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Jungfraujoch/common/CUDAWrapper.cu
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leonarski_fandFilip Leonarski 19b135186d
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v1.0.0-rc.175 (#85)
* Rugnux: Processes a collection live while jfjoch_broker writes it (`rugnux <master.h5> <broker URL>`).
* Rugnux: Processing starts on the first images and confirms its choices once all are in, so analysis can begin during collection.
* Rugnux: Faster processing, especially on servers with several GPUs and CPU sockets and on computers without a GPU (`--no-gpu`, macOS).
* Rugnux: Uses much less GPU memory, so large data sets stay on the GPU of smaller cards, and a data set too large for the card is processed on the CPU instead.
* Rugnux: On macOS, Bragg integration runs on the Apple GPU.
* Rugnux: Better handling of twinning and pseudo-symmetry, with the twin hypothesis written as `<prefix>_twin_<SG>.mtz`, and a wrong `--model` no longer confirms the data or decides the hand.
* Rugnux: `--model` accepts predicted (AlphaFold) models and falls back to molecular replacement when the model is not placed as a rigid body (experimental `--mr` forces it), settling space group, hand and twinning and writing a different answer as `<prefix>_mr.mtz`.
* Rugnux: Molecular replacement is faster and settles the space group in more cases with several copies in the asymmetric unit.
* Rugnux: Deposition-ready mmCIF, a richer report, and numbered steps on the terminal with the full log in `<prefix>_log.txt`; `_P1.mtz`, `--estimate-beam-center` and `--beam-center-search` are removed.
* Rugnux: The beam-stop shadow is found correctly on tilted detectors.
* Rugnux: Stills files that record a stationary goniometer axis get the default stills geometry refinement.
* jfjoch_viewer: "Analyze dataset" uses the same defaults as a bare `rugnux <file>`, and shows the results of processed CBF, marCCD and SMV sweeps.
* jfjoch_viewer: The Files panel refreshes on F5 and every few seconds, and the plot type and other selections stay put during live collection.
* jfjoch_writer: Memory stays bounded and old data files are closed efficiently on long runs, any failure ends the run in an error state the broker is told about, and the master file appears only after its data files; the ZeroMQ pusher logs when a stalled writer makes it drop images.
* Fixes: The TCP image pusher no longer blocks the broker's receiver, GPU out-of-memory failures stop with a clear message, and the XDS plugin masks module and chip edges.

---------

Co-authored-by: Filip Leonarski <jungfrau@filips-mac-mini.home>
Reviewed-on: #85
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-10-16 15:34:43 +02:00

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// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include <algorithm>
#include <cstdlib>
#include <fstream>
#include <string>
#include <thread>
#include <atomic>
#include <mutex>
#include <vector>
#include <cuda.h>
#include "CUDAWrapper.h"
#include "ThreadAffinity.h"
#include "JFJochException.h"
inline void cuda_err(cudaError_t val) {
if (val != cudaSuccess)
throw JFJochException(JFJochExceptionCategory::GPUCUDAError, cudaGetErrorString(val));
}
namespace {
std::atomic<bool> gpus_hidden{false};
}
void hide_gpus() {
gpus_hidden = true;
}
bool gpus_are_hidden() {
return gpus_hidden;
}
int32_t get_gpu_count() {
if (gpus_hidden)
return 0;
int device_count;
cudaError_t val = cudaGetDeviceCount(&device_count);
switch (val) {
case cudaSuccess:
return device_count;
case cudaErrorNoDevice:
case cudaErrorInsufficientDriver:
return 0;
default:
throw JFJochException(JFJochExceptionCategory::GPUCUDAError, cudaGetErrorString(val));
}
}
std::vector<std::string> get_gpu_names() {
std::vector<std::string> names;
const int32_t count = get_gpu_count();
names.reserve(count);
for (int32_t i = 0; i < count; i++) {
cudaDeviceProp prop{};
// A device that cannot be queried still exists and still gets work, so it is listed - just
// without a name. Losing the whole list over one unreadable device would be worse.
if (cudaGetDeviceProperties(&prop, i) == cudaSuccess)
names.emplace_back(prop.name);
else
names.emplace_back("unknown GPU");
}
return names;
}
size_t get_gpu_total_memory(int32_t dev_id) {
cudaDeviceProp prop{};
if (cudaGetDeviceProperties(&prop, dev_id) != cudaSuccess)
return 0;
return prop.totalGlobalMem;
}
bool get_gpu_free_memory(size_t &free_bytes, size_t &total_bytes) {
if (cudaMemGetInfo(&free_bytes, &total_bytes) != cudaSuccess)
return false;
#ifdef __linux__
// Asked once: whether each card shares the host's memory.
static const std::vector<int> integrated = [] {
std::vector<int> v(std::max(get_gpu_count(), 0));
for (int i = 0; i < static_cast<int>(v.size()); i++)
if (cudaDeviceGetAttribute(&v[i], cudaDevAttrIntegrated, i) != cudaSuccess) {
v[i] = 0;
cudaGetLastError();
}
return v;
}();
int device = 0;
if (cudaGetDevice(&device) != cudaSuccess || device >= static_cast<int>(integrated.size()) || !integrated[device])
return true;
std::ifstream meminfo("/proc/meminfo");
std::string line;
while (std::getline(meminfo, line))
if (line.rfind("MemAvailable:", 0) == 0) {
const size_t available = std::stoull(line.substr(13)) * 1024; // given in kB
const size_t headroom = total_bytes / 10; // the host's own processes live in the same memory
if (available > headroom)
free_bytes = std::max(free_bytes, std::min(available - headroom, total_bytes));
break;
}
#endif
return true;
}
bool gpu_direct_host_read() {
// Pageable memory access through the host's page tables is the hardware-coherent case (ATS over
// NVLink-C2C); without the second attribute the access is HMM-emulated, page faults and migration,
// and slower than a copy.
static const std::vector<bool> direct = [] {
const bool force = std::getenv("JFJOCH_FORCE_DIRECT_HOST_READ") != nullptr;
std::vector<bool> ret(get_gpu_count(), force);
for (int d = 0; d < static_cast<int>(ret.size()); d++) {
int pageable = 0, host_page_tables = 0;
cudaDeviceGetAttribute(&pageable, cudaDevAttrPageableMemoryAccess, d);
cudaDeviceGetAttribute(&host_page_tables, cudaDevAttrPageableMemoryAccessUsesHostPageTables, d);
if (pageable && host_page_tables)
ret[d] = true;
}
return ret;
}();
int device = 0;
if (cudaGetDevice(&device) != cudaSuccess || device >= static_cast<int>(direct.size()))
return false;
return direct[device];
}
void set_gpu(int32_t dev_id) {
auto dev_count = get_gpu_count();
// Ignore if no GPU present
if (dev_count > 0) {
if ((dev_id < 0) || (dev_id >= dev_count))
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Device ID cannot be negative");
cuda_err(cudaSetDevice(dev_id));
}
}
namespace {
std::atomic<bool> gpu_numa_binding{false};
// The NUMA node of each device, read once.
int GpuNumaNode(int32_t dev_id) {
static std::mutex m;
static std::vector<int> node;
std::lock_guard<std::mutex> lock(m);
if (node.empty()) {
const int32_t count = get_gpu_count();
node.assign(count, -1);
for (int32_t i = 0; i < count; i++) {
char bus_id[32] = {};
if (cudaDeviceGetPCIBusId(bus_id, sizeof(bus_id), i) == cudaSuccess)
node[i] = NumaNodeOfPciDevice(bus_id);
}
}
return dev_id < static_cast<int32_t>(node.size()) ? node[dev_id] : -1;
}
}
std::vector<int> get_gpu_numa_nodes() {
std::vector<int> nodes;
for (int32_t i = 0; i < get_gpu_count(); i++)
nodes.push_back(GpuNumaNode(i));
return nodes;
}
void enable_gpu_numa_binding() {
gpu_numa_binding = true;
}
void pin_gpu(int32_t dev_id) {
if (get_gpu_count() == 0)
return;
set_gpu(dev_id);
if (gpu_numa_binding)
PinThreadToNumaNode(GpuNumaNode(dev_id));
}
ScopedGpuPin::ScopedGpuPin(int32_t dev_id) {
if (get_gpu_count() == 0)
return;
cuda_err(cudaGetDevice(&prev_device));
const int node = gpu_numa_binding ? GpuNumaNode(dev_id) : -1;
if (node >= 0)
prev_cpus = GetThreadCpus();
set_gpu(dev_id);
PinThreadToNumaNode(node);
}
ScopedGpuPin::~ScopedGpuPin() {
SetThreadCpus(prev_cpus);
if (prev_device >= 0)
cudaSetDevice(prev_device); // not set_gpu: a destructor must not throw
}
void pin_gpu() {
static std::atomic<uint32_t> counter{0};
auto dev_count = get_gpu_count();
if (dev_count > 0)
pin_gpu(static_cast<int32_t>(counter.fetch_add(1) % dev_count));
}
void set_gpu_blocking_sync() {
// Through the driver's primary-context flags, which a context created later takes: the runtime's
// cudaSetDevice creates the device's context, serially, and on four cards that was most of a
// second before the run had started. The function is taken from the driver at run time, so the
// program does not link against it and still starts on a machine without one.
// Without a device nothing is called at all: even cudaGetLastError() would load the driver.
if (get_gpu_count() == 0)
return;
void *fn = nullptr;
cudaDriverEntryPointQueryResult found{};
if (cudaGetDriverEntryPointByVersion("cuDevicePrimaryCtxSetFlags", &fn, 12000, cudaEnableDefault, &found)
!= cudaSuccess
|| found != cudaDriverEntryPointSuccess) {
cudaGetLastError();
return;
}
const auto set_flags = reinterpret_cast<CUresult (*)(CUdevice, unsigned int)>(fn);
for (int32_t i = 0; i < get_gpu_count(); i++)
set_flags(i, CU_CTX_SCHED_BLOCKING_SYNC);
}
void create_gpu_contexts(int32_t first_device) {
std::vector<std::thread> threads;
for (int32_t i = first_device; i < get_gpu_count(); i++)
threads.emplace_back([i] {
// A device that fails here fails again, with its error, where it is used.
if (cudaSetDevice(i) != cudaSuccess || cudaFree(nullptr) != cudaSuccess)
cudaGetLastError();
});
for (auto &t : threads)
t.join();
}
void release_gpu_contexts() {
std::vector<std::thread> threads;
for (int32_t i = 0; i < get_gpu_count(); i++)
threads.emplace_back([i] {
if (cudaSetDevice(i) != cudaSuccess || cudaDeviceReset() != cudaSuccess)
cudaGetLastError();
});
for (auto &t : threads)
t.join();
}
void cuda_clear_error() {
if (!gpus_hidden) // hidden, nothing has used CUDA, and this call would still load the driver
cudaGetLastError();
}
void cuda_throw_if_context_lost() {
if (gpus_hidden)
return;
// cudaFree(nullptr) frees nothing, but a lost context fails it. The last error cannot say the same:
// once cudaGetLastError() has returned a sticky error, it and cudaPeekAtLastError() report success.
const cudaError_t err = cudaFree(nullptr);
if (err != cudaSuccess)
throw JFJochException(JFJochExceptionCategory::GPUCUDAError,
std::string("CUDA device unusable after an unrecoverable error: ")
+ cudaGetErrorString(err));
}