replace mutex with tryable spin lock

include/TryableSpinLock.hpp

@@ -0,0 +1,25 @@
+#ifndef __TRYABLE_SPIN_LOCK_HPP__
+#define __TRYABLE_SPIN_LOCK_HPP__
+
+#include <atomic>
+
+// Taken from http://stackoverflow.com/questions/26583433/c11-implementation-of-spinlock-using-atomic
+class TryableSpinLock {
+    std::atomic_flag locked = ATOMIC_FLAG_INIT ;
+public:
+    void lock() {
+        while (locked.test_and_set(std::memory_order_acquire)) { ; }
+    }
+
+    // from http://stackoverflow.com/questions/19742993/implementing-a-spinlock-in-boost-example-neededhttp://stackoverflow.com/questions/19742993/implementing-a-spinlock-in-boost-example-needed
+    // is this legit?
+    bool try_lock() {
+        return !locked.test_and_set(std::memory_order_acquire);
+    }
+
+    void unlock() {
+        locked.clear(std::memory_order_release);
+    }
+};
+
+#endif //__TRYABLE_SPIN_LOCK_HPP__

src/SalmonUtils.cpp

@@ -25,6 +25,7 @@
 #include "SalmonMath.hpp"
 #include "SalmonUtils.hpp"
 #include "UnpairedRead.hpp"
+#include "TryableSpinLock.hpp"
 
 #include "spdlog/fmt/ostr.h"
 #include "spdlog/fmt/fmt.h"
@@ -1799,7 +1800,8 @@ Eigen::VectorXd updateEffectiveLengths(SalmonOpts& sopt, ReadExpT& readExp,
   size_t stepSize = static_cast<size_t>(transcripts.size() * 0.1);
   size_t nextUpdate{0};
 
-  std::mutex updateMutex;
+  //std::mutex updateMutex;
+  TryableSpinLock tsl;
   /**
    * Compute the effective lengths of each transcript (in parallel)
    */
@@ -1922,7 +1924,7 @@ Eigen::VectorXd updateEffectiveLengths(SalmonOpts& sopt, ReadExpT& readExp,
             } // end sequence-specific factor calculation
 
             if (numProcessed > nextUpdate) {
-                if (updateMutex.try_lock()) {
+                if (tsl.try_lock()) {
                     if (numProcessed > nextUpdate) {
                         sopt.jointLog->info(
                                             "processed bias for {:3.1f}% of the transcripts",
@@ -1933,7 +1935,7 @@ Eigen::VectorXd updateEffectiveLengths(SalmonOpts& sopt, ReadExpT& readExp,
                             nextUpdate = numTranscripts - 1;
                         }
                     }
-                    updateMutex.unlock();
+                    tsl.unlock();
                 }
             }
             ++numProcessed;