linking problem

Hdf-forum archives
1

Dear Sir/Madam,

I am trying to use HDF5/parallel for a Fortran Code (Fleur code).
the code uses MKL (which contains scalapack openmpi/blacs). I built HDF5 using the mpif90 (the ifort intel compiler wrapper). the compilation of the code looks ok. But right at the end when it tries to link to libraries I have the error message:
ssubredist2.o:ssubredist2.F:(.text+0x1606): more undefined references to `flush__' follow
make: *** [fleur.x] Error 1

I would be grateful if you could help me solving the problem.
Many thanks.

···

--
Dr. Samir ABDELOUAHED
Postdoctoral Research Fellow
Department of Physics
University of York
Heslington, York, YO10 5DD, UK
Tel: 0044 (0) 1904 322208
Office: N003

2

Do you mean you have a

CALL FLUSH (lunit)

in your Fortran program? HDF5 does not use FLUSH and does not have a function called flush. You might want to 'nm' the other libraries you have and see what provides flush__

Scot

···

________________________________________
From: Hdf-forum <hdf-forum-bounces@lists.hdfgroup.org> on behalf of Samir ABDELOUAHED <abdelouahed.samir@gmail.com>
Sent: Wednesday, February 19, 2014 8:48 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] linking problem

Dear Sir/Madam,

I am trying to use HDF5/parallel for a Fortran Code (Fleur code).
the code uses MKL (which contains scalapack openmpi/blacs). I built HDF5
using the mpif90 (the ifort intel compiler wrapper). the compilation of
the code looks ok. But right at the end when it tries to link to
libraries I have the error message:
ssubredist2.o:ssubredist2.F:(.text+0x1606): more undefined references to
`flush__' follow
make: *** [fleur.x] Error 1

I would be grateful if you could help me solving the problem.
Many thanks.

--
Dr. Samir ABDELOUAHED
Postdoctoral Research Fellow
Department of Physics
University of York
Heslington, York, YO10 5DD, UK
Tel: 0044 (0) 1904 322208
Office: N003

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

3

Dear Scott,
I understand what do you mean. But at the same time I compiled Fleur without using HDF successfully.
So the problem comes from the HDF libraries and/or how to link Fleur to it.
I need to use HDF to make Fleur faster and to have small size output files.
Thanks,
Samir

···

On 19/02/14 16:21, Scot Breitenfeld wrote:

Do you mean you have a

CALL FLUSH (lunit)

in your Fortran program? HDF5 does not use FLUSH and does not have a function called flush. You might want to 'nm' the other libraries you have and see what provides flush__

Scot
________________________________________
From: Hdf-forum <hdf-forum-bounces@lists.hdfgroup.org> on behalf of Samir ABDELOUAHED <abdelouahed.samir@gmail.com>
Sent: Wednesday, February 19, 2014 8:48 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] linking problem

Dear Sir/Madam,

I am trying to use HDF5/parallel for a Fortran Code (Fleur code).
the code uses MKL (which contains scalapack openmpi/blacs). I built HDF5
using the mpif90 (the ifort intel compiler wrapper). the compilation of
the code looks ok. But right at the end when it tries to link to
libraries I have the error message:
ssubredist2.o:ssubredist2.F:(.text+0x1606): more undefined references to
`flush__' follow
make: *** [fleur.x] Error 1

I would be grateful if you could help me solving the problem.
Many thanks.

--
Dr. Samir ABDELOUAHED
Postdoctoral Research Fellow
Department of Physics
University of York
Heslington, York, YO10 5DD, UK
Tel: 0044 (0) 1904 322208
Office: N003

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

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

--
Dr. Samir ABDELOUAHED
Postdoctoral Research Fellow
Department of Physics
University of York
Heslington, York, YO10 5DD, UK
Tel: 0044 (0) 1904 322208
Office: N003

4

If the Flush call is in a part of fleur that is not exercised when hdf5 is
not used some linkers
will recognize this and not report an error. You should be able to use
the nm command as Scot suggested to find the location from which the flush
command is being called.

···

On Wed, Feb 19, 2014 at 10:41 AM, Samir ABDELOUAHED < abdelouahed.samir@gmail.com> wrote:

Dear Scott,
I understand what do you mean. But at the same time I compiled Fleur
without using HDF successfully.
So the problem comes from the HDF libraries and/or how to link Fleur to it.
I need to use HDF to make Fleur faster and to have small size output files.
Thanks,
Samir

On 19/02/14 16:21, Scot Breitenfeld wrote:

Do you mean you have a

CALL FLUSH (lunit)

in your Fortran program? HDF5 does not use FLUSH and does not have a
function called flush. You might want to 'nm' the other libraries you have
and see what provides flush__

Scot
________________________________________
From: Hdf-forum <hdf-forum-bounces@lists.hdfgroup.org> on behalf of
Samir ABDELOUAHED <abdelouahed.samir@gmail.com>
Sent: Wednesday, February 19, 2014 8:48 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] linking problem

Dear Sir/Madam,

I am trying to use HDF5/parallel for a Fortran Code (Fleur code).
the code uses MKL (which contains scalapack openmpi/blacs). I built HDF5
using the mpif90 (the ifort intel compiler wrapper). the compilation of
the code looks ok. But right at the end when it tries to link to
libraries I have the error message:
ssubredist2.o:ssubredist2.F:(.text+0x1606): more undefined references to
`flush__' follow
make: *** [fleur.x] Error 1

I would be grateful if you could help me solving the problem.
Many thanks.

--
Dr. Samir ABDELOUAHED
Postdoctoral Research Fellow
Department of Physics
University of York
Heslington, York, YO10 5DD, UK
Tel: 0044 (0) 1904 322208
Office: N003

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

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

--
Dr. Samir ABDELOUAHED
Postdoctoral Research Fellow
Department of Physics
University of York
Heslington, York, YO10 5DD, UK
Tel: 0044 (0) 1904 322208
Office: N003

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

--
Jim Edwards

CESM Software Engineering Group
National Center for Atmospheric Research
Boulder, CO
303-497-1842

5

Hi Jim,
Thank you for your help.
As Scott suggested I made nm /usr/local/hdf5/lib/libhdf5.a | grep "flush*" > flush-list .
Please find attached the flush-list file. It looks that flush is there!
Many thanks,
Samir

flush-list (2.73 KB)

···

On 19/02/14 18:47, Jim Edwards wrote:

If the Flush call is in a part of fleur that is not exercised when hdf5 is not used some linkers
will recognize this and not report an error. You should be able to use the nm command as Scot suggested to find the location from which the flush command is being called.

On Wed, Feb 19, 2014 at 10:41 AM, Samir ABDELOUAHED > <abdelouahed.samir@gmail.com <mailto:abdelouahed.samir@gmail.com>> wrote:

    Dear Scott,
    I understand what do you mean. But at the same time I compiled
    Fleur without using HDF successfully.
    So the problem comes from the HDF libraries and/or how to link
    Fleur to it.
    I need to use HDF to make Fleur faster and to have small size
    output files.
    Thanks,
    Samir

    On 19/02/14 16:21, Scot Breitenfeld wrote:

        Do you mean you have a

        CALL FLUSH (lunit)

        in your Fortran program? HDF5 does not use FLUSH and does not
        have a function called flush. You might want to 'nm' the other
        libraries you have and see what provides flush__

        Scot
        ________________________________________
        From: Hdf-forum <hdf-forum-bounces@lists.hdfgroup.org
        <mailto:hdf-forum-bounces@lists.hdfgroup.org>> on behalf of
        Samir ABDELOUAHED <abdelouahed.samir@gmail.com
        <mailto:abdelouahed.samir@gmail.com>>
        Sent: Wednesday, February 19, 2014 8:48 AM
        To: hdf-forum@lists.hdfgroup.org
        <mailto:hdf-forum@lists.hdfgroup.org>
        Subject: [Hdf-forum] linking problem

        Dear Sir/Madam,

        I am trying to use HDF5/parallel for a Fortran Code (Fleur code).
        the code uses MKL (which contains scalapack openmpi/blacs). I
        built HDF5
        using the mpif90 (the ifort intel compiler wrapper). the
        compilation of
        the code looks ok. But right at the end when it tries to link to
        libraries I have the error message:
        ssubredist2.o:ssubredist2.F:(.text+0x1606): more undefined
        references to
        `flush__' follow
        make: *** [fleur.x] Error 1

        I would be grateful if you could help me solving the problem.
        Many thanks.

        --
        Dr. Samir ABDELOUAHED
        Postdoctoral Research Fellow
        Department of Physics
        University of York
        Heslington, York, YO10 5DD, UK
        Tel: 0044 (0) 1904 322208
        Office: N003

        _______________________________________________
        Hdf-forum is for HDF software users discussion.
        Hdf-forum@lists.hdfgroup.org <mailto:Hdf-forum@lists.hdfgroup.org>
        http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

        _______________________________________________
        Hdf-forum is for HDF software users discussion.
        Hdf-forum@lists.hdfgroup.org <mailto:Hdf-forum@lists.hdfgroup.org>
        http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

    -- Dr. Samir ABDELOUAHED
    Postdoctoral Research Fellow
    Department of Physics
    University of York
    Heslington, York, YO10 5DD, UK
    Tel: 0044 (0) 1904 322208
    Office: N003

    _______________________________________________
    Hdf-forum is for HDF software users discussion.
    Hdf-forum@lists.hdfgroup.org <mailto:Hdf-forum@lists.hdfgroup.org>
    http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

--
Jim Edwards

CESM Software Engineering Group
National Center for Atmospheric Research
Boulder, CO
303-497-1842

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

--
Dr. Samir ABDELOUAHED
Postdoctoral Research Fellow
Department of Physics
University of York
Heslington, York, YO10 5DD, UK
Tel: 0044 (0) 1904 322208
Office: N003

6

I don't think so - you are looking for flush__ not fflush or HDF5_flush.
Check your other libraries.

···

On Wed, Feb 19, 2014 at 12:06 PM, Samir ABDELOUAHED < abdelouahed.samir@gmail.com> wrote:

Hi Jim,
Thank you for your help.
As Scott suggested I made nm /usr/local/hdf5/lib/libhdf5.a | grep "flush*"
> flush-list .
Please find attached the flush-list file. It looks that flush is there!
Many thanks,
Samir

On 19/02/14 18:47, Jim Edwards wrote:

If the Flush call is in a part of fleur that is not exercised when hdf5
is not used some linkers
will recognize this and not report an error. You should be able to use
the nm command as Scot suggested to find the location from which the flush
command is being called.

On Wed, Feb 19, 2014 at 10:41 AM, Samir ABDELOUAHED < > abdelouahed.samir@gmail.com> wrote:

Dear Scott,
I understand what do you mean. But at the same time I compiled Fleur
without using HDF successfully.
So the problem comes from the HDF libraries and/or how to link Fleur to
it.
I need to use HDF to make Fleur faster and to have small size output
files.
Thanks,
Samir

On 19/02/14 16:21, Scot Breitenfeld wrote:

Do you mean you have a

CALL FLUSH (lunit)

in your Fortran program? HDF5 does not use FLUSH and does not have a
function called flush. You might want to 'nm' the other libraries you have
and see what provides flush__

Scot
________________________________________
From: Hdf-forum <hdf-forum-bounces@lists.hdfgroup.org> on behalf of
Samir ABDELOUAHED <abdelouahed.samir@gmail.com>
Sent: Wednesday, February 19, 2014 8:48 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] linking problem

Dear Sir/Madam,

I am trying to use HDF5/parallel for a Fortran Code (Fleur code).
the code uses MKL (which contains scalapack openmpi/blacs). I built HDF5
using the mpif90 (the ifort intel compiler wrapper). the compilation of
the code looks ok. But right at the end when it tries to link to
libraries I have the error message:
ssubredist2.o:ssubredist2.F:(.text+0x1606): more undefined references to
`flush__' follow
make: *** [fleur.x] Error 1

I would be grateful if you could help me solving the problem.
Many thanks.

--
Dr. Samir ABDELOUAHED
Postdoctoral Research Fellow
Department of Physics
University of York
Heslington, York, YO10 5DD, UK
Tel: 0044 (0) 1904 322208
Office: N003

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org

http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org

http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

--
Dr. Samir ABDELOUAHED
Postdoctoral Research Fellow
Department of Physics
University of York
Heslington, York, YO10 5DD, UK
Tel: 0044 (0) 1904 322208
Office: N003

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org

http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

--
Jim Edwards

CESM Software Engineering Group
National Center for Atmospheric Research
Boulder, CO
303-497-1842

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

--
Dr. Samir ABDELOUAHED
Postdoctoral Research Fellow
Department of Physics
University of York
Heslington, York, YO10 5DD, UK
Tel: 0044 (0) 1904 322208
Office: N003

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org

http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

--
Jim Edwards

CESM Software Engineering Group
National Center for Atmospheric Research
Boulder, CO
303-497-1842