New upstream version 2.00~a2-191128+dfsg (a4515579) · Commits · Debian Med / plink2

plink2.cc

+106 −88

File changed.

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plink2_base.h

+12 −6

Original line number	Diff line number	Diff line
		@@ -77,6 +77,12 @@
		// valid input types, NOT counting VecW*.


		#if (__GNUC__ < 4)
		// may eventually add MSVC support to gain access to MKL on Windows, but can't
		// justify doing that before all major features are implemented.
		# error "gcc 4.x+ or clang equivalent required."
		#endif

		// The -Wshorten-64-to-32 diagnostic forces the code to be cluttered with
		// meaningless uintptr_t -> uint32_t static casts (number known to be < 2^32,
		// just stored in a uintptr_t because there's no speed penalty and we generally
		@@ -91,7 +97,7 @@
		// 10000 * major + 100 * minor + patch
		// Exception to CONSTI32, since we want the preprocessor to have access
		// to this value. Named with all caps as a consequence.
		#define PLINK2_BASE_VERNUM 600
		#define PLINK2_BASE_VERNUM 601


		#define _FILE_OFFSET_BITS 64
		@@ -208,7 +214,7 @@ namespace plink2 {
		# define CSINLINE static inline
		# define CSINLINE2 static inline
		// _Static_assert() should work in gcc 4.6+
		# if (__GNUC__ <= 4) && (__GNUC_MINOR__ < 6)
		# if (__GNUC__ == 4) && (__GNUC_MINOR__ < 6)
		# if defined(__clang__) && defined(__has_feature) && defined(__has_extension)
		# if __has_feature(c_static_assert) \|\| __has_extension(c_static_assert)
		# define static_assert _Static_assert
		@@ -568,7 +574,7 @@ HEADER_INLINE uint32_t bsrw(unsigned long ulii) {
		}
		# ifndef __LP64__
		// needed to prevent GCC 6 build failure
		# if (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8)
		# if (__GNUC__ == 4) && (__GNUC_MINOR__ < 8)
		# if (__cplusplus < 201103L) && !defined(__APPLE__)
		# ifndef uintptr_t
		# define uintptr_t unsigned long
		@@ -607,7 +613,7 @@ HEADER_INLINE uint32_t bsrw(unsigned long ulii) {
		// without this, we get ridiculous warning spew...
		// not 100% sure this is the right cutoff, but this has been tested on 4.7
		// and 4.8 build machines, so it plausibly is.
		# if (__GNUC__ <= 4) && (__GNUC_MINOR__ < 8) && (__cplusplus < 201103L)
		# if (__GNUC__ == 4) && (__GNUC_MINOR__ < 8) && (__cplusplus < 201103L)
		# undef PRIuPTR
		# undef PRIdPTR
		# define PRIuPTR "lu"
		@@ -1810,7 +1816,7 @@ extern uintptr_t g_failed_alloc_attempt_size;
		// number is printed as well; see e.g.
		// https://stackoverflow.com/questions/15884793/how-to-get-the-name-or-file-and-line-of-caller-method

		#if (__GNUC__ <= 4) && (__GNUC_MINOR__ < 7) && !defined(__APPLE__)
		#if (__GNUC__ == 4) && (__GNUC_MINOR__ < 7) && !defined(__APPLE__)
		// putting this in the header file caused a bunch of gcc 4.4 strict-aliasing
		// warnings, while not doing so seems to inhibit some malloc-related compiler
		// optimizations, bleah
		@@ -2123,7 +2129,7 @@ HEADER_INLINE uint32_t VecIsAligned(const void* ptr) {

		HEADER_INLINE void VecAlignUp(void* pp) {
		uintptr_t addr = S_CAST(uintptr_t, pp);
		#if (__GNUC__ <= 4) && (__GNUC_MINOR__ < 7) && !defined(__APPLE__)
		#if (__GNUC__ == 4) && (__GNUC_MINOR__ < 7) && !defined(__APPLE__)
		// bleah, need to write this way to avoid gcc 4.4 strict-aliasing warning
		addr = RoundUpPow2(addr, kBytesPerVec);
		memcpy(pp, &addr, sizeof(intptr_t));

plink2_bgzf.cc

+1 −2

Original line number	Diff line number	Diff line
		@@ -562,8 +562,7 @@ THREAD_FUNC_DECL BgzfCompressorThread(void* raw_arg) {
		BgzfCompressCommWithW** cwws = bgzfp->cwws;
		uintptr_t* next_job_idxp = bgzfp->next_job_idxp;
		while (1) {
		// make this depend on gcc version?
		const uint32_t slot_idx = __sync_fetch_and_add(next_job_idxp, 1) & slot_mask;
		const uint32_t slot_idx = __atomic_fetch_add(next_job_idxp, 1, __ATOMIC_ACQ_REL) & slot_mask;
		BgzfCompressCommWithP* cwp = cwps[slot_idx];
		BgzfCompressCommWithW* cww = cwws[slot_idx];
		#ifdef _WIN32

plink2_bgzf.h

+4 −3

Original line number	Diff line number	Diff line
		@@ -178,12 +178,13 @@ void CleanupBgzfRawMtStream(BgzfRawMtDecompressStream* bgzfp);
		// threads), but that proved to be slightly slower than htslib's bgzf writer
		// in my testing; it didn't do a good enough job of managing the
		// split-between-production-and-compression core.
		// So I've switched to a more flexible thread pool using
		// __sync_fetch_and_add() to distribute compression jobs.
		// So I've switched to a more flexible thread pool using __atomic_fetch_add()
		// to distribute compression jobs.
		// - There's a dedicated writer thread which flushes the compression results.
		// I will look into adding direct support for this parallelization pattern to
		// plink2_thread; the benefit is small (~5%), but applies to a lot of
		// workloads.
		// workloads. It may also be worthwhile to implement some form of
		// work-stealing.
		//
		// I tried making this less granular (each job contains two blocks instead of
		// one) to see if there was still meaningful room for improvement re: reducing

plink2_cmdline.cc

+10 −5

Original line number	Diff line number	Diff line
		@@ -2456,8 +2456,7 @@ void DupflagHtableMakerMain(uint32_t tidx, uint32_t thread_ct, DupflagHtableMake
		for (uint32_t hashval = Hashceil(sptr, slen, id_htable_size); ; ) {
		uint32_t old_htable_entry = id_htable[hashval];
		if (old_htable_entry == UINT32_MAX) {
		old_htable_entry = __sync_val_compare_and_swap(&(id_htable[hashval]), UINT32_MAX, item_uidx);
		if (old_htable_entry == UINT32_MAX) {
		if (ATOMIC_COMPARE_EXCHANGE_N_U32(&(id_htable[hashval]), &old_htable_entry, item_uidx, 0, __ATOMIC_ACQ_REL, __ATOMIC_ACQUIRE)) {
		break;
		}
		}
		@@ -2505,10 +2504,16 @@ PglErr MakeDupflagHtable(const uintptr_t* subset_mask, const char* const* item_i
		DupflagHtableMaker ctx;
		{
		uint32_t thread_ct = item_ct / 65536;
		if (!thread_ct) {
		thread_ct = 1;
		} else {
		if (thread_ct > max_thread_ct) {
		thread_ct = max_thread_ct;
		} else if (!thread_ct) {
		thread_ct = 1;
		}
		// bugfix (26 Nov 2019): forgot to force this
		if (thread_ct > kMaxDupflagThreads) {
		thread_ct = kMaxDupflagThreads;
		}
		}
		if (unlikely(SetThreadCt0(thread_ct - 1, &tg))) {
		goto MakeDupflagHtable_ret_NOMEM;