Improve locking

core/src/main/scala/eu/nomad_lab/h5/FileH5.scala

@@ -239,8 +239,10 @@ class FileH5(
 
   override def release0(): Unit = {
     logger.debug(s"closing file $path")
-    if (h5FileGroup >= 0)
+    if (h5FileGroup >= 0) {
+      H5Lib.fileFlush(h5FileGroup)
       H5Lib.fileClose(h5FileGroup)
+    }
     if (releaseLock)
       FileH5.release(path, writeable)
   }

core/src/main/scala/eu/nomad_lab/parsers/CalculationBackend.scala

@@ -130,19 +130,18 @@ class CalculationBackend(
         try {
           parsingResult match {
             case ParseResult.ParseSuccess | ParseResult.ParseWithWarnings =>
-              if (Files.exists(targetPath)) {
-                val targetF = h5.FileH5.open(targetPath, write = true, acquired = true)
-                val sourceF = h5.FileH5.open(tmpPath)
-                try {
-                  lab.h5.Merge.fileInFile(sourceF, targetF)
-                } finally {
-                  targetF.release()
-                }
-                sourceF.release()
-              } else {
-                Files.move(tmpPath, targetPath, StandardCopyOption.ATOMIC_MOVE)
-                Files.copy(targetPath, tmpPath, StandardCopyOption.COPY_ATTRIBUTES)
+              val targetF = if (!Files.exists(targetPath))
+                h5.FileH5.create(targetPath, acquired = true)
+              else
+                h5.FileH5.open(targetPath, write = true, acquired = true)
+              val sourceF = h5.FileH5.open(tmpPath)
+              try {
+                lab.h5.Merge.fileInFile(sourceF, targetF)
+              } finally {
+                targetF.release()
+                Thread.sleep(1000)
               }
+              sourceF.release()
             case ParseResult.ParseFailure =>
               Files.delete(tmpPath) // should be logged in the hdf5
             case ParseResult.ParseSkipped =>

hdf5/hdf5-placeholder/src/main/scala/eu/nomad_lab/H5Lib.scala

@@ -57,6 +57,10 @@ object H5Lib extends StrictLogging {
     throw new HdfException(errorMsg)
   }
 
+  def fileFlush(fileId: Long): Unit = {
+    throw new HdfException(errorMsg)
+  }
+
   def fileClose(fileId: Long): Unit = {
     throw new HdfException(errorMsg)
   }

hdf5/hdf5-support/src/main/scala/eu/nomad_lab/H5Lib.scala

@@ -76,6 +76,12 @@ object H5Lib extends StrictLogging {
     H5.H5Fopen(filePath, flags, HDF5Constants.H5P_DEFAULT)
   }
 
+  def fileFlush(fileId: Long): Unit = {
+    val err = H5.H5Fflush(fileId, HDF5Constants.H5F_SCOPE_GLOBAL)
+    if (err < 0)
+      logger.warn(s"Error $err while closing file with id $fileId")
+  }
+
   def fileClose(fileId: Long): Unit = {
     val err = H5.H5Fclose(fileId)
     if (err < 0)