Merge branch 'bug_fixes'

BenLangmead · Sep 14, 2021 · 73821b4 · 73821b4
2 parents da7b440 + 5a4d538
commit 73821b4
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diff --git a/.github/workflows/random_tests.yml b/.github/workflows/random_tests.yml
@@ -0,0 +1,53 @@
+name: Run bowtie random tests for all commits to master on Ubuntu and MacOS
+on:
+  push:
+    branches:
+      - 'master'
+    paths:
+      - '**.c'
+      - '**.h'
+      - '**.cpp'
+      - 'bowtie'
+      - 'bowtie-build'
+      - 'bowtie-inspect'
+      - 'Makefile'
+      - 'scripts/test/**'
+  pull_request:
+    branches:
+      - 'master'
+    paths:
+      - '**.c'
+      - '**.h'
+      - '**.cpp'
+      - 'bowtie'
+      - 'bowtie-build'
+      - 'bowtie-inspect'
+      - 'Makefile'
+      - 'scripts/test/**'
+jobs:
+  setup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v2
+      - name: Install zlib development files
+        run: |
+          sudo apt-get update
+          sudo apt-get install zlib1g-dev
+  linux:
+    runs-on: ubuntu-latest
+    needs: setup
+    steps:
+      - uses: actions/checkout@v2
+      - name: Run random tests
+        run: |
+          make allall
+          make random-test
+  macos:
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Run random tests
+        run: |
+          make allall
+          make random-test
diff --git a/.github/workflows/simple_tests.yml b/.github/workflows/simple_tests.yml
@@ -0,0 +1,54 @@
+name: Run bowtie simple tests on Ubuntu and MacOS
+on:
+  push:
+    branches:
+      - 'bug_fixes'
+      - 'master'
+    paths:
+      - '**.c'
+      - '**.h'
+      - '**.cpp'
+      - 'bowtie'
+      - 'bowtie-build'
+      - 'bowtie-inspect'
+      - 'Makefile'
+      - 'scripts/test/**'
+  pull_request:
+    branches:
+      - 'master'
+    paths:
+      - '**.c'
+      - '**.h'
+      - '**.cpp'
+      - 'bowtie'
+      - 'bowtie-build'
+      - 'bowtie-inspect'
+      - 'Makefile'
+      - 'scripts/test/**'
+jobs:
+  setup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v2
+      - name: Install zlib development files
+        run: |
+          sudo apt-get update
+          sudo apt-get install zlib1g-dev
+  linux:
+    runs-on: ubuntu-latest
+    needs: setup
+    steps:
+      - uses: actions/checkout@v2
+      - name: Run simple tests
+        run: |
+          make allall
+          make simple-test
+  macos:
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Run simple tests
+        run: |
+          make allall
+          make simple-test
diff --git a/.travis.yml b/.travis.yml
@@ -7,46 +7,6 @@ branches:
     - bug_fixes
 matrix:
   include:
-    # Linux (gcc4.9)
-    - os: linux
-      language: python
-      python: "3.4"
-      dist: xenial
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-4.9
-            - zlib1g-dev
-      env:
-        - CC=gcc-4.9
-        - CXX=g++-4.9
-    # Linux (gcc8)
-    - os: linux
-      language: python
-      python: "3.8"
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-8
-            - zlib1g-dev
-      env:
-        - CC=gcc-8
-        - CXX=g++-8
-        - CXXFLAGS="-fuse-ld=gold"
-    # MacOS
-    - os: osx
-      osx_image: xcode11.2
-      compiler: clang
-      env:
-        - CC=clang
-        - CXX=clang++
-        - NPROC="$(sysctl -n hw.activecpu)"
-      before_install:
-        - brew unlink python@2
     # ARM 64-bit
     - os: linux
       arch: arm64

diff --git a/Makefile b/Makefile
@@ -7,7 +7,7 @@ bindir = $(prefix)/bin
 
 ARCH = $(shell uname -m)
 INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) -I third_party
-LIBS = $(LDFLAGS) $(if $(RELEASE_BUILD),-L$(CURDIR)/.lib) -lz
+LIBS = $(LDFLAGS) $(if $(RELEASE_BUILD),-L$(CURDIR)/.lib) -lz -lpthread
 HEADERS = $(wildcard *.h)
 BOWTIE_MM = 1
 BOWTIE_SHARED_MEM = 1
@@ -65,25 +65,9 @@ SHMEM_DEF =
 ifeq (1,$(BOWTIE_SHARED_MEM))
     SHMEM_DEF = -DBOWTIE_SHARED_MEM
 endif
-PTHREAD_PKG =
-PTHREAD_LIB =
-PTHREAD_DEF =
 
 ifeq (1,$(MINGW))
-	PTHREAD_LIB = 
 	override EXTRA_FLAGS += -static-libgcc -static-libstdc++
-else
-    PTHREAD_LIB = -lpthread
-endif
-
-ifeq (1,$(NO_SPINLOCK))
-	override EXTRA_FLAGS += -DNO_SPINLOCK
-endif
-
-
-LIBS += $(PTHREAD_LIB)
-ifeq (1, $(WITH_TBBMALLOC))
-	LIBS += -ltbbmalloc
 endif
 
 POPCNT_CAPABILITY ?= 1
@@ -92,7 +76,6 @@ ifeq (aarch64,$(shell uname -m))
 endif
 ifeq (1, $(POPCNT_CAPABILITY))
     override EXTRA_FLAGS += -DPOPCNT_CAPABILITY
-    INC += -I third_party
 endif
 
 PREFETCH_LOCALITY = 2
@@ -113,15 +96,16 @@ ifeq (1,$(WITH_THREAD_PROFILING))
 endif
 
 OTHER_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \
-             edit.cpp ebwt.cpp
+             edit.cpp ebwt.cpp bt2_locks.cpp
 
-ifneq (1, $(NO_SPINLOCK))
-	OTHER_CPPS += bt2_locks.cpp
+ifeq (1,$(WITH_QUEUELOCK))
+	NO_SPINLOCK = 1
+	override EXTRA_FLAGS += -DWITH_QUEUELOCK
 endif
 
-ifeq (1,$(WITH_QUEUELOCK))
-	OTHER_CPPS += bt2_locks.cpp
-	override EXTRA_FLAGS += -DWITH_QUEUELOCK=1
+ifeq (1,$(NO_SPINLOCK))
+$(info $(NO_SPINLOCK))
+	override EXTRA_FLAGS += -DNO_SPINLOCK
 endif
 
 ifeq (1,$(WITH_FINE_TIMER))
@@ -242,8 +226,8 @@ DEFS=-fno-strict-aliasing \
      $(SHMEM_DEF)
 
 ALL_FLAGS = $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)
-DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(ALL_FLAGS)\""
-RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(ALL_FLAGS)\""
+DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)\""
+RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS) $(CFLAGS) $(CXXFLAGS)\""
 
 #
 # bowtie-build targets

diff --git a/NEWS b/NEWS
@@ -5,7 +5,7 @@ Bowtie NEWS
 
    Bowtie is now available for download.  0.9.0 is the first version to
 be released under the OSI Artistic License (see `LICENSE') and freely
-available to the public for download.  The current version is 1.3.0.
+available to the public for download.  The current version is 1.3.1.
 
 Reporting Issues
 ================
@@ -23,6 +23,18 @@ Keep up with our releases on the GitHub releases page:
 
 Version Release History
 =======================
+Version 1.3.1 - Sep 13, 2021
+
+    * Fixed an overflow issue in `bowtie-build` that would sometimes
+      yield corrupt "large" (64-bit) indexes; the resulting index
+      would sometimes cause `bowtie` to hang. Note: `bowtie2-build`
+      does not have this issue.
+    * Fixed an issue in `bowtie` causing XM:i SAM optional field to
+      sometimes be off by 1 when using the `-m/-M` flags.
+    * Fixed an issue that would sometimes cause deadlocks in `bowtie`
+      when running multithreaded.
+    * Fixed an issue causing build errors when compiling against
+      a pre-C++11 standard.
 
 Version 1.3.0 - Jul 22, 2020
 

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-1.3.0
+1.3.1
diff --git a/bt2_locks.cpp b/bt2_locks.cpp
@@ -1,32 +1,31 @@
-#include "bt2_locks.h"
-
 #if (__cplusplus >= 201103L)
 
-void mcs_lock::lock() {
+#include "bt2_locks.h"
+
+void mcs_lock::lock(mcs_node &node) {
 	node.next = nullptr;
-	node.unlocked = false;
 
-	mcs_node *pred = q.exchange(&node, std::memory_order_release);
+	mcs_node *pred = q.exchange(&node, std::memory_order_acq_rel);
 	if (pred) {
-		pred->next = &node;
+		node.unlocked = false;
+		pred->next.store(&node, std::memory_order_release);
 		spin_while_eq(node.unlocked, false);
 	}
 	node.unlocked.load(std::memory_order_acquire);
 }
 
-void mcs_lock::unlock() {
-	if (!node.next) {
+void mcs_lock::unlock(mcs_node &node) {
+	if (!node.next.load(std::memory_order_acquire)) {
 		mcs_node *node_ptr = &node;
 		if (q.compare_exchange_strong(node_ptr,
 					      (mcs_node *)nullptr,
 					      std::memory_order_release))
 			return;
 		spin_while_eq(node.next, (mcs_node *)nullptr);
 	}
-	node.next->unlocked.store(true, std::memory_order_release);
+	node.next.load(std::memory_order_acquire)->unlocked.store(true, std::memory_order_release);
 }
 
-thread_local mcs_lock::mcs_node mcs_lock::node;
 
 void spin_lock::lock() {
 	cpu_backoff backoff;
@@ -37,4 +36,5 @@ void spin_lock::lock() {
 void spin_lock::unlock() {
 	flag.clear(std::memory_order_release);
 }
+
 #endif
diff --git a/bt2_locks.h b/bt2_locks.h
@@ -48,27 +48,27 @@ class mcs_lock {
 public:
 	mcs_lock(): q(nullptr) {}
         struct mcs_node {
-		mcs_node *next;
+		std::atomic<mcs_node *> next;
 		std::atomic_bool unlocked;
         };
 
-	void lock();
-	void unlock();
-	typedef mcs_node* mcs_node_ptr;
+	void lock(mcs_node &node);
+	void unlock(mcs_node &node);
+	typedef std::atomic<mcs_node *> mcs_node_ptr;
 private:
-	void spin_while_eq(const volatile mcs_node_ptr& value, mcs_node *expected) {
+	void spin_while_eq(const volatile mcs_node_ptr& value, const volatile mcs_node *expected) {
 		cpu_backoff backoff;
-		while (value == expected)
+		while (value.load(std::memory_order_acquire) == expected)
 			backoff.pause();
 	}
 
-	void spin_while_eq(const volatile std::atomic_bool& value, bool expected) {
+	void spin_while_eq(const volatile std::atomic_bool& value, const volatile bool expected) {
 	 	cpu_backoff backoff;
 	 	while (value.load(std::memory_order_acquire) == expected)
 	 		backoff.pause();
 	}
         std::atomic<mcs_node *> q;
-        static thread_local mcs_node node;
 };
-#endif
+
+#endif // if (__cplusplus >= 201103L)
 #endif // __MCS_LOCK_H__
diff --git a/doc/website/manual.ssi b/doc/website/manual.ssi
@@ -1,5 +1,5 @@
 <h1>Table of Contents</h1>
-<p>Bowtie 1.3.0</p>
+<p>Bowtie 1.3.1</p>
 
 <nav id="TOC" role="doc-toc">
 <ul>

diff --git a/doc/website/recent_news.ssi b/doc/website/recent_news.ssi
@@ -1,3 +1,11 @@
+<h2>1.3.1 - 09/13/2021</h2>
+<ul>
+    <li>Fixed an overflow issue in <code>bowtie-build</code> that would sometimes yield corrupt "large" (64-bit) indexes; the resulting index would sometimes cause <code>bowtie</code> to hang. Note: <code>bowtie2-build</code> does not have this issue.</li>
+    <li>Fixed an issue in <code>bowtie</code> causing XM:i SAM optional field to sometimes be off by 1 when using the <code><a href="manual.shtml#bowtie-options-m">-m</a>/<a href="manual.shtml#bowtie-options-M">-M</a></code> flags.</li>
+    <li>Fixed an issue that would sometimes cause deadlocks in <code>bowtie</code> when running multithreaded.</li>
+    <li>Fixed an issue causing build errors when compiling against a pre-C++11 standard.</li>
+</ul>
+
 <h2>1.3.0 - 07/22/2020</h2>
 <ul>
     <li>Fixed an issue causing <code>bowtie</code> to report incorrect results when using a Bowtie 2 index.</li>

diff --git a/doc/website/rhsidebar.ssi b/doc/website/rhsidebar.ssi
@@ -18,10 +18,10 @@
 	</tr>
         <tr>
           <td>
-            <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.3.0">Bowtie 1.3.0</a>
+            <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.3.1">Bowtie 1.3.1</a>
           </td>
           <td align="right">
-            07/22/20
+            09/13/21
           </td>
         </tr>
         <tr>