Thank you for the report, H5F_provisional was missing from HDF5mpi.f90, which is used when --enable-parallel is specified. The fix will be in the next release, but for now the patch is:
--- HDF5mpio.f90 (revision 24616) +++ HDF5mpio.f90 (working copy) @@ -28,6 +28,7 @@ MODULE HDF5 USE H5GLOBAL USE H5F + USE H5F_PROVISIONAL USE H5G USE H5E USE H5E_PROVISIONAL Scot _______________________________________ From: Hdf-forum <[email protected]> on behalf of Christopher Harrop - NOAA Affiliate <[email protected]> Sent: Tuesday, January 07, 2014 12:52 PM To: HDF Users Discussion List Subject: Re: [Hdf-forum] HDF5-1.8.11 PGI link error Sean, Thank you for that patch. It does indeed solve the build problem for me. Chris > I noticed this too and observed that when using pgi to build a parallel > variant (with hdf5 1.8.12) the symbols where part of HF5_PROVISIONAL. So I > was able to make it build by applying the following mod: > > Index: fortran/test/tH5F_F03.f90 > =================================================================== > --- fortran/test/tH5F_F03.f90 (revision 1324) > +++ fortran/test/tH5F_F03.f90 (working copy) > @@ -41,6 +41,7 @@ > ! Tests the wrapper for h5fget_file_image > ! > USE HDF5 > + USE H5F_PROVISIONAL > USE ISO_C_BINDING > > IMPLICIT NONE > > I'm not sure if this was appropriate. > > Sean B. > ________________________________________ > From: Hdf-forum [[email protected]] on behalf of > Christopher Harrop - NOAA Affiliate [[email protected]] > Sent: Tuesday, January 07, 2014 11:19 AM > To: [email protected] > Subject: [Hdf-forum] HDF5-1.8.11 PGI link error > > Hello, > > I am trying to build HDF5 1.8.11 with PGI 13.2-0 and mvapich2 1.8 and am > getting a link error. I haven't been able to find any references to this > issue in my searching thus far. > > The error: > > FCLD fortranlib_test_F03 > tH5F_F03.o: In function `test_get_file_image_': > /mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: > undefined reference to `h5fget_file_image_f_' > /mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: > undefined reference to `h5fget_file_image_f_' > /mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test/./tH5F_F03.f90:92: > undefined reference to `h5fget_file_image_f_' > make[3]: *** [fortranlib_test_F03] Error 2 > make[3]: Leaving directory > `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran/test' > make[2]: *** [all-recursive] Error 1 > make[2]: Leaving directory > `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8/fortran' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory > `/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/build/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8' > make: *** > [/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8] > Error 2 > > In looking at ...fortran/test/./tH5F_F03.f90 I see that there is a RETURN > statement at the top of the subroutine with a comment indicating that there > is a PGI bug. How do I disable the compilation of this unusable test? > > This is how I am configuring it: > > export CC=mpicc > export CXX=mpicxx > export F77=mpif90 > export F90=mpif90 > export FC=mpif90 > export LDFLAGS=" -Wl,--rpath > -Wl,/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/szip/2.1/gnu/4.4.6/lib" > > ./configure > --with-szlib=/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/szip/2.1/gnu/4.4.6 > --enable-parallel --enable-fortran --enable-fortran2003 --enable-shared > --prefix=/mnt/lfs2/projects/jetmgmt/Christopher.W.Harrop/bass/opt/hdf5-mvapich2/1.8.11/pgi/13.2-0/mvapich2/1.8 > > This does not occur when I build HDF5 without parallel support. > > Let me know if I did not supply enough information. > > Chris > ----------------------------------------------------------------------------------------------------------- > Christopher W. Harrop email: > [email protected] > Global Systems Division > voice: (303) 497-6808 > NOAA Earth System Research Laboratory fax: > (303) 497-7259 > 325 Broadway R/GSD2 > Boulder, CO 80303 > > > > > > > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org ----------------------------------------------------------------------------------------------------------- Christopher W. Harrop email: [email protected] Global Systems Division voice: (303) 497-6808 NOAA Earth System Research Laboratory fax: (303) 497-7259 325 Broadway R/GSD2 Boulder, CO 80303 _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
