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
<[email protected] <mailto:[email protected]>> 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 <[email protected]
<mailto:[email protected]>> on behalf of
Samir ABDELOUAHED <[email protected]
<mailto:[email protected]>>
Sent: Wednesday, February 19, 2014 8:48 AM
To: [email protected]
<mailto:[email protected]>
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.
[email protected] <mailto:[email protected]>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected] <mailto:[email protected]>
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.
[email protected] <mailto:[email protected]>
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.
[email protected]
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
U fflush
00000000000062d0 T H5AC_flush
0000000000000670 t H5AC_log_flushed_entry
00000000000010a0 t H5AC_propagate_flushed_and_still_clean_entries_list
0000000000004130 T H5AC_rsp__dist_md_write__flush
0000000000004460 T H5AC_rsp__dist_md_write__flush_to_min_clean
0000000000004ef0 T H5AC_rsp__p0_only__flush
00000000000050b0 T H5AC_rsp__p0_only__flush_to_min_clean
U H5C_flush_cache
U H5C_flush_to_min_clean
0000000000000660 t H5B__flush
0000000000001630 t H5B2__cache_hdr_flush
0000000000001e60 t H5B2__cache_internal_flush
0000000000001bd0 t H5B2__cache_leaf_flush
00000000000000f0 t H5C_epoch_marker_flush
00000000000033c0 T H5C_flush_cache
0000000000000f20 t H5C_flush_invalidate_cache
0000000000000450 t H5C_flush_single_entry
00000000000037c0 T H5C_flush_to_min_clean
0000000000001a50 t H5D__chunk_flush
0000000000001280 t H5D__chunk_flush_entry.isra.1
U H5D__flush_sieve_buf
00000000000001c0 t H5D__compact_flush
0000000000000fd0 t H5D__contig_flush
U H5D__flush_sieve_buf
00000000000044c0 T H5D_flush
0000000000000740 t H5D__flush_cb
0000000000003de0 T H5D__flush_real
0000000000003d30 T H5D__flush_sieve_buf
U H5D__flush_real
0000000000000000 t H5O__dset_flush
U H5AC_flush
U H5D_flush
U H5F_accum_flush
U H5FD_flush
00000000000041b0 T H5Fflush
0000000000003070 T H5F_flush
U H5F_flush_mounts
0000000000001b00 T H5F_accum_flush
U H5F_flush
00000000000014c0 T H5F_flush_mounts
0000000000000000 t H5F_flush_mounts_recurse
0000000000000090 t H5F_sblock_flush
00000000000032a0 T H5FDflush
0000000000003560 T H5FD_flush
00000000000007d0 t H5FD_core_flush
0000000000000600 t H5FD_core_flush.part.1
0000000000001330 t H5FD_family_flush
U H5FD_flush
0000000000000440 t H5FD_mpio_flush
U H5FDflush
0000000000000150 t H5FD_multi_flush
U fflush
0000000000000c30 t H5FD_stdio_flush
0000000000002040 t H5FS_cache_hdr_flush
0000000000001be0 t H5FS_cache_sinfo_flush
0000000000000550 t H5G_node_flush
0000000000003010 t H5HF_cache_dblock_flush
00000000000042d0 t H5HF_cache_hdr_flush
0000000000001eb0 t H5HF_cache_iblock_flush
0000000000000960 t H5HG_flush
0000000000001730 t H5HL_datablock_flush
0000000000000360 t H5HL_prefix_flush
0000000000001e30 t H5O_cache_chk_flush
0000000000001820 t H5O_flush
U H5O_msg_flush
U H5O_flush_msgs
0000000000003a10 T H5O_flush_msgs
00000000000038b0 T H5O_msg_flush
U H5O_msg_flush
0000000000001210 t H5SM_list_flush
0000000000000d10 t H5SM_table_flush
U H5O_msg_flush
U H5F_flush_mounts
0000000000000000 t H5Z__flush_file_cb
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