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Validation reads of the final merge only its French-Wilson amplitudes, which the analyses made last, from the anisotropy tensor. That tensor is a fit to the merged intensities alone (the unmerged observations only give its error bar), so AnisotropyPriorHKL computes it from the merge without the rest of the analysis, bit for bit what AnisotropyTensorHKL of the full analysis gives (test). The first ValidateAgainstModel now runs from the start of the analyses on a copy of the merge given those same amplitudes, on the caller's card (get_gpu), with its log held and replayed where it was printed before; nothing it decides is acted on earlier. The model's preparation (census wait, indexer pool, GPU hold, merge engine release) moves with it. Measured, --simulate-live 10 --fast-live, 4axt model, RTX 5080, analyses + validation steps: strong lysozyme 0.91 -> 0.63 s, reference lysozyme 1.02 -> 0.66 s (validation beside the analyses 0.60-0.62 s vs 0.39-0.45 s alone, CPU shared; analyses 0.53 -> 0.62 s). The analyses were 80% waiting for the anisotropy (0.43 of 0.53 s), so starting on the full analysis' tensor would have gained ~0.1 s. p.hkl, p_maps.mtz identical, p.mtz data identical, all validation numbers identical. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4
272 lines
9.0 KiB
Plaintext
272 lines
9.0 KiB
Plaintext
// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#include <algorithm>
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#include <cstdlib>
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#include <fstream>
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#include <string>
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#include <thread>
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#include <atomic>
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#include <mutex>
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#include <vector>
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#include <cuda.h>
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#include "CUDAWrapper.h"
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#include "ThreadAffinity.h"
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#include "JFJochException.h"
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inline void cuda_err(cudaError_t val) {
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if (val != cudaSuccess)
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throw JFJochException(JFJochExceptionCategory::GPUCUDAError, cudaGetErrorString(val));
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}
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namespace {
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std::atomic<bool> gpus_hidden{false};
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}
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void hide_gpus() {
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gpus_hidden = true;
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}
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bool gpus_are_hidden() {
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return gpus_hidden;
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}
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int32_t get_gpu_count() {
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if (gpus_hidden)
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return 0;
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int device_count;
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cudaError_t val = cudaGetDeviceCount(&device_count);
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switch (val) {
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case cudaSuccess:
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return device_count;
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case cudaErrorNoDevice:
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case cudaErrorInsufficientDriver:
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return 0;
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default:
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throw JFJochException(JFJochExceptionCategory::GPUCUDAError, cudaGetErrorString(val));
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}
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}
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std::vector<std::string> get_gpu_names() {
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std::vector<std::string> names;
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const int32_t count = get_gpu_count();
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names.reserve(count);
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for (int32_t i = 0; i < count; i++) {
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cudaDeviceProp prop{};
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// A device that cannot be queried still exists and still gets work, so it is listed - just
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// without a name. Losing the whole list over one unreadable device would be worse.
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if (cudaGetDeviceProperties(&prop, i) == cudaSuccess)
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names.emplace_back(prop.name);
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else
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names.emplace_back("unknown GPU");
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}
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return names;
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}
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size_t get_gpu_total_memory(int32_t dev_id) {
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cudaDeviceProp prop{};
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if (cudaGetDeviceProperties(&prop, dev_id) != cudaSuccess)
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return 0;
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return prop.totalGlobalMem;
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}
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bool get_gpu_free_memory(size_t &free_bytes, size_t &total_bytes) {
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if (cudaMemGetInfo(&free_bytes, &total_bytes) != cudaSuccess)
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return false;
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#ifdef __linux__
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// Asked once: whether each card shares the host's memory.
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static const std::vector<int> integrated = [] {
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std::vector<int> v(std::max(get_gpu_count(), 0));
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for (int i = 0; i < static_cast<int>(v.size()); i++)
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if (cudaDeviceGetAttribute(&v[i], cudaDevAttrIntegrated, i) != cudaSuccess) {
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v[i] = 0;
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cudaGetLastError();
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}
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return v;
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}();
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int device = 0;
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if (cudaGetDevice(&device) != cudaSuccess || device >= static_cast<int>(integrated.size()) || !integrated[device])
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return true;
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std::ifstream meminfo("/proc/meminfo");
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std::string line;
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while (std::getline(meminfo, line))
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if (line.rfind("MemAvailable:", 0) == 0) {
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const size_t available = std::stoull(line.substr(13)) * 1024; // given in kB
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const size_t headroom = total_bytes / 10; // the host's own processes live in the same memory
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if (available > headroom)
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free_bytes = std::max(free_bytes, std::min(available - headroom, total_bytes));
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break;
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}
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#endif
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return true;
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}
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bool gpu_direct_host_read() {
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// Pageable memory access through the host's page tables is the hardware-coherent case (ATS over
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// NVLink-C2C); without the second attribute the access is HMM-emulated, page faults and migration,
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// and slower than a copy.
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static const std::vector<bool> direct = [] {
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const bool force = std::getenv("JFJOCH_FORCE_DIRECT_HOST_READ") != nullptr;
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std::vector<bool> ret(get_gpu_count(), force);
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for (int d = 0; d < static_cast<int>(ret.size()); d++) {
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int pageable = 0, host_page_tables = 0;
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cudaDeviceGetAttribute(&pageable, cudaDevAttrPageableMemoryAccess, d);
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cudaDeviceGetAttribute(&host_page_tables, cudaDevAttrPageableMemoryAccessUsesHostPageTables, d);
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if (pageable && host_page_tables)
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ret[d] = true;
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}
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return ret;
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}();
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int device = 0;
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if (cudaGetDevice(&device) != cudaSuccess || device >= static_cast<int>(direct.size()))
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return false;
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return direct[device];
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}
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void set_gpu(int32_t dev_id) {
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auto dev_count = get_gpu_count();
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// Ignore if no GPU present
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if (dev_count > 0) {
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if ((dev_id < 0) || (dev_id >= dev_count))
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Device ID cannot be negative");
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cuda_err(cudaSetDevice(dev_id));
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}
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}
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namespace {
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std::atomic<bool> gpu_numa_binding{false};
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// The NUMA node of each device, read once.
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int GpuNumaNode(int32_t dev_id) {
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static std::mutex m;
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static std::vector<int> node;
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std::lock_guard<std::mutex> lock(m);
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if (node.empty()) {
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const int32_t count = get_gpu_count();
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node.assign(count, -1);
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for (int32_t i = 0; i < count; i++) {
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char bus_id[32] = {};
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if (cudaDeviceGetPCIBusId(bus_id, sizeof(bus_id), i) == cudaSuccess)
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node[i] = NumaNodeOfPciDevice(bus_id);
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}
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}
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return dev_id < static_cast<int32_t>(node.size()) ? node[dev_id] : -1;
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}
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}
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std::vector<int> get_gpu_numa_nodes() {
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std::vector<int> nodes;
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for (int32_t i = 0; i < get_gpu_count(); i++)
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nodes.push_back(GpuNumaNode(i));
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return nodes;
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}
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void enable_gpu_numa_binding() {
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gpu_numa_binding = true;
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}
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int32_t get_gpu() {
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int dev = 0;
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if (get_gpu_count() > 0)
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cuda_err(cudaGetDevice(&dev));
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return dev;
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}
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void pin_gpu(int32_t dev_id) {
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if (get_gpu_count() == 0)
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return;
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set_gpu(dev_id);
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if (gpu_numa_binding)
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PinThreadToNumaNode(GpuNumaNode(dev_id));
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}
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ScopedGpuPin::ScopedGpuPin(int32_t dev_id) {
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if (get_gpu_count() == 0)
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return;
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cuda_err(cudaGetDevice(&prev_device));
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const int node = gpu_numa_binding ? GpuNumaNode(dev_id) : -1;
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if (node >= 0)
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prev_cpus = GetThreadCpus();
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set_gpu(dev_id);
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PinThreadToNumaNode(node);
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}
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ScopedGpuPin::~ScopedGpuPin() {
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SetThreadCpus(prev_cpus);
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if (prev_device >= 0)
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cudaSetDevice(prev_device); // not set_gpu: a destructor must not throw
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}
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void pin_gpu() {
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static std::atomic<uint32_t> counter{0};
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auto dev_count = get_gpu_count();
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if (dev_count > 0)
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pin_gpu(static_cast<int32_t>(counter.fetch_add(1) % dev_count));
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}
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void set_gpu_blocking_sync() {
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// Through the driver's primary-context flags, which a context created later takes: the runtime's
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// cudaSetDevice creates the device's context, serially, and on four cards that was most of a
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// second before the run had started. The function is taken from the driver at run time, so the
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// program does not link against it and still starts on a machine without one.
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// Without a device nothing is called at all: even cudaGetLastError() would load the driver.
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if (get_gpu_count() == 0)
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return;
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void *fn = nullptr;
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cudaDriverEntryPointQueryResult found{};
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if (cudaGetDriverEntryPointByVersion("cuDevicePrimaryCtxSetFlags", &fn, 12000, cudaEnableDefault, &found)
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!= cudaSuccess
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|| found != cudaDriverEntryPointSuccess) {
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cudaGetLastError();
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return;
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}
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const auto set_flags = reinterpret_cast<CUresult (*)(CUdevice, unsigned int)>(fn);
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for (int32_t i = 0; i < get_gpu_count(); i++)
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set_flags(i, CU_CTX_SCHED_BLOCKING_SYNC);
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}
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void create_gpu_contexts(int32_t first_device) {
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std::vector<std::thread> threads;
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for (int32_t i = first_device; i < get_gpu_count(); i++)
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threads.emplace_back([i] {
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// A device that fails here fails again, with its error, where it is used.
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if (cudaSetDevice(i) != cudaSuccess || cudaFree(nullptr) != cudaSuccess)
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cudaGetLastError();
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});
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for (auto &t : threads)
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t.join();
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}
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void release_gpu_contexts() {
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std::vector<std::thread> threads;
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for (int32_t i = 0; i < get_gpu_count(); i++)
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threads.emplace_back([i] {
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if (cudaSetDevice(i) != cudaSuccess || cudaDeviceReset() != cudaSuccess)
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cudaGetLastError();
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});
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for (auto &t : threads)
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t.join();
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}
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void cuda_clear_error() {
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if (!gpus_hidden) // hidden, nothing has used CUDA, and this call would still load the driver
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cudaGetLastError();
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}
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void cuda_throw_if_context_lost() {
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if (gpus_hidden)
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return;
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// cudaFree(nullptr) frees nothing, but a lost context fails it. The last error cannot say the same:
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// once cudaGetLastError() has returned a sticky error, it and cudaPeekAtLastError() report success.
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const cudaError_t err = cudaFree(nullptr);
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if (err != cudaSuccess)
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throw JFJochException(JFJochExceptionCategory::GPUCUDAError,
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std::string("CUDA device unusable after an unrecoverable error: ")
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+ cudaGetErrorString(err));
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}
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