Is HDF 5 compiler specific ??

Hdf-forum archives
1

Hello,

  Can you please tell me if the HDF 5 compilation is tailored for specific
compilers ??

  I am able to compile the HDF 5 code base in cygwin using gcc and g95 but I
am having a hard time with pgcc and pgf90.
  Can you please help in this regard ?

Thanks & Regards,
Kunal

2

Kunal,

HDF5 can be built with the PGI compilers (except that for the new 10.6 version on Linux 64 one has to go with the lower levels of optimization).

The error messages suggest that something is wrong with the PGI compilers or their installation on your system.

Have you tried to compile a simple C program like "Hello world" with pgcc? Have you tried to compile a simple Fortran program? If both work,
try to configure and build just HDF5 C library. You may also try to use CMake in case HDF5 configure has problems on Cygwin.

Elena

···

On Jul 15, 2010, at 7:25 PM, Kunal Rao wrote:

Hello,

  Can you please tell me if the HDF 5 compilation is tailored for specific compilers ??

  I am able to compile the HDF 5 code base in cygwin using gcc and g95 but I am having a hard time with pgcc and pgf90.
  Can you please help in this regard ?

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

3

Just to be more specific about the new 10.6 version PGI, it can compile
HDF5.
However some HDF5 tools doesn't work correctly if built with optimization 2
or above on Linux 32 and 64, which seems to be issue from the compiler.

Jonathan

···

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org]
On Behalf Of Elena Pourmal
Sent: Thursday, July 15, 2010 10:07 PM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] Is HDF 5 compiler specific ??

Kunal,

HDF5 can be built with the PGI compilers (except that for the new 10.6
version on Linux 64 one has to go with the lower levels of optimization).

The error messages suggest that something is wrong with the PGI compilers or
their installation on your system.

Have you tried to compile a simple C program like "Hello world" with pgcc?
Have you tried to compile a simple Fortran program? If both work,
try to configure and build just HDF5 C library. You may also try to use
CMake in case HDF5 configure has problems on Cygwin.

Elena

On Jul 15, 2010, at 7:25 PM, Kunal Rao wrote:

Hello,

  Can you please tell me if the HDF 5 compilation is tailored for specific

compilers ??

  I am able to compile the HDF 5 code base in cygwin using gcc and g95 but

I am having a hard time with pgcc and pgf90.

  Can you please help in this regard ?

Thanks & Regards,
Kunal
_______________________________________________
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

4

Dear Elena/Jonathan,

  Thank you very much for your reply. Atleast now, I am convinced that HDF 5
can be compiled using PGI compilers although
  I am not successful yet.

  I am using the cygwin environment on windows and using PGI compilers (pgcc
and pgf90).
  The compilers are located at: /c/PROGRA~1/PGI/win64/10.5/bin

  As suggested by you Elena, I am able to execute "Hello World" using the
PGI compilers..

  I am having trouble with linking with fortran libraries during the
configuration of HDF 5 (1.8.5)

  I am configuring using the following command:

  $./configure --enable-fortran |tee configure.log

  The error that I am getting is:

config.log (53.2 KB)

configure.log (1.83 KB)

···

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

  checking for Fortran libraries of pgf90...
-libpath:C:\PROGRA~1\PGI/win64/10.5/lib
  checking for dummy main to link with Fortran libraries... unknown
  configure: error: in
`/c/Users/Administrator/Desktop/hdf5-1.8.5/hdf5-1.8.5':
  configure: error: linking to Fortran libraries from C fails
  See `config.log' for more details.

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

   and my config.log contains:

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

    configure:6030: pgcc -o conftest.exe conftest.c
-libpath:C:\PROGRA~1\PGI/win64/10.5/lib >&5
    LINK : fatal error LNK1104: cannot open file
'libibpath:C:\PROGRA~1\PGI/win64/10.5/lib.lib'

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

    I am attaching the config.log and configure.log file for your reference
for you to understand my system and platform in more detail.

    Kindly let me know if you have any suggestion.

Thanks & Regards,
Kunal

On Fri, Jul 16, 2010 at 10:45 AM, Jonathan Kim <jkm@hdfgroup.org> wrote:

Just to be more specific about the new 10.6 version PGI, it can compile
HDF5.
However some HDF5 tools doesn't work correctly if built with optimization 2
or above on Linux 32 and 64, which seems to be issue from the compiler.

Jonathan

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:
hdf-forum-bounces@hdfgroup.org]
On Behalf Of Elena Pourmal
Sent: Thursday, July 15, 2010 10:07 PM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] Is HDF 5 compiler specific ??

Kunal,

HDF5 can be built with the PGI compilers (except that for the new 10.6
version on Linux 64 one has to go with the lower levels of optimization).

The error messages suggest that something is wrong with the PGI compilers
or
their installation on your system.

Have you tried to compile a simple C program like "Hello world" with pgcc?
Have you tried to compile a simple Fortran program? If both work,
try to configure and build just HDF5 C library. You may also try to use
CMake in case HDF5 configure has problems on Cygwin.

Elena

On Jul 15, 2010, at 7:25 PM, Kunal Rao wrote:

> Hello,
>
> Can you please tell me if the HDF 5 compilation is tailored for
specific
compilers ??
>
> I am able to compile the HDF 5 code base in cygwin using gcc and g95
but
I am having a hard time with pgcc and pgf90.
> Can you please help in this regard ?
>
> Thanks & Regards,
> Kunal
> _______________________________________________
> 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

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

5

Kunal,

We probably need someone with the Cygwin and configure experience :slight_smile:

I assume you have tried to compile a Fortran program with PGI, right? Do you need to set some environment variable (such as LIBS?) for linker to find the PGI Fortran libraries?

If you look at config.log

configure:6001: pgcc -o conftest.exe conftest.c -libpath:C:\PROGRA~1\PGI/win64/10.5/lib >&5
LINK : fatal error LNK1104: cannot open file 'libibpath:C:\PROGRA~1\PGI/win64/10.5/lib.lib'

compilation line doesn't have fortran libraries, but only the path to them (is it a correct path?)

(see how the same line looks on Linux

configure:6001: pgcc -o conftest conftest.c -L/usr/pgi/10.4/linux86/10.4/lib -L/usr/lib -L/usr/lib/gcc/i386-redhat-linux/4.1.2 -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lpgsse1 -lpgsse2 -lnspgc -lpgc -lrt -lpthread -lm >&5
)

Sorry... not much help.

Elena

···

On Jul 17, 2010, at 12:05 AM, Kunal Rao wrote:

Dear Elena/Jonathan,

  Thank you very much for your reply. Atleast now, I am convinced that HDF 5 can be compiled using PGI compilers although
  I am not successful yet.

  I am using the cygwin environment on windows and using PGI compilers (pgcc and pgf90).
  The compilers are located at: /c/PROGRA~1/PGI/win64/10.5/bin

  As suggested by you Elena, I am able to execute "Hello World" using the PGI compilers..

  I am having trouble with linking with fortran libraries during the configuration of HDF 5 (1.8.5)

  I am configuring using the following command:

  $./configure --enable-fortran |tee configure.log

  The error that I am getting is:

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

  checking for Fortran libraries of pgf90... -libpath:C:\PROGRA~1\PGI/win64/10.5/lib
  checking for dummy main to link with Fortran libraries... unknown
  configure: error: in `/c/Users/Administrator/Desktop/hdf5-1.8.5/hdf5-1.8.5':
  configure: error: linking to Fortran libraries from C fails
  See `config.log' for more details.

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

   and my config.log contains:

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

    configure:6030: pgcc -o conftest.exe conftest.c -libpath:C:\PROGRA~1\PGI/win64/10.5/lib >&5
    LINK : fatal error LNK1104: cannot open file 'libibpath:C:\PROGRA~1\PGI/win64/10.5/lib.lib'

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

    I am attaching the config.log and configure.log file for your reference for you to understand my system and platform in more detail.
    
    Kindly let me know if you have any suggestion.

Thanks & Regards,
Kunal
  
On Fri, Jul 16, 2010 at 10:45 AM, Jonathan Kim <jkm@hdfgroup.org> wrote:
Just to be more specific about the new 10.6 version PGI, it can compile
HDF5.
However some HDF5 tools doesn't work correctly if built with optimization 2
or above on Linux 32 and 64, which seems to be issue from the compiler.

Jonathan

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org]
On Behalf Of Elena Pourmal
Sent: Thursday, July 15, 2010 10:07 PM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] Is HDF 5 compiler specific ??

Kunal,

HDF5 can be built with the PGI compilers (except that for the new 10.6
version on Linux 64 one has to go with the lower levels of optimization).

The error messages suggest that something is wrong with the PGI compilers or
their installation on your system.

Have you tried to compile a simple C program like "Hello world" with pgcc?
Have you tried to compile a simple Fortran program? If both work,
try to configure and build just HDF5 C library. You may also try to use
CMake in case HDF5 configure has problems on Cygwin.

Elena

On Jul 15, 2010, at 7:25 PM, Kunal Rao wrote:

> Hello,
>
> Can you please tell me if the HDF 5 compilation is tailored for specific
compilers ??
>
> I am able to compile the HDF 5 code base in cygwin using gcc and g95 but
I am having a hard time with pgcc and pgf90.
> Can you please help in this regard ?
>
> Thanks & Regards,
> Kunal
> _______________________________________________
> 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

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

<config.log><configure.log>

6

Hi Elena,

  Thanks for your reply and your help in this regard.

  Yes, I am able to compile a fortran program with PGI. It was not required
to set explicitly any env. variable like LIBS to link
  with fortran libraries.

  We do have the LIBS env. variable which I did set to configure HDF 5. Now
the error looks like this:

···

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

   configure:5967: checking for dummy main to link with Fortran libraries
  configure:6001: pgcc -o conftest.exe conftest.c
-L/c/PROGRA~1/PGI/win64/10
  .5/lib -libpath:c:/PROGRA~1/PGI/win64/10.5/lib
-libpath:c:\PROGRA~1\PGI/win64/1
  0.5/lib >&5
  LINK : fatal error LNK1104: cannot open file
'libibpath:c:/PROGRA~1/PGI/win64/10
  .5/lib.lib'

  ---------------------------

   I read in one of the articles "The flag -llibraryname is passed to the
Microsoft linker (LINK) as
  -libpath:libraryname and is resolved as "liblibraryname.lib" ".

    In my case the same thing is happening, -libpath:c:....... is resolved
as libibpath:c:/......
    which obviously does not exist. I am not sure how we can avoid this
default linking and only have the explicit linking
    using the LIBS env. variable.

    If anyone has had similar issue, can you please throw some light on it.

Thanks & Regards,
Kunal

On Sat, Jul 17, 2010 at 7:36 PM, Elena Pourmal <epourmal@hdfgroup.org>wrote:

Kunal,

We probably need someone with the Cygwin and configure experience :slight_smile:

I assume you have tried to compile a Fortran program with PGI, right? Do
you need to set some environment variable (such as LIBS?) for linker to find
the PGI Fortran libraries?

If you look at config.log

configure:6001: pgcc -o conftest.exe conftest.c
-libpath:C:\PROGRA~1\PGI/win64/10.5/lib >&5
LINK : fatal error LNK1104: cannot open file
'libibpath:C:\PROGRA~1\PGI/win64/10.5/lib.lib'

compilation line doesn't have fortran libraries, but only the path to them
(is it a correct path?)

(see how the same line looks on Linux

configure:6001: pgcc -o conftest conftest.c
-L/usr/pgi/10.4/linux86/10.4/lib -L/usr/lib
-L/usr/lib/gcc/i386-redhat-linux/4.1.2 -lpgf90 -lpgf90_rpm1 -lpgf902
-lpgf90rtl -lpgftnrtl -lpgsse1 -lpgsse2 -lnspgc -lpgc -lrt -lpthread -lm >&5
)

Sorry... not much help.

Elena

On Jul 17, 2010, at 12:05 AM, Kunal Rao wrote:

Dear Elena/Jonathan,

  Thank you very much for your reply. Atleast now, I am convinced that HDF
5 can be compiled using PGI compilers although
  I am not successful yet.

  I am using the cygwin environment on windows and using PGI compilers
(pgcc and pgf90).
  The compilers are located at: /c/PROGRA~1/PGI/win64/10.5/bin

  As suggested by you Elena, I am able to execute "Hello World" using the
PGI compilers..

  I am having trouble with linking with fortran libraries during the
configuration of HDF 5 (1.8.5)

  I am configuring using the following command:

  $./configure --enable-fortran |tee configure.log

  The error that I am getting is:

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

  checking for Fortran libraries of pgf90...
-libpath:C:\PROGRA~1\PGI/win64/10.5/lib
  checking for dummy main to link with Fortran libraries... unknown
  configure: error: in
`/c/Users/Administrator/Desktop/hdf5-1.8.5/hdf5-1.8.5':
  configure: error: linking to Fortran libraries from C fails
  See `config.log' for more details.

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

   and my config.log contains:

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

    configure:6030: pgcc -o conftest.exe conftest.c
-libpath:C:\PROGRA~1\PGI/win64/10.5/lib >&5
    LINK : fatal error LNK1104: cannot open file
'libibpath:C:\PROGRA~1\PGI/win64/10.5/lib.lib'

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

    I am attaching the config.log and configure.log file for your reference
for you to understand my system and platform in more detail.

    Kindly let me know if you have any suggestion.

Thanks & Regards,
Kunal

On Fri, Jul 16, 2010 at 10:45 AM, Jonathan Kim <jkm@hdfgroup.org> wrote:

Just to be more specific about the new 10.6 version PGI, it can compile
HDF5.
However some HDF5 tools doesn't work correctly if built with optimization
2
or above on Linux 32 and 64, which seems to be issue from the compiler.

Jonathan

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:
hdf-forum-bounces@hdfgroup.org]
On Behalf Of Elena Pourmal
Sent: Thursday, July 15, 2010 10:07 PM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] Is HDF 5 compiler specific ??

Kunal,

HDF5 can be built with the PGI compilers (except that for the new 10.6
version on Linux 64 one has to go with the lower levels of optimization).

The error messages suggest that something is wrong with the PGI compilers
or
their installation on your system.

Have you tried to compile a simple C program like "Hello world" with pgcc?
Have you tried to compile a simple Fortran program? If both work,
try to configure and build just HDF5 C library. You may also try to use
CMake in case HDF5 configure has problems on Cygwin.

Elena

On Jul 15, 2010, at 7:25 PM, Kunal Rao wrote:

> Hello,
>
> Can you please tell me if the HDF 5 compilation is tailored for
specific
compilers ??
>
> I am able to compile the HDF 5 code base in cygwin using gcc and g95
but
I am having a hard time with pgcc and pgf90.
> Can you please help in this regard ?
>
> Thanks & Regards,
> Kunal
> _______________________________________________
> 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

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

<config.log><configure.log>

7

Hi Elena/Jonathan,

  I finally could get over that linking issue. I had to set the FCLIBS env.
variable.

  Thanks for all your time and your help.

Thanks & Regards,
Kunal

···

On Sat, Jul 17, 2010 at 11:26 PM, Kunal Rao <kunalgrao@gmail.com> wrote:

Hi Elena,

  Thanks for your reply and your help in this regard.

  Yes, I am able to compile a fortran program with PGI. It was not required
to set explicitly any env. variable like LIBS to link
  with fortran libraries.

  We do have the LIBS env. variable which I did set to configure HDF 5. Now
the error looks like this:

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

   configure:5967: checking for dummy main to link with Fortran libraries
  configure:6001: pgcc -o conftest.exe conftest.c
-L/c/PROGRA~1/PGI/win64/10
  .5/lib -libpath:c:/PROGRA~1/PGI/win64/10.5/lib
-libpath:c:\PROGRA~1\PGI/win64/1
  0.5/lib >&5
  LINK : fatal error LNK1104: cannot open file
'libibpath:c:/PROGRA~1/PGI/win64/10
  .5/lib.lib'

  ---------------------------

   I read in one of the articles "The flag -llibraryname is passed to the
Microsoft linker (LINK) as
  -libpath:libraryname and is resolved as "liblibraryname.lib" ".

    In my case the same thing is happening, -libpath:c:....... is resolved
as libibpath:c:/......
    which obviously does not exist. I am not sure how we can avoid this
default linking and only have the explicit linking
    using the LIBS env. variable.

    If anyone has had similar issue, can you please throw some light on it.

Thanks & Regards,
Kunal

On Sat, Jul 17, 2010 at 7:36 PM, Elena Pourmal <epourmal@hdfgroup.org>wrote:

Kunal,

We probably need someone with the Cygwin and configure experience :slight_smile:

I assume you have tried to compile a Fortran program with PGI, right? Do
you need to set some environment variable (such as LIBS?) for linker to find
the PGI Fortran libraries?

If you look at config.log

configure:6001: pgcc -o conftest.exe conftest.c
-libpath:C:\PROGRA~1\PGI/win64/10.5/lib >&5
LINK : fatal error LNK1104: cannot open file
'libibpath:C:\PROGRA~1\PGI/win64/10.5/lib.lib'

compilation line doesn't have fortran libraries, but only the path to them
(is it a correct path?)

(see how the same line looks on Linux

configure:6001: pgcc -o conftest conftest.c
-L/usr/pgi/10.4/linux86/10.4/lib -L/usr/lib
-L/usr/lib/gcc/i386-redhat-linux/4.1.2 -lpgf90 -lpgf90_rpm1 -lpgf902
-lpgf90rtl -lpgftnrtl -lpgsse1 -lpgsse2 -lnspgc -lpgc -lrt -lpthread -lm >&5
)

Sorry... not much help.

Elena

On Jul 17, 2010, at 12:05 AM, Kunal Rao wrote:

Dear Elena/Jonathan,

  Thank you very much for your reply. Atleast now, I am convinced that HDF
5 can be compiled using PGI compilers although
  I am not successful yet.

  I am using the cygwin environment on windows and using PGI compilers
(pgcc and pgf90).
  The compilers are located at: /c/PROGRA~1/PGI/win64/10.5/bin

  As suggested by you Elena, I am able to execute "Hello World" using the
PGI compilers..

  I am having trouble with linking with fortran libraries during the
configuration of HDF 5 (1.8.5)

  I am configuring using the following command:

  $./configure --enable-fortran |tee configure.log

  The error that I am getting is:

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

  checking for Fortran libraries of pgf90...
-libpath:C:\PROGRA~1\PGI/win64/10.5/lib
  checking for dummy main to link with Fortran libraries... unknown
  configure: error: in
`/c/Users/Administrator/Desktop/hdf5-1.8.5/hdf5-1.8.5':
  configure: error: linking to Fortran libraries from C fails
  See `config.log' for more details.

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

   and my config.log contains:

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

    configure:6030: pgcc -o conftest.exe conftest.c
-libpath:C:\PROGRA~1\PGI/win64/10.5/lib >&5
    LINK : fatal error LNK1104: cannot open file
'libibpath:C:\PROGRA~1\PGI/win64/10.5/lib.lib'

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

    I am attaching the config.log and configure.log file for your
reference for you to understand my system and platform in more detail.

    Kindly let me know if you have any suggestion.

Thanks & Regards,
Kunal

On Fri, Jul 16, 2010 at 10:45 AM, Jonathan Kim <jkm@hdfgroup.org> wrote:

Just to be more specific about the new 10.6 version PGI, it can compile
HDF5.
However some HDF5 tools doesn't work correctly if built with optimization
2
or above on Linux 32 and 64, which seems to be issue from the compiler.

Jonathan

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:
hdf-forum-bounces@hdfgroup.org]
On Behalf Of Elena Pourmal
Sent: Thursday, July 15, 2010 10:07 PM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] Is HDF 5 compiler specific ??

Kunal,

HDF5 can be built with the PGI compilers (except that for the new 10.6
version on Linux 64 one has to go with the lower levels of optimization).

The error messages suggest that something is wrong with the PGI compilers
or
their installation on your system.

Have you tried to compile a simple C program like "Hello world" with
pgcc?
Have you tried to compile a simple Fortran program? If both work,
try to configure and build just HDF5 C library. You may also try to use
CMake in case HDF5 configure has problems on Cygwin.

Elena

On Jul 15, 2010, at 7:25 PM, Kunal Rao wrote:

> Hello,
>
> Can you please tell me if the HDF 5 compilation is tailored for
specific
compilers ??
>
> I am able to compile the HDF 5 code base in cygwin using gcc and g95
but
I am having a hard time with pgcc and pgf90.
> Can you please help in this regard ?
>
> Thanks & Regards,
> Kunal
> _______________________________________________
> 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

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

<config.log><configure.log>