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Help Compiling h5edit

Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]
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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
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Re: Help Compiling h5edit

Elena Pourmal
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] <[hidden email]> 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.
> [hidden email]
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
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Re: Help Compiling h5edit

Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]
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] <[hidden email]> 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. [hidden email]
>> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
>>
>>
Twitter: https://twitter.com/hdf5
>
> _______________________________________________ Hdf-forum is for HDF
> software users discussion. [hidden email]
> 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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
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Re: Help Compiling h5edit

Elena Pourmal
Thank you! Good to know.

Elena

> On Apr 27, 2017, at 2:29 PM, Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] <[hidden email]> 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] <[hidden email]> 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. [hidden email]
>>> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
>>>
>>>
> Twitter: https://twitter.com/hdf5
>>
>> _______________________________________________ Hdf-forum is for HDF
>> software users discussion. [hidden email]
>> 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.
> [hidden email]
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> Twitter: https://twitter.com/hdf5

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Re: Help Compiling h5edit

Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]
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] <[hidden email]> 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] <[hidden email]> 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. [hidden email]
>>>> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
>>>>
>>>>
>> Twitter: https://twitter.com/hdf5
>>>
>>> _______________________________________________ Hdf-forum is for HDF
>>> software users discussion. [hidden email]
>>> 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.
>> [hidden email]
>> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
>> Twitter: https://twitter.com/hdf5
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> [hidden email]
> 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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
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