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 <[email protected]> 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.
> [email protected]
> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> [email protected]
> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>
>
_______________________________________________
Hdf-forum is for HDF software users discussion.
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