IsoSpecPy 2.5.0__py3-none-win_arm64.whl

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Files changed (45) hide show
  1. IsoSpecPy/Advanced.py +32 -0
  2. IsoSpecPy/Distributions.py +93 -0
  3. IsoSpecPy/Formulas.py +71 -0
  4. IsoSpecPy/IsoSpec++/aligned_ptr.h +638 -0
  5. IsoSpecPy/IsoSpec++/allocator.h +69 -0
  6. IsoSpecPy/IsoSpec++/btrd.h +206 -0
  7. IsoSpecPy/IsoSpec++/composition.h +126 -0
  8. IsoSpecPy/IsoSpec++/conf.h +38 -0
  9. IsoSpecPy/IsoSpec++/cwrapper.h +271 -0
  10. IsoSpecPy/IsoSpec++/dirtyAllocator.h +58 -0
  11. IsoSpecPy/IsoSpec++/element_lookup.h +36 -0
  12. IsoSpecPy/IsoSpec++/element_tables.h +50 -0
  13. IsoSpecPy/IsoSpec++/fasta.h +70 -0
  14. IsoSpecPy/IsoSpec++/fasta_mods.h +70 -0
  15. IsoSpecPy/IsoSpec++/fixedEnvelopes.h +418 -0
  16. IsoSpecPy/IsoSpec++/isa_kernel_impl.h +192 -0
  17. IsoSpecPy/IsoSpec++/isa_kernels.h +172 -0
  18. IsoSpecPy/IsoSpec++/isoMath.h +121 -0
  19. IsoSpecPy/IsoSpec++/isoSpec++.h +801 -0
  20. IsoSpecPy/IsoSpec++/iso_simd.h +48 -0
  21. IsoSpecPy/IsoSpec++/marginalTrek++.h +614 -0
  22. IsoSpecPy/IsoSpec++/misc.h +229 -0
  23. IsoSpecPy/IsoSpec++/mman.h +67 -0
  24. IsoSpecPy/IsoSpec++/operators.h +150 -0
  25. IsoSpecPy/IsoSpec++/platform.h +180 -0
  26. IsoSpecPy/IsoSpec++/platform_incl.h +33 -0
  27. IsoSpecPy/IsoSpec++/pod_vector.h +400 -0
  28. IsoSpecPy/IsoSpec++/summator.h +118 -0
  29. IsoSpecPy/IsoSpec++/unimod.h +80 -0
  30. IsoSpecPy/IsoSpec++/unimod_support.h +2169 -0
  31. IsoSpecPy/IsoSpec++/unimod_table_data.h +1027 -0
  32. IsoSpecPy/IsoSpecPy.py +1088 -0
  33. IsoSpecPy/IsoSpecPyOld.py +290 -0
  34. IsoSpecPy/PeriodicTbl.py +51 -0
  35. IsoSpecPy/__init__.py +19 -0
  36. IsoSpecPy/__main__.py +25 -0
  37. IsoSpecPy/approximations.py +122 -0
  38. IsoSpecPy/confs_passthrough.py +16 -0
  39. IsoSpecPy/isoFFI.py +290 -0
  40. bin/IsoSpecCppPy.dll +0 -0
  41. isospecpy-2.5.0.dist-info/METADATA +220 -0
  42. isospecpy-2.5.0.dist-info/RECORD +45 -0
  43. isospecpy-2.5.0.dist-info/WHEEL +5 -0
  44. isospecpy-2.5.0.dist-info/licenses/LICENCE +35 -0
  45. lib/IsoSpecCppPy.lib +0 -0
@@ -0,0 +1,638 @@
1
+ /*
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+ * Copyright (C) 2026 Mateusz Łącki and Michał Startek.
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+ *
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+ * This file is part of IsoSpec.
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+ *
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+ * IsoSpec is free software: you can redistribute it and/or modify
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+ * it under the terms of the Simplified ("2-clause") BSD licence.
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+ *
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+ * IsoSpec is distributed in the hope that it will be useful,
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+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
11
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
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+ *
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+ * You should have received a copy of the Simplified BSD Licence
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+ * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.
15
+ */
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+
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+ #pragma once
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+
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+ #include <cstddef> // std::size_t, std::nullptr_t
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+ #include <cstdint> // std::uintptr_t (only if doing runtime alignment checks)
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+ #include <cstdlib> // std::aligned_alloc, std::malloc, std::free
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+ #include <cstring> // std::memcpy
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+ #include <algorithm> // std::min
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+ #include <limits> // std::numeric_limits
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+ #include <memory> // std::assume_aligned (C++20)
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+ #include <new> // std::bad_alloc
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+ #include <utility> // std::exchange
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+ #include <type_traits> // std::is_trivial_v
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+
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+ #include "platform.h" // ISOSPEC_WE_ARE_ON_WINDOWS / ISOSPEC_WE_ARE_ON_UNIX_YAY
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+
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+ // aligned_unique_ptr's realloc() grows/shrinks without copying once the
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+ // allocation is big enough to be worth mapping directly from the OS. Below
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+ // that size it stays on the plain aligned_alloc/copy/free path. Deliberately
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+ // bypasses this project's own mman.h shim/ISOSPEC_GOT_MMAN machinery (used
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+ // elsewhere for plain huge-page mmap): that layer has no remap concept at
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+ // all on Windows and no equivalent of mremap on Darwin, so each platform's
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+ // real growth primitive is used directly instead:
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+ // - Linux / other real-mman UNIX: mmap + mremap(MREMAP_MAYMOVE) + munmap.
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+ // - Apple: mmap/munmap for create/destroy (Darwin has no mremap); growth
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+ // re-wires pages into a fresh mapping via mach_vm_remap instead of
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+ // copying, shrink just munmaps the tail in place.
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+ // - Windows: VirtualAlloc(MEM_RESERVE) a generously oversized address
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+ // range once, then VirtualAlloc(MEM_COMMIT)/VirtualFree(MEM_DECOMMIT)
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+ // to grow/shrink within it -- the base address never moves, so there is
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+ // no copy at all in the common case (only if growth ever outgrows the
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+ // initial reservation does it fall back to allocating a fresh, larger
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+ // reservation and copying, same as a real mremap() that has to move).
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+ // On any other platform (no mmap-family primitive available at all) the
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+ // VM-backed path is simply never engaged; realloc() keeps using the
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+ // aligned_alloc/copy/free path regardless of size.
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+ #if ISOSPEC_WE_ARE_ON_WINDOWS || ISOSPEC_WE_ARE_ON_UNIX_YAY
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+ #define ISOSPEC_ALIGNED_PTR_HAVE_VM_REALLOC 1
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+ #else
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+ #define ISOSPEC_ALIGNED_PTR_HAVE_VM_REALLOC 0
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+ #endif
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+
58
+ // The small-allocation backend needs an aligned allocator that can also be
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+ // deallocated with a plain std::free() (release() promises exactly that).
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+ // glibc/libc++'s std::aligned_alloc satisfies both at once. MSVC's CRT has
61
+ // no C11 aligned_alloc at all, only _aligned_malloc/_aligned_free -- and
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+ // memory from those two is NOT free()-compatible (the CRT stores its own
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+ // offset bookkeeping ahead of the returned pointer, which plain free() does
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+ // not know how to unwind). So on MSVC the small backend uses
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+ // _aligned_malloc/_aligned_free for its own storage (still genuinely
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+ // Alignment-aligned, as marginalTrek++.h's use of this class relies on),
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+ // and release() falls back to materialising a fresh plain-malloc()'d copy
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+ // to keep its free()-compatibility promise -- the same thing it already
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+ // does to escape a VM-backed region.
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+ #if defined(_MSC_VER)
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+ #define ISOSPEC_ALIGNED_PTR_SMALL_BACKEND_FREE_COMPATIBLE 0
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+ #else
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+ #define ISOSPEC_ALIGNED_PTR_SMALL_BACKEND_FREE_COMPATIBLE 1
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+ #endif
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+
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+ #if ISOSPEC_WE_ARE_ON_WINDOWS
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+ #include <windows.h>
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+ #if defined(_MSC_VER)
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+ #include <malloc.h> // _aligned_malloc / _aligned_free
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+ #endif
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+ #elif ISOSPEC_WE_ARE_ON_UNIX_YAY
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+ #include <sys/mman.h> // real system mmap/munmap (+ mremap on Linux)
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+ #include <unistd.h> // sysconf
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+ #if defined(__APPLE__) && defined(__MACH__)
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+ #include <mach/mach.h>
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+ #include <mach/mach_vm.h>
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+ #endif
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+ #endif
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+
90
+
91
+ #if ISOSPEC_ALIGNED_PTR_HAVE_VM_REALLOC
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+ namespace aligned_ptr_detail {
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+
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+ // A namespace-scope initializer runs once, single-threaded, before this
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+ // library is reachable from anywhere else -- unlike a function-local static,
96
+ // whose first-use initialization needs a runtime guard (a lock, on most
97
+ // ABIs) to stay safe if two threads race to initialize it. realloc() below
98
+ // queries this on every call regardless of size, making it the earliest and
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+ // most frequently hit point such a guard could be contended.
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+ inline std::size_t compute_os_page_size() noexcept
101
+ {
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+ #if ISOSPEC_WE_ARE_ON_WINDOWS
103
+ SYSTEM_INFO si;
104
+ GetSystemInfo(&si);
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+ return static_cast<std::size_t>(si.dwPageSize);
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+ #else
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+ return static_cast<std::size_t>(sysconf(_SC_PAGESIZE));
108
+ #endif
109
+ }
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+
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+ inline const std::size_t os_page_size_ = compute_os_page_size();
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+
113
+ inline std::size_t os_page_size() noexcept
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+ {
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+ return os_page_size_;
116
+ }
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+
118
+ inline std::size_t round_up_to_page(std::size_t bytes) noexcept
119
+ {
120
+ const std::size_t ps = os_page_size();
121
+ return (bytes + ps - 1) / ps * ps;
122
+ }
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+
124
+ // Smallest allocation realloc() will move onto the VM-backed backend.
125
+ //
126
+ // Not simply "one page": mapping fresh anonymous memory makes the kernel hand
127
+ // out zero pages that then fault in one by one on first touch, and for a buffer
128
+ // that is about to be overwritten wholesale that zeroing is pure waste. malloc,
129
+ // by contrast, hands back memory the process already owns and has already
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+ // faulted -- which, in the loop-over-many-molecules pattern this library is
131
+ // mostly used in, it almost always has. Measured on Alder Lake: routing a
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+ // ~1 MiB one-shot envelope fill through mmap instead of aligned_alloc cost
133
+ // 1.85x. So the VM backend has to earn its faults, and it only can by saving
134
+ // copies on repeated growth -- which needs the buffer to be big enough for
135
+ // those copies to hurt more than the faults do. The same measurements put the
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+ // crossover for the doubling-growth fills at a few hundred KiB.
137
+ //
138
+ // Consequently: allocate once, at a known size -> stay on the small backend
139
+ // (reset()); grow repeatedly -> realloc(), and cross over here. Overridable at
140
+ // build time for retuning.
141
+ #ifndef ISOSPEC_ALIGNED_PTR_VM_THRESHOLD
142
+ #define ISOSPEC_ALIGNED_PTR_VM_THRESHOLD (std::size_t(256) << 10) // 256 KiB
143
+ #endif
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+
145
+ inline std::size_t vm_backend_threshold() noexcept
146
+ {
147
+ const std::size_t ps = os_page_size();
148
+ return ISOSPEC_ALIGNED_PTR_VM_THRESHOLD < ps ? ps : ISOSPEC_ALIGNED_PTR_VM_THRESHOLD;
149
+ }
150
+
151
+ // Releases a VM-backed block given just (ptr, bytes), without the rest of a
152
+ // vm_region's bookkeeping -- used by aligned_unique_ptr::release_with_deleter()
153
+ // once ownership has been handed off to a caller who only has those two
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+ // values. bytes must be the actual backing size (region_.size / .reserved
155
+ // above), not a logical/unrounded request size; Windows ignores it (a
156
+ // placeholder-free VirtualFree(MEM_RELEASE) always frees the whole
157
+ // reservation from its base).
158
+ inline void vm_release_raw(void* ptr, std::size_t bytes) noexcept
159
+ {
160
+ #if ISOSPEC_WE_ARE_ON_WINDOWS
161
+ (void)bytes;
162
+ ::VirtualFree(ptr, 0, MEM_RELEASE);
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+ #else
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+ ::munmap(ptr, bytes);
165
+ #endif
166
+ }
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+
168
+
169
+ #if ISOSPEC_WE_ARE_ON_WINDOWS
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+ // Reservation only consumes address space, not RAM or page tables, so we can
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+ // afford to be wasteful up front in order to (almost) never have to move
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+ // the block: growth just commits further pages of the same reservation.
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+ struct vm_region {
174
+ void* base = nullptr;
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+ std::size_t reserved = 0;
176
+ std::size_t committed = 0;
177
+ };
178
+
179
+ inline std::size_t reservation_size_for(std::size_t bytes) noexcept
180
+ {
181
+ constexpr std::size_t min_reservation = std::size_t{1} << 26; // 64 MiB
182
+ constexpr std::size_t growth_factor = 16;
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+ std::size_t reserved = round_up_to_page(bytes) * growth_factor;
184
+ if (reserved < min_reservation)
185
+ reserved = min_reservation;
186
+ return reserved;
187
+ }
188
+
189
+ inline vm_region vm_create(std::size_t bytes)
190
+ {
191
+ vm_region r;
192
+ r.committed = round_up_to_page(bytes);
193
+ r.reserved = reservation_size_for(bytes);
194
+
195
+ r.base = ::VirtualAlloc(nullptr, r.reserved, MEM_RESERVE, PAGE_NOACCESS);
196
+ if (!r.base)
197
+ throw std::bad_alloc();
198
+
199
+ if (r.committed > 0 &&
200
+ !::VirtualAlloc(r.base, r.committed, MEM_COMMIT, PAGE_READWRITE)) {
201
+ ::VirtualFree(r.base, 0, MEM_RELEASE);
202
+ throw std::bad_alloc();
203
+ }
204
+ return r;
205
+ }
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+
207
+ inline void vm_destroy(vm_region& r) noexcept
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+ {
209
+ if (r.base)
210
+ ::VirtualFree(r.base, 0, MEM_RELEASE);
211
+ r = vm_region{};
212
+ }
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+
214
+ inline void vm_resize(vm_region& r, std::size_t new_bytes)
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+ {
216
+ const std::size_t new_committed = round_up_to_page(new_bytes);
217
+ if (new_committed == r.committed)
218
+ return;
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+
220
+ if (new_committed > r.reserved) {
221
+ // Outgrew the initial reservation (rare): there is no way to extend
222
+ // a VirtualAlloc reservation in place, so relocate -- same as a real
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+ // mremap() that cannot grow in place and has to move.
224
+ vm_region moved = vm_create(new_bytes);
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+ std::memcpy(moved.base, r.base, r.committed);
226
+ vm_destroy(r);
227
+ r = moved;
228
+ return;
229
+ }
230
+
231
+ if (new_committed > r.committed) {
232
+ if (!::VirtualAlloc(static_cast<char*>(r.base) + r.committed,
233
+ new_committed - r.committed, MEM_COMMIT, PAGE_READWRITE))
234
+ throw std::bad_alloc();
235
+ } else {
236
+ ::VirtualFree(static_cast<char*>(r.base) + new_committed,
237
+ r.committed - new_committed, MEM_DECOMMIT);
238
+ }
239
+ r.committed = new_committed;
240
+ }
241
+
242
+ #else // ISOSPEC_WE_ARE_ON_UNIX_YAY
243
+
244
+ struct vm_region {
245
+ void* base = nullptr;
246
+ std::size_t size = 0;
247
+ };
248
+
249
+ inline vm_region vm_create(std::size_t bytes)
250
+ {
251
+ vm_region r;
252
+ r.size = round_up_to_page(bytes);
253
+ r.base = ::mmap(nullptr, r.size, PROT_READ | PROT_WRITE,
254
+ MAP_PRIVATE | MAP_ANONYMOUS, -1, 0);
255
+ if (r.base == MAP_FAILED)
256
+ throw std::bad_alloc();
257
+ return r;
258
+ }
259
+
260
+ inline void vm_destroy(vm_region& r) noexcept
261
+ {
262
+ if (r.base)
263
+ ::munmap(r.base, r.size);
264
+ r = vm_region{};
265
+ }
266
+
267
+ #if defined(__APPLE__) && defined(__MACH__)
268
+
269
+ inline void vm_resize(vm_region& r, std::size_t new_bytes)
270
+ {
271
+ const std::size_t new_size = round_up_to_page(new_bytes);
272
+ if (new_size == r.size)
273
+ return;
274
+
275
+ if (new_size < r.size) {
276
+ // Shrink in place: base address is untouched, just drop the tail.
277
+ ::munmap(static_cast<char*>(r.base) + new_size, r.size - new_size);
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+ r.size = new_size;
279
+ return;
280
+ }
281
+
282
+ // Grow: Darwin has no mremap(). Allocate a fresh region and use
283
+ // mach_vm_remap to re-wire the old pages (not copy them) into its head,
284
+ // then release the old mapping.
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+ mach_vm_address_t new_addr = 0;
286
+ if (mach_vm_allocate(mach_task_self(), &new_addr, new_size, VM_FLAGS_ANYWHERE) != KERN_SUCCESS)
287
+ throw std::bad_alloc();
288
+
289
+ mach_vm_address_t target = new_addr;
290
+ vm_prot_t cur_prot, max_prot;
291
+ const kern_return_t kr = mach_vm_remap(
292
+ mach_task_self(), &target, r.size, 0, VM_FLAGS_OVERWRITE,
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+ mach_task_self(), reinterpret_cast<mach_vm_address_t>(r.base),
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+ FALSE /* share the same physical pages, don't copy */,
295
+ &cur_prot, &max_prot, VM_INHERIT_COPY);
296
+ if (kr != KERN_SUCCESS) {
297
+ mach_vm_deallocate(mach_task_self(), new_addr, new_size);
298
+ throw std::bad_alloc();
299
+ }
300
+
301
+ ::munmap(r.base, r.size);
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+ r.base = reinterpret_cast<void*>(new_addr);
303
+ r.size = new_size;
304
+ }
305
+
306
+ #else // Linux / other real-mman UNIX with an actual mremap()
307
+
308
+ inline void vm_resize(vm_region& r, std::size_t new_bytes)
309
+ {
310
+ const std::size_t new_size = round_up_to_page(new_bytes);
311
+ if (new_size == r.size)
312
+ return;
313
+
314
+ void* p = ::mremap(r.base, r.size, new_size, MREMAP_MAYMOVE);
315
+ if (p == MAP_FAILED)
316
+ throw std::bad_alloc();
317
+ r.base = p;
318
+ r.size = new_size;
319
+ }
320
+
321
+ #endif // __APPLE__
322
+ #endif // ISOSPEC_WE_ARE_ON_WINDOWS
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+
324
+ } // namespace aligned_ptr_detail
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+ #endif // ISOSPEC_ALIGNED_PTR_HAVE_VM_REALLOC
326
+
327
+
328
+ template<class T, std::size_t Alignment>
329
+ class aligned_unique_ptr {
330
+ static_assert((Alignment & (Alignment - 1)) == 0); // meaning: Alignment is a power of two
331
+ static_assert(Alignment >= alignof(T));
332
+ static_assert(Alignment <= 4096, "Alignment must not exceed the smallest page size assumed across supported platforms");
333
+ // Storage is acquired/released as raw bytes (aligned_alloc/free, or
334
+ // mmap/VirtualAlloc) with no constructor/destructor ever run over it --
335
+ // matches how this class has always behaved (it never invoked T's ctor
336
+ // even before this rework, since it called the operator new[] *function*
337
+ // directly rather than a `new T[n]` *expression*), just made explicit.
338
+ static_assert(std::is_trivial_v<T>, "aligned_unique_ptr never runs T's constructor/destructor; T must be trivial");
339
+
340
+ T* ptr_ = nullptr;
341
+ std::size_t capacity_bytes_ = 0;
342
+
343
+ #if ISOSPEC_ALIGNED_PTR_HAVE_VM_REALLOC
344
+ bool is_mapped_ = false;
345
+ aligned_ptr_detail::vm_region region_{};
346
+ #endif
347
+
348
+ // C11 aligned_alloc requires size to be a multiple of alignment.
349
+ static std::size_t round_up_to_alignment(std::size_t bytes) noexcept
350
+ {
351
+ return (bytes + Alignment - 1) / Alignment * Alignment;
352
+ }
353
+
354
+ // n * sizeof(T), then rounding up to Alignment, must not silently wrap:
355
+ // that would turn a request for a huge buffer into a tiny allocation,
356
+ // which the caller (having asked for n elements) would then write past.
357
+ static std::size_t bytes_for(std::size_t n)
358
+ {
359
+ constexpr std::size_t max_size = (std::numeric_limits<std::size_t>::max)();
360
+ if (n > max_size / sizeof(T))
361
+ throw std::bad_alloc();
362
+ const std::size_t bytes = n * sizeof(T);
363
+ if (bytes > max_size - (Alignment - 1))
364
+ throw std::bad_alloc();
365
+ return bytes;
366
+ }
367
+
368
+ static T* allocate_small(std::size_t n)
369
+ {
370
+ if (n == 0)
371
+ return nullptr;
372
+ const std::size_t bytes = bytes_for(n);
373
+ #if ISOSPEC_ALIGNED_PTR_SMALL_BACKEND_FREE_COMPATIBLE
374
+ void* p = std::aligned_alloc(Alignment, round_up_to_alignment(bytes));
375
+ #else
376
+ void* p = ::_aligned_malloc(bytes, Alignment);
377
+ #endif
378
+ if (!p)
379
+ throw std::bad_alloc();
380
+ return static_cast<T*>(p);
381
+ }
382
+
383
+ static void free_small(void* p) noexcept
384
+ {
385
+ #if ISOSPEC_ALIGNED_PTR_SMALL_BACKEND_FREE_COMPATIBLE
386
+ std::free(p);
387
+ #else
388
+ ::_aligned_free(p);
389
+ #endif
390
+ }
391
+
392
+ void free_current() noexcept
393
+ {
394
+ if (!ptr_)
395
+ return;
396
+ #if ISOSPEC_ALIGNED_PTR_HAVE_VM_REALLOC
397
+ if (is_mapped_) {
398
+ aligned_ptr_detail::vm_destroy(region_);
399
+ return;
400
+ }
401
+ #endif
402
+ free_small(ptr_);
403
+ }
404
+
405
+ static void deleter_free(void* p, std::size_t) noexcept
406
+ {
407
+ std::free(p);
408
+ }
409
+
410
+ static void deleter_small(void* p, std::size_t) noexcept
411
+ {
412
+ free_small(p);
413
+ }
414
+
415
+ public:
416
+ static constexpr std::size_t alignment = Alignment;
417
+
418
+ // Returned by release_with_deleter(): the raw pointer plus everything
419
+ // needed to free it correctly, whichever backend actually produced it.
420
+ // Unlike release(), never copies -- deleter(ptr, size) must be called
421
+ // exactly once to avoid leaking it.
422
+ struct release_result {
423
+ T* ptr;
424
+ std::size_t size;
425
+ void (*deleter)(void*, std::size_t) noexcept;
426
+ };
427
+
428
+ T* allocate(std::size_t n)
429
+ {
430
+ return allocate_small(n);
431
+ }
432
+
433
+ explicit aligned_unique_ptr(std::size_t n)
434
+ : ptr_(allocate(n))
435
+ , capacity_bytes_(n * sizeof(T))
436
+ {}
437
+
438
+ aligned_unique_ptr() noexcept
439
+ : ptr_(nullptr)
440
+ {}
441
+
442
+ ~aligned_unique_ptr()
443
+ {
444
+ free_current();
445
+ }
446
+
447
+ aligned_unique_ptr(const aligned_unique_ptr&) = delete;
448
+ aligned_unique_ptr& operator=(const aligned_unique_ptr&) = delete;
449
+
450
+ aligned_unique_ptr(aligned_unique_ptr&& other) noexcept
451
+ : ptr_(std::exchange(other.ptr_, nullptr))
452
+ , capacity_bytes_(std::exchange(other.capacity_bytes_, 0))
453
+ #if ISOSPEC_ALIGNED_PTR_HAVE_VM_REALLOC
454
+ , is_mapped_(std::exchange(other.is_mapped_, false))
455
+ , region_(std::exchange(other.region_, aligned_ptr_detail::vm_region{}))
456
+ #endif
457
+ {}
458
+
459
+ aligned_unique_ptr& operator=(aligned_unique_ptr&& other) noexcept
460
+ {
461
+ if (this != &other) {
462
+ free_current();
463
+ ptr_ = std::exchange(other.ptr_, nullptr);
464
+ capacity_bytes_ = std::exchange(other.capacity_bytes_, 0);
465
+ #if ISOSPEC_ALIGNED_PTR_HAVE_VM_REALLOC
466
+ is_mapped_ = std::exchange(other.is_mapped_, false);
467
+ region_ = std::exchange(other.region_, aligned_ptr_detail::vm_region{});
468
+ #endif
469
+ }
470
+ return *this;
471
+ }
472
+
473
+ T* get() noexcept
474
+ {
475
+ return std::assume_aligned<Alignment>(ptr_);
476
+ }
477
+
478
+ const T* get() const noexcept
479
+ {
480
+ return std::assume_aligned<Alignment>(ptr_);
481
+ }
482
+
483
+ T& operator[](std::size_t i) noexcept
484
+ {
485
+ return get()[i];
486
+ }
487
+
488
+ const T& operator[](std::size_t i) const noexcept
489
+ {
490
+ return get()[i];
491
+ }
492
+
493
+ explicit operator bool() const noexcept
494
+ {
495
+ return ptr_ != nullptr;
496
+ }
497
+
498
+ // Allocate n elements, discarding whatever was held before and keeping none
499
+ // of its contents. Always uses the small backend -- see
500
+ // ISOSPEC_ALIGNED_PTR_VM_THRESHOLD for why a one-shot allocation of a known
501
+ // size does not want the VM one. (Not noexcept: allocation can throw.)
502
+ void reset(std::size_t n)
503
+ {
504
+ free_current();
505
+ #if ISOSPEC_ALIGNED_PTR_HAVE_VM_REALLOC
506
+ is_mapped_ = false;
507
+ region_ = aligned_ptr_detail::vm_region{};
508
+ #endif
509
+ if (n > 0) {
510
+ ptr_ = allocate_small(n);
511
+ capacity_bytes_ = n * sizeof(T);
512
+ } else {
513
+ ptr_ = nullptr;
514
+ capacity_bytes_ = 0;
515
+ }
516
+ }
517
+
518
+ // Grows or shrinks the buffer to hold n elements, preserving the first
519
+ // min(old capacity, new capacity) bytes. Below the page-size threshold
520
+ // this is the same aligned_alloc/copy/free pattern reset() uses; once a
521
+ // given instance has crossed that threshold it switches permanently to
522
+ // a VM-backed region that the OS resizes in place (see the backends
523
+ // above), so further growth/shrinkage stops needing to copy at all.
524
+ void realloc(std::size_t n)
525
+ {
526
+ const std::size_t new_bytes = n == 0 ? 0 : bytes_for(n);
527
+
528
+ if (new_bytes == 0) {
529
+ free_current();
530
+ ptr_ = nullptr;
531
+ capacity_bytes_ = 0;
532
+ #if ISOSPEC_ALIGNED_PTR_HAVE_VM_REALLOC
533
+ is_mapped_ = false;
534
+ region_ = aligned_ptr_detail::vm_region{};
535
+ #endif
536
+ return;
537
+ }
538
+
539
+ #if ISOSPEC_ALIGNED_PTR_HAVE_VM_REALLOC
540
+ if (is_mapped_) {
541
+ aligned_ptr_detail::vm_resize(region_, new_bytes);
542
+ ptr_ = static_cast<T*>(region_.base);
543
+ capacity_bytes_ = new_bytes;
544
+ return;
545
+ }
546
+
547
+ if (new_bytes >= aligned_ptr_detail::vm_backend_threshold()) {
548
+ // Crossing the threshold: switch backend. This one transition
549
+ // still has to copy -- there is nothing yet to remap.
550
+ aligned_ptr_detail::vm_region r = aligned_ptr_detail::vm_create(new_bytes);
551
+ if (ptr_) {
552
+ std::memcpy(r.base, ptr_, std::min(capacity_bytes_, new_bytes));
553
+ free_small(ptr_);
554
+ }
555
+ region_ = r;
556
+ ptr_ = static_cast<T*>(region_.base);
557
+ capacity_bytes_ = new_bytes;
558
+ is_mapped_ = true;
559
+ return;
560
+ }
561
+ #endif
562
+
563
+ T* new_ptr = allocate_small(n);
564
+ if (ptr_) {
565
+ std::memcpy(new_ptr, ptr_, std::min(capacity_bytes_, new_bytes));
566
+ free_small(ptr_);
567
+ }
568
+ ptr_ = new_ptr;
569
+ capacity_bytes_ = new_bytes;
570
+ }
571
+
572
+ // Hands back ownership as a plain T* that the caller can free with a
573
+ // bare std::free() / C free(), regardless of which backend produced it.
574
+ // Whenever the current backend isn't already free()-compatible on its
575
+ // own -- a VM-backed region always needs this, and so does the small
576
+ // backend on MSVC (see ISOSPEC_ALIGNED_PTR_SMALL_BACKEND_FREE_COMPATIBLE
577
+ // above) -- this materialises a fresh plain-malloc()'d copy instead.
578
+ // That copy is the whole cost of calling this in those cases;
579
+ // release_with_deleter() below avoids it when the caller can accept a
580
+ // deleter instead of assuming free().
581
+ T* release()
582
+ {
583
+ if (!ptr_) {
584
+ capacity_bytes_ = 0;
585
+ return nullptr;
586
+ }
587
+
588
+ bool needs_materialize = !ISOSPEC_ALIGNED_PTR_SMALL_BACKEND_FREE_COMPATIBLE;
589
+ #if ISOSPEC_ALIGNED_PTR_HAVE_VM_REALLOC
590
+ needs_materialize = needs_materialize || is_mapped_;
591
+ #endif
592
+ if (needs_materialize) {
593
+ void* copy = std::malloc(capacity_bytes_);
594
+ if (!copy)
595
+ throw std::bad_alloc();
596
+ std::memcpy(copy, ptr_, capacity_bytes_);
597
+ free_current();
598
+ ptr_ = nullptr;
599
+ #if ISOSPEC_ALIGNED_PTR_HAVE_VM_REALLOC
600
+ is_mapped_ = false;
601
+ region_ = aligned_ptr_detail::vm_region{};
602
+ #endif
603
+ capacity_bytes_ = 0;
604
+ return static_cast<T*>(copy);
605
+ }
606
+
607
+ capacity_bytes_ = 0;
608
+ return std::assume_aligned<Alignment>(std::exchange(ptr_, nullptr));
609
+ }
610
+
611
+ // Fast counterpart to release(): never copies. Returns the raw pointer
612
+ // together with the (size, deleter) pair needed to free it correctly --
613
+ // the caller must invoke result.deleter(result.ptr, result.size) exactly
614
+ // once (or not at all, if it hands the triple further on).
615
+ release_result release_with_deleter() noexcept
616
+ {
617
+ T* p = std::exchange(ptr_, nullptr);
618
+ std::size_t bytes = capacity_bytes_;
619
+ capacity_bytes_ = 0;
620
+ #if ISOSPEC_ALIGNED_PTR_HAVE_VM_REALLOC
621
+ if (is_mapped_) {
622
+ is_mapped_ = false;
623
+ #if ISOSPEC_WE_ARE_ON_WINDOWS
624
+ const std::size_t region_bytes = region_.reserved;
625
+ #else
626
+ const std::size_t region_bytes = region_.size;
627
+ #endif
628
+ region_ = aligned_ptr_detail::vm_region{};
629
+ return release_result{p, region_bytes, &aligned_ptr_detail::vm_release_raw};
630
+ }
631
+ #endif
632
+ #if ISOSPEC_ALIGNED_PTR_SMALL_BACKEND_FREE_COMPATIBLE
633
+ return release_result{p, bytes, &deleter_free};
634
+ #else
635
+ return release_result{p, bytes, &deleter_small};
636
+ #endif
637
+ }
638
+ };
@@ -0,0 +1,69 @@
1
+ /*
2
+ * Copyright (C) 2015-2020 Mateusz Łącki and Michał Startek.
3
+ *
4
+ * This file is part of IsoSpec.
5
+ *
6
+ * IsoSpec is free software: you can redistribute it and/or modify
7
+ * it under the terms of the Simplified ("2-clause") BSD licence.
8
+ *
9
+ * IsoSpec is distributed in the hope that it will be useful,
10
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
11
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
12
+ *
13
+ * You should have received a copy of the Simplified BSD Licence
14
+ * along with IsoSpec. If not, see <https://opensource.org/licenses/BSD-2-Clause>.
15
+ */
16
+
17
+ #pragma once
18
+
19
+ #include <cstring>
20
+ #include "conf.h"
21
+ #include "pod_vector.h"
22
+
23
+ namespace IsoSpec
24
+ {
25
+
26
+ template <typename T> inline void copyConf(
27
+ const T* source, T* destination,
28
+ int dim
29
+ ){
30
+ memcpy(destination, source, dim*sizeof(T));
31
+ }
32
+
33
+ template <typename T> class Allocator
34
+ {
35
+ private:
36
+ T* currentTab;
37
+ int currentId;
38
+ const int dim, tabSize;
39
+ pod_vector<T*> prevTabs;
40
+
41
+ public:
42
+ explicit Allocator(const int dim, const int tabSize = 10000);
43
+ ~Allocator();
44
+
45
+ Allocator(const Allocator& other) = delete;
46
+ Allocator& operator=(const Allocator& other) = delete;
47
+
48
+ void shiftTables();
49
+
50
+ inline T* newConf()
51
+ {
52
+ currentId++;
53
+
54
+ if (currentId >= tabSize)
55
+ shiftTables();
56
+
57
+ return &(currentTab[ currentId * dim ]);
58
+ }
59
+
60
+ inline T* makeCopy(const T* conf)
61
+ {
62
+ T* currentPlace = newConf();
63
+ copyConf<T>( conf, currentPlace, dim );
64
+
65
+ return currentPlace;
66
+ }
67
+ };
68
+
69
+ } // namespace IsoSpec