Re: [netcdfgroup] Problem with netCDF "classic" files larger than 2GB on Windows

Try to compile with 64 bit off_t and lseek. E.g. in config.h

#define SIZEOF_OFF_T 8
#define lseek _lseeki64
#define off_t __int64
#define _off_t __int64
#define _OFF_T_DEFINED
Your test_big_classic.c works for me. The config.h I'm using with msvc9 is attached. 

Christoph


On 7/5/2011 3:13 PM, Mark Rivers wrote:

Hi Russ and Ed,

Thanks for your replies.

I have now upgraded from netCDF 3.6.3 to 4.1.3 as you suggested.

I have reproduced the problem in a simple test program, which I have
attached. The test program creates a netCDF file of the following format
as revealed by ncdump:

corvette:areaDetector/ADApp/netCDFSrc>ncdump -k /home/epics/scratch/test.nc

classic

corvette:areaDetector/ADApp/netCDFSrc>ncdump -h /home/epics/scratch/test.nc

netcdf test {

dimensions:

numArrays = UNLIMITED ; // (4100 currently)

YSize = 1024 ;

XSize = 1024 ;

variables:

byte array_data(numArrays, YSize, XSize) ;

}

So it writes a 1024x1024 byte array to the file 4100 times, where 4100
is the unlimited dimension. This tests writing files that are larger
than both the 2GB and 4GB potential limits.

The test program runs fine on Linux and Cygwin.

However, when compiled with the Microsoft Visual Studio 2008 compiler,
it fails with exactly the same error I got in netCDF 3.6.3, except it is
now in line 342 rather than 325 of posixio.c.

writing record 2047/4100

writing record 2048/4100

Assertion failed: pxp->bf_offset <= offset && offset < pxp->bf_offset +
(off_t) pxp->bf_extent, file ..\..\..\ADApp\netCDFSrc\libsrc\posixio.c,
line 342

By way of background on why I need to use the Microsoft compiler:

I run a fairly large NSF-funded user facility at the Advanced Photon
Source at Argonne National Laboratory. We collect data using a wide
variety of x-ray and other detectors under a distributed real-time
control system called EPICS. Some of these detectors can be controlled
from Linux and Cygwin, but many of them have vendor-supplied drivers
that can only be called from code compiled with the Microsoft compiler.
I also need to build my application to run on the vxWorks and RTEMS
real-time operating systems, which we use to control specialized VME
hardware. These use the gcc compiler, but cross-compiling for the
real-time target on a Linux host.

I am building with gnumake, not the Visual Studio application
development environment on all platforms, including when building with
the Microsoft VC++ compiler on Windows.

I have also attached a copy of the config.h file I am using, which has
been modified from the version built by "configure" on Linux to do
things differently if _WIN32 or vxWorks are defined.

I had to make some minor changes to the 4.1.3 source code in order to
allow it to build with the Microsoft VS 2008 compiler, and to build on
vxWorks. I will send those changes in a separate e-mail.

I have also attached an IDL version of the same program. It should be
completely equivalent to the C program. It works fine on both Linux and
on Windows. It appears to me that the idl_netcdf.dll file that ITT
provides with IDL on Windows is built with the Microsoft compiler
(judging from dumpbin /imports), but I am not certain of this. If so, it
indicates that it is possible to write netCDF classic files when
compiling with Visual Studio, and I am probably just doing something wrong.

Perhaps it is in my flags to the compiler. Here is the output when I
compile posixio.c as an example of the flags I am using:

J:\epics\devel\areaDetector\ADApp\netCDFSrc>make install.win32-x86

make -C O.win32-x86 -f ../Makefile TOP=../../.. T_A=win32-x86 install

make[1]: Entering directory
`J:/epics/devel/areaDetector/ADApp/netCDFSrc/O.win32-x86'

cl -c /nologo /D__STDC__=0 /D_CRT_SECURE_NO_DEPRECATE
/D_CRT_NONSTDC_NO_DEPRECATE /Ox /GL /W3 /w44355 /D_WIN32_WINNT=0x0503
-DHAVE_CONFIG_H /MT -DEPICS_DLL_NO - I. -I..\\O.Common - I. -I..
-I..\\..\\..\\ADApp\\netCDFSrc\\include
-I..\\..\\..\\ADApp\\netCDFSrc\\libsrc
-I..\\..\\..\\ADApp\\netCDFSrc\\libdispatch
-I..\\..\\..\\ADApp\\netCDFSrc\\liblib -I..\\..\\..\\include\\os\\WIN32
-I..\\..\\..\\include -IJ:\\epics\\devel\\asyn-4-17\\include
-IJ:\\epics\\devel\\calc-2-8\\include
-IJ:\\epics\\devel\\busy-1-3\\include
-IJ:\\epics\\devel\\sscan-2-6-6\\include
-IJ:\\epics\\devel\\mca-6-12-4\\include
-IJ:\\epics\\devel\\autosave-4-7\\include\\os\\WIN32
-IJ:\\epics\\devel\\autosave-4-7\\include
-IJ:\\epics\\devel\\areaDetector-1-7beta1\\include\\os\\WIN32
-IJ:\\epics\\devel\\areaDetector-1-7beta1\\include
-IH:\\epics\\base-3.14.12.1\\include\\os\\WIN32
-IH:\\epics\\base-3.14.12.1\\include
-I..\\..\\..\\ADApp\\netCDFSrc\\include
..\\..\\..\\ADApp\\netCDFSrc\\libsrc\\posixio.c

posixio.c

..\..\..\ADApp\netCDFSrc\libsrc\posixio.c(433) : warning C4018: '<' :
signed/unsigned mismatch

..\..\..\ADApp\netCDFSrc\libsrc\posixio.c(441) : warning C4018: '<=' :
signed/unsigned mismatch

..\..\..\ADApp\netCDFSrc\libsrc\posixio.c(449) : warning C4018: '<=' :
signed/unsigned mismatch

..\..\..\ADApp\netCDFSrc\libsrc\posixio.c(454) : warning C4018: '>' :
signed/unsigned mismatch

Thanks,

Mark

-----Original Message-----
From: Russ Rew [mailto:russ@xxxxxxxxxxxxxxxx]
Sent: Wednesday, June 29, 2011 1:34 PM
To: Mark Rivers
Cc: netcdfgroup@xxxxxxxxxxxxxxxx
Subject: Re: [netcdfgroup] Problem with netCDF "classic" files larger
than 2GB on Windows

Hi Mark,


 I am having a problem writing netCDF "classic" files larger than 2GB



 when building with the Microsoft Visual Studio 2008 compiler. The same



 code works fine when build on Linux, and on Cygwin.







 A bit of background. This is a project to build generic file writers



 for cameras and detectors in the areaDetector package



 (http://cars9.uchicago.edu/software/epics/areaDetectorDoc.html) for the



 EPICS (http://www.aps.anl.gov/epics/) real-time control system. This is



 a large project, with its own build system based on gnumake. I am



 building the basic netCDF library from the same source code on all



 supported platforms (Linux 32 and 64-bit, Windows 32 and 64-bit with



 Microsoft compiler, Windows with Cygwin gcc compilet, vxWorks, Darwin ,



 Solaris, etc.). Because I have another file writer that handles HDF5, I



 am using netCDF 3.6.3, since I only want to netCDF to create "classic"



 files. I am using 3.6.3 because it is less complex than 4.x, not



 requiring any HDF5 support, etc.


I recommend you use the latest netCDF-4 release, 4.1.3. If you don't

have and HDF5 library installed, it will be built without support for

netCDF-4, but with bug fixes since 3.6.3 was released 3 years ago. For

example, these bug fixes were mentioned in the RELEASE_NOTES for 4.1.2:

Fixed two large-file bugs with using classic format or

64-bit offset format and accessing multidimensional

variables with more than 2**32 values.

If the problem you're seeing still occurs in releases since 4.1.2, it

may be something new.

--Russ


 The application is typically streaming uncompressed images, using the



 UNLIMITED dimension as the streaming dimension. Thus, each record is



 small, only a few MB, and the file size limitations of the classic



 format are not a problem. Here is an ncdump of a file header created



 with this file writer on Linux:







 corvette:ADApp/op/adl>ncdump -h /home/epics/scratch/netcdf_test_1.nc



 netcdf netcdf_test_1 {



 dimensions:



 numArrays =3D UNLIMITED ; // (4100 currently)



 dim0 =3D 1024 ;



 dim1 =3D 1024 ;



 attrStringSize =3D 256 ;



 variables:



 int uniqueId(numArrays) ;



 double timeStamp(numArrays) ;



 byte array_data(numArrays, dim0, dim1) ;



 int Attr_ColorMode(numArrays) ;



 double Attr_AcquireTime(numArrays) ;



 double Attr_RingCurrent(numArrays) ;



 char Attr_RingCurrent_EGU(numArrays, attrStringSize) ;



 double Attr_ID_Energy(numArrays) ;



 char Attr_ID_Energy_EGU(numArrays, attrStringSize) ;



 int Attr_ImageCounter(numArrays) ;



 int Attr_MaxSizeX(numArrays) ;



 int Attr_MaxSizeY(numArrays) ;



 char Attr_CameraModel(numArrays, attrStringSize) ;



 char Attr_CameraManufacturer(numArrays, attrStringSize) ;







 // global attributes:



 :dataType =3D 1 ;



 :NDNetCDFFileVersion =3D 3. ;



 :numArrayDims =3D 2 ;



 :dimSize =3D 1024, 1024 ;



 ...







 So the only large array is called "array_data", and in this case it is



 [4100, 1024, 1024], where 4100 is the unlimited dimension. Thus, this



 file is over 4GB, and it can be written and read with no problems on



 Linux and Cygwin. It also works fine when writing files on Windows with



 the Microsoft compiler, up to file sizes of 2GB.







 However, when I try to write a file on Windows larger than 2GB using the



 program built with the Visual Studio compiler I get the following error:







 Assertion failed: pxp->bf_offset <=3D offset && offset < pxp->bf_offset =



 +



 (off_t) pxp->bf_extent, file ..\posixio.c, line 325







 When I look at the code at line 325 in posixio.c, I see that offset and



 pdxp->bf_offset are of type off_t. I added a printf() in that code to



 print the sizeof(offset) and sizeof(off_t), and it comes up as 4, not 8.











 But when I look at the config.h file that comes in the win32/NET



 directory in netCDF 3.6.3 it has the following:



 corvette:areaDetector/ADApp/netCDFSrc>grep -C3 off_t



 /usr/local/netcdf/netcdf-3.6.3/win32/NET/config.h



 /* #undef HAVE_ST_BLKSIZE */







 /* Define to `long' if <sys/types.h> doesn't define. */



 /* #undef off_t */







 /* Define to `unsigned' if <sys/types.h> doesn't define. */



 /* #undef size_t */



 --



 /* The number of bytes in a size_t */



 #define SIZEOF_SIZE_T 4







 /* The number of bytes in a off_t */



 #define SIZEOF_OFF_T 8







 /* Define to `int' if system doesn't define. */











 So it defines SIZEOF_OFF_T to be 8, not 4.







 I have generated the netCDF config.h file on Linux, but then edited it



 to correctly (?) define things on other platforms, like _WIN32 and



 vxWorks.







 The compiler flags being used on Windows are illustrated in the



 following output when I build:







 cl -c /nologo /D__STDC__=3D0 /D_CRT_SECURE_NO_DEPRECATE



 /D_CRT_NONSTDC_NO_DEPRECATE /Ox /GL /W3 /w44355



 /D_WIN32_WINNT=3D0x0503 -D_FILE_OFFSET_BITS=3D64 /MT -DEPICS_DLL_NO =



 -I.



 -I..\\O.Common - I. -I.. -I..\\..\\..\\include\\os\\WIN32



 -I..\\..\\..\\include -IJ:\\epics\\devel\\asyn-4-17\\include



 -IJ:\\epics\\devel\\calc-2-8\\include



 -IJ:\\epics\\devel\\busy-1-3\\include



 -IJ:\\epics\\devel\\sscan-2-6-6\\include



 -IJ:\\epics\\devel\\mca-6-12-4\\include



 -IJ:\\epics\\devel\\autosave-4-7\\include\\os\\WIN32



 -IJ:\\epics\\devel\\autosave-4-7\\include



 -IJ:\\epics\\devel\\areaDetector-1-7beta1\\include\\os\\WIN32



 -IJ:\\epics\\devel\\areaDetector-1-7beta1\\include



 -IH:\\epics\\base-3.14.12.1\\include\\os\\WIN32



 -IH:\\epics\\base-3.14.12.1\\include ..\\var.c







 There is something I don't understand here.







 Has netCDF 3.6.3 been tested to correctly write classic files > 2GB with



 the Microsoft compiler? Why am I getting the assert error?







 Thanks very much,



 Mark Rivers




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/* #undef USE_PARALLEL_POSIX */

/* if true, build libsrc code with renamed API functions */
#define USE_RENAMEV3 1

/* if true, compile in zlib compression in netCDF-4 variables */
#define USE_ZLIB 1

/* Version number of package */
//#define VERSION "4.1.3"

/* Define WORDS_BIGENDIAN to 1 if your processor stores words with the most
   significant byte first (like Motorola and SPARC, unlike Intel and VAX). */
#if defined __BIG_ENDIAN__
# define WORDS_BIGENDIAN 1
#elif ! defined __LITTLE_ENDIAN__
/* # undef WORDS_BIGENDIAN */
#endif

/* xdr float32 */
/* #undef XDR_FLOAT32 */

/* xdr float64 */
/* #undef XDR_FLOAT64 */

/* xdr int16 */
/* #undef XDR_INT16 */

/* xdr int32 */
/* #undef XDR_INT32 */

/* xdr uint16 */
/* #undef XDR_UINT16 */

/* xdr uint32 */
/* #undef XDR_UINT32 */

/* Number of bits in a file offset, on hosts where this is settable. */
/* #undef _FILE_OFFSET_BITS */

/* Needed by HPUX with c89 compiler. */
/* #undef _HPUX_SOURCE */

/* Define for large files, on AIX-style hosts. */
/* #undef _LARGE_FILES */

/* Define to 1 if type `char' is unsigned and you are not using gcc.  */
#ifndef __CHAR_UNSIGNED__
/* # undef __CHAR_UNSIGNED__ */
#endif

/* Define to empty if `const' does not conform to ANSI C. */
/* #undef const */

/* Turned on by netCDF configure. */
/* #undef f2cFortran */

/* Turned on by netCDF configure. */
/* #undef gFortran */

/* Define to `long int' if <sys/types.h> does not define. */
/* #undef off_t */

/* Turned on by netCDF configure. */
/*#define pgiFortran 1*/

/* Define to `unsigned int' if <sys/types.h> does not define. */
/* #undef size_t */

/* Define to empty if the keyword `volatile' does not work. Warning: valid
   code using `volatile' can become incorrect without. Disable with care. */
/* #undef volatile */

/* Shorthand for gcc's unused attribute feature */
#if defined(__GNUG__) || defined(__GNUC__)
#define not_used __attribute__ ((unused))
#else
#define not_used 
#endif /* __GNUG__ || __GNUC__ */

/* I added the following to this config.h file by hand, after being abducted by 
   aliens last week in Kansas. (All Hail Zorlock, Mighty Destroyer of Worlds!) 
*/
#include <io.h>
#include <process.h>
#define lseek _lseeki64
#define off_t __int64
#define _off_t __int64
#define _OFF_T_DEFINED
#define snprintf sprintf_s
#define strcasecmp _stricmp

#define HAVE_STRDUP 1
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