feat: native ARM64 / Apple Silicon and macOS clang build support#2694
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BenjaminDEMAILLE wants to merge 2 commits into
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feat: native ARM64 / Apple Silicon and macOS clang build support#2694BenjaminDEMAILLE wants to merge 2 commits into
BenjaminDEMAILLE wants to merge 2 commits into
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…nMP + STARforMac Make the build work out-of-the-box on non-x86 and on macOS, instead of failing with 'unrecognized command-line option -mavx2' (issues alexdobin#2104, alexdobin#1754) or missing OpenMP/link flags on Apple Silicon (issues alexdobin#1901, alexdobin#2108). - Detect uname -s/-m. On x86_64/amd64 use -mavx2; on arm64/aarch64 use -march=armv8-a+simd so opal's SIMDe maps AVX2 intrinsics onto NEON. - macOS + Apple clang OpenMP: -Xpreprocessor -fopenmp with a Homebrew libomp include/lib path (brew --prefix libomp, with /opt/homebrew and /usr/local fallbacks) and -lomp at link time. - macOS link flags: no -static-libgcc / full -static (unsupported by Apple clang); link htslib as a static archive and libomp dynamically. Add STARforMac / STARlongForMac (dynamic) targets. - Portable build date for BSD/macOS date(1). Supersedes the stale, broken PR alexdobin#1863 (variable typo + inverted x86 logic). Verified: native arm64 build via 'make STARforMac CXX=clang++'. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…dobin#1833) The README stated x86-64 only and the macOS instructions required Homebrew gcc. STAR builds and runs on ARM64/AArch64 (incl. Apple Silicon) via SIMDe, and now has a native Apple clang target. - Hardware requirements: note ARM64/Apple Silicon support via SIMDe. - macOS: document 'make STARforMac CXX=clang++' with Homebrew libomp as the recommended native build (arm64 or x86_64), keeping the gcc path as an alternative. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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…ndian support (#7) * fix(macos): spawn readFilesCommand via posix_spawnp The POSIX path used vfork()+execlp()+exit(0) to run the generated readsCommand script. On macOS this fails ("Failed spawning readFilesCommand", upstream issue alexdobin#2663) because the script has no shebang and posix_spawn-style exec has no ENOEXEC->/bin/sh fallback; calling exit() in a vfork child is also undefined behavior. Replace with posix_spawnp invoking "<shell> <script>" explicitly, with proper error checking. POSIX-only branch; the Windows system()-based path is unchanged. Ported from upstream PR alexdobin#2693. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * feat: big-endian support with guarded little-endian fast path STAR read the genome, suffix array and packed arrays through native uint*/uint128* casts, assuming little-endian byte order, which caused "next index is smaller than previous" failures on big-endian hosts (s390x, ppc64). Add byteOrder.h with loadUintLE/storeUintLE helpers and route the four endian-sensitive sites (PackedArray::operator[]/writePacked, funCompareSuffixes, funCalcSAiFromSA) through them. The helpers are guarded by STAR_BIG_ENDIAN: little-endian builds keep the original single-instruction native load (zero performance/behavior change), and only known big-endian compiles take the portable byte-wise path. The existing MSVC byte-access path in funCalcSAiFromSA is reused for BE. The byte-wise implementation is exposed by name and unit-tested (test_byteOrder.cpp) so the BE algorithm is validated on the LE CI runner. Ported from the patch in upstream issue alexdobin#2690. Note: compile-validated only; CI has no big-endian runner. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * feat: referenceless CRAM output (--outSAMtype CRAM) Add CRAM as an output container. STAR produces its BAM via the proven output path, then transcodes it to referenceless CRAM at finalization (cramOutput.cpp, using bundled HTSlib with CRAM_OPT_NO_REF, so no external reference FASTA is required). On conversion failure the original BAM is kept and the run continues. - Parameters_runtimeSetup: accept "CRAM" as outSAMtype[0], reusing the BAM Unsorted/SortedByCoordinate logic; set outCRAMbool and CRAM names. - STAR.cpp: transcode Aligned.out.bam / Aligned.sortedByCoord.out.bam to .cram after wiggle output, removing the intermediate BAM. - Hot per-record output code is untouched; the transcriptome BAM stays BAM for RSEM/Salmon. CRAM is incompatible with --outStd. - WebUI: CRAM options in the outSAMtype dropdown, .cram artifacts and MIME type. - Registered cramOutput in CMake build. Implemented properly rather than porting the incomplete upstream draft PR alexdobin#2670 (which wrote a NULL header and rerouted the working BAM path). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * build: Makefile ARM64/macOS/libomp parity and cramOutput Port the platform-detection from upstream PR alexdobin#2694 to the Makefile (CI uses CMake, which already handles ARM64; this is for `make` users): - detect UNAME_S/UNAME_M; select -mavx2 on x86_64, -march=armv8-a+simd on ARM64/AArch64 - macOS + Apple clang OpenMP: -Xpreprocessor -fopenmp + libomp include, -lomp at link; add native STARforMac target (dynamic libomp) - portable BSD/macOS date fallback for the build timestamp - add cramOutput.o to OBJECTS Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> * docs: document CRAM output, ARM64/macOS, and big-endian support Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
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Summary
Make STAR build out-of-the-box on ARM64 / Apple Silicon and on macOS with Apple clang, instead of failing with
unrecognized command-line option -mavx2(#2104, #1754) or missing OpenMP / link flags (#1901, #2108). Addresses the long-standing "Plans for ARM Support?" request (#1833).Changes (
source/Makefile)uname -m: x86_64/amd64 use-mavx2; arm64/aarch64 use-march=armv8-a+simd, so opal's SIMDe maps AVX2 intrinsics onto NEON automatically (building on the already-merged SIMDe support, simple, but inelegant support for non-x86 using SIMDe #1163).-Xpreprocessor -fopenmpwith a Homebrewlibompinclude/lib path (brew --prefix libomp, with/opt/homebrewand/usr/localfallbacks) and-lompat link time.-static-libgcc/ full-static(unsupported by Apple clang); link htslib as a static archive and libomp dynamically. AddSTARforMac/STARlongForMactargets.date(1).README is updated to document ARM64/Apple Silicon support and the native
make STARforMac CXX=clang++build.This supersedes the stale, broken #1863 (variable typo
avxCXXFLAGS_SIMD+ inverted x86 logic).Verification
make STARforMac CXX=clang++produces an arm64-native binary on Apple Silicon; genome generation + alignment verified working.Closes #2104, closes #1754, closes #1901, closes #2108, closes #1833.
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