Matt, h5edit is a sequential tool. Is there any reason for using h5pcc vs. h5cc? We don't test h5edit with the parallel HDF5 library and we haven't move to gcc version 6.3 yet.
I would suggest to use h5cc with the earlier versions of gcc. We will look into this problem when we start using gcc 6.3. Thank you for reporting! Elena > On Apr 27, 2017, at 11:41 AM, Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND > APPLICATIONS INC] <[email protected]> wrote: > > All, > > I'm not sure if this is the place for h5edit help, but I can't find anywhere > better. > > The issue I'm having is during compilation where: > >> /nobackup/gmao_SIteam/Baselibs/ESMA-Baselibs-5.0.3/x86_64-unknown-linux-gnu/ifort_2017.0.098-mpt_2.14r19-gcc_6.3.0/Linux/bin/h5pcc >> -DHAVE_CONFIG_H -I. -DpgiFortran >> -I/nobackup/gmao_SIteam/Baselibs/ESMA-Baselibs-5.0.3/x86_64-unknown-linux-gnu/ifort_2017.0.098-mpt_2.14r19-gcc_6.3.0/Linux/include/ >> >> -I/nobackup/gmao_SIteam/Baselibs/ESMA-Baselibs-5.0.3/x86_64-unknown-linux-gnu/ifort_2017.0.098-mpt_2.14r19-gcc_6.3.0/Linux/include/zlib >> >> -I/nobackup/gmao_SIteam/Baselibs/ESMA-Baselibs-5.0.3/x86_64-unknown-linux-gnu/ifort_2017.0.098-mpt_2.14r19-gcc_6.3.0/Linux/include/szlib >> >> -I/nobackup/gmao_SIteam/Baselibs/ESMA-Baselibs-5.0.3/x86_64-unknown-linux-gnu/ifort_2017.0.098-mpt_2.14r19-gcc_6.3.0/Linux/include/jpeg >> >> -I/nobackup/gmao_SIteam/Baselibs/ESMA-Baselibs-5.0.3/x86_64-unknown-linux-gnu/ifort_2017.0.098-mpt_2.14r19-gcc_6.3.0/Linux/include/hdf5 >> >> -I/nobackup/gmao_SIteam/Baselibs/ESMA-Baselibs-5.0.3/x86_64-unknown-linux-gnu/ifort_2017.0.098-mpt_2.14r19-gcc_6.3.0/Linux/include/hdf >> >> -I/nobackup/gmao_SIteam/Baselibs/ESMA-Baselibs-5.0.3/x86_64-unknown-linux-gnu/ifort_2017.0.098-mpt_2.14r19-gcc_6.3.0/Linux/include/uuid >> >> -I/nobackup/gmao_SIteam/Baselibs/ESMA-Baselibs-5.0.3/x86_64-unknown-linux-gnu/ifort_2017.0.098-mpt_2.14r19-gcc_6.3.0/Linux/include/netcdf >> >> -I/nobackup/gmao_SIteam/Baselibs/ESMA-Baselibs-5.0.3/x86_64-unknown-linux-gnu/ifort_2017.0.098-mpt_2.14r19-gcc_6.3.0/Linux/include/udunits2 >> >> -I/nobackup/gmao_SIteam/Baselibs/ESMA-Baselibs-5.0.3/x86_64-unknown-linux-gnu/ifort_2017.0.098-mpt_2.14r19-gcc_6.3.0/Linux/include/gsl >> >> -I/nobackup/gmao_SIteam/Baselibs/ESMA-Baselibs-5.0.3/x86_64-unknown-linux-gnu/ifort_2017.0.098-mpt_2.14r19-gcc_6.3.0/Linux/include/antlr >> -fPIC -MT parse.o -MD -MP -MF .deps/parse.Tpo -c -o parse.o parse.c >> parse.y: In function ‘H5EDITyyparse’: >> parse.y:342:53: warning: implicit declaration of function >> ‘split_object_component’ [-Wimplicit-function-declaration] >> source_attribute_part = split_object_component( >> source_object_name, >> ^~~~~~~~~~~~~~~~~~~~~~ >> parse.y:342:51: warning: assignment makes pointer from integer without a >> cast [-Wint-conversion] >> source_attribute_part = split_object_component( >> source_object_name, >> ^ >> parse.y:353:56: warning: assignment makes pointer from integer without a >> cast [-Wint-conversion] >> destination_attribute_part = >> split_object_component( copy_param2_name, >> ^ >> parse.y:624:17: warning: implicit declaration of function >> ‘split_object_attribute’ [-Wimplicit-function-declaration] >> if (0 != split_object_attribute(group_name, dataset_name)){ >> ^~~~~~~~~~~~~~~~~~~~~~ >> parse.y: At top level: >> parse.y:1119:8: error: conflicting types for ‘split_object_component’ >> char * split_object_component ( char *pathname, char **trim_pathname ) >> ^~~~~~~~~~~~~~~~~~~~~~ >> parse.y:342:53: note: previous implicit declaration of >> ‘split_object_component’ was here >> source_attribute_part = split_object_component( >> source_object_name, >> ^~~~~~~~~~~~~~~~~~~~~~ >> make[1]: *** [parse.o] Error 1 >> make[1]: Leaving directory >> `/nobackupp9/gmao_SIteam/Baselibs/ESMA-Baselibs-5.0.3/src/h5edit/src' >> make: *** [install-recursive] Error 1 > > In this case, h5pcc is based on gcc 6.3.0: > >> $ h5pcc --version >> gcc (GCC) 6.3.0 >> Copyright (C) 2016 Free Software Foundation, Inc. >> This is free software; see the source for copying conditions. There is NO >> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. > > Now on some systems I don't see this, on some I do. Is this a yacc issue? > Once I see a .y file, I'm way out of my league. > > Maybe preprocessing? Not sure. > > -- > Matt Thompson, SSAI, Sr Scientific Programmer/Analyst > NASA GSFC, Global Modeling and Assimilation Office > Code 610.1, 8800 Greenbelt Rd, Greenbelt, MD 20771 > Phone: 301-614-6712 Fax: 301-614-6246 > http://science.gsfc.nasa.gov/sed/bio/matthew.thompson > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > Twitter: https://twitter.com/hdf5 _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
