Dear Albert,
Thank you very much. I did as you suggested, but the following error occurred.
Testing h5dump thyperslab.h5 PASSED
Testing h5dump -d integer -o /gpfs1/home/rajesh/test/hdf5-1.6.10/tools PASSED
Testing h5dump -d integer -o /gpfs1/home/rajesh/test/hdf5-1.6.10/tools PASSED
Running h5import /gpfs1/home/rajesh/test/hdf5-1.6.10/tools/h5dump/../ PASSED
Running h5diff tbinary.h5 /gpfs1/home/rajesh/test/hdf5-1.6.10/tools/h PASSED
Testing h5dump -b BE -d float -o /gpfs1/home/rajesh/test/hdf5-1.6.10/t PASSED
Testing h5dump -d integer -o /gpfs1/home/rajesh/test/hdf5-1.6.10/tools PASSED
Running h5import /gpfs1/home/rajesh/test/hdf5-1.6.10/tools/h5dump/../ PASSED
Running h5diff tbinary.h5 /gpfs1/home/rajesh/test/hdf5-1.6.10/tools/h PASSED
Testing h5dump -d double -b FILE -o /gpfs1/home/rajesh/test/hdf5-1.6.1 PASSED
All h5dump tests passed.
Real 5.10
User 1.42
System 0.87
Finished testing testh5dump.sh
============================
Target "_check-s" is up to date.
make _check-p
===Tests in h5dump ended Mon Mar 22 11:16:19 IST 2010===
+ cd fortran
+ make check
+ cd src
+ make check
/usr/vac/bin/xlc -qlanglvl=stdc99 -D_LARGE_FILES -q64 -I. -I../../src
-I../../src -I/usr/lib/include -c H5f90kit.c
echo timestamp > H5f90kit.lo
/usr/vac/bin/xlc -qlanglvl=stdc99 -D_LARGE_FILES -q64 -I. -I../../src
-I../../src -I/usr/lib/include -c H5_f.c
echo timestamp > H5_f.lo
/usr/vac/bin/xlc -qlanglvl=stdc99 -D_LARGE_FILES -q64 -I. -I../../src
-I../../src -I/usr/lib/include -c H5Rf.c
echo timestamp > H5Rf.lo
/usr/vac/bin/xlc -qlanglvl=stdc99 -D_LARGE_FILES -q64 -I. -I../../src
-I../../src -I/usr/lib/include -c H5Ff.c
echo timestamp > H5Ff.lo
/usr/vac/bin/xlc -qlanglvl=stdc99 -D_LARGE_FILES -q64 -I. -I../../src
-I../../src -I/usr/lib/include -c H5Sf.c
echo timestamp > H5Sf.lo
/usr/vac/bin/xlc -qlanglvl=stdc99 -D_LARGE_FILES -q64 -I. -I../../src
-I../../src -I/usr/lib/include -c H5Df.c
"H5Df.c", line 273.141: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Df.c", line 804.140: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
echo timestamp > H5Df.lo
/usr/vac/bin/xlc -qlanglvl=stdc99 -D_LARGE_FILES -q64 -I. -I../../src
-I../../src -I/usr/lib/include -c H5Gf.c
echo timestamp > H5Gf.lo
/usr/vac/bin/xlc -qlanglvl=stdc99 -D_LARGE_FILES -q64 -I. -I../../src
-I../../src -I/usr/lib/include -c H5Af.c
"H5Af.c", line 209.80: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 218.80: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 227.80: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 236.80: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 245.80: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 254.80: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 263.80: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 272.80: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 281.77: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 290.77: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 299.77: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 308.77: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 317.77: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 326.77: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 335.77: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 344.77: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 353.79: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 362.79: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 371.79: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 380.79: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 389.79: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 398.79: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 407.79: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 416.79: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 425.70: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 558.69: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 573.79: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 582.79: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 591.79: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 600.79: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 609.79: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 618.79: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 627.79: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 636.79: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 645.76: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 654.76: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 663.76: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 672.76: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 681.76: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 690.76: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 699.76: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 708.76: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 717.78: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 726.78: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 735.78: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 744.78: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 753.78: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 762.78: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 771.78: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Af.c", line 780.78: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
echo timestamp > H5Af.lo
/usr/vac/bin/xlc -qlanglvl=stdc99 -D_LARGE_FILES -q64 -I. -I../../src
-I../../src -I/usr/lib/include -c H5Tf.c
echo timestamp > H5Tf.lo
/usr/vac/bin/xlc -qlanglvl=stdc99 -D_LARGE_FILES -q64 -I. -I../../src
-I../../src -I/usr/lib/include -c H5Pf.c
"H5Pf.c", line 2268.95: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Pf.c", line 2293.81: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Pf.c", line 2357.93: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Pf.c", line 2382.79: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Pf.c", line 2756.74: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Pf.c", line 2780.60: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Pf.c", line 2840.74: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Pf.c", line 2864.60: 1506-1108 (I) The use of keyword
'__attribute__' is non-portable.
"H5Pf.c", line 3111.65: 1506-280 (E) Function argument assignment
between types "const char* const*" and "char**" is not allowed.
echo timestamp > H5Pf.lo
/usr/vac/bin/xlc -qlanglvl=stdc99 -D_LARGE_FILES -q64 -I. -I../../src
-I../../src -I/usr/lib/include -c H5If.c
echo timestamp > H5If.lo
/usr/vac/bin/xlc -qlanglvl=stdc99 -D_LARGE_FILES -q64 -I. -I../../src
-I../../src -I/usr/lib/include -c H5Ef.c
echo timestamp > H5Ef.lo
/usr/vac/bin/xlc -qlanglvl=stdc99 -D_LARGE_FILES -q64 -I. -I../../src
-I../../src -I/usr/lib/include -c H5Zf.c
echo timestamp > H5Zf.lo
/bin/xlf90 -I. -O -qsuffix=f=f90 -O -I. -I./ -I../src -c H5fortran_types.f90
** h5fortran_types === End of Compilation 1 ===
1501-510 Compilation successful for file H5fortran_types.f90.
echo timestamp > H5fortran_types.lo
/bin/xlf90 -I. -O -qsuffix=f=f90 -O -I. -I./ -I../src -c H5fortran_flags.f90
** h5fortran_flags === End of Compilation 1 ===
1501-510 Compilation successful for file H5fortran_flags.f90.
echo timestamp > H5fortran_flags.lo
/bin/xlf90 -I. -O -qsuffix=f=f90 -O -I. -I./ -I../src -c H5f90global.f90
** h5global === End of Compilation 1 ===
1501-510 Compilation successful for file H5f90global.f90.
echo timestamp > H5f90global.lo
/bin/xlf90 -I. -O -qsuffix=f=f90 -O -I. -I./ -I../src -c H5_ff.f90
** h5lib === End of Compilation 1 ===
1501-510 Compilation successful for file H5_ff.f90.
echo timestamp > H5_ff.lo
/bin/xlf90 -I. -O -qsuffix=f=f90 -O -I. -I./ -I../src -c H5Rff.f90
** h5r === End of Compilation 1 ===
1501-510 Compilation successful for file H5Rff.f90.
echo timestamp > H5Rff.lo
/bin/xlf90 -I. -O -qsuffix=f=f90 -O -I. -I./ -I../src -c H5Fff.f90
** h5f === End of Compilation 1 ===
1501-510 Compilation successful for file H5Fff.f90.
echo timestamp > H5Fff.lo
/bin/xlf90 -I. -O -qsuffix=f=f90 -O -I. -I./ -I../src -c H5Sff.f90
** h5s === End of Compilation 1 ===
1501-510 Compilation successful for file H5Sff.f90.
echo timestamp > H5Sff.lo
/bin/xlf90 -I. -O -qsuffix=f=f90 -O -I. -I./ -I../src -c H5Dff.f90
** h5d === End of Compilation 1 ===
1501-510 Compilation successful for file H5Dff.f90.
echo timestamp > H5Dff.lo
/bin/xlf90 -I. -O -qsuffix=f=f90 -O -I. -I./ -I../src -c H5Gff.f90
** h5g === End of Compilation 1 ===
1501-510 Compilation successful for file H5Gff.f90.
echo timestamp > H5Gff.lo
/bin/xlf90 -I. -O -qsuffix=f=f90 -O -I. -I./ -I../src -c H5Aff.f90
** h5a === End of Compilation 1 ===
1501-510 Compilation successful for file H5Aff.f90.
echo timestamp > H5Aff.lo
/bin/xlf90 -I. -O -qsuffix=f=f90 -O -I. -I./ -I../src -c H5Tff.f90
** h5t === End of Compilation 1 ===
1501-510 Compilation successful for file H5Tff.f90.
echo timestamp > H5Tff.lo
/bin/xlf90 -I. -O -qsuffix=f=f90 -O -I. -I./ -I../src -c H5Pff.f90
** h5p === End of Compilation 1 ===
1501-510 Compilation successful for file H5Pff.f90.
echo timestamp > H5Pff.lo
/bin/xlf90 -I. -O -qsuffix=f=f90 -O -I. -I./ -I../src -c H5Iff.f90
** h5i === End of Compilation 1 ===
1501-510 Compilation successful for file H5Iff.f90.
echo timestamp > H5Iff.lo
/bin/xlf90 -I. -O -qsuffix=f=f90 -O -I. -I./ -I../src -c H5Eff.f90
** h5e === End of Compilation 1 ===
1501-510 Compilation successful for file H5Eff.f90.
echo timestamp > H5Eff.lo
/bin/xlf90 -I. -O -qsuffix=f=f90 -O -I. -I./ -I../src -c H5Zff.f90
** h5z === End of Compilation 1 ===
1501-510 Compilation successful for file H5Zff.f90.
echo timestamp > H5Zff.lo
/bin/xlf90 -I. -O -qsuffix=f=f90 -O -I. -I./ -I../src -c HDF5.f90
** hdf5 === End of Compilation 1 ===
1501-510 Compilation successful for file HDF5.f90.
echo timestamp > HDF5.lo
mkdir .libs
rm -fr .libs/libhdf5_fortran.la .libs/libhdf5_fortran.* .libs/libhdf5_fortran.*
ar -X 64 cru .libs/libhdf5_fortran.a H5f90kit.o H5_f.o H5Rf.o H5Ff.o
H5Sf.o H5Df.o H5Gf.o H5Af.o H5Tf.o H5Pf.o H5If.o H5Ef.o H5Zf.o
H5fortran_types.o H5fortran_flags.o H5f90global.o H5_ff.o H5Rff.o
H5Fff.o H5Sff.o H5Dff.o H5Gff.o H5Aff.o H5Tff.o H5Pff.o H5Iff.o
H5Eff.o H5Zff.o HDF5.o
ar: 0707-126 H5fortran_types.o is not valid with the current object file mode.
Use the -X option to specify the desired object mode.
ar: 0707-126 H5fortran_flags.o is not valid with the current object file mode.
Use the -X option to specify the desired object mode.
ar: 0707-126 H5f90global.o is not valid with the current object file mode.
Use the -X option to specify the desired object mode.
ar: 0707-126 H5_ff.o is not valid with the current object file mode.
Use the -X option to specify the desired object mode.
ar: 0707-126 H5Rff.o is not valid with the current object file mode.
Use the -X option to specify the desired object mode.
ar: 0707-126 H5Fff.o is not valid with the current object file mode.
Use the -X option to specify the desired object mode.
ar: 0707-126 H5Sff.o is not valid with the current object file mode.
Use the -X option to specify the desired object mode.
ar: 0707-126 H5Dff.o is not valid with the current object file mode.
Use the -X option to specify the desired object mode.
ar: 0707-126 H5Gff.o is not valid with the current object file mode.
Use the -X option to specify the desired object mode.
ar: 0707-126 H5Aff.o is not valid with the current object file mode.
Use the -X option to specify the desired object mode.
ar: 0707-126 H5Tff.o is not valid with the current object file mode.
Use the -X option to specify the desired object mode.
ar: 0707-126 H5Pff.o is not valid with the current object file mode.
Use the -X option to specify the desired object mode.
ar: 0707-126 H5Iff.o is not valid with the current object file mode.
Use the -X option to specify the desired object mode.
ar: 0707-126 H5Eff.o is not valid with the current object file mode.
Use the -X option to specify the desired object mode.
ar: 0707-126 H5Zff.o is not valid with the current object file mode.
Use the -X option to specify the desired object mode.
ar: 0707-126 HDF5.o is not valid with the current object file mode.
Use the -X option to specify the desired object mode.
make: 1254-004 The error code from the last command is 16.
Stop.
+ exit 1
make: 1254-004 The error code from the last command is 1.
Stop.
+ exit 1
make: 1254-004 The error code from the last command is 1.
Stop.
bash-3.2$
What could be wrong? any help would greatly be appreciated.
Thanking you,
Rajesh
On Fri, Mar 19, 2010 at 9:02 PM, Albert Cheng <acheng@hdfgroup.org> wrote:
The error indicated that during configure, HDF5 concluded the
sizeof (long) is 8 bytes but when testhdf5 was compiled,
sizeof (long) is only 4 bytes. Similar meanings for the other 3
data types.
I think your system has 32bits as the default mode. You changed it
to the 64bits object mode by the "export OBJECT_MODE=64 ... configure"
but did not do so during the "make" stage. Therefore, xlc
continued with the default 32bits mode and generated 32bits mode
objects. If you go to the test/ directory and do "file testhdf5",
you would find it is actually a 32bits object file, not as a
"64-bit XCOFF executable".
To "fix" this, you need to have $OBJECT_MODE set to 64 in all
stages of configure/make/make check. I have a caution that if
this built library is used later to compile other applications,
the users must use the same $OBJECT_MODE value of 64, otherwise
you will get mixed mode objects. That usually resulted in linking
errors.
According to the following IBM document, it is advised to use
-q64 instead of using OBJECT_MODE=64.
http://publib.boulder.ibm.com/infocenter/comphelp/v8v101/index.jsp?topic=/com.ibm.xlf101a.doc/xlfcr/objmode.htm
Important note
Using OBJECT_MODE to determine the default bit mode can have serious
implications if you are not aware of the setting of OBJECT_MODE at the time
of invocation. For example, you may not be aware that OBJECT_MODE has been
set to 64, and you may unexpectedly obtain 64-bit object files.
We strongly urge you to be aware of the setting of OBJECT_MODE at all times
and to set OBJECT_MODE yourself to ensure that the compiler is invoked for
the correct bit mode. Instead, you can always use the -q32 or -q64 option to
specify the bit mode. Therefore, I would advise you to change your configure
command to this:
export CC=/usr/vac/bin/xlc
export CFLAGS=-q64
export FC=/bin/xlf90
export FCFLAGS=-q64
export CPP=/bin/cpp
export CXX=/usr/vacpp/bin/xlC
export CXXFLAGS=-q64
export AR="ar -X 64" # need to tell ar to use 64bits mode too
./configure --prefix=/gpfs1/home/rajesh/test/hdf5-1.6.10
--with-zlib=/usr/lib --enable-fortran --enable-netcdf-4
--disable-shared
Then you can simply run "make", "make check" and "make install".
Everything will run in the 64bits mode. Even the installed "h5cc/h5fc/h5c++"
will compile and link in the 64bit mode.
BTW, I am not sure why you have "--enable-netcdf-4" in the
configure command. "--enable-netcdf-4" is NOT a recognized
option by the HDF5 configure and is ignored by the configure
command.
I hope this helps.
-Albert
THG Developer
At 02:04 AM 3/19/2010, you wrote:
Hi HDF users,
While trying to install HDF5 on AIX5.3 the following error occurred.
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
============================
Testing testhdf5
testhdf5 Test Log
For help use: ./testhdf5 -help
Linked with hdf5 version 1.6 release 10
Testing -- Configure definitions (config)
Error: sizeof(long) is 4 but H5_SIZEOF_LONG is 8
Error: sizeof(unsigned long) is 4 but H5_SIZEOF_LONG is 8
Error: sizeof(size_t) is 4 but H5_SIZEOF_SIZE_T is 8
Error: sizeof(ssize_t) is 4 but H5_SIZEOF_SSIZE_T is 8
Testing -- Encode/decode metadata code (metadata)
Testing -- Ternary Search Trees (tst)
Testing -- Memory Heaps (heap)
Testing -- Skip Lists (skiplist)
Testing -- Reference Counted Strings (refstr)
Testing -- Low-Level File I/O (file)
Testing -- Dataspaces (h5s)
Testing -- Dataspace coordinates (coords)
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
The command I gave is
export OBJECT_MODE=64
export CC=/usr/vac/bin/xlc
export FC=/bin/xlf90
export CPP=/bin/cpp
export CXX=/usr/vacpp/bin/xlC
./configure --prefix=/gpfs1/home/rajesh/test/hdf5-1.6.10
--with-zlib=/usr/lib --enable-fortran --enable-netcdf-4
--disable-shared
Could anyone please help in this regard?
Thanks,
Rajesh
Consultant,
('PRITHVI' High Performance Computing System,
Indian Institute of Tropical Meteorology, Pune)
HCL Infosystems Ltd.
Arena 10, Pune Nagar Road, Viman Nagar, Pune
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
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_______________________________________________
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
