I am attempting to build hdf5 1.8.3 with a pathscale 3.2 compiler. I am encountering the following issue:
% export CC=pathcc CXX=pathCC F77=pathf90 F90=pathf90
% ./configure --enable-fortran --enable-shared
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
...
compiler 'pathcc' is GNU gcc-4.2.0
...
SUMMARY OF THE HDF5 CONFIGURATION
···
=================================
General Information:
-------------------
HDF5 Version: 1.8.3
Configured on: Wed Jul 29 11:24:18 MDT 2009
Configured by: jgatenc@glory144
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux glory144 2.6.18-63chaos #1 SMP Fri Dec 19 15:37:16 EST 2008 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries:
Installation point: /gscratch1/jgatenc/hdf5-1.8.3/hdf5
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /projects/global/x86_64/compilers/pathscale/3.2/bin/pathcc (gcc-4.2.0)
CFLAGS/H5_CFLAGS: /-std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -O -fomit-frame-pointer -finline-functions
CPPFLAGS/H5_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE / -DNDEBUG -UH5_DEBUG_API
Shared Libraries: yes
Static Libraries: yes
Statically Linked Executables: no
Extra libraries: -lz -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: yes
Fortran Compiler: pathf90
Fortran Flags: -I.
C++: no
Features:
---------
Parallel HDF5: no
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Linux Large File Support (LFS): yes
% make
Making all in src
make[1]: Entering directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
make all-am
make[2]: Entering directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
/bin/sh ../libtool --tag=CC --mode=compile pathcc -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -DNDEBUG -UH5_DEBUG_API -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -O -fomit-frame-pointer -finline-functions -MT H5.lo -MD -MP -MF .deps/H5.Tpo -c -o H5.lo H5.c
libtool: compile: pathcc -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -DNDEBUG -UH5_DEBUG_API -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -O -fomit-frame-pointer -finline-functions -MT H5.lo -MD -MP -MF .deps/H5.Tpo -c H5.c -fPIC -DPIC -o .libs/H5.o
pathcc WARNING: -Wdisabled-optimization is ignored
pathcc ERROR parsing -Wold-style-definition: unknown flag
pathcc ERROR parsing -Wvariadic-macros: unknown flag
pathcc ERROR parsing -Winit-self: unknown flag
pathcc ERROR parsing -Wmissing-include-dirs: unknown flag
pathcc ERROR parsing -Wc++-compat: unknown flag
pathcc ERROR parsing -Wvolatile-register-var: unknown flag
pathcc ERROR parsing -Wstrict-overflow: unknown flag
PathScale(TM) Compiler Suite: Version 3.2
Changeset: 1192db93e3df4f01cddf0b957c29dbd9632cf61c
Built by: gautam@eng-05.pathscale.com in /scratch/gautam/nightly-compiler-build-pending/ekopath-pending
Built on: 2008-06-16 16:45:36 -0700
Thread model: posix
GNU gcc version 4.2.0 (PathScale 3.2 driver)
make[2]: *** [H5.lo] Error 1
make[2]: Leaving directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
make: *** [all-recursive] Error 1
For some reason, we are passing GNU options to pathscale. Your help is greatly appreciated.
Thanks,
Jonathan
I ran into this too and wondered the same thing. Why is HDF5's configure
script passing GNU flags to a non-GNU compiler?
I fixed by setting CFLAGS/CXXFLAGS explicitly in the configuration...
./configure CC=pathcc CXX=pathCC FC=pathf90 F77=pathf90 CFLAGS=-fPIC CXXFLAGS=-fPIC --enable-production
Mark
···
On Wed, 2009-07-29 at 11:32 -0600, Atencio, Jonathan Gerald wrote:
I am attempting to build hdf5 1.8.3 with a pathscale 3.2 compiler. I am encountering the following issue:
% export CC=pathcc CXX=pathCC F77=pathf90 F90=pathf90
% ./configure --enable-fortran --enable-shared
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
...
compiler 'pathcc' is GNU gcc-4.2.0
...
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.3
Configured on: Wed Jul 29 11:24:18 MDT 2009
Configured by: jgatenc@glory144
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux glory144 2.6.18-63chaos #1 SMP Fri Dec 19 15:37:16 EST 2008 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries:
Installation point: /gscratch1/jgatenc/hdf5-1.8.3/hdf5
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /projects/global/x86_64/compilers/pathscale/3.2/bin/pathcc (gcc-4.2.0)
CFLAGS/H5_CFLAGS: /-std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -O -fomit-frame-pointer -finline-functions
CPPFLAGS/H5_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE / -DNDEBUG -UH5_DEBUG_API
Shared Libraries: yes
Static Libraries: yes
Statically Linked Executables: no
Extra libraries: -lz -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: yes
Fortran Compiler: pathf90
Fortran Flags: -I.
C++: no
Features:
---------
Parallel HDF5: no
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Linux Large File Support (LFS): yes
% make
Making all in src
make[1]: Entering directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
make all-am
make[2]: Entering directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
/bin/sh ../libtool --tag=CC --mode=compile pathcc -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -DNDEBUG -UH5_DEBUG_API -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -O -fomit-frame-pointer -finline-functions -MT H5.lo -MD -MP -MF .deps/H5.Tpo -c -o H5.lo H5.c
libtool: compile: pathcc -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -DNDEBUG -UH5_DEBUG_API -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -O -fomit-frame-pointer -finline-functions -MT H5.lo -MD -MP -MF .deps/H5.Tpo -c H5.c -fPIC -DPIC -o .libs/H5.o
pathcc WARNING: -Wdisabled-optimization is ignored
pathcc ERROR parsing -Wold-style-definition: unknown flag
pathcc ERROR parsing -Wvariadic-macros: unknown flag
pathcc ERROR parsing -Winit-self: unknown flag
pathcc ERROR parsing -Wmissing-include-dirs: unknown flag
pathcc ERROR parsing -Wc++-compat: unknown flag
pathcc ERROR parsing -Wvolatile-register-var: unknown flag
pathcc ERROR parsing -Wstrict-overflow: unknown flag
PathScale(TM) Compiler Suite: Version 3.2
Changeset: 1192db93e3df4f01cddf0b957c29dbd9632cf61c
Built by: gautam@eng-05.pathscale.com in /scratch/gautam/nightly-compiler-build-pending/ekopath-pending
Built on: 2008-06-16 16:45:36 -0700
Thread model: posix
GNU gcc version 4.2.0 (PathScale 3.2 driver)
make[2]: *** [H5.lo] Error 1
make[2]: Leaving directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
make: *** [all-recursive] Error 1
For some reason, we are passing GNU options to pathscale. Your help is greatly appreciated.
Thanks,
Jonathan
_______________________________________________
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
email: mailto:miller86@llnl.gov
(M/T/W) (925)-423-5901 (!!LLNL BUSINESS ONLY!!)
(Th/F) (530)-753-8511 (!!LLNL BUSINESS ONLY!!)
Just to let you know that it is a known problem and we have been working on the fix.
Current status: we can configure and compile with the fix we have, but there are failures in the datatype conversion tests. It may take a while to resolve those issues.
Thank you!
Elena
···
On Jul 29, 2009, at 12:32 PM, Atencio, Jonathan Gerald wrote:
I am attempting to build hdf5 1.8.3 with a pathscale 3.2 compiler. I am encountering the following issue:
% export CC=pathcc CXX=pathCC F77=pathf90 F90=pathf90
% ./configure --enable-fortran --enable-shared
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
...
compiler 'pathcc' is GNU gcc-4.2.0
...
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.3
Configured on: Wed Jul 29 11:24:18 MDT 2009
Configured by: jgatenc@glory144
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux glory144 2.6.18-63chaos #1 SMP Fri Dec 19 15:37:16 EST 2008 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries:
Installation point: /gscratch1/jgatenc/hdf5-1.8.3/hdf5
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /projects/global/x86_64/compilers/pathscale/3.2/bin/pathcc (gcc-4.2.0)
CFLAGS/H5_CFLAGS: /-std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -O -fomit-frame-pointer -finline-functions
CPPFLAGS/H5_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE / -DNDEBUG -UH5_DEBUG_API
Shared Libraries: yes
Static Libraries: yes
Statically Linked Executables: no
Extra libraries: -lz -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: yes
Fortran Compiler: pathf90
Fortran Flags: -I.
C++: no
Features:
---------
Parallel HDF5: no
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Linux Large File Support (LFS): yes
% make
Making all in src
make[1]: Entering directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
make all-am
make[2]: Entering directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
/bin/sh ../libtool --tag=CC --mode=compile pathcc -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -DNDEBUG -UH5_DEBUG_API -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -O -fomit-frame-pointer -finline-functions -MT H5.lo -MD -MP -MF .deps/H5.Tpo -c -o H5.lo H5.c
libtool: compile: pathcc -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -DNDEBUG -UH5_DEBUG_API -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -O -fomit-frame-pointer -finline-functions -MT H5.lo -MD -MP -MF .deps/H5.Tpo -c H5.c -fPIC -DPIC -o .libs/H5.o
pathcc WARNING: -Wdisabled-optimization is ignored
pathcc ERROR parsing -Wold-style-definition: unknown flag
pathcc ERROR parsing -Wvariadic-macros: unknown flag
pathcc ERROR parsing -Winit-self: unknown flag
pathcc ERROR parsing -Wmissing-include-dirs: unknown flag
pathcc ERROR parsing -Wc++-compat: unknown flag
pathcc ERROR parsing -Wvolatile-register-var: unknown flag
pathcc ERROR parsing -Wstrict-overflow: unknown flag
PathScale(TM) Compiler Suite: Version 3.2
Changeset: 1192db93e3df4f01cddf0b957c29dbd9632cf61c
Built by: gautam@eng-05.pathscale.com in /scratch/gautam/nightly-compiler-build-pending/ekopath-pending
Built on: 2008-06-16 16:45:36 -0700
Thread model: posix
GNU gcc version 4.2.0 (PathScale 3.2 driver)
make[2]: *** [H5.lo] Error 1
make[2]: Leaving directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
make: *** [all-recursive] Error 1
For some reason, we are passing GNU options to pathscale. Your help is greatly appreciated.
Thanks,
Jonathan
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
I ran into this too and wondered the same thing. Why is HDF5's configure
script passing GNU flags to a non-GNU compiler?
The problem is that the Pathscale compiler is at least partially based on GCC and spits out a string containing "gcc" (or something like that) when passed the '-v' command line parameter, so our configure script decides it's actually GCC.
Quincey
···
On Jul 29, 2009, at 12:43 PM, Mark Miller wrote:
I fixed by setting CFLAGS/CXXFLAGS explicitly in the configuration...
./configure CC=pathcc CXX=pathCC FC=pathf90 F77=pathf90 CFLAGS=-fPIC CXXFLAGS=-fPIC --enable-production
Mark
On Wed, 2009-07-29 at 11:32 -0600, Atencio, Jonathan Gerald wrote:
I am attempting to build hdf5 1.8.3 with a pathscale 3.2 compiler. I am encountering the following issue:
% export CC=pathcc CXX=pathCC F77=pathf90 F90=pathf90
% ./configure --enable-fortran --enable-shared
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
...
compiler 'pathcc' is GNU gcc-4.2.0
...
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.3
Configured on: Wed Jul 29 11:24:18 MDT 2009
Configured by: jgatenc@glory144
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux glory144 2.6.18-63chaos #1 SMP Fri Dec 19 15:37:16 EST 2008 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries:
Installation point: /gscratch1/jgatenc/hdf5-1.8.3/hdf5
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /projects/global/x86_64/compilers/pathscale/3.2/bin/pathcc (gcc-4.2.0)
CFLAGS/H5_CFLAGS: /-std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -O -fomit-frame-pointer -finline-functions
CPPFLAGS/H5_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE / -DNDEBUG -UH5_DEBUG_API
Shared Libraries: yes
Static Libraries: yes
Statically Linked Executables: no
Extra libraries: -lz -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: yes
Fortran Compiler: pathf90
Fortran Flags: -I.
C++: no
Features:
---------
Parallel HDF5: no
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Linux Large File Support (LFS): yes
% make
Making all in src
make[1]: Entering directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
make all-am
make[2]: Entering directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
/bin/sh ../libtool --tag=CC --mode=compile pathcc -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -DNDEBUG -UH5_DEBUG_API -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -O -fomit-frame-pointer -finline-functions -MT H5.lo -MD -MP -MF .deps/H5.Tpo -c -o H5.lo H5.c
libtool: compile: pathcc -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -DNDEBUG -UH5_DEBUG_API -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -O -fomit-frame-pointer -finline-functions -MT H5.lo -MD -MP -MF .deps/H5.Tpo -c H5.c -fPIC -DPIC -o .libs/H5.o
pathcc WARNING: -Wdisabled-optimization is ignored
pathcc ERROR parsing -Wold-style-definition: unknown flag
pathcc ERROR parsing -Wvariadic-macros: unknown flag
pathcc ERROR parsing -Winit-self: unknown flag
pathcc ERROR parsing -Wmissing-include-dirs: unknown flag
pathcc ERROR parsing -Wc++-compat: unknown flag
pathcc ERROR parsing -Wvolatile-register-var: unknown flag
pathcc ERROR parsing -Wstrict-overflow: unknown flag
PathScale(TM) Compiler Suite: Version 3.2
Changeset: 1192db93e3df4f01cddf0b957c29dbd9632cf61c
Built by: gautam@eng-05.pathscale.com in /scratch/gautam/nightly-compiler-build-pending/ekopath-pending
Built on: 2008-06-16 16:45:36 -0700
Thread model: posix
GNU gcc version 4.2.0 (PathScale 3.2 driver)
make[2]: *** [H5.lo] Error 1
make[2]: Leaving directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
make: *** [all-recursive] Error 1
For some reason, we are passing GNU options to pathscale. Your help is greatly appreciated.
Thanks,
Jonathan
_______________________________________________
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
email: mailto:miller86@llnl.gov
(M/T/W) (925)-423-5901 (!!LLNL BUSINESS ONLY!!)
(Th/F) (530)-753-8511 (!!LLNL BUSINESS ONLY!!)
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Hi Elena,
I did see a slew of warnings from H55conv.c in 1.8.1 with pathscale
compilers.
Mark
/usr/gapps/silo/hdf5/src/hdf5-1.8.1/src/H5Tconv.c: In function
'H5T_conv_uchar_short':
/usr/gapps/silo/hdf5/src/hdf5-1.8.1/src/H5Tconv.c:4619: warning:
comparison is always false due to limited range of data type
'H5T_conv_uchar_int':
/usr/gapps/silo/hdf5/src/hdf5-1.8.1/src/H5Tconv.c:4748: warning:
comparison is always false due to limited range of data type
/usr/gapps/silo/hdf5/src/hdf5-1.8.1/src/H5Tconv.c: In function
'H5T_conv_uchar_long':
/usr/gapps/silo/hdf5/src/hdf5-1.8.1/src/H5Tconv.c:4877: warning:
comparison is always false due to limited range of data type
/usr/gapps/silo/hdf5/src/hdf5-1.8.1/src/H5Tconv.c: In function
'H5T_conv_uchar_llong':
/usr/gapps/silo/hdf5/src/hdf5-1.8.1/src/H5Tconv.c:5009: warning:
comparison is always false due to limited range of data type
/usr/gapps/silo/hdf5/src/hdf5-1.8.1/src/H5Tconv.c: In function
'H5T_conv_ushort_int':
/usr/gapps/silo/hdf5/src/hdf5-1.8.1/src/H5Tconv.c:5339: warning:
comparison is always false due to limited range of data type
/usr/gapps/silo/hdf5/src/hdf5-1.8.1/src/H5Tconv.c: In function
'H5T_conv_ushort_long':
/usr/gapps/silo/hdf5/src/hdf5-1.8.1/src/H5Tconv.c:5471: warning:
comparison is always false due to limited range of data type
/usr/gapps/silo/hdf5/src/hdf5-1.8.1/src/H5Tconv.c: In function
'H5T_conv_ushort_llong':
/usr/gapps/silo/hdf5/src/hdf5-1.8.1/src/H5Tconv.c:5603: warning:
comparison is always false due to limited range of data type
/usr/gapps/silo/hdf5/src/hdf5-1.8.1/src/H5Tconv.c: In function
'H5T_conv_uint_long':
/usr/gapps/silo/hdf5/src/hdf5-1.8.1/src/H5Tconv.c:6060: warning:
comparison is always false due to limited range of data type
/usr/gapps/silo/hdf5/src/hdf5-1.8.1/src/H5Tconv.c: In function
'H5T_conv_uint_llong':
/usr/gapps/silo/hdf5/src/hdf5-1.8.1/src/H5Tconv.c:6188: warning:
comparison is always false due to limited range of data type
mv -f .deps/H5Tconv.Tpo .deps/H5Tconv.Plo
···
Just to let you know that it is a known problem and we have been
working on the fix.
Current status: we can configure and compile with the fix we have,
but there are failures in the datatype conversion tests. It may take
a while to resolve those issues.
Thank you!
Elena
On Jul 29, 2009, at 12:32 PM, Atencio, Jonathan Gerald wrote:
> I am attempting to build hdf5 1.8.3 with a pathscale 3.2 compiler. I
> am encountering the following issue:
>
> % export CC=pathcc CXX=pathCC F77=pathf90 F90=pathf90
> % ./configure --enable-fortran --enable-shared
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> ...
> compiler 'pathcc' is GNU gcc-4.2.0
> ...
> SUMMARY OF THE HDF5 CONFIGURATION
> =================================
>
> General Information:
> -------------------
> HDF5 Version: 1.8.3
> Configured on: Wed Jul 29 11:24:18 MDT 2009
> Configured by: jgatenc@glory144
> Configure mode: production
> Host system: x86_64-unknown-linux-gnu
> Uname information: Linux glory144 2.6.18-63chaos #1 SMP
> Fri Dec 19 15:37:16 EST 2008 x86_64 x86_64 x86_64 GNU/Linux
> Byte sex: little-endian
> Libraries:
> Installation point: /gscratch1/jgatenc/hdf5-1.8.3/hdf5
>
> Compiling Options:
> ------------------
> Compilation Mode: production
> C Compiler: /projects/global/x86_64/compilers/
> pathscale/3.2/bin/pathcc (gcc-4.2.0)
> CFLAGS/H5_CFLAGS: /-std=c99 -pedantic -Wall -Wextra -
> Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -
> Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-
> prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-
> decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -
> Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-
> optimization -Wformat=2 -Wunreachable-code -Wendif-labels -
> Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -
> Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -
> Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-
> optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow
> -O -fomit-frame-pointer -finline-functions
> CPPFLAGS/H5_CPPFLAGS: -D_LARGEFILE_SOURCE -
> D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -
> D_BSD_SOURCE / -DNDEBUG -UH5_DEBUG_API
> Shared Libraries: yes
> Static Libraries: yes
> Statically Linked Executables: no
> Extra libraries: -lz -lm
> Archiver: ar
> Ranlib: ranlib
> Debugged Packages:
> API Tracing: no
>
> Languages:
> ----------
> Fortran: yes
> Fortran Compiler: pathf90
> Fortran Flags: -I.
> C++: no
>
> Features:
> ---------
> Parallel HDF5: no
> High Level library: yes
> Threadsafety: no
> Default API Mapping: v18
> With Deprecated Public Symbols: yes
> I/O filters (external): deflate(zlib)
> I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
> MPE: no
> Direct VFD: no
> dmalloc: no
> Clear file buffers before write: yes
> Using memory checker: no
> Function Stack Tracing: no
> GPFS: no
> Strict File Format Checks: no
> Optimization Instrumentation: no
> Linux Large File Support (LFS): yes
>
> % make
> Making all in src
> make[1]: Entering directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
> make all-am
> make[2]: Entering directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
> /bin/sh ../libtool --tag=CC --mode=compile pathcc -DHAVE_CONFIG_H -
> I. -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -
> D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -DNDEBUG -
> UH5_DEBUG_API -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -
> Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-
> strings -Wconversion -Waggregate-return -Wstrict-prototypes -
> Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -
> Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-
> format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization
> -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-
> statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -
> Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -
> Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-
> compat -Wvolatile-register-var -Wstrict-overflow -O -fomit-frame-
> pointer -finline-functions -MT H5.lo -MD -MP -MF .deps/H5.Tpo -c -o
> H5.lo H5.c
> libtool: compile: pathcc -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -
> D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -
> D_BSD_SOURCE -DNDEBUG -UH5_DEBUG_API -std=c99 -pedantic -Wall -
> Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-
> qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -
> Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -
> Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-
> equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -
> Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -
> Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -
> Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -
> Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-
> optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow
> -O -fomit-frame-pointer -finline-functions -MT H5.lo -MD -MP -
> MF .deps/H5.Tpo -c H5.c -fPIC -DPIC -o .libs/H5.o
> pathcc WARNING: -Wdisabled-optimization is ignored
> pathcc ERROR parsing -Wold-style-definition: unknown flag
> pathcc ERROR parsing -Wvariadic-macros: unknown flag
> pathcc ERROR parsing -Winit-self: unknown flag
> pathcc ERROR parsing -Wmissing-include-dirs: unknown flag
> pathcc ERROR parsing -Wc++-compat: unknown flag
> pathcc ERROR parsing -Wvolatile-register-var: unknown flag
> pathcc ERROR parsing -Wstrict-overflow: unknown flag
> PathScale(TM) Compiler Suite: Version 3.2
> Changeset: 1192db93e3df4f01cddf0b957c29dbd9632cf61c
> Built by: gautam@eng-05.pathscale.com in /scratch/gautam/nightly-
> compiler-build-pending/ekopath-pending
> Built on: 2008-06-16 16:45:36 -0700
> Thread model: posix
> GNU gcc version 4.2.0 (PathScale 3.2 driver)
> make[2]: *** [H5.lo] Error 1
> make[2]: Leaving directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
> make: *** [all-recursive] Error 1
>
>
> For some reason, we are passing GNU options to pathscale. Your help
> is greatly appreciated.
>
> Thanks,
>
> Jonathan
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@hdfgroup.org
> http://*mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
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
email: mailto:miller86@llnl.gov
(M/T/W) (925)-423-5901 (!!LLNL BUSINESS ONLY!!)
(Th/F) (530)-753-8511 (!!LLNL BUSINESS ONLY!!)
Out of curiosity, is that really "HDF5's" configure script that is the
cause of Autoconf's test to determine if the compiler is a GNU
compiler?
My impression from -v info is that pathscale is somehow using a GCC
frontend but maybe a proprietary code-generator backend?
FYI, dtransform tests all passed on my pathscale build for 1.8.1.
Mark
···
On Wed, 2009-07-29 at 16:09 -0500, Quincey Koziol wrote:
On Jul 29, 2009, at 12:43 PM, Mark Miller wrote:
> I ran into this too and wondered the same thing. Why is HDF5's
> configure
> script passing GNU flags to a non-GNU compiler?
The problem is that the Pathscale compiler is at least partially
based on GCC and spits out a string containing "gcc" (or something
like that) when passed the '-v' command line parameter, so our
configure script decides it's actually GCC.
Quincey
>
> I fixed by setting CFLAGS/CXXFLAGS explicitly in the configuration...
>
> ./configure CC=pathcc CXX=pathCC FC=pathf90 F77=pathf90 CFLAGS=-fPIC
> CXXFLAGS=-fPIC --enable-production
>
> Mark
>
> On Wed, 2009-07-29 at 11:32 -0600, Atencio, Jonathan Gerald wrote:
>> I am attempting to build hdf5 1.8.3 with a pathscale 3.2 compiler.
>> I am encountering the following issue:
>>
>> % export CC=pathcc CXX=pathCC F77=pathf90 F90=pathf90
>> % ./configure --enable-fortran --enable-shared
>> checking for a BSD-compatible install... /usr/bin/install -c
>> checking whether build environment is sane... yes
>> ...
>> compiler 'pathcc' is GNU gcc-4.2.0
>> ...
>> SUMMARY OF THE HDF5 CONFIGURATION
>> =================================
>>
>> General Information:
>> -------------------
>> HDF5 Version: 1.8.3
>> Configured on: Wed Jul 29 11:24:18 MDT 2009
>> Configured by: jgatenc@glory144
>> Configure mode: production
>> Host system: x86_64-unknown-linux-gnu
>> Uname information: Linux glory144 2.6.18-63chaos #1
>> SMP Fri Dec 19 15:37:16 EST 2008 x86_64 x86_64 x86_64 GNU/Linux
>> Byte sex: little-endian
>> Libraries:
>> Installation point: /gscratch1/jgatenc/hdf5-1.8.3/hdf5
>>
>> Compiling Options:
>> ------------------
>> Compilation Mode: production
>> C Compiler: /projects/global/x86_64/compilers/
>> pathscale/3.2/bin/pathcc (gcc-4.2.0)
>> CFLAGS/H5_CFLAGS: /-std=c99 -pedantic -Wall -Wextra -
>> Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -
>> Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -
>> Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -
>> Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-
>> equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -
>> Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels
>> -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -
>> Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -
>> Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-
>> optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-
>> overflow -O -fomit-frame-pointer -finline-functions
>> CPPFLAGS/H5_CPPFLAGS: -D_LARGEFILE_SOURCE -
>> D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -
>> D_BSD_SOURCE / -DNDEBUG -UH5_DEBUG_API
>> Shared Libraries: yes
>> Static Libraries: yes
>> Statically Linked Executables: no
>> Extra libraries: -lz -lm
>> Archiver: ar
>> Ranlib: ranlib
>> Debugged Packages:
>> API Tracing: no
>>
>> Languages:
>> ----------
>> Fortran: yes
>> Fortran Compiler: pathf90
>> Fortran Flags: -I.
>> C++: no
>>
>> Features:
>> ---------
>> Parallel HDF5: no
>> High Level library: yes
>> Threadsafety: no
>> Default API Mapping: v18
>> With Deprecated Public Symbols: yes
>> I/O filters (external): deflate(zlib)
>> I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
>> MPE: no
>> Direct VFD: no
>> dmalloc: no
>> Clear file buffers before write: yes
>> Using memory checker: no
>> Function Stack Tracing: no
>> GPFS: no
>> Strict File Format Checks: no
>> Optimization Instrumentation: no
>> Linux Large File Support (LFS): yes
>>
>> % make
>> Making all in src
>> make[1]: Entering directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
>> make all-am
>> make[2]: Entering directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
>> /bin/sh ../libtool --tag=CC --mode=compile pathcc -DHAVE_CONFIG_H
>> -I. -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -
>> D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -DNDEBUG -
>> UH5_DEBUG_API -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -
>> Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-
>> strings -Wconversion -Waggregate-return -Wstrict-prototypes -
>> Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -
>> Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-
>> format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-
>> optimization -Wformat=2 -Wunreachable-code -Wendif-labels -
>> Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -
>> Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -
>> Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-
>> optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-
>> overflow -O -fomit-frame-pointer -finline-functions -MT H5.lo -MD -
>> MP -MF .deps/H5.Tpo -c -o H5.lo H5.c
>> libtool: compile: pathcc -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -
>> D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -
>> D_BSD_SOURCE -DNDEBUG -UH5_DEBUG_API -std=c99 -pedantic -Wall -
>> Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-
>> qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -
>> Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -
>> Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-
>> equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -
>> Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels
>> -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -
>> Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -
>> Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-
>> optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-
>> overflow -O -fomit-frame-pointer -finline-functions -MT H5.lo -MD -
>> MP -MF .deps/H5.Tpo -c H5.c -fPIC -DPIC -o .libs/H5.o
>> pathcc WARNING: -Wdisabled-optimization is ignored
>> pathcc ERROR parsing -Wold-style-definition: unknown flag
>> pathcc ERROR parsing -Wvariadic-macros: unknown flag
>> pathcc ERROR parsing -Winit-self: unknown flag
>> pathcc ERROR parsing -Wmissing-include-dirs: unknown flag
>> pathcc ERROR parsing -Wc++-compat: unknown flag
>> pathcc ERROR parsing -Wvolatile-register-var: unknown flag
>> pathcc ERROR parsing -Wstrict-overflow: unknown flag
>> PathScale(TM) Compiler Suite: Version 3.2
>> Changeset: 1192db93e3df4f01cddf0b957c29dbd9632cf61c
>> Built by: gautam@eng-05.pathscale.com in /scratch/gautam/nightly-
>> compiler-build-pending/ekopath-pending
>> Built on: 2008-06-16 16:45:36 -0700
>> Thread model: posix
>> GNU gcc version 4.2.0 (PathScale 3.2 driver)
>> make[2]: *** [H5.lo] Error 1
>> make[2]: Leaving directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
>> make[1]: *** [all] Error 2
>> make[1]: Leaving directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
>> make: *** [all-recursive] Error 1
>>
>>
>> For some reason, we are passing GNU options to pathscale. Your help
>> is greatly appreciated.
>>
>> Thanks,
>>
>> Jonathan
>>
>> _______________________________________________
>> 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
> email: mailto:miller86@llnl.gov
> (M/T/W) (925)-423-5901 (!!LLNL BUSINESS ONLY!!)
> (Th/F) (530)-753-8511 (!!LLNL BUSINESS ONLY!!)
>
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@hdfgroup.org
> http://*mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
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
email: mailto:miller86@llnl.gov
(M/T/W) (925)-423-5901 (!!LLNL BUSINESS ONLY!!)
(Th/F) (530)-753-8511 (!!LLNL BUSINESS ONLY!!)
Hi Mark,
Out of curiosity, is that really "HDF5's" configure script that is the
cause of Autoconf's test to determine if the compiler is a GNU
compiler?
Yup. 
My impression from -v info is that pathscale is somehow using a GCC
frontend but maybe a proprietary code-generator backend?
Could be, sure.
FYI, dtransform tests all passed on my pathscale build for 1.8.1.
It could be that older/newer versions of the Pathscale compiler exhibit the bug. Additionally, the GCC folks have pointed us in the correct direction for fixing it, so hopefully we can address it in a future release.
Quincey
···
On Jul 29, 2009, at 4:25 PM, Mark Miller wrote:
Mark
On Wed, 2009-07-29 at 16:09 -0500, Quincey Koziol wrote:
On Jul 29, 2009, at 12:43 PM, Mark Miller wrote:
I ran into this too and wondered the same thing. Why is HDF5's
configure
script passing GNU flags to a non-GNU compiler?
The problem is that the Pathscale compiler is at least partially
based on GCC and spits out a string containing "gcc" (or something
like that) when passed the '-v' command line parameter, so our
configure script decides it's actually GCC.
Quincey
I fixed by setting CFLAGS/CXXFLAGS explicitly in the configuration...
./configure CC=pathcc CXX=pathCC FC=pathf90 F77=pathf90 CFLAGS=-fPIC
CXXFLAGS=-fPIC --enable-production
Mark
On Wed, 2009-07-29 at 11:32 -0600, Atencio, Jonathan Gerald wrote:
I am attempting to build hdf5 1.8.3 with a pathscale 3.2 compiler.
I am encountering the following issue:
% export CC=pathcc CXX=pathCC F77=pathf90 F90=pathf90
% ./configure --enable-fortran --enable-shared
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
...
compiler 'pathcc' is GNU gcc-4.2.0
...
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.3
Configured on: Wed Jul 29 11:24:18 MDT 2009
Configured by: jgatenc@glory144
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux glory144 2.6.18-63chaos #1
SMP Fri Dec 19 15:37:16 EST 2008 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries:
Installation point: /gscratch1/jgatenc/hdf5-1.8.3/hdf5
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /projects/global/x86_64/compilers/
pathscale/3.2/bin/pathcc (gcc-4.2.0)
CFLAGS/H5_CFLAGS: /-std=c99 -pedantic -Wall -Wextra -
Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -
Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -
Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -
Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-
equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -
Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels
-Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -
Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -
Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-
optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-
overflow -O -fomit-frame-pointer -finline-functions
CPPFLAGS/H5_CPPFLAGS: -D_LARGEFILE_SOURCE -
D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -
D_BSD_SOURCE / -DNDEBUG -UH5_DEBUG_API
Shared Libraries: yes
Static Libraries: yes
Statically Linked Executables: no
Extra libraries: -lz -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: yes
Fortran Compiler: pathf90
Fortran Flags: -I.
C++: no
Features:
---------
Parallel HDF5: no
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Linux Large File Support (LFS): yes
% make
Making all in src
make[1]: Entering directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
make all-am
make[2]: Entering directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
/bin/sh ../libtool --tag=CC --mode=compile pathcc -DHAVE_CONFIG_H
-I. -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -
D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -DNDEBUG -
UH5_DEBUG_API -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -
Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-
strings -Wconversion -Waggregate-return -Wstrict-prototypes -
Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -
Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-
format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-
optimization -Wformat=2 -Wunreachable-code -Wendif-labels -
Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -
Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -
Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-
optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-
overflow -O -fomit-frame-pointer -finline-functions -MT H5.lo -MD -
MP -MF .deps/H5.Tpo -c -o H5.lo H5.c
libtool: compile: pathcc -DHAVE_CONFIG_H -I. -D_LARGEFILE_SOURCE -
D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -
D_BSD_SOURCE -DNDEBUG -UH5_DEBUG_API -std=c99 -pedantic -Wall -
Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-
qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -
Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -
Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-
equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -
Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels
-Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -
Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -
Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-
optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-
overflow -O -fomit-frame-pointer -finline-functions -MT H5.lo -MD -
MP -MF .deps/H5.Tpo -c H5.c -fPIC -DPIC -o .libs/H5.o
pathcc WARNING: -Wdisabled-optimization is ignored
pathcc ERROR parsing -Wold-style-definition: unknown flag
pathcc ERROR parsing -Wvariadic-macros: unknown flag
pathcc ERROR parsing -Winit-self: unknown flag
pathcc ERROR parsing -Wmissing-include-dirs: unknown flag
pathcc ERROR parsing -Wc++-compat: unknown flag
pathcc ERROR parsing -Wvolatile-register-var: unknown flag
pathcc ERROR parsing -Wstrict-overflow: unknown flag
PathScale(TM) Compiler Suite: Version 3.2
Changeset: 1192db93e3df4f01cddf0b957c29dbd9632cf61c
Built by: gautam@eng-05.pathscale.com in /scratch/gautam/nightly-
compiler-build-pending/ekopath-pending
Built on: 2008-06-16 16:45:36 -0700
Thread model: posix
GNU gcc version 4.2.0 (PathScale 3.2 driver)
make[2]: *** [H5.lo] Error 1
make[2]: Leaving directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/gscratch1/jgatenc/hdf5-1.8.3/src'
make: *** [all-recursive] Error 1
For some reason, we are passing GNU options to pathscale. Your help
is greatly appreciated.
Thanks,
Jonathan
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--
Mark C. Miller, Lawrence Livermore National Laboratory
email: mailto:miller86@llnl.gov
(M/T/W) (925)-423-5901 (!!LLNL BUSINESS ONLY!!)
(Th/F) (530)-753-8511 (!!LLNL BUSINESS ONLY!!)
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://*mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
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
email: mailto:miller86@llnl.gov
(M/T/W) (925)-423-5901 (!!LLNL BUSINESS ONLY!!)
(Th/F) (530)-753-8511 (!!LLNL BUSINESS ONLY!!)
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
