rewrote parallelization of calcCI.cpp

[rsem.git] / Buffer.h

diff --git a/Buffer.h b/Buffer.h
index 1ce28bca18d4e21193965886cd92e0d64e5a927e..1c5a2d6f5415a901a9ec7ee335207a2644d2d6d6 100644 (file)
--- a/Buffer.h
+++ b/Buffer.h
@@ -3,48 +3,36 @@
 
 #include<cstdio>
 #include<fstream>
-#include<pthread.h>
-
-#include "my_assert.h"
 
 typedef unsigned long long bufsize_type;
 const int FLOATSIZE = sizeof(float);
 
 class Buffer {
 public:
-       Buffer(int nMB, int nSamples, int cvlen, const char* tmpF) {
+       Buffer(bufsize_type size, int sp, int nSamples, int cvlen, const char* tmpF) {
                cpos = 0;
-               size = bufsize_type(nMB) * 1024 * 1024 / FLOATSIZE / cvlen;
-               if (size > (bufsize_type)nSamples) size = nSamples;
-               general_assert(size > 0, "Memory allocated for credibility intervals is not enough!");
-               size *= cvlen;
-
+               this->size = size;
                buffer = new float[size];
                ftmpOut.open(tmpF, std::ios::binary);
-               pthread_mutex_init(&lock, NULL);
 
-               fr = to = 0;
+               fr = to = sp;
                this->nSamples = nSamples;
                this->cvlen = cvlen;
+
        }
 
        ~Buffer() {
                if (fr < to) flushToTempFile();
 
                delete[] buffer;
-               pthread_mutex_destroy(&lock);
                ftmpOut.close();
        }
 
-       void write(int n, float **vecs) {
-               pthread_assert(pthread_mutex_lock(&lock), "pthread_mutex_lock", "Error occurred while acquiring the lock!");
-               for (int i = 0; i < n; i++) {
-                       if (size - cpos < bufsize_type(cvlen)) flushToTempFile();
-                       memcpy(buffer + cpos, vecs[i], FLOATSIZE * cvlen);
-                       cpos += cvlen;
-                       ++to;
-               }
-               pthread_assert(pthread_mutex_unlock(&lock), "pthread_mutex_unlock", "Error occurred while releasing the lock!");
+       void write(float *vec) {
+               if (size - cpos < bufsize_type(cvlen)) flushToTempFile();
+               memcpy(buffer + cpos, vec, FLOATSIZE * cvlen);
+               cpos += cvlen;
+               ++to;
        }
 
 private:
@@ -52,7 +40,6 @@ private:
 
        float *buffer;
        std::ofstream ftmpOut;
-       pthread_mutex_t lock;
 
        int fr, to; // each flush, sample fr .. to - 1
        int nSamples, cvlen;
@@ -62,15 +49,15 @@ private:
                std::streampos gap2 = std::streampos(nSamples - to) * FLOATSIZE;
                float *p = NULL;
 
-               ftmpOut.seekp(0, std::ios_base::beg);
+               ftmpOut.seekp(0, std::ios::beg);
                for (int i = 0; i < cvlen; i++) {
                        p = buffer + i;
-                       ftmpOut.seekp(gap1, std::ios_base::cur);
+                       ftmpOut.seekp(gap1, std::ios::cur);
                        for (int j = fr; j < to; j++) {
                                ftmpOut.write((char*)p, FLOATSIZE);
                                p += cvlen;
                        }
-                       ftmpOut.seekp(gap2, std::ios_base::cur);
+                       ftmpOut.seekp(gap2, std::ios::cur);
                }
 
                cpos = 0;