Hello,
I am hoping someone here can suggest work-around.
HDF5-1.8.5 compilation is failing on pgcc-6.2 in H5Pdcpl.c
The particular code that is failing involves lines bracketed with
conditional compilation logic...
#ifdef H5_HAVE_C99_DESIGNATED_INITIALIZER
But, HDF5's configure script seems to decide that pgcc-6.2 has this
feature and there is no easy way to turn it off. I mean, I cannot
concoct a configure incantation that will turn OFF this macro symbol. I
can manually edit header files and remove the definition but that
doesn't really help.
Has anyone encountered this? Anyone have a workaround? If you do, please
'reply-all' to this email with answer. Thanks.
Mark
···
--
Mark C. Miller, Lawrence Livermore National Laboratory
================!!LLNL BUSINESS ONLY!!================
miller86@llnl.gov urgent: miller86@pager.llnl.gov
T:8-6 (925)-423-5901 M/W/Th:7-12,2-7 (530)-753-8511
Hi Mark,
Hello,
I am hoping someone here can suggest work-around.
HDF5-1.8.5 compilation is failing on pgcc-6.2 in H5Pdcpl.c
The particular code that is failing involves lines bracketed with
conditional compilation logic...
#ifdef H5_HAVE_C99_DESIGNATED_INITIALIZER
But, HDF5's configure script seems to decide that pgcc-6.2 has this
feature and there is no easy way to turn it off. I mean, I cannot
concoct a configure incantation that will turn OFF this macro symbol. I
can manually edit header files and remove the definition but that
doesn't really help.
Has anyone encountered this? Anyone have a workaround? If you do, please
'reply-all' to this email with answer. Thanks.
That a _really_ old version of pgcc (the current version is 10.6+), is there any way to use a newer one? If not, you can edit the H5config.h and H5pubconf.h files in 'src' subdirectory after running configure, but before building everything with 'make'. You want to change the line:
#define HAVE_C99_DESIGNATED_INITIALIZER 1
to
/* #undef HAVE_C99_DESIGNATED_INITIALIZER */
in H5config.h and
#define H5_HAVE_C99_DESIGNATED_INITIALIZER 1
to
/* #undef H5_HAVE_C99_DESIGNATED_INITIALIZER */
in H5pubconf.h (note that the macro has a leading "H5_" in the H5pubconf.h header file)
Quincey
···
On Jul 1, 2010, at 8:27 PM, Mark Miller wrote:
Mark
--
Mark C. Miller, Lawrence Livermore National Laboratory
================!!LLNL BUSINESS ONLY!!================
miller86@llnl.gov urgent: miller86@pager.llnl.gov
T:8-6 (925)-423-5901 M/W/Th:7-12,2-7 (530)-753-8511
From: Laura C Murguia <murguia1@llnl.gov>
Date: July 1, 2010 7:35:30 PM CDT
To: "Miller, Mark C." <miller86@llnl.gov>
Cc: "Arrighi, Bill" <arrighi2@llnl.gov>
Subject: Re: Hdf5-1.8.5 compilation error on pgi compiler (heine)
Mark Miller wrote:
What platform is this? which version of pgcc?
Mark
On Thu, 2010-07-01 at 17:24, Laura C Murguia wrote:
make[4]: Entering directory
`/misc/lc/shale/perforce/Release_4_12_new_hdf5_1.8.5/imports/hdf5/src'
/bin/sh ../libtool --tag=CC --mode=compile pgcc -DHAVE_CONFIG_H -I.
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE
-D_BSD_SOURCE -D_POSIX_SOURCE -DNDEBUG -UH5_DEBUG_API -c99
-Minform=inform -fast -s -fast -Minform,inform -c -o H5Pdcpl.lo H5Pdcpl.c
libtool: compile: pgcc -DHAVE_CONFIG_H -I. -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE -D_POSIX_SOURCE
-DNDEBUG -UH5_DEBUG_API -c99 -Minform=inform -fast -s -fast
-Minform,inform -c H5Pdcpl.c -o H5Pdcpl.o
PGC-I-0222-Redundant definition for symbol __THROW
(/usr/include/sys/cdefs.h: 57)
PGC-I-0222-Redundant definition for symbol __extension__
(/usr/include/sys/cdefs.h: 234)
PGC-I-0222-Redundant definition for symbol __need_size_t
(/usr/include/_G_config.h: 10)
PGC-I-0222-Redundant definition for symbol __need_NULL
(/usr/include/_G_config.h: 13)
PGC-I-0222-Redundant definition for symbol __need_wint_t
(/usr/include/wchar.h: 47)
PGC-I-0222-Redundant definition for symbol __need_wint_t
(/usr/include/wchar.h: 47)
PGC-I-0222-Redundant definition for symbol __need_size_t
(/usr/include/gconv.h: 29)
PGC-I-0222-Redundant definition for symbol __need_wchar_t
(/usr/include/gconv.h: 30)
PGC-I-0222-Redundant definition for symbol __need_size_t
(/usr/include/stdlib.h: 28)
PGC-I-0222-Redundant definition for symbol __need_wchar_t
(/usr/include/stdlib.h: 30)
PGC-I-0222-Redundant definition for symbol __need_NULL
(/usr/include/stdlib.h: 31)
PGC-I-0222-Redundant definition for symbol __need_size_t
(/usr/local/pgi/linux86/6.2/include/alloca.h: 24)
PGC-I-0222-Redundant definition for symbol __need_size_t
(/usr/include/string.h: 31)
PGC-I-0222-Redundant definition for symbol __need_NULL
(/usr/include/string.h: 32)
PGC-I-0222-Redundant definition for symbol __need_size_t
(/usr/include/unistd.h: 193)
PGC-I-0222-Redundant definition for symbol __need_NULL
(/usr/include/unistd.h: 194)
PGC-I-0222-Redundant definition for symbol __need_size_t
(/usr/include/pwd.h: 32)
PGC-I-0222-Redundant definition for symbol __need_size_t
(/usr/include/time.h: 36)
PGC-I-0222-Redundant definition for symbol __need_NULL
(/usr/include/time.h: 37)
PGC-W-0114-More than one type specified (/usr/include/unistd.h: 189)
PGC-W-0143-Useless typedef declaration (no declarators present)
(/usr/include/unistd.h: 189)
PGC-S-0170-Designated initializers are not supported (H5Pdcpl.c: 153)
PGC-S-0073-Too many initializers for H5D_def_layout_compact_g
(H5Pdcpl.c: 153)
PGC-S-0170-Designated initializers are not supported (H5Pdcpl.c: 154)
PGC-S-0170-Designated initializers are not supported (H5Pdcpl.c: 155)
PGC-S-0073-Too many initializers for H5D_def_layout_chunk_g (H5Pdcpl.c: 155)
PGC-W-0170-Designated initializers are not supported (H5Pdcpl.c: 179)
PGC/x86 Linux/x86 6.2-3: compilation completed with severe errors
make[4]: *** [H5Pdcpl.lo] Error 1
make[4]: Leaving directory
`/misc/lc/shale/perforce/Release_4_12_new_hdf5_1.8.5/imports/hdf5/src'
make[3]: *** [install-recursive] Error 1
make[3]: Leaving directory
`/misc/lc/shale/perforce/Release_4_12_new_hdf5_1.8.5/imports/hdf5'
make[2]: *** [hdf5-install] Error 2
make[2]: Leaving directory
`/misc/lc/shale/perforce/Release_4_12_new_hdf5_1.8.5/imports'
make[1]: *** [hdf5] Error 2
make[1]: Leaving directory
`/misc/lc/shale/perforce/Release_4_12_new_hdf5_1.8.5/imports'
make: *** [imports] Error 2
--Laura
Mark,
This is on Open b-div; heine.llnl.gov; /usr/local/pgi/linux86/6.2/bin/pgcc
--Laura
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
I figured that was the problem. I don't have any control over this but
knowing the pgcc is really, really old, I'll consider the problem
closed. Thanks for advice.
Mark
···
On Tue, 2010-07-06 at 05:31 -0700, Quincey Koziol wrote:
Hi Mark,
On Jul 1, 2010, at 8:27 PM, Mark Miller wrote:
> Hello,
>
> I am hoping someone here can suggest work-around.
>
> HDF5-1.8.5 compilation is failing on pgcc-6.2 in H5Pdcpl.c
>
> The particular code that is failing involves lines bracketed with
> conditional compilation logic...
>
> #ifdef H5_HAVE_C99_DESIGNATED_INITIALIZER
>
> But, HDF5's configure script seems to decide that pgcc-6.2 has this
> feature and there is no easy way to turn it off. I mean, I cannot
> concoct a configure incantation that will turn OFF this macro
> symbol. I
> can manually edit header files and remove the definition but that
> doesn't really help.
>
> Has anyone encountered this? Anyone have a workaround? If you do,
> please
> 'reply-all' to this email with answer. Thanks.
That a _really_ old version of pgcc (the current version is 10.6+), is
there any way to use a newer one? If not, you can edit the H5config.h
and H5pubconf.h files in 'src' subdirectory after running configure,
but before building everything with 'make'. You want to change the
line:
#define HAVE_C99_DESIGNATED_INITIALIZER 1
to
/* #undef HAVE_C99_DESIGNATED_INITIALIZER */
in H5config.h and
#define H5_HAVE_C99_DESIGNATED_INITIALIZER 1
to
/* #undef H5_HAVE_C99_DESIGNATED_INITIALIZER */
in H5pubconf.h (note that the macro has a leading "H5_" in the
H5pubconf.h header file)
Quincey
> Mark
>
>
> --
> Mark C. Miller, Lawrence Livermore National Laboratory
> ================!!LLNL BUSINESS ONLY!!================
> miller86@llnl.gov urgent: miller86@pager.llnl.gov
> T:8-6 (925)-423-5901 M/W/Th:7-12,2-7 (530)-753-8511
>
> From: Laura C Murguia <murguia1@llnl.gov>
>
> Date: July 1, 2010 7:35:30 PM CDT
>
> To: "Miller, Mark C." <miller86@llnl.gov>
>
> Cc: "Arrighi, Bill" <arrighi2@llnl.gov>
>
> Subject: Re: Hdf5-1.8.5 compilation error on pgi compiler (heine)
>
>
>
> Mark Miller wrote:
> > What platform is this? which version of pgcc?
> >
> > Mark
> >
> > On Thu, 2010-07-01 at 17:24, Laura C Murguia wrote:
> >
> > > make[4]: Entering directory
> > > `/misc/lc/shale/perforce/Release_4_12_new_hdf5_1.8.5/imports/hdf5/src'
> > > /bin/sh ../libtool --tag=CC --mode=compile pgcc
> > > -DHAVE_CONFIG_H -I.
> > > -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> > > -D_LARGEFILE64_SOURCE
> > > -D_BSD_SOURCE -D_POSIX_SOURCE -DNDEBUG -UH5_DEBUG_API -c99
> > > -Minform=inform -fast -s -fast -Minform,inform -c -o H5Pdcpl.lo
> > > H5Pdcpl.c
> > > libtool: compile: pgcc -DHAVE_CONFIG_H -I.
> > > -D_FILE_OFFSET_BITS=64
> > > -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE
> > > -D_POSIX_SOURCE
> > > -DNDEBUG -UH5_DEBUG_API -c99 -Minform=inform -fast -s -fast
> > > -Minform,inform -c H5Pdcpl.c -o H5Pdcpl.o
> > > PGC-I-0222-Redundant definition for symbol __THROW
> > > (/usr/include/sys/cdefs.h: 57)
> > > PGC-I-0222-Redundant definition for symbol __extension__
> > > (/usr/include/sys/cdefs.h: 234)
> > > PGC-I-0222-Redundant definition for symbol __need_size_t
> > > (/usr/include/_G_config.h: 10)
> > > PGC-I-0222-Redundant definition for symbol __need_NULL
> > > (/usr/include/_G_config.h: 13)
> > > PGC-I-0222-Redundant definition for symbol __need_wint_t
> > > (/usr/include/wchar.h: 47)
> > > PGC-I-0222-Redundant definition for symbol __need_wint_t
> > > (/usr/include/wchar.h: 47)
> > > PGC-I-0222-Redundant definition for symbol __need_size_t
> > > (/usr/include/gconv.h: 29)
> > > PGC-I-0222-Redundant definition for symbol __need_wchar_t
> > > (/usr/include/gconv.h: 30)
> > > PGC-I-0222-Redundant definition for symbol __need_size_t
> > > (/usr/include/stdlib.h: 28)
> > > PGC-I-0222-Redundant definition for symbol __need_wchar_t
> > > (/usr/include/stdlib.h: 30)
> > > PGC-I-0222-Redundant definition for symbol __need_NULL
> > > (/usr/include/stdlib.h: 31)
> > > PGC-I-0222-Redundant definition for symbol __need_size_t
> > > (/usr/local/pgi/linux86/6.2/include/alloca.h: 24)
> > > PGC-I-0222-Redundant definition for symbol __need_size_t
> > > (/usr/include/string.h: 31)
> > > PGC-I-0222-Redundant definition for symbol __need_NULL
> > > (/usr/include/string.h: 32)
> > > PGC-I-0222-Redundant definition for symbol __need_size_t
> > > (/usr/include/unistd.h: 193)
> > > PGC-I-0222-Redundant definition for symbol __need_NULL
> > > (/usr/include/unistd.h: 194)
> > > PGC-I-0222-Redundant definition for symbol __need_size_t
> > > (/usr/include/pwd.h: 32)
> > > PGC-I-0222-Redundant definition for symbol __need_size_t
> > > (/usr/include/time.h: 36)
> > > PGC-I-0222-Redundant definition for symbol __need_NULL
> > > (/usr/include/time.h: 37)
> > > PGC-W-0114-More than one type specified (/usr/include/unistd.h:
> > > 189)
> > > PGC-W-0143-Useless typedef declaration (no declarators present)
> > > (/usr/include/unistd.h: 189)
> > > PGC-S-0170-Designated initializers are not supported (H5Pdcpl.c:
> > > 153)
> > > PGC-S-0073-Too many initializers for H5D_def_layout_compact_g
> > > (H5Pdcpl.c: 153)
> > > PGC-S-0170-Designated initializers are not supported (H5Pdcpl.c:
> > > 154)
> > > PGC-S-0170-Designated initializers are not supported (H5Pdcpl.c:
> > > 155)
> > > PGC-S-0073-Too many initializers for H5D_def_layout_chunk_g
> > > (H5Pdcpl.c: 155)
> > > PGC-W-0170-Designated initializers are not supported (H5Pdcpl.c:
> > > 179)
> > > PGC/x86 Linux/x86 6.2-3: compilation completed with severe
> > > errors
> > > make[4]: *** [H5Pdcpl.lo] Error 1
> > > make[4]: Leaving directory
> > > `/misc/lc/shale/perforce/Release_4_12_new_hdf5_1.8.5/imports/hdf5/src'
> > > make[3]: *** [install-recursive] Error 1
> > > make[3]: Leaving directory
> > > `/misc/lc/shale/perforce/Release_4_12_new_hdf5_1.8.5/imports/hdf5'
> > > make[2]: *** [hdf5-install] Error 2
> > > make[2]: Leaving directory
> > > `/misc/lc/shale/perforce/Release_4_12_new_hdf5_1.8.5/imports'
> > > make[1]: *** [hdf5] Error 2
> > > make[1]: Leaving directory
> > > `/misc/lc/shale/perforce/Release_4_12_new_hdf5_1.8.5/imports'
> > > make: *** [imports] Error 2
> > >
> > > --Laura
> > >
> Mark,
> This is on Open b-div;
> heine.llnl.gov; /usr/local/pgi/linux86/6.2/bin/pgcc
>
> --Laura
>
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@hdfgroup.org
> http://*mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
--
Mark C. Miller, Lawrence Livermore National Laboratory
================!!LLNL BUSINESS ONLY!!================
miller86@llnl.gov urgent: miller86@pager.llnl.gov
T:8-6 (925)-423-5901 M/W/Th:7-12,2-7 (530)-753-8511
