Fix posix_madvise on FreeBSD returning error if size=0 (See #460)

milot-mirdita · milot-mirdita · commit 15ace29a276b · 2021-06-25T17:51:12.000+02:00
diff --git a/src/commons/DBReader.cpp b/src/commons/DBReader.cpp
@@ -1000,7 +1000,7 @@ void DBReader<T>::setSequentialAdvice() {
 #ifdef HAVE_POSIX_MADVISE
     for(size_t i = 0; i < dataFileCnt; i++){
         size_t dataSize = dataSizeOffset[i+1] - dataSizeOffset[i];
-        if (posix_madvise (dataFiles[i], dataSize, POSIX_MADV_SEQUENTIAL) != 0){
+        if (dataSize > 0 && posix_madvise (dataFiles[i], dataSize, POSIX_MADV_SEQUENTIAL) != 0){
             Debug(Debug::ERROR) << "posix_madvise returned an error " << dataFileName << "\n";
         }
     }
diff --git a/src/commons/Util.cpp b/src/commons/Util.cpp
@@ -389,7 +389,7 @@ uint64_t Util::getL2CacheSize() {
 
 char Util::touchMemory(const char *memory, size_t size) {
 #ifdef HAVE_POSIX_MADVISE
-    if (posix_madvise ((void*)memory, size, POSIX_MADV_WILLNEED) != 0){
+    if (size > 0 && posix_madvise ((void*)memory, size, POSIX_MADV_WILLNEED) != 0){
         Debug(Debug::ERROR) << "posix_madvise returned an error (touchMemory)\n";
     }
 #endif
diff --git a/src/linclust/KmerIndex.h b/src/linclust/KmerIndex.h
@@ -183,7 +183,7 @@ class KmerIndex{
         this->indexGridSize = MathUtil::ceilIntDivision( MathUtil::ipow<size_t>(alphabetSize, kmerSize), gridResolution );
         this->entryOffsets = (size_t *) entriesOffetData;
 #if HAVE_POSIX_MADVISE
-        if (posix_madvise (entriesData, entryCount* sizeof(KmerEntryRelative), POSIX_MADV_SEQUENTIAL) != 0){
+        if (entryCount > 0 && posix_madvise (entriesData, entryCount* sizeof(KmerEntryRelative), POSIX_MADV_SEQUENTIAL) != 0){
             Debug(Debug::ERROR) << "KmerIndex posix_madvise returned an error\n";
         }
 #endif
diff --git a/src/prefiltering/Prefiltering.cpp b/src/prefiltering/Prefiltering.cpp
@@ -406,7 +406,7 @@ void Prefiltering::mergeTargetSplits(const std::string &outDB, const std::string
         files[i] = FileUtil::openFileOrDie(fileNames[i].first.c_str(), "r", true);
         dataFile[i] = static_cast<char*>(FileUtil::mmapFile(files[i], &dataFileSize[i]));
 #ifdef HAVE_POSIX_MADVISE
-        if (posix_madvise (dataFile[i], dataFileSize[i], POSIX_MADV_SEQUENTIAL) != 0){
+        if (dataFileSize[i] > 0 && posix_madvise (dataFile[i], dataFileSize[i], POSIX_MADV_SEQUENTIAL) != 0){
             Debug(Debug::ERROR) << "posix_madvise returned an error " << fileNames[i].first << "\n";
         }
 #endif

Original file line number	Diff line number	Diff line change
`@@ -1000,7 +1000,7 @@ void DBReader<T>::setSequentialAdvice() {`
`1000`	`1000`	`#ifdef HAVE_POSIX_MADVISE`
`1001`	`1001`	`for(size_t i = 0; i < dataFileCnt; i++){`
`1002`	`1002`	`size_t dataSize = dataSizeOffset[i+1] - dataSizeOffset[i];`
`1003`		`- if (posix_madvise (dataFiles[i], dataSize, POSIX_MADV_SEQUENTIAL) != 0){`
	`1003`	`+ if (dataSize > 0 && posix_madvise (dataFiles[i], dataSize, POSIX_MADV_SEQUENTIAL) != 0){`
`1004`	`1004`	`Debug(Debug::ERROR) << "posix_madvise returned an error " << dataFileName << "\n";`
`1005`	`1005`	`}`
`1006`	`1006`	`}`
Original file line number	Diff line number	Diff line change
`@@ -389,7 +389,7 @@ uint64_t Util::getL2CacheSize() {`
`389`	`389`
`390`	`390`	`char Util::touchMemory(const char *memory, size_t size) {`
`391`	`391`	`#ifdef HAVE_POSIX_MADVISE`
`392`		`- if (posix_madvise ((void*)memory, size, POSIX_MADV_WILLNEED) != 0){`
	`392`	`+ if (size > 0 && posix_madvise ((void*)memory, size, POSIX_MADV_WILLNEED) != 0){`
`393`	`393`	`Debug(Debug::ERROR) << "posix_madvise returned an error (touchMemory)\n";`
`394`	`394`	`}`
`395`	`395`	`#endif`
Original file line number	Diff line number	Diff line change
`@@ -183,7 +183,7 @@ class KmerIndex{`
`183`	`183`	`this->indexGridSize = MathUtil::ceilIntDivision( MathUtil::ipow<size_t>(alphabetSize, kmerSize), gridResolution );`
`184`	`184`	`this->entryOffsets = (size_t *) entriesOffetData;`
`185`	`185`	`#if HAVE_POSIX_MADVISE`
`186`		`- if (posix_madvise (entriesData, entryCount* sizeof(KmerEntryRelative), POSIX_MADV_SEQUENTIAL) != 0){`
	`186`	`+ if (entryCount > 0 && posix_madvise (entriesData, entryCount* sizeof(KmerEntryRelative), POSIX_MADV_SEQUENTIAL) != 0){`
`187`	`187`	`Debug(Debug::ERROR) << "KmerIndex posix_madvise returned an error\n";`
`188`	`188`	`}`
`189`	`189`	`#endif`
Original file line number	Diff line number	Diff line change
`@@ -406,7 +406,7 @@ void Prefiltering::mergeTargetSplits(const std::string &outDB, const std::string`
`406`	`406`	`files[i] = FileUtil::openFileOrDie(fileNames[i].first.c_str(), "r", true);`
`407`	`407`	`dataFile[i] = static_cast<char*>(FileUtil::mmapFile(files[i], &dataFileSize[i]));`
`408`	`408`	`#ifdef HAVE_POSIX_MADVISE`
`409`		`- if (posix_madvise (dataFile[i], dataFileSize[i], POSIX_MADV_SEQUENTIAL) != 0){`
	`409`	`+ if (dataFileSize[i] > 0 && posix_madvise (dataFile[i], dataFileSize[i], POSIX_MADV_SEQUENTIAL) != 0){`
`410`	`410`	`Debug(Debug::ERROR) << "posix_madvise returned an error " << fileNames[i].first << "\n";`
`411`	`411`	`}`
`412`	`412`	`#endif`