Thank you! Good to know. Elena > On Apr 27, 2017, at 2:29 PM, Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND > APPLICATIONS INC] <[email protected]> wrote: > > Elena, > > The main reason I use h5pcc is because these libraries (the Baselibs) are > nearly always compiled for parallel HDF5/netCDF4. Thus, my make file then > says to use 'h5pcc' rather than 'h5cc' in some subsequent make steps (like > wise using mpifort rather than ifort). > > I'll try and see what happens if I use h5cc rather than h5pcc. > > Matt > > > > On 04/27/2017 03:22 PM, Elena Pourmal wrote: >> 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 >> > > > -- > 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
