prompt_size;
-  const std::vector<int> prompt = InterleaveQueries(
-      prompts, runtime_config, min_prompt_size, max_prompt_size);
+  ScanQueryLengths(queries_prompt, min_prompt_size, max_prompt_size);
 
   size_t max_tokens = runtime_config.max_tokens;
   size_t max_generated_tokens = runtime_config.max_generated_tokens;
   RangeChecks<TConfig>(max_tokens, max_generated_tokens, max_prompt_size);
-  for (auto i = pos.cbegin(); i != pos.cend(); ++i) {
-    if (*i >= max_tokens) {
-      fprintf(stderr, "Warning: pos %zu >= max_tokens %zu, aborting.\n", *i,
+  for (size_t pos : queries_pos_copy) {
+    if (pos >= max_tokens) {
+      fprintf(stderr, "Warning: pos %zu >= max_tokens %zu, aborting.\n", pos,
               max_tokens);
       return;
     }
@@ -967,17 +945,13 @@ void GenerateT(const ByteStorageT& weights_u8, Activations& activations,
     prefill.Init<TConfig>(num_queries, runtime_config.prefill_tbatch_size,
                           pools);
     prefill_start = hwy::platform::Now();
-    prefill.Prefill<TConfig>(prompts, prefill_per_query, pos, query_idx_start,
-                             weights, runtime_config, div_seq_len, kv_caches,
-                             pools);
+    prefill.Prefill<TConfig>(queries_prompt, prefill_per_query,
+                             queries_mutable_pos, query_idx_start, weights,
+                             runtime_config, div_seq_len, kv_caches, pools);
     timing_info.NotifyPrefill(prefill_per_query * num_queries, prefill_start);
+    // queries_pos are incremented by Prefill.
   }
 
-  std::vector<size_t> interleaved_pos(pos.size());
-  std::transform(
-      pos.cbegin(), pos.cend(), interleaved_pos.begin(),
-      [&](size_t v) { return (v + prefill_per_query) * num_queries; });
-
   // Storage for the last generated token from each query, passed to the next
   // Transformer() call.
   std::vector<int> gen_tokens(num_queries);
@@ -985,25 +959,19 @@ void GenerateT(const ByteStorageT& weights_u8, Activations& activations,
   // Stream the last prompt token from each query and fill gen_tokens.
   TokenStreamer token_streamer(runtime_config);
   for (size_t query_idx = 0; query_idx < num_queries; ++query_idx) {
-    gen_tokens[query_idx] = prompts[query_idx][prefill_per_query];
+    gen_tokens[query_idx] = queries_prompt[query_idx][prefill_per_query];
     (void)token_streamer(query_idx_start + query_idx,
-                         pos[query_idx] + prefill_per_query,
-                         gen_tokens[query_idx], 0.0f);
+                         queries_mutable_pos[query_idx], gen_tokens[query_idx],
+                         0.0f);
   }
 
   const double gen_start = hwy::platform::Now();
-  for (size_t gen_per_query = 0;
-       gen_per_query < HWY_MIN(max_tokens, max_generated_tokens);
-       ++gen_per_query) {
-    // Decode: generate one token for each query.
-    Transformer<TConfig>(
-        gen_tokens.data(), /*num_tokens=*/1, num_queries,
-        MultiplePositions(interleaved_pos.data(), interleaved_pos.size()),
-        weights, activations, div_seq_len, kv_caches, pool,
-        runtime_config.layers_output);
-    for (auto& v : interleaved_pos) {
-      v += num_queries;
-    }
+  for (size_t gen = 0; gen < HWY_MIN(max_tokens, max_generated_tokens); ++gen) {
+    // Decode generates one token per query and increments queries_mutable_pos.
+    Transformer<TConfig>(QueriesToken(gen_tokens.data(), num_queries),
+                         queries_mutable_pos, weights, activations, div_seq_len,
+                         kv_caches, pool, runtime_config.layers_output);
+    // queries_pos are incremented by Transformer.
 
     bool all_queries_eos = true;
     PROFILER_ZONE("Gen.Embedding");
@@ -1022,8 +990,7 @@ void GenerateT(const ByteStorageT& weights_u8, Activations& activations,
 
       const bool is_eos =
           token_streamer(query_idx_start + query_idx,
-                         pos[query_idx] + prefill_per_query + 1 + gen_per_query,
-                         token, logits[token]);
+                         queries_mutable_pos[query_idx], token, logits[token]);
       all_queries_eos &= is_eos;
       gen_tokens[query_idx] = is_eos ? runtime_config.eos_id : token;
     }
@@ -1038,28 +1005,29 @@ void GenerateSingleT(const ByteStorageT& weights_u8,
                      const RuntimeConfig& runtime_config,
                      const PromptTokens& prompt, size_t pos, KVCache& kv_cache,
                      PerClusterPools& pools, TimingInfo& timing_info) {
-  const size_t num_queries = 1;
+  constexpr size_t kNumQueries = 1;
   const size_t qbatch_start = 0;
 
   Activations activations;
-  activations.Allocate<TConfig>(num_queries);
+  activations.Allocate<TConfig>(kNumQueries);
 
-  const MultiplePromptsTokens prompts(&prompt, num_queries);
-  const MultiplePositions positions(&pos, num_queries);
-  const KVCaches kv_caches{&kv_cache, num_queries};
+  const QueriesPromptTokens prompt_span(&prompt, kNumQueries);
+  QueriesPos pos_span(&pos, kNumQueries);
+  const KVCaches kv_caches{&kv_cache, kNumQueries};
 
-  GenerateT<TConfig>(weights_u8, activations, runtime_config, prompts,
-                     positions, qbatch_start, kv_caches, pools, timing_info);
+  GenerateT<TConfig>(weights_u8, activations, runtime_config, prompt_span,
+                     pos_span, qbatch_start, kv_caches, pools, timing_info);
 }
 
 template <class TConfig>
 void GenerateBatchT(const ByteStorageT& weights_u8,
                     const RuntimeConfig& runtime_config,
-                    const MultiplePromptsTokens& prompts,
-                    const MultiplePositions& pos, const KVCaches& kv_caches,
+                    const QueriesPromptTokens& queries_prompt,
+                    const QueriesPos& queries_pos, const KVCaches& kv_caches,
                     PerClusterPools& pools, TimingInfo& timing_info) {
-  HWY_ASSERT(prompts.size() == pos.size() &&
-             prompts.size() == kv_caches.size());
+  const size_t num_queries = queries_prompt.size();
+  HWY_ASSERT(queries_pos.size() == num_queries);
+  HWY_ASSERT(kv_caches.size() == num_queries);
   // Griffin does not support query batching.
   const size_t max_qbatch_size =
       (TConfig::kGriffinLayers > 0) ? 1 : runtime_config.decode_qbatch_size;
@@ -1067,15 +1035,14 @@ void GenerateBatchT(const ByteStorageT& weights_u8,
   Activations activations;
   activations.Allocate<TConfig>(max_qbatch_size);
 
-  const size_t num_queries = prompts.size();
   for (size_t qbatch_start = 0; qbatch_start < num_queries;
        qbatch_start += max_qbatch_size) {
     // Generate one batch of tokens from `qbatch_size` queries.
     const size_t qbatch_size =
         HWY_MIN(num_queries - qbatch_start, max_qbatch_size);
-    const MultiplePromptsTokens qbatch_prompts(&prompts[qbatch_start],
+    const QueriesPromptTokens qbatch_prompts(&queries_prompt[qbatch_start],
                                              qbatch_size);
-    const MultiplePositions qbatch_pos(&pos[qbatch_start], qbatch_size);
+    QueriesPos qbatch_pos(&queries_pos[qbatch_start], qbatch_size);
     const KVCaches qbatch_kv(&kv_caches[qbatch_start], qbatch_size);
     GenerateT<TConfig>(weights_u8, activations, runtime_config, qbatch_prompts,
                        qbatch_pos, qbatch_start, qbatch_kv, pools, timing_info);
@@ -1098,11 +1065,13 @@ void GenerateSingle(  // NOLINT(misc-definitions-in-headers)
 
 void GenerateBatch(  // NOLINT(misc-definitions-in-headers)
     GEMMA_CONFIG, const ByteStorageT& weights_u8,
-    const RuntimeConfig& runtime_config, const MultiplePromptsTokens& prompts,
-    const MultiplePositions& pos, const KVCaches& kv_caches,
-    PerClusterPools& pools, TimingInfo& timing_info) {
+    const RuntimeConfig& runtime_config,
+    const QueriesPromptTokens& queries_prompt, const QueriesPos& queries_pos,
+    const KVCaches& kv_caches, PerClusterPools& pools,
+    TimingInfo& timing_info) {
   HWY_EXPORT_AND_DYNAMIC_DISPATCH_T(GenerateBatchT<GEMMA_CONFIG>)
-  (weights_u8, runtime_config, prompts, pos, kv_caches, pools, timing_info);
+  (weights_u8, runtime_config, queries_prompt, queries_pos, kv_caches, pools,
+   timing_info);
 }
 
 #endif  // HWY_ONCE

gemma/gemma.cc

@@ -64,12 +64,11 @@ Gemma::~Gemma() {
                              const PromptTokens& prompt, size_t pos,           \
                              KVCache& kv_cache, PerClusterPools& pools,        \
                              TimingInfo& timing_info);                         \
-  extern void GenerateBatch(CONFIGT<TWEIGHT>, const ByteStorageT& weights_u8,  \
-                            const RuntimeConfig& runtime_config,               \
-                            const MultiplePromptsTokens& prompts,              \
-                            const MultiplePositions& pos,                      \
-                            const KVCaches& kv_caches, PerClusterPools& pools, \
-                            TimingInfo& timing_info);
+  extern void GenerateBatch(                                                   \
+      CONFIGT<TWEIGHT>, const ByteStorageT& weights_u8,                        \
+      const RuntimeConfig& runtime_config, const QueriesPromptTokens& prompts, \
+      const QueriesPos& queries_pos, const KVCaches& kv_caches,                \
+      PerClusterPools& pools, TimingInfo& timing_info);
 GEMMA_FOREACH_CONFIG_AND_WEIGHT(GEMMA_DECLARE);
 
 // Adapters to select from the above overloads via CallForModelAndWeight.
@@ -88,35 +87,35 @@ template <class TConfig>
 struct GenerateBatchT {
   void operator()(const ByteStorageT& weights_u8,
                   const RuntimeConfig& runtime_config,
-                  const MultiplePromptsTokens& prompts,
-                  const MultiplePositions& pos, const KVCaches& kv_caches,
+                  const QueriesPromptTokens& queries_prompt,
+                  const QueriesPos& queries_pos, const KVCaches& kv_caches,
                   PerClusterPools& pools, TimingInfo& timing_info) const {
-    GenerateBatch(TConfig(), weights_u8, runtime_config, prompts, pos,
-                  kv_caches, pools, timing_info);
+    GenerateBatch(TConfig(), weights_u8, runtime_config, queries_prompt,
+                  queries_pos, kv_caches, pools, timing_info);
   }
 };
 
 void Gemma::Generate(const RuntimeConfig& runtime_config,
-                     const PromptTokens& prompt, size_t start_pos,
-                     KVCache& kv_cache, TimingInfo& timing_info) {
+                     const PromptTokens& prompt, size_t pos, KVCache& kv_cache,
+                     TimingInfo& timing_info) {
   pools_.StartSpinning();
 
   CallForModelAndWeight<GenerateSingleT>(info_.model, info_.weight, weights_u8_,
-                                         runtime_config, prompt, start_pos,
-                                         kv_cache, pools_, timing_info);
+                                         runtime_config, prompt, pos, kv_cache,
+                                         pools_, timing_info);
 
   pools_.StopSpinning();
 }
 
 void Gemma::GenerateBatch(const RuntimeConfig& runtime_config,
-                          const MultiplePromptsTokens& prompts,
-                          const MultiplePositions& start_pos,
+                          const QueriesPromptTokens& queries_prompt,
+                          const QueriesPos& queries_pos,
                           const KVCaches& kv_caches, TimingInfo& timing_info) {
   pools_.StartSpinning();
 
-  CallForModelAndWeight<GenerateBatchT>(info_.model, info_.weight, weights_u8_,
-                                        runtime_config, prompts, start_pos,
-                                        kv_caches, pools_, timing_info);
+  CallForModelAndWeight<GenerateBatchT>(
+      info_.model, info_.weight, weights_u8_, runtime_config, queries_prompt,
+      queries_pos, kv_caches, pools_, timing_info);
 
   pools_.StopSpinning();
 }

gemma/gemma.h

@@ -142,8 +142,12 @@ struct TimingInfo {
 };
 
 using PromptTokens = hwy::Span<const int>;
-using MultiplePromptsTokens = hwy::Span<const PromptTokens>;
-using MultiplePositions = hwy::Span<const size_t>;
+
+// Batches of independent queries have their own prompt, previous token,
+// position in the sequence, and KVCache.
+using QueriesPromptTokens = hwy::Span<const PromptTokens>;
+using QueriesToken = hwy::Span<const int>;
+using QueriesPos = hwy::Span<const size_t>;
 using KVCaches = hwy::Span<KVCache>;
 
 class Gemma {
@@ -161,13 +165,17 @@ class Gemma {
   const ByteStorageT& Weights() const { return weights_u8_; }
   ByteStorageT& MutableWeights() { return weights_u8_; }
 
+  // `pos` is the position in the KV cache. Users are responsible for
+  // incrementing it in the `*StreamFunc`, or setting to zero for single-turn.
   void Generate(const RuntimeConfig& runtime_config, const PromptTokens& prompt,
-                size_t start_pos, KVCache& kv_cache, TimingInfo& timing_info);
+                size_t pos, KVCache& kv_cache, TimingInfo& timing_info);
 
+  // `queries_pos` are the positions in the KV cache. Users are responsible for
+  // incrementing them in `BatchStreamFunc`, or setting to zero for single-turn.
   void GenerateBatch(const RuntimeConfig& runtime_config,
-                     const MultiplePromptsTokens& prompts,
-                     const MultiplePositions& start_pos,
-                     const KVCaches& kv_caches, TimingInfo& timing_info);
+                     const QueriesPromptTokens& queries_prompt,
+                     const QueriesPos& queries_pos, const KVCaches& kv_caches,
+                     TimingInfo& timing_info);
 
  private:
   PerClusterPools& pools_;

gemma/run.cc

@@ -80,20 +80,19 @@ void ReplGemma(Gemma& model, KVCache& kv_cache, const InferenceArgs& args,
                int verbosity, const AcceptFunc& accept_token,
                std::string& eot_line) {
   PROFILER_ZONE("Gen.misc");
-  size_t abs_pos = 0;   // absolute token index over all turns
-  int current_pos = 0;  // token index within the current turn
-  int prompt_size{};
+  size_t abs_pos = 0;                     // across turns
+  size_t tokens_generated_this_turn = 0;  // differentiates prefill from reply
+  size_t prompt_size = 0;
 
   std::mt19937 gen;
   InitGenerator(args, gen);
 
   // callback function invoked for each generated token.
-  auto stream_token = [&abs_pos, &current_pos, &args, &gen, &prompt_size,
-                       &model, verbosity](int token, float) {
+  auto stream_token = [&](int token, float) {
     ++abs_pos;
-    ++current_pos;
+    ++tokens_generated_this_turn;
     // <= since position is incremented before
-    if (current_pos <= prompt_size) {
+    if (tokens_generated_this_turn <= prompt_size) {
       std::cerr << "." << std::flush;
     } else if (token == EOS_ID) {
       if (!args.multiturn) {
@@ -108,7 +107,7 @@ void ReplGemma(Gemma& model, KVCache& kv_cache, const InferenceArgs& args,
       HWY_ASSERT(
           model.Tokenizer().Decode(std::vector<int>{token}, &token_text));
       // +1 since position is incremented above
-      if (current_pos == prompt_size + 1) {
+      if (tokens_generated_this_turn == prompt_size + 1) {
         // first token of response
         token_text.erase(0, token_text.find_first_not_of(" \t\n"));
         if (verbosity >= 1) {
@@ -121,7 +120,7 @@ void ReplGemma(Gemma& model, KVCache& kv_cache, const InferenceArgs& args,
   };
 
   while (abs_pos < args.max_tokens) {
-    current_pos = 0;
+    tokens_generated_this_turn = 0;
     std::string prompt_string = GetPrompt(std::cin, verbosity, eot_line);
     if (!std::cin) return;
     // If !eot_line.empty(), we append \n, so only look at the first 2 chars.