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Jungfraujoch/tests/CUDAMemHelpersTest.cpp
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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

433 lines
17 KiB
C++

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute
// SPDX-License-Identifier: GPL-3.0-only
#include <catch2/catch_all.hpp>
#include "../common/CUDAWrapper.h"
#include <atomic>
#include <optional>
#include <thread>
#ifdef JFJOCH_USE_CUDA
#include <cstring>
#include <future>
#include <latch>
#include <set>
#include <thread>
#include "../image_analysis/indexing/CUDAMemHelpers.h"
#include "../image_analysis/indexing/IndexerThreadPool.h"
// Whether the current GPU shares the host's memory (GB10, Jetson). A test that fills the card until an
// allocation fails would there fill the host's RAM - every process on the machine runs out with it.
static bool gpu_is_integrated() {
int device = 0, integrated = 0;
return cudaGetDevice(&device) == cudaSuccess
&& cudaDeviceGetAttribute(&integrated, cudaDevAttrIntegrated, device) == cudaSuccess && integrated;
}
// The broker starts fresh worker threads for every data collection. A stream per thread ever started
// is a device-memory leak that ends a long-running broker, so threads that follow one another have to
// end up on the same stream.
TEST_CASE("CudaAllocationStream_ReusedByLaterThreads", "[CUDAMemHelpers]") {
if (get_gpu_count() == 0)
SKIP("No CUDA GPU present");
std::set<cudaStream_t> seen;
for (int i = 0; i < 100; i++)
std::thread([&seen] {
CudaDevicePtr<uint8_t> buffer(1 << 16);
seen.insert(cuda_allocation_stream());
}).join();
CHECK(seen.size() == 1);
CHECK(*seen.begin() != nullptr);
}
TEST_CASE("CudaAllocationStream_DistinctForConcurrentThreads", "[CUDAMemHelpers]") {
if (get_gpu_count() == 0)
SKIP("No CUDA GPU present");
// Neither thread may exit - and hand its stream back - before the other has taken its own.
std::latch both_have_one(2);
auto take = [&both_have_one] {
const cudaStream_t stream = cuda_allocation_stream();
both_have_one.count_down();
both_have_one.wait();
return stream;
};
auto a = std::async(std::launch::async, take);
auto b = std::async(std::launch::async, take);
const cudaStream_t stream_a = a.get();
const cudaStream_t stream_b = b.get();
CHECK(stream_a != nullptr);
CHECK(stream_b != nullptr);
CHECK(stream_a != stream_b);
}
// The shadow finder builds its GPU accumulator on a throw-away thread and frees it from another one
// long after. The free is ordered on the allocating thread's stream, so that stream has to outlive
// the thread - including while a later thread has borrowed it.
TEST_CASE("CudaDevicePtr_FreedAfterAllocatingThreadExited", "[CUDAMemHelpers]") {
if (get_gpu_count() == 0)
SKIP("No CUDA GPU present");
auto buffer = std::async(std::launch::async, [] {
return std::make_unique<CudaDevicePtr<uint8_t>>(1 << 20);
}).get();
std::thread([] { CudaDevicePtr<uint8_t> other(1 << 16); }).join();
REQUIRE(cudaMemset(buffer->get(), 0, 1 << 20) == cudaSuccess);
buffer.reset();
CHECK(cudaDeviceSynchronize() == cudaSuccess);
CHECK(cudaGetLastError() == cudaSuccess);
}
// A pool that cannot serve the request is not an error: the buffer comes from cudaMalloc instead. It
// must then not stay behind as the thread's last error, or the cudaGetLastError() after the next
// kernel launch throws "out of memory" over work that went fine.
TEST_CASE("CudaDevicePtr_HandledPoolFailureLeavesNoError", "[CUDAMemHelpers]") {
if (get_gpu_count() == 0)
SKIP("No CUDA GPU present");
int device = 0;
REQUIRE(cudaGetDevice(&device) == cudaSuccess);
cudaMemPoolProps props{};
props.allocType = cudaMemAllocationTypePinned;
props.location.type = cudaMemLocationTypeDevice;
props.location.id = device;
props.maxSize = 4 << 20;
cudaMemPool_t previous = nullptr, capped = nullptr;
REQUIRE(cudaDeviceGetMemPool(&previous, device) == cudaSuccess);
REQUIRE(cudaMemPoolCreate(&capped, &props) == cudaSuccess);
REQUIRE(cudaDeviceSetMemPool(device, capped) == cudaSuccess);
{
CudaDevicePtr<uint8_t> buffer(64 << 20);
CHECK(buffer.get() != nullptr);
CHECK(cudaGetLastError() == cudaSuccess);
}
REQUIRE(cudaDeviceSetMemPool(device, previous) == cudaSuccess);
cudaMemPoolDestroy(capped);
}
// Engines built one after another take the pinned buffers the previous one gave back - also a little
// larger ones, within the size class - while a frame-sized buffer is not kept at all.
TEST_CASE("CudaPinnedPool_ReusedByTheNextEngine", "[CUDAMemHelpers]") {
if (get_gpu_count() == 0)
SKIP("No CUDA GPU present");
cuda_release_pinned_pool();
void *first = nullptr;
{
CudaHostPtr<float> a(1000);
first = a.get();
}
{
PinnedVector<float> b(1020);
CHECK(static_cast<void *>(b.data()) == first);
}
{
CudaHostPtr<uint8_t> large(CUDA_PINNED_POOL_MAX_BUFFER + 1);
large.get()[CUDA_PINNED_POOL_MAX_BUFFER] = 1;
}
CHECK(cuda_release_pinned_pool() == 4096);
CHECK(cuda_release_pinned_pool() == 0);
}
// Within a scope a cuFFT plan is kept once made and lent to one user at a time: two users at once get
// two plans, the next one after them gets one of those back, and a transform on a lent plan - another
// stream, a work area of the caller's - gives the same result bit for bit. When the scope ends, every
// kept plan is destroyed; outside a scope nothing is kept.
TEST_CASE("CudaFFTPlan_KeptAndLentToOneUserAtATime", "[CUDAMemHelpers]") {
if (get_gpu_count() == 0)
SKIP("No CUDA GPU present");
REQUIRE(jfjoch_cufft_plans::kept() == 0);
auto scope = std::make_unique<CudaFFTPlanScope>();
const int n = 1000, batch = 7, nc = n / 2 + 1;
const CudaFFTShape shape{.n = {n}, .idist = n, .odist = nc, .type = CUFFT_R2C, .batch = batch};
std::vector<float> input(n * batch);
for (size_t i = 0; i < input.size(); i++)
input[i] = static_cast<float>((i * 7919) % 1013) - 500.0f;
CudaDevicePtr<float> d_in(input.size());
CudaDevicePtr<cufftComplex> d_out(nc * batch);
REQUIRE(cudaMemcpy(d_in, input.data(), input.size() * sizeof(float), cudaMemcpyHostToDevice) == cudaSuccess);
auto transform = [&](const CudaFFTPlan &plan, cudaStream_t stream) {
REQUIRE(cufftExecR2C(plan, d_in, d_out) == CUFFT_SUCCESS);
std::vector<cufftComplex> out(nc * batch);
REQUIRE(cudaMemcpyAsync(out.data(), d_out, out.size() * sizeof(cufftComplex), cudaMemcpyDeviceToHost,
stream) == cudaSuccess);
REQUIRE(cudaStreamSynchronize(stream) == cudaSuccess);
return out;
};
CudaStream stream_a, stream_c;
std::vector<cufftComplex> first;
cufftHandle handle_a = 0;
{
CudaFFTPlan a(shape, stream_a);
CudaFFTPlan b(shape);
handle_a = a.get();
CHECK(handle_a != b.get());
first = transform(a, stream_a);
}
const size_t work = CudaFFTPlan::WorkBytes(shape);
CudaDevicePtr<char> work_area(std::max<size_t>(work, 1));
CudaFFTPlan c(shape, stream_c, work_area);
CHECK(c.get() == handle_a);
CHECK(c.WorkBytes() == work);
const std::vector<cufftComplex> again = transform(c, stream_c);
REQUIRE(again.size() == first.size());
CHECK(memcmp(again.data(), first.data(), first.size() * sizeof(cufftComplex)) == 0);
CHECK(jfjoch_cufft_plans::kept() == 1); // b; a is lent to c
c = CudaFFTPlan();
CHECK(jfjoch_cufft_plans::kept() == 2);
scope.reset();
CHECK(jfjoch_cufft_plans::kept() == 0);
CHECK(CudaFFTPlan::WorkBytes(shape) == work);
{ CudaFFTPlan d(shape); }
CHECK(jfjoch_cufft_plans::kept() == 0);
}
// An FFT indexer that finds the card full waits for the GPU work beside it to give its memory back, and
// is built then: the main line's for the probes, a probe's for the main line's image pass - never for a
// probe, itself included. With nothing to wait for it fails at once, as one that does not fit always has.
TEST_CASE("IndexerThreadPool_FFTIndexerWaitsForGPUWorkBeside", "[CUDAMemHelpers]") {
if (get_gpu_count() == 0)
SKIP("No CUDA GPU present");
if (gpu_is_integrated())
SKIP("Fills the card, which on an integrated GPU is the host's memory");
IndexingSettings settings;
settings.Algorithm(IndexingAlgorithmEnum::FFT).IndexingThreads(1);
DiffractionExperiment x;
x.ImportIndexingSettings(settings);
const std::vector<Coord> recip{{0.1, 0, 0}, {0, 0.1, 0}, {0, 0, 0.1}};
// Every card, held by the work beside: an indexer worker takes its card round-robin (pin_gpu), so on
// a machine with several the one it lands on is not the test thread's. Topped up right before each
// Run, so memory something else gave back in between does not let the indexer fit.
const int gpus = get_gpu_count();
std::vector<std::vector<CudaDevicePtr<uint8_t>>> held(gpus);
const auto fill = [&] {
for (int d = 0; d < gpus; d++) {
ScopedGpuPin pin(d);
for (size_t chunk = size_t(256) << 20; chunk >= (size_t(1) << 20); chunk /= 2)
while (true) {
try {
held[d].emplace_back(chunk, CudaAlloc::Synchronous);
} catch (const JFJochException &) {
break;
}
}
}
};
const auto release = [&] {
for (int d = 0; d < gpus; d++) {
ScopedGpuPin pin(d);
held[d].clear();
}
};
// The pools' indexers go back to the allocation pool when they are destroyed; trim it after them, so
// the next test finds the cards free.
{
IndexerThreadPool probe(settings, IndexerConstruction::OnFirstUse, /*beside=*/true);
IndexerThreadPool pool(settings, IndexerConstruction::OnFirstUse);
{
GPUWorkBeside work;
fill();
CHECK(probe.Run(x, recip).error != nullptr);
}
{
std::optional<GPUImagePass> image_pass(std::in_place);
GPUWorkBeside work;
fill();
std::thread ends([&] {
std::this_thread::sleep_for(std::chrono::milliseconds(500));
release();
image_pass.reset();
});
CHECK(probe.Run(x, recip).error == nullptr);
ends.join();
}
{
std::optional<GPUWorkBeside> work(std::in_place);
fill();
std::thread ends([&] {
std::this_thread::sleep_for(std::chrono::milliseconds(500));
release();
work.reset();
});
CHECK(pool.Run(x, recip).error == nullptr);
ends.join();
}
}
for (int d = 0; d < gpus; d++) {
ScopedGpuPin pin(d);
cuda_trim_allocation_pool();
}
}
// A merge helper's buffer that finds the card full while a probe pass holds the rest of it waits for
// that work to end and its memory to come back (CudaAlloc::SynchronousAfterWorkBeside); a plain
// synchronous one fails at once.
TEST_CASE("CudaDevicePtr_AfterWorkBesideWaitsForItsMemory", "[CUDAMemHelpers]") {
if (get_gpu_count() == 0)
SKIP("no GPU");
if (gpu_is_integrated())
SKIP("Fills the card, which on an integrated GPU is the host's memory");
std::vector<CudaDevicePtr<uint8_t>> held;
const auto fill = [&] {
for (size_t chunk = size_t(256) << 20; chunk >= (size_t(1) << 20); chunk /= 2)
while (true) {
try {
held.emplace_back(chunk, CudaAlloc::Synchronous);
} catch (const JFJochException &) {
break;
}
}
};
constexpr size_t BYTES = size_t(64) << 20;
{
std::optional<GPUWorkBeside> work(std::in_place);
fill();
CHECK_THROWS_AS(CudaDevicePtr<uint8_t>(BYTES, CudaAlloc::Synchronous), JFJochException);
std::thread ends([&] {
std::this_thread::sleep_for(std::chrono::milliseconds(500));
held.clear();
work.reset();
});
CHECK_NOTHROW(CudaDevicePtr<uint8_t>(BYTES, CudaAlloc::SynchronousAfterWorkBeside));
ends.join();
}
cuda_trim_allocation_pool();
}
// The free memory waited on is cudaMemGetInfo's on a discrete card. On one that shares the host's memory
// (GB10, Jetson) it also counts the page cache the host hands back, less a tenth of the card for the host:
// never less than cudaMemGetInfo's. Allocations between the readings move them, hence the 1 GB slack.
TEST_CASE("GetGpuFreeMemory_IntegratedCountsThePageCache", "[CUDAMemHelpers]") {
if (get_gpu_count() == 0)
SKIP("No CUDA GPU present");
constexpr double SLACK = 1e9;
size_t free_bytes = 0, total_bytes = 0;
REQUIRE(get_gpu_free_memory(free_bytes, total_bytes));
size_t cuda_free = 0, cuda_total = 0;
REQUIRE(cudaMemGetInfo(&cuda_free, &cuda_total) == cudaSuccess);
CHECK(total_bytes == cuda_total);
CHECK(free_bytes <= total_bytes);
CHECK(double(free_bytes) >= double(cuda_free) - SLACK);
if (!gpu_is_integrated())
CHECK(double(free_bytes) == Catch::Approx(double(cuda_free)).margin(SLACK));
}
// The pool's indexers go back to the card - not only to the allocation pool - when it is asked, and the
// next frame builds them again.
TEST_CASE("IndexerThreadPool_ReleaseIndexersGivesTheCardBack", "[CUDAMemHelpers]") {
if (get_gpu_count() == 0)
SKIP("No CUDA GPU present");
IndexingSettings settings;
settings.Algorithm(IndexingAlgorithmEnum::FFT).IndexingThreads(1);
DiffractionExperiment x;
x.ImportIndexingSettings(settings);
const std::vector<Coord> recip{{0.1, 0, 0}, {0, 0.1, 0}, {0, 0, 0.1}};
// What the allocation pools of all cards hand out: an indexer worker takes its card round-robin.
const auto pooled = [] {
uint64_t sum = 0;
for (int d = 0; d < get_gpu_count(); d++) {
cudaMemPool_t pool = nullptr;
uint64_t used = 0;
if (cudaDeviceGetDefaultMemPool(&pool, d) == cudaSuccess
&& cudaMemPoolGetAttribute(pool, cudaMemPoolAttrUsedMemCurrent, &used) == cudaSuccess)
sum += used;
}
return sum;
};
const auto reserved = [] {
uint64_t sum = 0;
for (int d = 0; d < get_gpu_count(); d++) {
cudaMemPool_t pool = nullptr;
uint64_t r = 0;
if (cudaDeviceGetDefaultMemPool(&pool, d) == cudaSuccess
&& cudaMemPoolGetAttribute(pool, cudaMemPoolAttrReservedMemCurrent, &r) == cudaSuccess)
sum += r;
}
return sum;
};
const uint64_t before = pooled();
const uint64_t reserved_before = reserved();
{
IndexerThreadPool pool(settings, IndexerConstruction::OnFirstUse);
const IndexerResult first = pool.Run(x, recip);
REQUIRE(first.error == nullptr);
REQUIRE(pooled() > before + (uint64_t(100) << 20));
pool.ReleaseIndexers();
CHECK(pooled() <= before + (uint64_t(16) << 20));
CHECK(reserved() <= reserved_before + (uint64_t(64) << 20));
const IndexerResult again = pool.Run(x, recip);
CHECK(again.error == nullptr);
CHECK(again.executed == first.executed);
CHECK(again.lattice.size() == first.lattice.size());
}
for (int d = 0; d < get_gpu_count(); d++) {
ScopedGpuPin pin(d);
cuda_trim_allocation_pool();
}
}
#endif
// A merge that finds the card full waits for the GPU work running beside it: until the last one
// ends, and not forever.
TEST_CASE("GPUWorkBeside_WaitEndsWithTheWork", "[CUDAMemHelpers]") {
CHECK(wait_for_gpu_work_beside(std::chrono::seconds(0)));
std::optional<GPUWorkBeside> work;
work.emplace();
CHECK_FALSE(wait_for_gpu_work_beside(std::chrono::seconds(0)));
std::thread ends([&work] {
std::this_thread::sleep_for(std::chrono::milliseconds(100));
work.reset();
});
CHECK(wait_for_gpu_work_beside(std::chrono::seconds(60)));
ends.join();
}
// The speculative geometry probe waits for the main line's merge on a card too small for both, and on a
// larger one runs beside it; the rest of the work beside never waits for a merge.
TEST_CASE("GPUWorkBeside_AfterMergesTakesTurnsOnASmallCard", "[CUDAMemHelpers]") {
// As take_turns() in CUDAWrapper.cpp.
const bool small = get_gpu_count() > 0 && get_gpu_total_memory(0) < 12'000'000'000ull;
std::optional<GPUMerge> merge(std::in_place);
{ GPUWorkBeside other; } // does not wait
std::atomic<bool> started = false;
std::thread probe([&started] {
GPUWorkBeside beside(/*after_merges=*/true);
started = true;
});
if (small) {
std::this_thread::sleep_for(std::chrono::milliseconds(200));
CHECK_FALSE(started);
}
merge.reset();
probe.join();
CHECK(started);
}