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Jungfraujoch/tests/ParallelForTest.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

280 lines
11 KiB
C++

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include <catch2/catch_all.hpp>
#include <algorithm>
#include <cmath>
#include <mutex>
#include <numeric>
#include <stdexcept>
#include <thread>
#include <vector>
#include "../common/CUDAWrapper.h"
#include "../common/ParallelFor.h"
#include "../common/ThreadAffinity.h"
namespace {
const std::vector<size_t> THREAD_COUNTS = {0, 1, 2, 3, 8, 64};
const std::vector<int> SIZES = {0, 1, 2, 7, 64, 1000};
}
// The split is fixed and contiguous, which is what lets a pass whose per-element work is independent
// give the serial answer bit for bit. Every element has to land in exactly one slice, the slices have
// to tile [0, n) in order, and there must never be an empty one.
TEST_CASE("ParallelChunks_SlicesTileTheRange", "[ParallelFor]") {
for (int n: SIZES) {
for (size_t nthreads: THREAD_COUNTS) {
CAPTURE(n, nthreads);
std::mutex m;
std::vector<std::pair<int, int>> slices;
std::vector<int> visits(static_cast<size_t>(std::max(n, 1)), 0);
ParallelChunks(n, nthreads, [&](int lo, int hi) {
{
std::scoped_lock lock(m);
slices.emplace_back(lo, hi);
}
for (int i = lo; i < hi; i++)
visits[static_cast<size_t>(i)]++; // slices are disjoint, so no lock needed
});
std::sort(slices.begin(), slices.end());
int expected_lo = 0;
for (const auto &[lo, hi]: slices) {
CHECK(lo == expected_lo);
CHECK(hi > lo); // never an empty slice
expected_lo = hi;
}
CHECK(expected_lo == n); // and they reach the end
CHECK(slices.size() <= static_cast<size_t>(std::max(n, 0)));
for (int i = 0; i < n; i++)
CHECK(visits[static_cast<size_t>(i)] == 1);
}
}
}
// Work stealing, so a worker takes whatever is next rather than a fixed slice - but every item still
// has to be done exactly once, whatever order they come out in.
TEST_CASE("ParallelFor_VisitsEveryItemOnce", "[ParallelFor]") {
for (int n: SIZES) {
for (size_t nthreads: THREAD_COUNTS) {
CAPTURE(n, nthreads);
std::vector<std::atomic<int>> visits(static_cast<size_t>(std::max(n, 1)));
for (auto &v: visits)
v.store(0);
ParallelFor(n, nthreads, [&](int i) { visits[static_cast<size_t>(i)].fetch_add(1); });
for (int i = 0; i < n; i++)
CHECK(visits[static_cast<size_t>(i)].load() == 1);
}
}
}
// One thread means the caller's loop, in order - the property the serial fallbacks rely on.
TEST_CASE("ParallelFor_IsSerialAndInOrderForOneThread", "[ParallelFor]") {
for (size_t nthreads: {size_t{0}, size_t{1}}) {
CAPTURE(nthreads);
std::vector<int> order;
ParallelFor(16, nthreads, [&](int i) { order.push_back(i); });
std::vector<int> expected(16);
std::iota(expected.begin(), expected.end(), 0);
CHECK(order == expected);
}
}
// Splitting the work must not change the answer. Each element is written by exactly one worker, so
// the result has to match the serial loop element for element, at every thread count.
TEST_CASE("ParallelFor_SplitDoesNotChangeTheResult", "[ParallelFor]") {
constexpr int N = 1000;
std::vector<double> serial(N);
for (int i = 0; i < N; i++)
serial[static_cast<size_t>(i)] = std::sin(i * 0.001) * 1e6 + i;
for (size_t nthreads: THREAD_COUNTS) {
CAPTURE(nthreads);
std::vector<double> chunked(N, 0.0), stolen(N, 0.0);
ParallelChunks(N, nthreads, [&](int lo, int hi) {
for (int i = lo; i < hi; i++)
chunked[static_cast<size_t>(i)] = std::sin(i * 0.001) * 1e6 + i;
});
ParallelFor(N, nthreads, [&](int i) {
stolen[static_cast<size_t>(i)] = std::sin(i * 0.001) * 1e6 + i;
});
CHECK(chunked == serial); // bit for bit, not approximately
CHECK(stolen == serial);
}
}
// The blocks depend on n alone: the same tiling of [0, n), block b always the same range, whatever the
// thread count.
TEST_CASE("ParallelBlocks_PartitionIgnoresTheThreadCount", "[ParallelFor]") {
for (int n: {0, 1, 7, 4095, 4096, 100000, 5000000}) {
const int nb = ReductionBlocks(n);
CHECK(nb <= MAX_REDUCTION_BLOCKS);
std::vector<std::pair<int, int>> reference;
for (size_t nthreads: THREAD_COUNTS) {
CAPTURE(n, nthreads);
std::vector<std::pair<int, int>> range(static_cast<size_t>(nb), {-1, -1});
ParallelBlocks(n, nthreads, [&](int b, int lo, int hi) { range[static_cast<size_t>(b)] = {lo, hi}; });
int expected_lo = 0;
for (const auto &[lo, hi]: range) {
CHECK(lo == expected_lo);
CHECK(hi > lo);
expected_lo = hi;
}
CHECK(expected_lo == n);
if (reference.empty()) reference = range;
CHECK(range == reference);
}
}
}
// What the blocks are for: a floating-point sum folded per block and added up in block order has the
// same bits at any thread count. The terms span many decades, so any change of grouping would show.
TEST_CASE("ParallelBlocks_SumIsTheSameAtAnyThreadCount", "[ParallelFor]") {
constexpr int N = 1000003;
constexpr int NCELL = 37;
std::vector<double> term(N);
for (int i = 0; i < N; i++)
term[static_cast<size_t>(i)] = std::exp(std::sin(i * 0.37) * 20.0) * (i % 3 == 0 ? -1.0 : 1.0);
auto blocked_sums = [&](size_t nthreads) {
const int nb = ReductionBlocks(N);
std::vector<double> part(static_cast<size_t>(nb), 0.0);
std::vector<std::vector<double>> cell_part(static_cast<size_t>(nb), std::vector<double>(NCELL, 0.0));
ParallelBlocks(N, nthreads, [&](int b, int lo, int hi) {
for (int i = lo; i < hi; i++) {
part[static_cast<size_t>(b)] += term[static_cast<size_t>(i)];
cell_part[static_cast<size_t>(b)][static_cast<size_t>(i % NCELL)] += term[static_cast<size_t>(i)];
}
});
std::vector<double> out(NCELL + 1, 0.0);
for (int b = 0; b < nb; b++) {
out[NCELL] += part[static_cast<size_t>(b)];
for (int c = 0; c < NCELL; c++)
out[static_cast<size_t>(c)] += cell_part[static_cast<size_t>(b)][static_cast<size_t>(c)];
}
return out;
};
const std::vector<double> one = blocked_sums(1);
for (size_t nthreads: {size_t{3}, size_t{7}, size_t{32}}) {
CAPTURE(nthreads);
CHECK(blocked_sums(nthreads) == one); // bit for bit, not approximately
}
}
// A negative or zero count is a no-op rather than an error - callers pass a computed size.
TEST_CASE("ParallelFor_DoesNothingForAnEmptyRange", "[ParallelFor]") {
int calls = 0;
for (int n: {0, -1, -1000}) {
ParallelChunks(n, 8, [&](int, int) { calls++; });
ParallelFor(n, 8, [&](int) { calls++; });
ParallelBlocks(n, 8, [&](int, int, int) { calls++; });
}
CHECK(calls == 0);
}
// An exception thrown in a worker reaches the caller rather than terminating: the futures are waited
// on, so the other workers finish first and only then does it propagate.
TEST_CASE("ParallelFor_PropagatesAnException", "[ParallelFor]") {
CHECK_THROWS_AS(ParallelChunks(64, 4, [](int lo, int) {
if (lo == 0) throw std::runtime_error("from a chunk");
}), std::runtime_error);
CHECK_THROWS_AS(ParallelFor(64, 4, [](int i) {
if (i == 0) throw std::runtime_error("from an item");
}), std::runtime_error);
}
#ifdef __linux__
// The merging engine's ScopedGpuPin keeps its thread by the card only while it lives: a thread kept to
// one CPU before is kept to that CPU after, and the pool's workers keep the process's CPUs while a
// narrowed thread hands them work.
TEST_CASE("ScopedGpuPin_GivesTheThreadItsCpusBack", "[ParallelFor]") {
const std::vector<int> all = GetThreadCpus();
REQUIRE(all.size() >= 2);
std::vector<int> after_pin;
std::vector<std::vector<int>> seen_by_task(4);
std::thread([&] {
SetThreadCpus({all.front()});
{
const ScopedGpuPin pin(0);
ParallelChunks(4, 4, [&](int lo, int) { seen_by_task[lo] = GetThreadCpus(); });
}
after_pin = GetThreadCpus();
}).join();
CHECK(after_pin == std::vector<int>{all.front()});
for (int t = 1; t < 4; t++)
CHECK(seen_by_task[t] == all);
}
#endif
namespace {
std::vector<int> CpuRange(int lo, int hi) { // [lo, hi]
std::vector<int> v(hi - lo + 1);
std::iota(v.begin(), v.end(), lo);
return v;
}
std::vector<int> Concat(std::vector<int> a, const std::vector<int> &b) {
a.insert(a.end(), b.begin(), b.end());
return a;
}
}
// Synthetic machines: which CPUs a GPU run keeps to, given the CPUs it may use, the package of every
// CPU and the package of every card.
TEST_CASE("CpusOfGpuPackages_KeepsToTheCardsPackages", "[ParallelFor]") {
// Four packages of 12 CPUs, four cards on packages 2 and 3.
std::vector<int> four(48);
for (int c = 0; c < 48; c++)
four[c] = c / 12;
CHECK(CpusOfGpuPackages(CpuRange(0, 47), four, {2, 2, 3, 3}) == CpuRange(24, 47));
// Two packages of 12 cores with hyper-threading, numbered as Linux does: CPUs 0-11 and 24-35 on
// package 0, 12-23 and 36-47 on package 1.
std::vector<int> two(48);
for (int c = 0; c < 48; c++)
two[c] = (c / 12) % 2;
const std::vector<int> package1 = Concat(CpuRange(12, 23), CpuRange(36, 47));
CHECK(CpusOfGpuPackages(CpuRange(0, 47), two, {1}) == package1);
CHECK(CpusOfGpuPackages(CpuRange(0, 47), two, {1, 1}) == package1);
// Cards on both packages: nothing to keep to.
CHECK(CpusOfGpuPackages(CpuRange(0, 47), two, {0, 1}).empty());
// No card (a CPU build, or none visible), or a card whose package is not known.
CHECK(CpusOfGpuPackages(CpuRange(0, 47), two, {}).empty());
CHECK(CpusOfGpuPackages(CpuRange(0, 47), two, {1, -1}).empty());
// One package, as on a desktop.
CHECK(CpusOfGpuPackages(CpuRange(0, 31), std::vector<int>(32, 0), {0}).empty());
}
// A process started on fewer CPUs (taskset, numactl, a cpuset) keeps within them.
TEST_CASE("CpusOfGpuPackages_RespectsARestrictedMask", "[ParallelFor]") {
std::vector<int> four(48);
for (int c = 0; c < 48; c++)
four[c] = c / 12;
// Already on one package - with the cards or without them - stays where it is.
CHECK(CpusOfGpuPackages(CpuRange(0, 11), four, {2, 3}).empty());
CHECK(CpusOfGpuPackages(CpuRange(24, 35), four, {2, 3}).empty());
// Already on the cards' packages only.
CHECK(CpusOfGpuPackages(CpuRange(24, 47), four, {2, 3}).empty());
// Over packages 1 and 2, cards on 2 and 3: the part on package 2.
CHECK(CpusOfGpuPackages(CpuRange(18, 29), four, {2, 3}) == CpuRange(24, 29));
}
// Without a card nothing is confined, so the process keeps the CPUs it started with.
TEST_CASE("ConfineToGpuPackages_DoesNothingWithoutACard", "[ParallelFor]") {
const unsigned before = AvailableCpus();
const std::vector<int> cpus = GetThreadCpus();
CHECK(ConfineToGpuPackages({}).empty());
CHECK(AvailableCpus() == before);
CHECK(GetThreadCpus() == cpus);
}