Build failed HDF 4.2r4 on MacOS X 10.6 with intel fortran

Hdf-forum archives
1

Hello,

Recently I upgraded to OS 10.6 with Xcode 3.1.2(gcc 4.2.1).
But, I failed to build HDF 4.2r4 with intel fortran 11.1.

As the HDF release note said that "only the 32-bit version of
the Intel compiler is supported", I followed it.

I can build zlib and jpeg libraries, but can't HDF as stated below.

Are there any tips or suggestions?

Best,
Yuichiro Hagihara

$ tar xzf zlib-1.2.3.tar.gz
$ cd zlib-1.2.3
$ ./configure
$ make test
$ sudo make install

$ tar xzf jpegsrc.v6b.tar.gz
$ cd jpeg-6b
$ cp /usr/share/libtool/config/config.guess .
$ cp /usr/share/libtool/config/config.sub .
$ ./configure --enable-shared --enable-static
$ make
$ sudo make install

$ tar xzf HDF4.2r3
$ cd HDF4.2r3
$ ./configure --with-jpeg=/usr/local --with-zlib=/usr/local --prefix=/usr/local

Configure summary
Compiling Options:

···

------------------
               Compilation Mode: Default
                     C Compiler: gcc
                         CFLAGS: -O2
                       CPPFLAGS: -I/usr/include/rpc -I/usr/local/include -I/usr/local/include -DBIG_LONGS -DSWAP
                        LDFLAGS: -L/usr/local/lib -L/usr/local/lib
               Shared Libraries: no
               Static Libraries: yes

Languages:
----------
                        Fortran: Yes
               Fortran Compiler: ifort
                         FFLAGS:

Features:
---------
               SZIP compression: disabled

HDF support for NetCDF-3 APIs:
------------------------------
                    HDF4-NetCDF: Yes

$ make
Making all in hdf
Making all in src
make all-am
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -I/usr/local/include -I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT atom.lo -MD -MP -MF .deps/atom.Tpo -c -o atom.lo atom.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -I/usr/local/include -I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT atom.lo -MD -MP -MF .deps/atom.Tpo -c atom.c -o atom.o
In file included from hdf.h:20,
                 from atom.c:64:
hdfi.h:1352: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'you'
In file included from hdf.h:20,
                 from atom.c:64:
hdfi.h:1355:1: warning: "GOT_MACHINE" redefined
hdfi.h:760:1: warning: this is the location of the previous definition
hdfi.h:1359:1: warning: "DF_MT" redefined
hdfi.h:775:1: warning: this is the location of the previous definition
hdfi.h:1361: error: redefinition of typedef 'VOIDP'
hdfi.h:779: error: previous declaration of 'VOIDP' was here
hdfi.h:1362: error: redefinition of typedef '_fcd'
hdfi.h:780: error: previous declaration of '_fcd' was here
hdfi.h:1363: error: redefinition of typedef 'char8'
hdfi.h:781: error: previous declaration of 'char8' was here
hdfi.h:1364: error: redefinition of typedef 'uchar8'
hdfi.h:782: error: previous declaration of 'uchar8' was here
hdfi.h:1365: error: redefinition of typedef 'int8'
hdfi.h:783: error: previous declaration of 'int8' was here
hdfi.h:1366: error: redefinition of typedef 'uint8'
hdfi.h:784: error: previous declaration of 'uint8' was here
hdfi.h:1367: error: redefinition of typedef 'int16'
hdfi.h:785: error: previous declaration of 'int16' was here
hdfi.h:1368: error: redefinition of typedef 'uint16'
hdfi.h:786: error: previous declaration of 'uint16' was here
hdfi.h:1369: error: redefinition of typedef 'int32'
hdfi.h:787: error: previous declaration of 'int32' was here
hdfi.h:1370: error: redefinition of typedef 'uint32'
hdfi.h:788: error: previous declaration of 'uint32' was here
hdfi.h:1371: error: redefinition of typedef 'intn'
hdfi.h:789: error: previous declaration of 'intn' was here
hdfi.h:1372: error: redefinition of typedef 'uintn'
hdfi.h:790: error: previous declaration of 'uintn' was here
hdfi.h:1373: error: redefinition of typedef 'intf'
hdfi.h:793: error: previous declaration of 'intf' was here
hdfi.h:1374: error: redefinition of typedef 'float32'
hdfi.h:791: error: previous declaration of 'float32' was here
hdfi.h:1375: error: redefinition of typedef 'float64'
hdfi.h:792: error: previous declaration of 'float64' was here
hdfi.h:1376: error: conflicting types for 'hdf_pint_t'
hdfi.h:794: error: previous declaration of 'hdf_pint_t' was here
make[3]: *** [atom.lo] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

2

Hi Yuichiro,

I'm not exactly sure what the problem is, but it seemed that you built HDF
4.2r3 not 4.2r4. You might want to try 4.2r4, perhaps, new configuration
was added between r3 and r4.

Binh-Minh

···

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-
bounces@hdfgroup.org] On Behalf Of HAGIHARA Yuichiro
Sent: Tuesday, November 17, 2009 2:57 AM
To: hdf-forum@hdfgroup.org
Subject: [Hdf-forum] Build failed HDF 4.2r4 on MacOS X 10.6 with
intelfortran

Hello,

Recently I upgraded to OS 10.6 with Xcode 3.1.2(gcc 4.2.1).
But, I failed to build HDF 4.2r4 with intel fortran 11.1.

As the HDF release note said that "only the 32-bit version of
the Intel compiler is supported", I followed it.

I can build zlib and jpeg libraries, but can't HDF as stated below.

Are there any tips or suggestions?

Best,
Yuichiro Hagihara

$ tar xzf zlib-1.2.3.tar.gz
$ cd zlib-1.2.3
$ ./configure
$ make test
$ sudo make install

$ tar xzf jpegsrc.v6b.tar.gz
$ cd jpeg-6b
$ cp /usr/share/libtool/config/config.guess .
$ cp /usr/share/libtool/config/config.sub .
$ ./configure --enable-shared --enable-static
$ make
$ sudo make install

$ tar xzf HDF4.2r3
$ cd HDF4.2r3
$ ./configure --with-jpeg=/usr/local --with-zlib=/usr/local --
prefix=/usr/local

Configure summary
Compiling Options:
------------------
              Compilation Mode: Default
                    C Compiler: gcc
                        CFLAGS: -O2
                      CPPFLAGS: -I/usr/include/rpc -I/usr/local/include
-I/usr/local/include -DBIG_LONGS -DSWAP
                       LDFLAGS: -L/usr/local/lib -L/usr/local/lib
              Shared Libraries: no
              Static Libraries: yes

Languages:
----------
                       Fortran: Yes
              Fortran Compiler: ifort
                        FFLAGS:

Features:
---------
              SZIP compression: disabled

HDF support for NetCDF-3 APIs:
------------------------------
                   HDF4-NetCDF: Yes

$ make
Making all in hdf
Making all in src
make all-am
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -
I/usr/include/rpc -I/usr/local/include -I/usr/local/include -DBIG_LONGS -
DSWAP -O2 -MT atom.lo -MD -MP -MF .deps/atom.Tpo -c -o atom.lo atom.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -
I/usr/local/include -I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT atom.lo
-MD -MP -MF .deps/atom.Tpo -c atom.c -o atom.o
In file included from hdf.h:20,
                from atom.c:64:
hdfi.h:1352: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'you'
In file included from hdf.h:20,
                from atom.c:64:
hdfi.h:1355:1: warning: "GOT_MACHINE" redefined
hdfi.h:760:1: warning: this is the location of the previous definition
hdfi.h:1359:1: warning: "DF_MT" redefined
hdfi.h:775:1: warning: this is the location of the previous definition
hdfi.h:1361: error: redefinition of typedef 'VOIDP'
hdfi.h:779: error: previous declaration of 'VOIDP' was here
hdfi.h:1362: error: redefinition of typedef '_fcd'
hdfi.h:780: error: previous declaration of '_fcd' was here
hdfi.h:1363: error: redefinition of typedef 'char8'
hdfi.h:781: error: previous declaration of 'char8' was here
hdfi.h:1364: error: redefinition of typedef 'uchar8'
hdfi.h:782: error: previous declaration of 'uchar8' was here
hdfi.h:1365: error: redefinition of typedef 'int8'
hdfi.h:783: error: previous declaration of 'int8' was here
hdfi.h:1366: error: redefinition of typedef 'uint8'
hdfi.h:784: error: previous declaration of 'uint8' was here
hdfi.h:1367: error: redefinition of typedef 'int16'
hdfi.h:785: error: previous declaration of 'int16' was here
hdfi.h:1368: error: redefinition of typedef 'uint16'
hdfi.h:786: error: previous declaration of 'uint16' was here
hdfi.h:1369: error: redefinition of typedef 'int32'
hdfi.h:787: error: previous declaration of 'int32' was here
hdfi.h:1370: error: redefinition of typedef 'uint32'
hdfi.h:788: error: previous declaration of 'uint32' was here
hdfi.h:1371: error: redefinition of typedef 'intn'
hdfi.h:789: error: previous declaration of 'intn' was here
hdfi.h:1372: error: redefinition of typedef 'uintn'
hdfi.h:790: error: previous declaration of 'uintn' was here
hdfi.h:1373: error: redefinition of typedef 'intf'
hdfi.h:793: error: previous declaration of 'intf' was here
hdfi.h:1374: error: redefinition of typedef 'float32'
hdfi.h:791: error: previous declaration of 'float32' was here
hdfi.h:1375: error: redefinition of typedef 'float64'
hdfi.h:792: error: previous declaration of 'float64' was here
hdfi.h:1376: error: conflicting types for 'hdf_pint_t'
hdfi.h:794: error: previous declaration of 'hdf_pint_t' was here
make[3]: *** [atom.lo] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

--
Internal Virus Database is out-of-date.
Checked by AVG.
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2:14 PM

3

OS X 10.6 defaults to a 64 bit build for GCC. You may have to add the "-arch i386" to the CFLAGS and CPPFLAGS to force a 32 bit build.

···

_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

On Nov 17, 2009, at 2:57 AM, HAGIHARA Yuichiro wrote:

Hello,

Recently I upgraded to OS 10.6 with Xcode 3.1.2(gcc 4.2.1).
But, I failed to build HDF 4.2r4 with intel fortran 11.1.

As the HDF release note said that "only the 32-bit version of
the Intel compiler is supported", I followed it.

I can build zlib and jpeg libraries, but can't HDF as stated below.

Are there any tips or suggestions?

Best,
Yuichiro Hagihara

$ tar xzf zlib-1.2.3.tar.gz
$ cd zlib-1.2.3
$ ./configure
$ make test
$ sudo make install

$ tar xzf jpegsrc.v6b.tar.gz
$ cd jpeg-6b
$ cp /usr/share/libtool/config/config.guess .
$ cp /usr/share/libtool/config/config.sub .
$ ./configure --enable-shared --enable-static
$ make
$ sudo make install

$ tar xzf HDF4.2r3
$ cd HDF4.2r3
$ ./configure --with-jpeg=/usr/local --with-zlib=/usr/local --prefix=/usr/local

Configure summary
Compiling Options:
------------------
              Compilation Mode: Default
                    C Compiler: gcc
                        CFLAGS: -O2
                      CPPFLAGS: -I/usr/include/rpc -I/usr/local/include -I/usr/local/include -DBIG_LONGS -DSWAP
                       LDFLAGS: -L/usr/local/lib -L/usr/local/lib
              Shared Libraries: no
              Static Libraries: yes

Languages:
----------
                       Fortran: Yes
              Fortran Compiler: ifort
                        FFLAGS:

Features:
---------
              SZIP compression: disabled

HDF support for NetCDF-3 APIs:
------------------------------
                   HDF4-NetCDF: Yes

$ make
Making all in hdf
Making all in src
make all-am
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -I/usr/local/include -I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT atom.lo -MD -MP -MF .deps/atom.Tpo -c -o atom.lo atom.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -I/usr/local/include -I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT atom.lo -MD -MP -MF .deps/atom.Tpo -c atom.c -o atom.o
In file included from hdf.h:20,
                from atom.c:64:
hdfi.h:1352: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'you'
In file included from hdf.h:20,
                from atom.c:64:
hdfi.h:1355:1: warning: "GOT_MACHINE" redefined
hdfi.h:760:1: warning: this is the location of the previous definition
hdfi.h:1359:1: warning: "DF_MT" redefined
hdfi.h:775:1: warning: this is the location of the previous definition
hdfi.h:1361: error: redefinition of typedef 'VOIDP'
hdfi.h:779: error: previous declaration of 'VOIDP' was here
hdfi.h:1362: error: redefinition of typedef '_fcd'
hdfi.h:780: error: previous declaration of '_fcd' was here
hdfi.h:1363: error: redefinition of typedef 'char8'
hdfi.h:781: error: previous declaration of 'char8' was here
hdfi.h:1364: error: redefinition of typedef 'uchar8'
hdfi.h:782: error: previous declaration of 'uchar8' was here
hdfi.h:1365: error: redefinition of typedef 'int8'
hdfi.h:783: error: previous declaration of 'int8' was here
hdfi.h:1366: error: redefinition of typedef 'uint8'
hdfi.h:784: error: previous declaration of 'uint8' was here
hdfi.h:1367: error: redefinition of typedef 'int16'
hdfi.h:785: error: previous declaration of 'int16' was here
hdfi.h:1368: error: redefinition of typedef 'uint16'
hdfi.h:786: error: previous declaration of 'uint16' was here
hdfi.h:1369: error: redefinition of typedef 'int32'
hdfi.h:787: error: previous declaration of 'int32' was here
hdfi.h:1370: error: redefinition of typedef 'uint32'
hdfi.h:788: error: previous declaration of 'uint32' was here
hdfi.h:1371: error: redefinition of typedef 'intn'
hdfi.h:789: error: previous declaration of 'intn' was here
hdfi.h:1372: error: redefinition of typedef 'uintn'
hdfi.h:790: error: previous declaration of 'uintn' was here
hdfi.h:1373: error: redefinition of typedef 'intf'
hdfi.h:793: error: previous declaration of 'intf' was here
hdfi.h:1374: error: redefinition of typedef 'float32'
hdfi.h:791: error: previous declaration of 'float32' was here
hdfi.h:1375: error: redefinition of typedef 'float64'
hdfi.h:792: error: previous declaration of 'float64' was here
hdfi.h:1376: error: conflicting types for 'hdf_pint_t'
hdfi.h:794: error: previous declaration of 'hdf_pint_t' was here
make[3]: *** [atom.lo] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

4

Is that also a typo? Mac OS X 10.6 does not support Xcode 3.1.x, you
need to use 3.2 or later.

···

On 11/17/09 4:57 PM, HAGIHARA Yuichiro said:

Recently I upgraded to OS 10.6 with Xcode 3.1.2(gcc 4.2.1).

--
____________________________________________________________
Sean McBride, B. Eng sean@rogue-research.com
Rogue Research www.rogue-research.com
Mac Software Developer Montréal, Québec, Canada

5

Hi Guys,

I failed to read dataset from one of my HDF5 file.
Function H5Dread did not report error; but output data buffer filled with nonsense characters.

The dataset is simple one rank string and I want read whole string.

This file can be opened by application HDFView without problem.
How does HDFView read these dataset?
I really can not find any problem within my code.
What am I doing wrong or what am I missing?

Can somebody help me to check?

Many thanks,

Kathryn Yao Peng
Software Developer
Phone:905-764-0614 Ext:2233
Fax:905-764-0153
Email:peng@pcigeomatics.com
WebSite:www.pcigeomatics.com

hdf5read.cpp (11 KB)

···

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org] On Behalf Of Sean McBride
Sent: Tuesday, November 17, 2009 10:51 AM
To: hdf-forum@hdfgroup.org
Subject: Re: [Hdf-forum] Build failed HDF 4.2r4 on MacOS X 10.6 with intel fortran

On 11/17/09 4:57 PM, HAGIHARA Yuichiro said:

Recently I upgraded to OS 10.6 with Xcode 3.1.2(gcc 4.2.1).

Is that also a typo? Mac OS X 10.6 does not support Xcode 3.1.x, you
need to use 3.2 or later.

--
____________________________________________________________
Sean McBride, B. Eng sean@rogue-research.com
Rogue Research www.rogue-research.com
Mac Software Developer Montréal, Québec, Canada

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

6

Yes, Mike's suggestion should work.

I am working on the 64-bit port. It should be available for the HDF4.2r5 release coming January 2010. I will be more than happy to share the port as soon as becomes available.

Elena

···

On Nov 17, 2009, at 8:17 AM, Michael Jackson wrote:

OS X 10.6 defaults to a 64 bit build for GCC. You may have to add the "-arch i386" to the CFLAGS and CPPFLAGS to force a 32 bit build.

_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

On Nov 17, 2009, at 2:57 AM, HAGIHARA Yuichiro wrote:

Hello,

Recently I upgraded to OS 10.6 with Xcode 3.1.2(gcc 4.2.1).
But, I failed to build HDF 4.2r4 with intel fortran 11.1.

As the HDF release note said that "only the 32-bit version of
the Intel compiler is supported", I followed it.

I can build zlib and jpeg libraries, but can't HDF as stated below.

Are there any tips or suggestions?

Best,
Yuichiro Hagihara

$ tar xzf zlib-1.2.3.tar.gz
$ cd zlib-1.2.3
$ ./configure
$ make test
$ sudo make install

$ tar xzf jpegsrc.v6b.tar.gz
$ cd jpeg-6b
$ cp /usr/share/libtool/config/config.guess .
$ cp /usr/share/libtool/config/config.sub .
$ ./configure --enable-shared --enable-static
$ make
$ sudo make install

$ tar xzf HDF4.2r3
$ cd HDF4.2r3
$ ./configure --with-jpeg=/usr/local --with-zlib=/usr/local --prefix=/usr/local

Configure summary
Compiling Options:
------------------
             Compilation Mode: Default
                   C Compiler: gcc
                       CFLAGS: -O2
                     CPPFLAGS: -I/usr/include/rpc -I/usr/local/include -I/usr/local/include -DBIG_LONGS -DSWAP
                      LDFLAGS: -L/usr/local/lib -L/usr/local/lib
             Shared Libraries: no
             Static Libraries: yes

Languages:
----------
                      Fortran: Yes
             Fortran Compiler: ifort
                       FFLAGS:

Features:
---------
             SZIP compression: disabled

HDF support for NetCDF-3 APIs:
------------------------------
                  HDF4-NetCDF: Yes

$ make
Making all in hdf
Making all in src
make all-am
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -I/usr/local/include -I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT atom.lo -MD -MP -MF .deps/atom.Tpo -c -o atom.lo atom.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -I/usr/local/include -I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT atom.lo -MD -MP -MF .deps/atom.Tpo -c atom.c -o atom.o
In file included from hdf.h:20,
               from atom.c:64:
hdfi.h:1352: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'you'
In file included from hdf.h:20,
               from atom.c:64:
hdfi.h:1355:1: warning: "GOT_MACHINE" redefined
hdfi.h:760:1: warning: this is the location of the previous definition
hdfi.h:1359:1: warning: "DF_MT" redefined
hdfi.h:775:1: warning: this is the location of the previous definition
hdfi.h:1361: error: redefinition of typedef 'VOIDP'
hdfi.h:779: error: previous declaration of 'VOIDP' was here
hdfi.h:1362: error: redefinition of typedef '_fcd'
hdfi.h:780: error: previous declaration of '_fcd' was here
hdfi.h:1363: error: redefinition of typedef 'char8'
hdfi.h:781: error: previous declaration of 'char8' was here
hdfi.h:1364: error: redefinition of typedef 'uchar8'
hdfi.h:782: error: previous declaration of 'uchar8' was here
hdfi.h:1365: error: redefinition of typedef 'int8'
hdfi.h:783: error: previous declaration of 'int8' was here
hdfi.h:1366: error: redefinition of typedef 'uint8'
hdfi.h:784: error: previous declaration of 'uint8' was here
hdfi.h:1367: error: redefinition of typedef 'int16'
hdfi.h:785: error: previous declaration of 'int16' was here
hdfi.h:1368: error: redefinition of typedef 'uint16'
hdfi.h:786: error: previous declaration of 'uint16' was here
hdfi.h:1369: error: redefinition of typedef 'int32'
hdfi.h:787: error: previous declaration of 'int32' was here
hdfi.h:1370: error: redefinition of typedef 'uint32'
hdfi.h:788: error: previous declaration of 'uint32' was here
hdfi.h:1371: error: redefinition of typedef 'intn'
hdfi.h:789: error: previous declaration of 'intn' was here
hdfi.h:1372: error: redefinition of typedef 'uintn'
hdfi.h:790: error: previous declaration of 'uintn' was here
hdfi.h:1373: error: redefinition of typedef 'intf'
hdfi.h:793: error: previous declaration of 'intf' was here
hdfi.h:1374: error: redefinition of typedef 'float32'
hdfi.h:791: error: previous declaration of 'float32' was here
hdfi.h:1375: error: redefinition of typedef 'float64'
hdfi.h:792: error: previous declaration of 'float64' was here
hdfi.h:1376: error: conflicting types for 'hdf_pint_t'
hdfi.h:794: error: previous declaration of 'hdf_pint_t' was here
make[3]: *** [atom.lo] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

7

Hi Binh-Minh,

Sorry, typo, it's HDF4.2r4 not r3.
I failed to build HDF4.2"r4".

Best,
Yuichiro Hagihara

···

On Tue, 17 Nov 2009 03:26:44 -0500, Binh-Minh Ribler wrote:

Hi Yuichiro,

I'm not exactly sure what the problem is, but it seemed that you built HDF
4.2r3 not 4.2r4. You might want to try 4.2r4, perhaps, new configuration
was added between r3 and r4.

Binh-Minh

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-
bounces@hdfgroup.org] On Behalf Of HAGIHARA Yuichiro
Sent: Tuesday, November 17, 2009 2:57 AM
To: hdf-forum@hdfgroup.org
Subject: [Hdf-forum] Build failed HDF 4.2r4 on MacOS X 10.6 with
intelfortran

Hello,

Recently I upgraded to OS 10.6 with Xcode 3.1.2(gcc 4.2.1).
But, I failed to build HDF 4.2r4 with intel fortran 11.1.

As the HDF release note said that "only the 32-bit version of
the Intel compiler is supported", I followed it.

I can build zlib and jpeg libraries, but can't HDF as stated below.

Are there any tips or suggestions?

Best,
Yuichiro Hagihara

$ tar xzf zlib-1.2.3.tar.gz
$ cd zlib-1.2.3
$ ./configure
$ make test
$ sudo make install

$ tar xzf jpegsrc.v6b.tar.gz
$ cd jpeg-6b
$ cp /usr/share/libtool/config/config.guess .
$ cp /usr/share/libtool/config/config.sub .
$ ./configure --enable-shared --enable-static
$ make
$ sudo make install

$ tar xzf HDF4.2r3
$ cd HDF4.2r3
$ ./configure --with-jpeg=/usr/local --with-zlib=/usr/local --
prefix=/usr/local

Configure summary
Compiling Options:
------------------
              Compilation Mode: Default
                    C Compiler: gcc
                        CFLAGS: -O2
                      CPPFLAGS: -I/usr/include/rpc -I/usr/local/include
-I/usr/local/include -DBIG_LONGS -DSWAP
                       LDFLAGS: -L/usr/local/lib -L/usr/local/lib
              Shared Libraries: no
              Static Libraries: yes

Languages:
----------
                       Fortran: Yes
              Fortran Compiler: ifort
                        FFLAGS:

Features:
---------
              SZIP compression: disabled

HDF support for NetCDF-3 APIs:
------------------------------
                   HDF4-NetCDF: Yes

$ make
Making all in hdf
Making all in src
make all-am
/bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -
I/usr/include/rpc -I/usr/local/include -I/usr/local/include -DBIG_LONGS -
DSWAP -O2 -MT atom.lo -MD -MP -MF .deps/atom.Tpo -c -o atom.lo atom.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -
I/usr/local/include -I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT atom.lo
-MD -MP -MF .deps/atom.Tpo -c atom.c -o atom.o
In file included from hdf.h:20,
                from atom.c:64:
hdfi.h:1352: error: expected '=', ',', ';', 'asm' or '__attribute__' before
'you'
In file included from hdf.h:20,
                from atom.c:64:
hdfi.h:1355:1: warning: "GOT_MACHINE" redefined
hdfi.h:760:1: warning: this is the location of the previous definition
hdfi.h:1359:1: warning: "DF_MT" redefined
hdfi.h:775:1: warning: this is the location of the previous definition
hdfi.h:1361: error: redefinition of typedef 'VOIDP'
hdfi.h:779: error: previous declaration of 'VOIDP' was here
hdfi.h:1362: error: redefinition of typedef '_fcd'
hdfi.h:780: error: previous declaration of '_fcd' was here
hdfi.h:1363: error: redefinition of typedef 'char8'
hdfi.h:781: error: previous declaration of 'char8' was here
hdfi.h:1364: error: redefinition of typedef 'uchar8'
hdfi.h:782: error: previous declaration of 'uchar8' was here
hdfi.h:1365: error: redefinition of typedef 'int8'
hdfi.h:783: error: previous declaration of 'int8' was here
hdfi.h:1366: error: redefinition of typedef 'uint8'
hdfi.h:784: error: previous declaration of 'uint8' was here
hdfi.h:1367: error: redefinition of typedef 'int16'
hdfi.h:785: error: previous declaration of 'int16' was here
hdfi.h:1368: error: redefinition of typedef 'uint16'
hdfi.h:786: error: previous declaration of 'uint16' was here
hdfi.h:1369: error: redefinition of typedef 'int32'
hdfi.h:787: error: previous declaration of 'int32' was here
hdfi.h:1370: error: redefinition of typedef 'uint32'
hdfi.h:788: error: previous declaration of 'uint32' was here
hdfi.h:1371: error: redefinition of typedef 'intn'
hdfi.h:789: error: previous declaration of 'intn' was here
hdfi.h:1372: error: redefinition of typedef 'uintn'
hdfi.h:790: error: previous declaration of 'uintn' was here
hdfi.h:1373: error: redefinition of typedef 'intf'
hdfi.h:793: error: previous declaration of 'intf' was here
hdfi.h:1374: error: redefinition of typedef 'float32'
hdfi.h:791: error: previous declaration of 'float32' was here
hdfi.h:1375: error: redefinition of typedef 'float64'
hdfi.h:792: error: previous declaration of 'float64' was here
hdfi.h:1376: error: conflicting types for 'hdf_pint_t'
hdfi.h:794: error: previous declaration of 'hdf_pint_t' was here
make[3]: *** [atom.lo] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

8

Hi,

I have a question about current support status of type H5T_VLEN.
I failed read this dataset because of my dataset type is H5T_VLEN.

I can see; function "H5T_vlen_disk_read" attached to this type of data.
During reading; it is actually read by function "H5D_scatgath_read".
I think some problem related this data type.

I did not get any error and buffer is filled with nonsense.

Thanks,
Kathryn

···

-----Original Message-----
From: Kathryn (Yao) Peng
Sent: Tuesday, November 17, 2009 11:32 AM
To: 'hdf-forum@hdfgroup.org'
Subject: RE: [Hdf-forum] Build failed HDF 4.2r4 on MacOS X 10.6 with intel fortran

Hi Guys,

I failed to read dataset from one of my HDF5 file.
Function H5Dread did not report error; but output data buffer filled with nonsense characters.

The dataset is simple one rank string and I want read whole string.

This file can be opened by application HDFView without problem.
How does HDFView read these dataset?
I really can not find any problem within my code.
What am I doing wrong or what am I missing?

Can somebody help me to check?

Many thanks,

Kathryn Yao Peng
Software Developer
Phone:905-764-0614 Ext:2233
Fax:905-764-0153
Email:peng@pcigeomatics.com
WebSite:www.pcigeomatics.com

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org] On Behalf Of Sean McBride
Sent: Tuesday, November 17, 2009 10:51 AM
To: hdf-forum@hdfgroup.org
Subject: Re: [Hdf-forum] Build failed HDF 4.2r4 on MacOS X 10.6 with intel fortran

On 11/17/09 4:57 PM, HAGIHARA Yuichiro said:

Recently I upgraded to OS 10.6 with Xcode 3.1.2(gcc 4.2.1).

Is that also a typo? Mac OS X 10.6 does not support Xcode 3.1.x, you
need to use 3.2 or later.

--
____________________________________________________________
Sean McBride, B. Eng sean@rogue-research.com
Rogue Research www.rogue-research.com
Mac Software Developer Montréal, Québec, Canada

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

9

Thanks for the response.

First of all, I used Xcode 3.2.1 not 3.1.2.

I succeeded in making HDF with "-arch i386" flags,

$ export CFLAGS="-arch i386"
$ export CPPFLAGS="-arch i386"
$ export LDFLAGS="-arch i386"

but I had an error at make check.

···

============================
HDF-nc C interface tests

srcdir="." ./hdfnctest
Testing read/write datasets with unlimited dimensions via SD API PASSED
Testing read/write variables with unlimited dimensions via nc API make[2]: *** [check] Abort trap
make[1]: *** [check-recursive] Error 1
make: *** [check-recursive] Error 1

While I tried to make with "--disalbed-netcdf", I got same error.
Any other ideas/suggestions are mostly welcome.

Best,
Yuichiro Hagihara

On Tue, 17 Nov 2009 09:17:37 -0500, Michael Jackson wrote:

OS X 10.6 defaults to a 64 bit build for GCC. You may have to add the
"-arch i386" to the CFLAGS and CPPFLAGS to force a 32 bit build.

_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

On Nov 17, 2009, at 2:57 AM, HAGIHARA Yuichiro wrote:

Hello,

Recently I upgraded to OS 10.6 with Xcode 3.1.2(gcc 4.2.1).
But, I failed to build HDF 4.2r4 with intel fortran 11.1.

As the HDF release note said that "only the 32-bit version of
the Intel compiler is supported", I followed it.

I can build zlib and jpeg libraries, but can't HDF as stated below.

Are there any tips or suggestions?

Best,
Yuichiro Hagihara

$ tar xzf zlib-1.2.3.tar.gz
$ cd zlib-1.2.3
$ ./configure
$ make test
$ sudo make install

$ tar xzf jpegsrc.v6b.tar.gz
$ cd jpeg-6b
$ cp /usr/share/libtool/config/config.guess .
$ cp /usr/share/libtool/config/config.sub .
$ ./configure --enable-shared --enable-static
$ make
$ sudo make install

$ tar xzf HDF4.2r3
$ cd HDF4.2r3
$ ./configure --with-jpeg=/usr/local --with-zlib=/usr/local --prefix=/usr/local

Configure summary
Compiling Options:
------------------
              Compilation Mode: Default
                    C Compiler: gcc
                        CFLAGS: -O2
                      
CPPFLAGS: -I/usr/include/rpc -I/usr/local/include -I/usr/local/include -DBIG_LONGS -DSWAP
                       LDFLAGS: -L/usr/local/lib -L/usr/local/lib
              Shared Libraries: no
              Static Libraries: yes

Languages:
----------
                       Fortran: Yes
              Fortran Compiler: ifort
                        FFLAGS:

Features:
---------
              SZIP compression: disabled

HDF support for NetCDF-3 APIs:
------------------------------
                   HDF4-NetCDF: Yes

$ make
Making all in hdf
Making all in src
make all-am
/bin/sh ../../libtool --tag=CC --mode=compile
gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -I/usr/local/include -I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT
atom.lo -MD -MP -MF .deps/atom.Tpo -c -o atom.lo atom.c
libtool: compile:
gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -I/usr/local/include -I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT
atom.lo -MD -MP -MF .deps/atom.Tpo -c atom.c -o atom.o
In file included from hdf.h:20,
                from atom.c:64:
hdfi.h:1352: error: expected '=', ',', ';', 'asm' or '__attribute__'
before 'you'
In file included from hdf.h:20,
                from atom.c:64:
hdfi.h:1355:1: warning: "GOT_MACHINE" redefined
hdfi.h:760:1: warning: this is the location of the previous definition
hdfi.h:1359:1: warning: "DF_MT" redefined
hdfi.h:775:1: warning: this is the location of the previous definition
hdfi.h:1361: error: redefinition of typedef 'VOIDP'
hdfi.h:779: error: previous declaration of 'VOIDP' was here
hdfi.h:1362: error: redefinition of typedef '_fcd'
hdfi.h:780: error: previous declaration of '_fcd' was here
hdfi.h:1363: error: redefinition of typedef 'char8'
hdfi.h:781: error: previous declaration of 'char8' was here
hdfi.h:1364: error: redefinition of typedef 'uchar8'
hdfi.h:782: error: previous declaration of 'uchar8' was here
hdfi.h:1365: error: redefinition of typedef 'int8'
hdfi.h:783: error: previous declaration of 'int8' was here
hdfi.h:1366: error: redefinition of typedef 'uint8'
hdfi.h:784: error: previous declaration of 'uint8' was here
hdfi.h:1367: error: redefinition of typedef 'int16'
hdfi.h:785: error: previous declaration of 'int16' was here
hdfi.h:1368: error: redefinition of typedef 'uint16'
hdfi.h:786: error: previous declaration of 'uint16' was here
hdfi.h:1369: error: redefinition of typedef 'int32'
hdfi.h:787: error: previous declaration of 'int32' was here
hdfi.h:1370: error: redefinition of typedef 'uint32'
hdfi.h:788: error: previous declaration of 'uint32' was here
hdfi.h:1371: error: redefinition of typedef 'intn'
hdfi.h:789: error: previous declaration of 'intn' was here
hdfi.h:1372: error: redefinition of typedef 'uintn'
hdfi.h:790: error: previous declaration of 'uintn' was here
hdfi.h:1373: error: redefinition of typedef 'intf'
hdfi.h:793: error: previous declaration of 'intf' was here
hdfi.h:1374: error: redefinition of typedef 'float32'
hdfi.h:791: error: previous declaration of 'float32' was here
hdfi.h:1375: error: redefinition of typedef 'float64'
hdfi.h:792: error: previous declaration of 'float64' was here
hdfi.h:1376: error: conflicting types for 'hdf_pint_t'
hdfi.h:794: error: previous declaration of 'hdf_pint_t' was here
make[3]: *** [atom.lo] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

10

Hmm... Looks bad. We will need to investigate.

Elena

···

On Nov 17, 2009, at 9:16 PM, HAGIHARA Yuichiro wrote:

Thanks for the response.

First of all, I used Xcode 3.2.1 not 3.1.2.

I succeeded in making HDF with "-arch i386" flags,

$ export CFLAGS="-arch i386"
$ export CPPFLAGS="-arch i386"
$ export LDFLAGS="-arch i386"

but I had an error at make check.

============================
HDF-nc C interface tests

srcdir="." ./hdfnctest
Testing read/write datasets with unlimited dimensions via SD API PASSED
Testing read/write variables with unlimited dimensions via nc API make[2]: *** [check] Abort trap
make[1]: *** [check-recursive] Error 1
make: *** [check-recursive] Error 1

While I tried to make with "--disalbed-netcdf", I got same error.
Any other ideas/suggestions are mostly welcome.

Best,
Yuichiro Hagihara

On Tue, 17 Nov 2009 09:17:37 -0500, Michael Jackson wrote:

OS X 10.6 defaults to a 64 bit build for GCC. You may have to add the
"-arch i386" to the CFLAGS and CPPFLAGS to force a 32 bit build.

_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

On Nov 17, 2009, at 2:57 AM, HAGIHARA Yuichiro wrote:

Hello,

Recently I upgraded to OS 10.6 with Xcode 3.1.2(gcc 4.2.1).
But, I failed to build HDF 4.2r4 with intel fortran 11.1.

As the HDF release note said that "only the 32-bit version of
the Intel compiler is supported", I followed it.

I can build zlib and jpeg libraries, but can't HDF as stated below.

Are there any tips or suggestions?

Best,
Yuichiro Hagihara

$ tar xzf zlib-1.2.3.tar.gz
$ cd zlib-1.2.3
$ ./configure
$ make test
$ sudo make install

$ tar xzf jpegsrc.v6b.tar.gz
$ cd jpeg-6b
$ cp /usr/share/libtool/config/config.guess .
$ cp /usr/share/libtool/config/config.sub .
$ ./configure --enable-shared --enable-static
$ make
$ sudo make install

$ tar xzf HDF4.2r3
$ cd HDF4.2r3
$ ./configure --with-jpeg=/usr/local --with-zlib=/usr/local --prefix=/usr/local

Configure summary
Compiling Options:
------------------
             Compilation Mode: Default
                   C Compiler: gcc
                       CFLAGS: -O2

CPPFLAGS: -I/usr/include/rpc -I/usr/local/include -I/usr/local/include -DBIG_LONGS -DSWAP
                      LDFLAGS: -L/usr/local/lib -L/usr/local/lib
             Shared Libraries: no
             Static Libraries: yes

Languages:
----------
                      Fortran: Yes
             Fortran Compiler: ifort
                       FFLAGS:

Features:
---------
             SZIP compression: disabled

HDF support for NetCDF-3 APIs:
------------------------------
                  HDF4-NetCDF: Yes

$ make
Making all in hdf
Making all in src
make all-am
/bin/sh ../../libtool --tag=CC --mode=compile
gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -I/usr/local/include -I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT
atom.lo -MD -MP -MF .deps/atom.Tpo -c -o atom.lo atom.c
libtool: compile:
gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -I/usr/local/include -I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT
atom.lo -MD -MP -MF .deps/atom.Tpo -c atom.c -o atom.o
In file included from hdf.h:20,
               from atom.c:64:
hdfi.h:1352: error: expected '=', ',', ';', 'asm' or '__attribute__'
before 'you'
In file included from hdf.h:20,
               from atom.c:64:
hdfi.h:1355:1: warning: "GOT_MACHINE" redefined
hdfi.h:760:1: warning: this is the location of the previous definition
hdfi.h:1359:1: warning: "DF_MT" redefined
hdfi.h:775:1: warning: this is the location of the previous definition
hdfi.h:1361: error: redefinition of typedef 'VOIDP'
hdfi.h:779: error: previous declaration of 'VOIDP' was here
hdfi.h:1362: error: redefinition of typedef '_fcd'
hdfi.h:780: error: previous declaration of '_fcd' was here
hdfi.h:1363: error: redefinition of typedef 'char8'
hdfi.h:781: error: previous declaration of 'char8' was here
hdfi.h:1364: error: redefinition of typedef 'uchar8'
hdfi.h:782: error: previous declaration of 'uchar8' was here
hdfi.h:1365: error: redefinition of typedef 'int8'
hdfi.h:783: error: previous declaration of 'int8' was here
hdfi.h:1366: error: redefinition of typedef 'uint8'
hdfi.h:784: error: previous declaration of 'uint8' was here
hdfi.h:1367: error: redefinition of typedef 'int16'
hdfi.h:785: error: previous declaration of 'int16' was here
hdfi.h:1368: error: redefinition of typedef 'uint16'
hdfi.h:786: error: previous declaration of 'uint16' was here
hdfi.h:1369: error: redefinition of typedef 'int32'
hdfi.h:787: error: previous declaration of 'int32' was here
hdfi.h:1370: error: redefinition of typedef 'uint32'
hdfi.h:788: error: previous declaration of 'uint32' was here
hdfi.h:1371: error: redefinition of typedef 'intn'
hdfi.h:789: error: previous declaration of 'intn' was here
hdfi.h:1372: error: redefinition of typedef 'uintn'
hdfi.h:790: error: previous declaration of 'uintn' was here
hdfi.h:1373: error: redefinition of typedef 'intf'
hdfi.h:793: error: previous declaration of 'intf' was here
hdfi.h:1374: error: redefinition of typedef 'float32'
hdfi.h:791: error: previous declaration of 'float32' was here
hdfi.h:1375: error: redefinition of typedef 'float64'
hdfi.h:792: error: previous declaration of 'float64' was here
hdfi.h:1376: error: conflicting types for 'hdf_pint_t'
hdfi.h:794: error: previous declaration of 'hdf_pint_t' was here
make[3]: *** [atom.lo] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

11

Hi Yuichiro,

In that test, there was a bug reported and fixed right after the release. I
think that bug was the reason of the failure you saw. If you want to try,
you may change line 62 in the file tncunlim.c from:

char varname[10]; /* variable name */
to:
char varname[11]; /* variable name */

Thank you!
Binh-Minh

···

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-
bounces@hdfgroup.org] On Behalf Of HAGIHARA Yuichiro
Sent: Tuesday, November 17, 2009 10:17 PM
To: hdf-forum@hdfgroup.org
Subject: Re: [Hdf-forum] Build failed HDF 4.2r4 on MacOS X 10.6 with intel
fortran

Thanks for the response.

First of all, I used Xcode 3.2.1 not 3.1.2.

I succeeded in making HDF with "-arch i386" flags,

$ export CFLAGS="-arch i386"
$ export CPPFLAGS="-arch i386"
$ export LDFLAGS="-arch i386"

but I had an error at make check.

============================
HDF-nc C interface tests

srcdir="." ./hdfnctest
Testing read/write datasets with unlimited dimensions via SD API
PASSED
Testing read/write variables with unlimited dimensions via nc API
make[2]: *** [check] Abort trap
make[1]: *** [check-recursive] Error 1
make: *** [check-recursive] Error 1

While I tried to make with "--disalbed-netcdf", I got same error.
Any other ideas/suggestions are mostly welcome.

Best,
Yuichiro Hagihara

On Tue, 17 Nov 2009 09:17:37 -0500, Michael Jackson wrote:

OS X 10.6 defaults to a 64 bit build for GCC. You may have to add the
"-arch i386" to the CFLAGS and CPPFLAGS to force a 32 bit build.

_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

On Nov 17, 2009, at 2:57 AM, HAGIHARA Yuichiro wrote:

Hello,

Recently I upgraded to OS 10.6 with Xcode 3.1.2(gcc 4.2.1).
But, I failed to build HDF 4.2r4 with intel fortran 11.1.

As the HDF release note said that "only the 32-bit version of
the Intel compiler is supported", I followed it.

I can build zlib and jpeg libraries, but can't HDF as stated below.

Are there any tips or suggestions?

Best,
Yuichiro Hagihara

$ tar xzf zlib-1.2.3.tar.gz
$ cd zlib-1.2.3
$ ./configure
$ make test
$ sudo make install

$ tar xzf jpegsrc.v6b.tar.gz
$ cd jpeg-6b
$ cp /usr/share/libtool/config/config.guess .
$ cp /usr/share/libtool/config/config.sub .
$ ./configure --enable-shared --enable-static
$ make
$ sudo make install

$ tar xzf HDF4.2r3
$ cd HDF4.2r3
$ ./configure --with-jpeg=/usr/local --with-zlib=/usr/local --

prefix=/usr/local

Configure summary
Compiling Options:
------------------
              Compilation Mode: Default
                    C Compiler: gcc
                        CFLAGS: -O2

CPPFLAGS: -I/usr/include/rpc -I/usr/local/include -I/usr/local/include

-DBIG_LONGS -DSWAP

                       LDFLAGS: -L/usr/local/lib -L/usr/local/lib
              Shared Libraries: no
              Static Libraries: yes

Languages:
----------
                       Fortran: Yes
              Fortran Compiler: ifort
                        FFLAGS:

Features:
---------
              SZIP compression: disabled

HDF support for NetCDF-3 APIs:
------------------------------
                   HDF4-NetCDF: Yes

$ make
Making all in hdf
Making all in src
make all-am
/bin/sh ../../libtool --tag=CC --mode=compile
gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -I/usr/local/include -

I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT

atom.lo -MD -MP -MF .deps/atom.Tpo -c -o atom.lo atom.c
libtool: compile:
gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -I/usr/local/include -

I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT

atom.lo -MD -MP -MF .deps/atom.Tpo -c atom.c -o atom.o
In file included from hdf.h:20,
                from atom.c:64:
hdfi.h:1352: error: expected '=', ',', ';', 'asm' or '__attribute__'
before 'you'
In file included from hdf.h:20,
                from atom.c:64:
hdfi.h:1355:1: warning: "GOT_MACHINE" redefined
hdfi.h:760:1: warning: this is the location of the previous definition
hdfi.h:1359:1: warning: "DF_MT" redefined
hdfi.h:775:1: warning: this is the location of the previous definition
hdfi.h:1361: error: redefinition of typedef 'VOIDP'
hdfi.h:779: error: previous declaration of 'VOIDP' was here
hdfi.h:1362: error: redefinition of typedef '_fcd'
hdfi.h:780: error: previous declaration of '_fcd' was here
hdfi.h:1363: error: redefinition of typedef 'char8'
hdfi.h:781: error: previous declaration of 'char8' was here
hdfi.h:1364: error: redefinition of typedef 'uchar8'
hdfi.h:782: error: previous declaration of 'uchar8' was here
hdfi.h:1365: error: redefinition of typedef 'int8'
hdfi.h:783: error: previous declaration of 'int8' was here
hdfi.h:1366: error: redefinition of typedef 'uint8'
hdfi.h:784: error: previous declaration of 'uint8' was here
hdfi.h:1367: error: redefinition of typedef 'int16'
hdfi.h:785: error: previous declaration of 'int16' was here
hdfi.h:1368: error: redefinition of typedef 'uint16'
hdfi.h:786: error: previous declaration of 'uint16' was here
hdfi.h:1369: error: redefinition of typedef 'int32'
hdfi.h:787: error: previous declaration of 'int32' was here
hdfi.h:1370: error: redefinition of typedef 'uint32'
hdfi.h:788: error: previous declaration of 'uint32' was here
hdfi.h:1371: error: redefinition of typedef 'intn'
hdfi.h:789: error: previous declaration of 'intn' was here
hdfi.h:1372: error: redefinition of typedef 'uintn'
hdfi.h:790: error: previous declaration of 'uintn' was here
hdfi.h:1373: error: redefinition of typedef 'intf'
hdfi.h:793: error: previous declaration of 'intf' was here
hdfi.h:1374: error: redefinition of typedef 'float32'
hdfi.h:791: error: previous declaration of 'float32' was here
hdfi.h:1375: error: redefinition of typedef 'float64'
hdfi.h:792: error: previous declaration of 'float64' was here
hdfi.h:1376: error: conflicting types for 'hdf_pint_t'
hdfi.h:794: error: previous declaration of 'hdf_pint_t' was here
make[3]: *** [atom.lo] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

--
Internal Virus Database is out-of-date.
Checked by AVG.
Version: 7.5.549 / Virus Database: 270.9.0/1778 - Release Date: 11/9/2008
2:14 PM

12

Hi Binh-Minh,

I tried to build with changed mfhdf/libsrc/tncunlim.c,
but failed to make check again.

Thanks for your suggestions.

Best,
Yuichiro Hagihara

···

On Wed, 18 Nov 2009 03:52:52 -0500, Binh-Minh Ribler wrote:

Hi Yuichiro,

In that test, there was a bug reported and fixed right after the release. I
think that bug was the reason of the failure you saw. If you want to try,
you may change line 62 in the file tncunlim.c from:

char varname[10]; /* variable name */
to:
char varname[11]; /* variable name */

Thank you!
Binh-Minh

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-
bounces@hdfgroup.org] On Behalf Of HAGIHARA Yuichiro
Sent: Tuesday, November 17, 2009 10:17 PM
To: hdf-forum@hdfgroup.org
Subject: Re: [Hdf-forum] Build failed HDF 4.2r4 on MacOS X 10.6 with intel
fortran

Thanks for the response.

First of all, I used Xcode 3.2.1 not 3.1.2.

I succeeded in making HDF with "-arch i386" flags,

$ export CFLAGS="-arch i386"
$ export CPPFLAGS="-arch i386"
$ export LDFLAGS="-arch i386"

but I had an error at make check.

============================
HDF-nc C interface tests

srcdir="." ./hdfnctest
Testing read/write datasets with unlimited dimensions via SD API
PASSED
Testing read/write variables with unlimited dimensions via nc API
make[2]: *** [check] Abort trap
make[1]: *** [check-recursive] Error 1
make: *** [check-recursive] Error 1

While I tried to make with "--disalbed-netcdf", I got same error.
Any other ideas/suggestions are mostly welcome.

Best,
Yuichiro Hagihara

On Tue, 17 Nov 2009 09:17:37 -0500, Michael Jackson wrote:

OS X 10.6 defaults to a 64 bit build for GCC. You may have to add the
"-arch i386" to the CFLAGS and CPPFLAGS to force a 32 bit build.

_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

On Nov 17, 2009, at 2:57 AM, HAGIHARA Yuichiro wrote:

Hello,

Recently I upgraded to OS 10.6 with Xcode 3.1.2(gcc 4.2.1).
But, I failed to build HDF 4.2r4 with intel fortran 11.1.

As the HDF release note said that "only the 32-bit version of
the Intel compiler is supported", I followed it.

I can build zlib and jpeg libraries, but can't HDF as stated below.

Are there any tips or suggestions?

Best,
Yuichiro Hagihara

$ tar xzf zlib-1.2.3.tar.gz
$ cd zlib-1.2.3
$ ./configure
$ make test
$ sudo make install

$ tar xzf jpegsrc.v6b.tar.gz
$ cd jpeg-6b
$ cp /usr/share/libtool/config/config.guess .
$ cp /usr/share/libtool/config/config.sub .
$ ./configure --enable-shared --enable-static
$ make
$ sudo make install

$ tar xzf HDF4.2r3
$ cd HDF4.2r3
$ ./configure --with-jpeg=/usr/local --with-zlib=/usr/local --

prefix=/usr/local

Configure summary
Compiling Options:
------------------
              Compilation Mode: Default
                    C Compiler: gcc
                        CFLAGS: -O2

CPPFLAGS: -I/usr/include/rpc -I/usr/local/include -I/usr/local/include

-DBIG_LONGS -DSWAP

                       LDFLAGS: -L/usr/local/lib -L/usr/local/lib
              Shared Libraries: no
              Static Libraries: yes

Languages:
----------
                       Fortran: Yes
              Fortran Compiler: ifort
                        FFLAGS:

Features:
---------
              SZIP compression: disabled

HDF support for NetCDF-3 APIs:
------------------------------
                   HDF4-NetCDF: Yes

$ make
Making all in hdf
Making all in src
make all-am
/bin/sh ../../libtool --tag=CC --mode=compile
gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -I/usr/local/include -

I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT

atom.lo -MD -MP -MF .deps/atom.Tpo -c -o atom.lo atom.c
libtool: compile:
gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -I/usr/local/include -

I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT

atom.lo -MD -MP -MF .deps/atom.Tpo -c atom.c -o atom.o
In file included from hdf.h:20,
                from atom.c:64:
hdfi.h:1352: error: expected '=', ',', ';', 'asm' or '__attribute__'
before 'you'
In file included from hdf.h:20,
                from atom.c:64:
hdfi.h:1355:1: warning: "GOT_MACHINE" redefined
hdfi.h:760:1: warning: this is the location of the previous definition
hdfi.h:1359:1: warning: "DF_MT" redefined
hdfi.h:775:1: warning: this is the location of the previous definition
hdfi.h:1361: error: redefinition of typedef 'VOIDP'
hdfi.h:779: error: previous declaration of 'VOIDP' was here
hdfi.h:1362: error: redefinition of typedef '_fcd'
hdfi.h:780: error: previous declaration of '_fcd' was here
hdfi.h:1363: error: redefinition of typedef 'char8'
hdfi.h:781: error: previous declaration of 'char8' was here
hdfi.h:1364: error: redefinition of typedef 'uchar8'
hdfi.h:782: error: previous declaration of 'uchar8' was here
hdfi.h:1365: error: redefinition of typedef 'int8'
hdfi.h:783: error: previous declaration of 'int8' was here
hdfi.h:1366: error: redefinition of typedef 'uint8'
hdfi.h:784: error: previous declaration of 'uint8' was here
hdfi.h:1367: error: redefinition of typedef 'int16'
hdfi.h:785: error: previous declaration of 'int16' was here
hdfi.h:1368: error: redefinition of typedef 'uint16'
hdfi.h:786: error: previous declaration of 'uint16' was here
hdfi.h:1369: error: redefinition of typedef 'int32'
hdfi.h:787: error: previous declaration of 'int32' was here
hdfi.h:1370: error: redefinition of typedef 'uint32'
hdfi.h:788: error: previous declaration of 'uint32' was here
hdfi.h:1371: error: redefinition of typedef 'intn'
hdfi.h:789: error: previous declaration of 'intn' was here
hdfi.h:1372: error: redefinition of typedef 'uintn'
hdfi.h:790: error: previous declaration of 'uintn' was here
hdfi.h:1373: error: redefinition of typedef 'intf'
hdfi.h:793: error: previous declaration of 'intf' was here
hdfi.h:1374: error: redefinition of typedef 'float32'
hdfi.h:791: error: previous declaration of 'float32' was here
hdfi.h:1375: error: redefinition of typedef 'float64'
hdfi.h:792: error: previous declaration of 'float64' was here
hdfi.h:1376: error: conflicting types for 'hdf_pint_t'
hdfi.h:794: error: previous declaration of 'hdf_pint_t' was here
make[3]: *** [atom.lo] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

13

Hi Yuichiro,

We will have to investigate it on the specific platform. In the meantime,
if you would like to disable that test, you may do so in hdfnctest.c.

Thank you for your patience!
Binh-Minh

···

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-
bounces@hdfgroup.org] On Behalf Of HAGIHARA Yuichiro
Sent: Wednesday, November 18, 2009 4:39 AM
To: hdf-forum@hdfgroup.org
Subject: Re: [Hdf-forum] Build failed HDF 4.2r4 on MacOS X 10.6 with intel
fortran

Hi Binh-Minh,

I tried to build with changed mfhdf/libsrc/tncunlim.c,
but failed to make check again.

Thanks for your suggestions.

Best,
Yuichiro Hagihara

On Wed, 18 Nov 2009 03:52:52 -0500, Binh-Minh Ribler wrote:

Hi Yuichiro,

In that test, there was a bug reported and fixed right after the release.

I

think that bug was the reason of the failure you saw. If you want to

try,

you may change line 62 in the file tncunlim.c from:

char varname[10]; /* variable name */
to:
char varname[11]; /* variable name */

Thank you!
Binh-Minh

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-
bounces@hdfgroup.org] On Behalf Of HAGIHARA Yuichiro
Sent: Tuesday, November 17, 2009 10:17 PM
To: hdf-forum@hdfgroup.org
Subject: Re: [Hdf-forum] Build failed HDF 4.2r4 on MacOS X 10.6 with

intel

fortran

Thanks for the response.

First of all, I used Xcode 3.2.1 not 3.1.2.

I succeeded in making HDF with "-arch i386" flags,

$ export CFLAGS="-arch i386"
$ export CPPFLAGS="-arch i386"
$ export LDFLAGS="-arch i386"

but I had an error at make check.

============================
HDF-nc C interface tests

srcdir="." ./hdfnctest
Testing read/write datasets with unlimited dimensions via SD API
PASSED
Testing read/write variables with unlimited dimensions via nc API
make[2]: *** [check] Abort trap
make[1]: *** [check-recursive] Error 1
make: *** [check-recursive] Error 1

While I tried to make with "--disalbed-netcdf", I got same error.
Any other ideas/suggestions are mostly welcome.

Best,
Yuichiro Hagihara

On Tue, 17 Nov 2009 09:17:37 -0500, Michael Jackson wrote:

OS X 10.6 defaults to a 64 bit build for GCC. You may have to add the
"-arch i386" to the CFLAGS and CPPFLAGS to force a 32 bit build.

_________________________________________________________
Mike Jackson mike.jackson@bluequartz.net
BlueQuartz Software www.bluequartz.net
Principal Software Engineer Dayton, Ohio

On Nov 17, 2009, at 2:57 AM, HAGIHARA Yuichiro wrote:

Hello,

Recently I upgraded to OS 10.6 with Xcode 3.1.2(gcc 4.2.1).
But, I failed to build HDF 4.2r4 with intel fortran 11.1.

As the HDF release note said that "only the 32-bit version of
the Intel compiler is supported", I followed it.

I can build zlib and jpeg libraries, but can't HDF as stated below.

Are there any tips or suggestions?

Best,
Yuichiro Hagihara

$ tar xzf zlib-1.2.3.tar.gz
$ cd zlib-1.2.3
$ ./configure
$ make test
$ sudo make install

$ tar xzf jpegsrc.v6b.tar.gz
$ cd jpeg-6b
$ cp /usr/share/libtool/config/config.guess .
$ cp /usr/share/libtool/config/config.sub .
$ ./configure --enable-shared --enable-static
$ make
$ sudo make install

$ tar xzf HDF4.2r3
$ cd HDF4.2r3
$ ./configure --with-jpeg=/usr/local --with-zlib=/usr/local --

prefix=/usr/local

Configure summary
Compiling Options:
------------------
              Compilation Mode: Default
                    C Compiler: gcc
                        CFLAGS: -O2

CPPFLAGS: -I/usr/include/rpc -I/usr/local/include -

I/usr/local/include

-DBIG_LONGS -DSWAP

                       LDFLAGS: -L/usr/local/lib -L/usr/local/lib
              Shared Libraries: no
              Static Libraries: yes

Languages:
----------
                       Fortran: Yes
              Fortran Compiler: ifort
                        FFLAGS:

Features:
---------
              SZIP compression: disabled

HDF support for NetCDF-3 APIs:
------------------------------
                   HDF4-NetCDF: Yes

$ make
Making all in hdf
Making all in src
make all-am
/bin/sh ../../libtool --tag=CC --mode=compile
gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -I/usr/local/include -

I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT

atom.lo -MD -MP -MF .deps/atom.Tpo -c -o atom.lo atom.c
libtool: compile:
gcc -DHAVE_CONFIG_H -I. -I/usr/include/rpc -I/usr/local/include -

I/usr/local/include -DBIG_LONGS -DSWAP -O2 -MT

atom.lo -MD -MP -MF .deps/atom.Tpo -c atom.c -o atom.o
In file included from hdf.h:20,
                from atom.c:64:
hdfi.h:1352: error: expected '=', ',', ';', 'asm' or '__attribute__'
before 'you'
In file included from hdf.h:20,
                from atom.c:64:
hdfi.h:1355:1: warning: "GOT_MACHINE" redefined
hdfi.h:760:1: warning: this is the location of the previous definition
hdfi.h:1359:1: warning: "DF_MT" redefined
hdfi.h:775:1: warning: this is the location of the previous definition
hdfi.h:1361: error: redefinition of typedef 'VOIDP'
hdfi.h:779: error: previous declaration of 'VOIDP' was here
hdfi.h:1362: error: redefinition of typedef '_fcd'
hdfi.h:780: error: previous declaration of '_fcd' was here
hdfi.h:1363: error: redefinition of typedef 'char8'
hdfi.h:781: error: previous declaration of 'char8' was here
hdfi.h:1364: error: redefinition of typedef 'uchar8'
hdfi.h:782: error: previous declaration of 'uchar8' was here
hdfi.h:1365: error: redefinition of typedef 'int8'
hdfi.h:783: error: previous declaration of 'int8' was here
hdfi.h:1366: error: redefinition of typedef 'uint8'
hdfi.h:784: error: previous declaration of 'uint8' was here
hdfi.h:1367: error: redefinition of typedef 'int16'
hdfi.h:785: error: previous declaration of 'int16' was here
hdfi.h:1368: error: redefinition of typedef 'uint16'
hdfi.h:786: error: previous declaration of 'uint16' was here
hdfi.h:1369: error: redefinition of typedef 'int32'
hdfi.h:787: error: previous declaration of 'int32' was here
hdfi.h:1370: error: redefinition of typedef 'uint32'
hdfi.h:788: error: previous declaration of 'uint32' was here
hdfi.h:1371: error: redefinition of typedef 'intn'
hdfi.h:789: error: previous declaration of 'intn' was here
hdfi.h:1372: error: redefinition of typedef 'uintn'
hdfi.h:790: error: previous declaration of 'uintn' was here
hdfi.h:1373: error: redefinition of typedef 'intf'
hdfi.h:793: error: previous declaration of 'intf' was here
hdfi.h:1374: error: redefinition of typedef 'float32'
hdfi.h:791: error: previous declaration of 'float32' was here
hdfi.h:1375: error: redefinition of typedef 'float64'
hdfi.h:792: error: previous declaration of 'float64' was here
hdfi.h:1376: error: conflicting types for 'hdf_pint_t'
hdfi.h:794: error: previous declaration of 'hdf_pint_t' was here
make[3]: *** [atom.lo] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

--
Internal Virus Database is out-of-date.
Checked by AVG.
Version: 7.5.549 / Virus Database: 270.9.0/1778 - Release Date: 11/9/2008
2:14 PM