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Re: netcdf 3.5.1 with pgi 5.2-2 in 3é bits mode

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  • Subject: Re: netcdf 3.5.1 with pgi 5.2-2 in 3é bits mode
  • Date: Thu, 21 Oct 2004 17:48:06 +0200

    Helo,

    I finnaly could compile, the errors was due to a bad pgf90 installation at first.
and after I forget to make clean make distclean before retrying.

        Thank you very much for help.
   

address@hidden a écrit:
Etienne,


  If you are tryingto create a double-precision version
of the netcf libs, here is some info we found
from the NetCDF known problems page:

---------------------------------------------------------------------

http://my.unidata.ucar.edu/content/software/netcdf/known_problems.html#r8

"Problem with simultaneous 8-byte reals and doubleprecisions in Fortran-90
interface

The Fortran-90 interface of the netCDF package doesn't support
environments where both real values and doubleprecision values are 8-bytes
wide (e.g. the Portland Group's Fortran-90 compiler with the "-r8"
option).

Workarounds include the following:

    * Not using the Fortran-90 interface (the Fortran-77 interface works
OK in this environment); and
    * Modifying the netCDF-using code, replacing the use of real values
with doubleprecision values."

-------------------------------------------------------------------------

We see in netcdf that the common data format uses 6 bytes to store
the real value, so an 8-byte real will need more room, and more changes will
be needed.


regards,
dave



  
I retry with pgi 5.2-4 + your modifications in

$PGI/linux86-64/5.2/include/sys/types.h

+

$PGI/linux86-64/5.2/include/bits/types.h


and had no more success to compile netcdf 3.5.1 ?!

    Etienne




address@hidden a écrit:

    
   That's it?

I haven't any troubles on a x86_64 system ?!


        
Just want to get past this one, and see if things improve.

Replace $PGI/linux86-64/5.2/include/sys/types.h
and
$PGI/linux86/5.2/include/sys/types.h

with the attached sys_types.h


Replace $PGI/linux86-64/5.2/include/bits/types.h
and
$PGI/linux86/5.2/include/bits/types.h

with the attached bits_types.h






      
address@hidden a écrit:



        
We can get rid of one problem.


Send us the files
/usr/include/sys/types.h
/usr/include/bits/types.h


and we will fix them to replace the ones in
$PGI/linux86/5.2/include/sys
                      /bits

and we can proceed from there.


dave







          
On the following systems redhat 9.0 :
+ uname -a
Linux px-master.mercator-ocean.fr 2.6.8-1.584smp #1 SMP Mon Sep 20
07:39:39 EDT 2004 i686 i686 i386 GNU/Linux

I tried to compile netcdf 3.5.1 with pgi 5.2-2 according your notices
on
the web in the following way
in double precision for real fortran.

env CC=pgcc CFLAGS="-O -Msignextend -V" FC=pgf90 F90=pgf90 FFLAGS="-g
-w
-V"  \
    CXX=pgCC CPPFLAGS="-DNDEBUG -DpgiFortran" ./configure
-prefix=/tmp/final >& config.log
and I got that in the configure

checking size of short... (cached) 0
checking size of int... (cached) 0
checking size of long... (cached) 0
checking size of float... (cached) 0
checking size of double... (cached) 0
checking size of off_t... (cached) 0
checking size of size_t... (cached) 0

configure.log
see also config.log in joint file?

How to compile netcdf 3.5.1 with pgi 5.2-2 to have double precisioon 8
byetes on real fortran.


CXX=pgCC CPPFLAGS="-DNDEBUG -DpgiFortran" ./configure
-prefix=/tmp/final
+ CXX=pgCC
+ CPPFLAGS=-DNDEBUG -DpgiFortran
+ ./configure -prefix=/tmp/final
loading cache ./config.cache
checking for top-level source-directory
/home/mercator-px/src/netcdf-3.5.1/src
checking for m4 preprocessor
checking for m4... (cached) m4
checking m4 flags... -B10000
checking C compiler "pgcc"... works
checking how to make dependencies... false
checking for pgCC... (cached) pgCC
checking C++ compiler "pgCC"... works
checking how to run the C preprocessor... (cached) pgcc -E
checking user-defined Fortran-77 compiler "pgf90"... works
checking for Fortran .F compiler...
checking if Fortran-77 compiler handles *.F files... yes
checking user-defined Fortran-90 compiler "pgf90"... works
checking for nm utility
checking for nm... (cached) nm
checking nm flags...
checking for C-equivalent to Fortran routine "SUB"... sub_
checking for Fortran "byte"... yes
checking for Fortran "integer*2"... yes
checking if Fortran "byte" is C "signed char"... yes
checking if Fortran "byte" is C "short"... no
checking if Fortran "byte" is C "int"... no
checking if Fortran "byte" is C "long"... no
checking if Fortran "integer*2" is C "short"... yes
checking if Fortran "integer*2" is C "int"... no
checking if Fortran "integer*2" is C "long"... no
checking if Fortran "integer" is C "int"... yes
checking if Fortran "real" is C "float"... no
checking if Fortran "real" is C "double"... yes
checking if Fortran "doubleprecision" is C "double"... yes
checking for Fortran-equivalent to netCDF "byte"... byte
checking for Fortran-equivalent to netCDF "short"... integer*2
checking for math library
checking for tanh in -lc... (cached) no
checking for tanh in -lm... (cached) no
checking for ar utility
checking for ar... (cached) ar
checking ar flags... cru
checking for nm utility
checking for nm... (cached) nm
checking nm flags...
checking for ranlib... (cached) ranlib
checking for stdlib.h... (cached) yes
checking for sys/types.h... (cached) yes
checking for strerror... (cached) no
checking for working ftruncate()... yes
checking for working alloca.h... (cached) no
checking for alloca... (cached) no
checking whether alloca needs Cray hooks... (cached) no
checking stack direction for C alloca... (cached) -1
checking for st_blksize in struct stat... (cached) yes
checking for IEEE floating point format... yes
checking for ANSI C header files... (cached) no
checking for size_t... (cached) yes
checking for off_t... (cached) yes
checking for ssize_t... (cached) yes
checking for ptrdiff_t... (cached) no
checking for uchar... (cached) no
checking whether char is unsigned... (cached) no
checking whether byte ordering is bigendian... (cached) no
checking size of short... (cached) 0
checking size of int... (cached) 0
checking size of long... (cached) 0
checking size of float... (cached) 0
checking size of double... (cached) 0
checking size of off_t... (cached) 0
checking size of size_t... (cached) 0
checking for manual-page index command...
checking binary distribution directory...
/home/ftp/pub/binary/dummy_system
creating ./config.status
creating macros.make
udcreating fortran/nfconfig.inc
fortran/nfconfig.inc is unchanged
creating libsrc/ncconfig.h
libsrc/ncconfig.h is unchanged


  Sincerely yours,
              Etienne Gondet.
GIP MERCATOR Océan
HPC coordinator
8-10 rue HERMES
31526 RAMONVILLE SAINT-AGNE CEDEX
France
tel:  05 61 39 38 11 (from France);       33 5 61 39 38 11 (other)
fax:  05 61 39 38 99 (from france);       33 5 61 39 38 99 (other)







            



          
------------------------------------------------------------------------

/* bits/types.h -- definitions of __*_t types underlying *_t types.
  Copyright (C) 2002 Free Software Foundation, Inc.
  This file is part of the GNU C Library.

  The GNU C Library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.

  The GNU C Library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.

  You should have received a copy of the GNU Lesser General Public
  License along with the GNU C Library; if not, write to the Free
  Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
  02111-1307 USA.  */

/*
* Never include this file directly; use <sys/types.h> instead.
*/

#ifndef	_BITS_TYPES_H
#define	_BITS_TYPES_H	1

#include <features.h>
#include <bits/wordsize.h>

#define __need_size_t
#include <stddef.h>

/* Convenience types.  */
typedef unsigned char __u_char;
typedef unsigned short int __u_short;
typedef unsigned int __u_int;
typedef unsigned long int __u_long;

/* Fixed-size types, underlying types depend on word size and compiler.
*/
typedef signed char __int8_t;
typedef unsigned char __uint8_t;
typedef signed short int __int16_t;
typedef unsigned short int __uint16_t;
typedef signed int __int32_t;
typedef unsigned int __uint32_t;
#if __WORDSIZE == 64
typedef signed long int __int64_t;
typedef unsigned long int __uint64_t;
/*  #elif defined __GLIBC_HAVE_LONG_LONG  */
#elif defined (__GLIBC_HAVE_LONG_LONG) || defined(__PGI)
__extension__ typedef signed long long int __int64_t;
__extension__ typedef unsigned long long int __uint64_t;
#endif

/* quad_t is also 64 bits, but is traditionally defined as `long long'
  even when `long' is also 64 bits.  */
/*  #ifdef __GLIBC_HAVE_LONG_LONG  */
#if defined (__GLIBC_HAVE_LONG_LONG) || defined(__PGI)
__extension__ typedef long long int __quad_t;
__extension__ typedef unsigned long long int __u_quad_t;
#elif __WORDSIZE == 64
typedef long int __quad_t;
typedef unsigned long int __u_quad_t;
#else
typedef struct
{
 long __val[2];
} __quad_t;
typedef struct
{
 __u_long __val[2];
} __u_quad_t;
#endif


/* The machine-dependent file <bits/typesizes.h> defines __*_T_TYPE
  macros for each of the OS types we define below.  The definitions
  of those macros must use the following macros for underlying types.
  We define __S<SIZE>_TYPE and __U<SIZE>_TYPE for the signed and
unsigned
  variants of each of the following integer types on this machine.

	16		-- "natural" 16-bit type (always short)
	32		-- "natural" 32-bit type (always int)
	64		-- "natural" 64-bit type (long or long long)
	LONG32		-- 32-bit type, traditionally long
	QUAD		-- 64-bit type, always long long
	WORD		-- natural type of __WORDSIZE bits (int or long)
	LONGWORD	-- type of __WORDSIZE bits, traditionally long

  We distinguish WORD/LONGWORD, 32/LONG32, and 64/QUAD so that the
  conventional uses of `long' or `long long' type modifiers match the
  types we define, even when a less-adorned type would be the same
size.
  This matters for (somewhat) portably writing printf/scanf formats for
  these types, where using the appropriate l or ll format modifiers can
  make the typedefs and the formats match up across all GNU platforms.
If
  we used `long' when it's 64 bits where `long long' is expected, then
the
  compiler would warn about the formats not matching the argument
types,
  and the programmer changing them to shut up the compiler would break
the
  program's portability.

  Here we assume what is presently the case in all the GCC
configurations
  we support: long long is always 64 bits, long is always word/address
size,
  and int is always 32 bits.  */

#define	__S16_TYPE		short int
#define __U16_TYPE		unsigned short int
#define	__S32_TYPE		int
#define __U32_TYPE		unsigned int
#define __SLONGWORD_TYPE	long int
#define __ULONGWORD_TYPE	unsigned long int
#define	__SQUAD_TYPE		long long int
#define	__UQUAD_TYPE		unsigned long long int
#if __WORDSIZE == 32
# define __SWORD_TYPE		int
# define __UWORD_TYPE		unsigned int
# define __SLONG32_TYPE		long int
# define __ULONG32_TYPE		unsigned long int
# define __S64_TYPE		__quad_t
# define __U64_TYPE		__u_quad_t
#elif __WORDSIZE == 64
# define __SWORD_TYPE		long int
# define __UWORD_TYPE		unsigned long int
# define __SLONG32_TYPE		int
# define __ULONG32_TYPE		unsigned int
# define __S64_TYPE		long int
# define __U64_TYPE		unsigned long int
#else
# error
#endif
#include <bits/typesizes.h>	/* Defines __*_T_TYPE macros.  */


typedef __DEV_T_TYPE __dev_t;	/* Type of device numbers.  */
typedef __UID_T_TYPE __uid_t;	/* Type of user identifications.  */
typedef __GID_T_TYPE __gid_t;	/* Type of group identifications.  */
typedef __INO_T_TYPE __ino_t;	/* Type of file serial numbers.  */
typedef __INO64_T_TYPE __ino64_t; /* Type of file serial numbers (LFS).
*/
typedef __MODE_T_TYPE __mode_t;	/* Type of file attribute bitmasks.  */
typedef __NLINK_T_TYPE __nlink_t; /* Type of file link counts.  */
typedef __OFF_T_TYPE __off_t;	/* Type of file sizes and offsets.  */
typedef __OFF64_T_TYPE __off64_t; /* Type of file sizes and offsets
(LFS).  */
typedef __PID_T_TYPE __pid_t;	/* Type of process identifications.  */
typedef __FSID_T_TYPE __fsid_t;	/* Type of file system IDs.  */
typedef __CLOCK_T_TYPE __clock_t; /* Type of CPU usage counts.  */
typedef __RLIM_T_TYPE __rlim_t;	/* Type for resource measurement.  */
typedef __RLIM64_T_TYPE __rlim64_t; /* Type for resource measurement
(LFS).  */
typedef __ID_T_TYPE __id_t;	/* General type for IDs.  */
typedef __TIME_T_TYPE __time_t;	/* Seconds since the Epoch.  */
typedef __USECONDS_T_TYPE __useconds_t; /* Count of microseconds.  */
typedef __SUSECONDS_T_TYPE __suseconds_t; /* Signed count of
microseconds.  */

typedef __DADDR_T_TYPE __daddr_t; /* The type of a disk address.  */
typedef __SWBLK_T_TYPE __swblk_t; /* Type of a swap block maybe?  */
typedef __KEY_T_TYPE __key_t;	/* Type of an IPC key */

/* Clock ID used in clock and timer functions.  */
typedef __CLOCKID_T_TYPE __clockid_t;

/* Timer ID returned by `timer_create'.  */
typedef __TIMER_T_TYPE __timer_t;

/* Type to represent block size.  */
typedef __BLKSIZE_T_TYPE __blksize_t;

/* Types from the Large File Support interface.  */

/* Type to count number of disk blocks.  */
typedef __BLKCNT_T_TYPE __blkcnt_t;
typedef __BLKCNT64_T_TYPE __blkcnt64_t;

/* Type to count file system blocks.  */
typedef __FSBLKCNT_T_TYPE __fsblkcnt_t;
typedef __FSBLKCNT64_T_TYPE __fsblkcnt64_t;

/* Type to count file system nodes.  */
typedef __FSFILCNT_T_TYPE __fsfilcnt_t;
typedef __FSFILCNT64_T_TYPE __fsfilcnt64_t;


/* These few don't really vary by system, they always correspond
  to one of the other defined types.  */
typedef __SWORD_TYPE __ssize_t; /* Type of a byte count, or error.  */
typedef __off64_t __loff_t;	/* Type of file sizes and offsets (LFS).  */
typedef __quad_t *__qaddr_t;
typedef char *__caddr_t;

/* Duplicates info from stdint.h but this is used in unistd.h.  */
typedef __SWORD_TYPE __intptr_t;

/* Duplicate info from sys/socket.h.  */
typedef __U32_TYPE __socklen_t;


#endif /* bits/types.h */

------------------------------------------------------------------------

/* Copyright (C) 1991,1992,1994,1995,1996,1997,1998,1999,2000,2001,2002
  	Free Software Foundation, Inc.
  This file is part of the GNU C Library.

  The GNU C Library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.

  The GNU C Library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.

  You should have received a copy of the GNU Lesser General Public
  License along with the GNU C Library; if not, write to the Free
  Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
  02111-1307 USA.  */

/*
*	POSIX Standard: 2.6 Primitive System Data Types	<sys/types.h>
*/

#ifndef	_SYS_TYPES_H
#define	_SYS_TYPES_H	1

#include <features.h>

__BEGIN_DECLS

#include <bits/types.h>

#ifdef	__USE_BSD
# ifndef __u_char_defined
typedef __u_char u_char;
typedef __u_short u_short;
typedef __u_int u_int;
typedef __u_long u_long;
typedef __quad_t quad_t;
typedef __u_quad_t u_quad_t;
typedef __fsid_t fsid_t;
#  define __u_char_defined
# endif
#endif

typedef __loff_t loff_t;

#ifndef __ino_t_defined
# ifndef __USE_FILE_OFFSET64
typedef __ino_t ino_t;
# else
typedef __ino64_t ino_t;
# endif
# define __ino_t_defined
#endif
#if defined __USE_LARGEFILE64 && !defined __ino64_t_defined
typedef __ino64_t ino64_t;
# define __ino64_t_defined
#endif

#ifndef __dev_t_defined
typedef __dev_t dev_t;
# define __dev_t_defined
#endif

#ifndef __gid_t_defined
typedef __gid_t gid_t;
# define __gid_t_defined
#endif

#ifndef __mode_t_defined
typedef __mode_t mode_t;
# define __mode_t_defined
#endif

#ifndef __nlink_t_defined
typedef __nlink_t nlink_t;
# define __nlink_t_defined
#endif

#ifndef __uid_t_defined
typedef __uid_t uid_t;
# define __uid_t_defined
#endif

#ifndef __off_t_defined
# ifndef __USE_FILE_OFFSET64
typedef __off_t off_t;
# else
typedef __off64_t off_t;
# endif
# define __off_t_defined
#endif
#if defined __USE_LARGEFILE64 && !defined __off64_t_defined
typedef __off64_t off64_t;
# define __off64_t_defined
#endif

#ifndef __pid_t_defined
typedef __pid_t pid_t;
# define __pid_t_defined
#endif

#if (defined __USE_SVID || defined __USE_XOPEN) && !defined
__id_t_defined
typedef __id_t id_t;
# define __id_t_defined
#endif

#ifndef __ssize_t_defined
typedef __ssize_t ssize_t;
# define __ssize_t_defined
#endif

#ifdef	__USE_BSD
# ifndef __daddr_t_defined
typedef __daddr_t daddr_t;
typedef __caddr_t caddr_t;
#  define __daddr_t_defined
# endif
#endif

#if (defined __USE_SVID || defined __USE_XOPEN) && !defined
__key_t_defined
typedef __key_t key_t;
# define __key_t_defined
#endif

#ifdef __USE_XOPEN
# define __need_clock_t
#endif
#define	__need_time_t
#define __need_timer_t
#define __need_clockid_t
#include <time.h>

#ifdef __USE_XOPEN
# ifndef __useconds_t_defined
typedef __useconds_t useconds_t;
#  define __useconds_t_defined
# endif
# ifndef __suseconds_t_defined
typedef __suseconds_t suseconds_t;
#  define __suseconds_t_defined
# endif
#endif

#define	__need_size_t
#include <stddef.h>

#ifdef __USE_MISC
/* Old compatibility names for C types.  */
typedef unsigned long int ulong;
typedef unsigned short int ushort;
typedef unsigned int uint;
#endif

/* These size-specific names are used by some of the inet code.  */

#if !__GNUC_PREREQ (2, 7)

/* These types are defined by the ISO C99 header <inttypes.h>. */
# ifndef __int8_t_defined
#  define __int8_t_defined
typedef	char int8_t;
typedef	short int int16_t;
typedef	int int32_t;
/*  #  if __GLIBC_HAVE_LONG_LONG  */
#  if  defined( __GLIBC_HAVE_LONG_LONG) || defined(__PGI)
__extension__ typedef long long int int64_t;
#  endif
# endif

/* But these were defined by ISO C without the first `_'.  */
typedef	unsigned char u_int8_t;
typedef	unsigned short int u_int16_t;
typedef	unsigned int u_int32_t;
/*  #  if __GLIBC_HAVE_LONG_LONG  */
#  if  defined( __GLIBC_HAVE_LONG_LONG) || defined(__PGI)
__extension__ typedef unsigned long long int u_int64_t;
# endif

typedef int register_t;

#else

/* For GCC 2.7 and later, we can use specific type-size attributes.  */
# define __intN_t(N, MODE) \
 typedef int int##N##_t __attribute__ ((__mode__ (MODE)))
# define __u_intN_t(N, MODE) \
 typedef unsigned int u_int##N##_t __attribute__ ((__mode__ (MODE)))

# ifndef __int8_t_defined
#  define __int8_t_defined
__intN_t (8, __QI__);
__intN_t (16, __HI__);
__intN_t (32, __SI__);
__intN_t (64, __DI__);
# endif

__u_intN_t (8, __QI__);
__u_intN_t (16, __HI__);
__u_intN_t (32, __SI__);
__u_intN_t (64, __DI__);

typedef int register_t __attribute__ ((__mode__ (__word__)));


/* Some code from BIND tests this macro to see if the types above are
  defined.  */
#endif
#define __BIT_TYPES_DEFINED__	1


#ifdef	__USE_BSD
/* In BSD <sys/types.h> is expected to define BYTE_ORDER.  */
# include <endian.h>

/* It also defines `fd_set' and the FD_* macros for `select'.  */
# include <sys/select.h>

/* BSD defines these symbols, so we follow.  */
# include <sys/sysmacros.h>
#endif /* Use BSD.  */


#if defined __USE_UNIX98 && !defined __blksize_t_defined
typedef __blksize_t blksize_t;
# define __blksize_t_defined
#endif

/* Types from the Large File Support interface.  */
#ifndef __USE_FILE_OFFSET64
# ifndef __blkcnt_t_defined
typedef __blkcnt_t blkcnt_t;	 /* Type to count number of disk blocks.
*/
#  define __blkcnt_t_defined
# endif
# ifndef __fsblkcnt_t_defined
typedef __fsblkcnt_t fsblkcnt_t; /* Type to count file system blocks.
*/
#  define __fsblkcnt_t_defined
# endif
# ifndef __fsfilcnt_t_defined
typedef __fsfilcnt_t fsfilcnt_t; /* Type to count file system inodes.
*/
#  define __fsfilcnt_t_defined
# endif
#else
# ifndef __blkcnt_t_defined
typedef __blkcnt64_t blkcnt_t;	   /* Type to count number of disk
blocks.  */
#  define __blkcnt_t_defined
# endif
# ifndef __fsblkcnt_t_defined
typedef __fsblkcnt64_t fsblkcnt_t; /* Type to count file system blocks.
*/
#  define __fsblkcnt_t_defined
# endif
# ifndef __fsfilcnt_t_defined
typedef __fsfilcnt64_t fsfilcnt_t; /* Type to count file system inodes.
*/
#  define __fsfilcnt_t_defined
# endif
#endif

#ifdef __USE_LARGEFILE64
typedef __blkcnt64_t blkcnt64_t;     /* Type to count number of disk
blocks. */
typedef __fsblkcnt64_t fsblkcnt64_t; /* Type to count file system
blocks.  */
typedef __fsfilcnt64_t fsfilcnt64_t; /* Type to count file system
inodes.  */
#endif


/* Now add the thread types.  */
#if defined __USE_POSIX199506 || defined __USE_UNIX98
# include <bits/pthreadtypes.h>
#endif

__END_DECLS

#endif /* sys/types.h */