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Jungfraujoch/common/ThreadAffinity.h
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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: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#pragma once
#include <string>
#include <vector>
// Keeping a GPU's worker threads on the socket the card hangs off, on a machine with more than one
// NUMA node, so the pinned host buffers they allocate and the copies to the card stay on that
// socket's memory controller and PCIe root. Read from /sys - no libnuma - and Linux only: elsewhere,
// and on a machine with a single node, every call is a no-op.
// The NUMA node of a PCI device, from its bus id as CUDA gives it ("0000:41:00.0"); -1 where it is
// not known or the machine has a single node.
int NumaNodeOfPciDevice(const std::string &pci_bus_id);
// How many CPUs this process may use: the CPUs it was started on (its affinity mask - what taskset,
// a cpuset or a Slurm job gives it), and no more than its cgroup's CPU quota where one is set (a
// container started with --cpus). std::thread::hardware_concurrency() counts every CPU of the
// machine, so a job given 16 of a node's 192 would otherwise start 192 threads. Read once, at the
// first call. Outside Linux it is hardware_concurrency(). At least 1.
unsigned AvailableCpus();
// The CPUs a process driving GPUs keeps to on a machine of several packages (sockets): those of the
// packages its cards hang off. `allowed` is what the process may use, `package_of_cpu[c]` the package
// of CPU c (-1 unknown) and `gpu_packages` the package of each card (-1 unknown). Empty where nothing
// changes: the allowed CPUs sit in one package, there is no card or one card's package is unknown, the
// cards' packages hold every allowed CPU, or none of them.
std::vector<int> CpusOfGpuPackages(const std::vector<int> &allowed, const std::vector<int> &package_of_cpu,
const std::vector<int> &gpu_packages);
// Keep the process to CpusOfGpuPackages for cards on the NUMA nodes `gpu_nodes` (-1 unknown): the
// calling thread, the CPUs RestoreThreadAffinity gives back and what AvailableCpus counts all become
// those, within the CPUs it was started on. Threads, and the memory they first touch, spread over
// sockets the cards are not on make the latency-bound scaling slower: on a 48-CPU server with its cards
// on two of four NUMA nodes, a rotation run kept to those two nodes' 24 CPUs took 12 % less wall time
// than on all 48, and the 12 CPUs of one node without a card still beat all 48. Call it on the main thread before any thread
// is started. Returns the CPUs it keeps to; empty where nothing changed. Linux only.
std::vector<int> ConfineToGpuPackages(const std::vector<int> &gpu_nodes);
// Restrict the calling thread to the CPUs of `node` that the process may run on. Nothing happens for
// node < 0, or where that would leave the thread no CPU.
void PinThreadToNumaNode(int node);
// Give the calling thread back the CPUs the process started with. A thread inherits the affinity of
// the thread that creates it, so a thread pool first reached from a pinned worker would otherwise
// run every later parallel pass of the process on one socket.
void RestoreThreadAffinity();
// The calling thread's CPUs now, for SetThreadCpus to give back after a while on one node. Empty
// outside Linux.
std::vector<int> GetThreadCpus();
// Keep the calling thread on exactly these CPUs. Nothing happens for an empty list.
void SetThreadCpus(const std::vector<int> &cpus);