Merge pull request #1629 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:feature/json_vol to feature/json_vol

* commit '799a732650735b8ad05a0398781d2a26ec47b288': (185 commits)
  Updated the VOL struct. The json_vol test fails, though, because the plugin can't be found. Will diagnose later.
  Correct examples for packaging
  HDFFV-10738 Wrong INTENT for H5LTread_dataset_double_f
  Changes that show the right way to iterate over enums.
  Changes that show the right way to iterate over enums.
  Test improvement Description     Moved the new tests to a more appropriate test function. Platforms tested:     Linux/64 (jelly)
  Used the H5_INC_ENUM macro to squash enum value increment warnings.
  Fixed HDFFV-10210 and HDFFV-10587 Description:     - Added parameter validation (HDFFV-10210)     - Added detection of division by zero (HDFFV-10587 - CVE-2018-17438)     - Fixed typos in various tests Platforms tested:     Linux/64 (jelly)     Linux/64 (platypus)     Darwin (osx1011test)
  Fix CMake error in name
  Commented out memcpy overlap check while we investigate parallel filters issues.
  Yanked check for memcpy n > 0
  - Added H5MMprivate.h #includes where needed - Added casts to quiet H5MM_memcpy warnings - Removed char * casts from HDmemcpy
  Added an H5MM_memcpy call that checks for buffer overlap.
  Added the HDopen work-around on windows to pio_engine.c
  Adds _wopen support on Windows so that files with UTF-8 names can be opened.
  CMake: fix pthread linking to only be private
  Add API routines to retrieve, restore, reset, and free library state.
  Added a note of bug fix for HDFFV-10705.
  Fixed the MANIFEST
  Fix issue with direct chunk write not updating the "last chunk" index cache.  Fix issues involving datasets being "no allocated" when they contain cached raw data.
  ...

1 files changed, 25 insertions, 7 deletions

diff --git a/src/H5FDsec2.c b/src/H5FDsec2.c
index c507387..0054a86 100644
--- a/src/H5FDsec2.c
+++ b/src/H5FDsec2.c
@@ -682,11 +682,13 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS
     if(REGION_OVERFLOW(addr, size))
         HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow, addr = %llu", (unsigned long long)addr)
 
-    /* Seek to the correct location */
+#ifndef H5_HAVE_PREADWRITE
+    /* Seek to the correct location (if we don't have pread) */
     if(addr != file->pos || OP_READ != file->op) {
         if(HDlseek(file->fd, (HDoff_t)addr, SEEK_SET) < 0)
             HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position")
     } /* end if */
+#endif /* H5_HAVE_PREADWRITE */
 
     /* Read data, being careful of interrupted system calls, partial results,
      * and the end of the file.
@@ -694,7 +696,8 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS
     while(size > 0) {
 
         h5_posix_io_t       bytes_in        = 0;    /* # of bytes to read       */
-        h5_posix_io_ret_t   bytes_read      = -1;   /* # of bytes actually read */ 
+        h5_posix_io_ret_t   bytes_read      = -1;   /* # of bytes actually read */
+        HDoff_t             offset          = (HDoff_t)addr;
 
         /* Trying to read more bytes than the return type can handle is
          * undefined behavior in POSIX.
@@ -705,15 +708,21 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNUS
             bytes_in = (h5_posix_io_t)size;
 
         do {
+#ifdef H5_HAVE_PREADWRITE
+            bytes_read = HDpread(file->fd, buf, bytes_in, offset);
+            offset += bytes_read;
+#else
             bytes_read = HDread(file->fd, buf, bytes_in);
+#endif /* H5_HAVE_PREADWRITE */
         } while(-1 == bytes_read && EINTR == errno);
         
         if(-1 == bytes_read) { /* error */
             int myerrno = errno;
             time_t mytime = HDtime(NULL);
-            HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
 
-            HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)myoffset);
+            offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
+
+            HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total read size = %llu, bytes this sub-read = %llu, bytes actually read = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_read, (unsigned long long)offset);
         } /* end if */
         
         if(0 == bytes_read) {
@@ -777,11 +786,13 @@ H5FD_sec2_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
     if(REGION_OVERFLOW(addr, size))
         HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow, addr = %llu, size = %llu", (unsigned long long)addr, (unsigned long long)size)
 
-    /* Seek to the correct location */
+#ifndef H5_HAVE_PREADWRITE
+    /* Seek to the correct location (if we don't have pwrite) */
     if(addr != file->pos || OP_WRITE != file->op) {
         if(HDlseek(file->fd, (HDoff_t)addr, SEEK_SET) < 0)
             HSYS_GOTO_ERROR(H5E_IO, H5E_SEEKERROR, FAIL, "unable to seek to proper position")
     } /* end if */
+#endif /* H5_HAVE_PREADWRITE */
 
     /* Write the data, being careful of interrupted system calls and partial
      * results
@@ -790,6 +801,7 @@ H5FD_sec2_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
 
         h5_posix_io_t       bytes_in        = 0;    /* # of bytes to write  */
         h5_posix_io_ret_t   bytes_wrote     = -1;   /* # of bytes written   */ 
+        HDoff_t             offset          = (HDoff_t)addr;
 
         /* Trying to write more bytes than the return type can handle is
          * undefined behavior in POSIX.
@@ -800,15 +812,21 @@ H5FD_sec2_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UNU
             bytes_in = (h5_posix_io_t)size;
 
         do {
+#ifdef H5_HAVE_PREADWRITE
+            bytes_wrote = HDpwrite(file->fd, buf, bytes_in, offset);
+            offset += bytes_wrote;
+#else
             bytes_wrote = HDwrite(file->fd, buf, bytes_in);
+#endif /* H5_HAVE_PREADWRITE */
         } while(-1 == bytes_wrote && EINTR == errno);
         
         if(-1 == bytes_wrote) { /* error */
             int myerrno = errno;
             time_t mytime = HDtime(NULL);
-            HDoff_t myoffset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
 
-            HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)myoffset);
+            offset = HDlseek(file->fd, (HDoff_t)0, SEEK_CUR);
+
+            HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed: time = %s, filename = '%s', file descriptor = %d, errno = %d, error message = '%s', buf = %p, total write size = %llu, bytes this sub-write = %llu, bytes actually written = %llu, offset = %llu", HDctime(&mytime), file->filename, file->fd, myerrno, HDstrerror(myerrno), buf, (unsigned long long)size, (unsigned long long)bytes_in, (unsigned long long)bytes_wrote, (unsigned long long)offset);
         } /* end if */
         
         HDassert(bytes_wrote > 0);