All,
I was able to try this again and using h5cc is, in fact, a non-starter.
Apparently when you build HDF5 with --enable-parallel, you only get h5pcc and
h5pfc, no h5cc or h5fc.
Also, weirdly, if all my compilers are GNU (gcc, gfortran) then I don't seem
to get this. If I have a mix (ifort + gcc), then I do. Yet h5edit has no
Fortran that I know of...
Matt
On 04/27/2017 03:43 PM, Elena Pourmal wrote:
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
--
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
