Help Compiling h5edit

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

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] <matthew.thompson@nasa.gov> 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.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

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

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

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. Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

Twitter: https://twitter.com/hdf5

_______________________________________________ Hdf-forum is for HDF
software users discussion. Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

Twitter: https://twitter.com/hdf5

···

On 04/27/2017 03:22 PM, Elena Pourmal wrote:

On Apr 27, 2017, at 11:41 AM, Thompson, Matt (GSFC-610.1)[SCIENCE >> SYSTEMS AND APPLICATIONS INC] <matthew.thompson@nasa.gov> wrote:

--
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

Thank you! Good to know.

Elena

···

On Apr 27, 2017, at 2:29 PM, Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] <matthew.thompson@nasa.gov> 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] <matthew.thompson@nasa.gov> 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. Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

Twitter: https://twitter.com/hdf5

_______________________________________________ Hdf-forum is for HDF
software users discussion. Hdf-forum@lists.hdfgroup.org
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.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

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] <matthew.thompson@nasa.gov> 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] <matthew.thompson@nasa.gov> 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. Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

Twitter: https://twitter.com/hdf5

_______________________________________________ Hdf-forum is for HDF
software users discussion. Hdf-forum@lists.hdfgroup.org
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.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
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