All, Thank you for the quick help. Much appreciated. Applying that simple patch in the interim is easy to do.
Chris > 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 ----------------------------------------------------------------------------------------------------------- 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. 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