My hdf5 1.8.7 appears to build okay but my make check fails. This is on a Sci Linux box:
uname -a
Linux redqueen.rcs.manchester.ac.uk 2.6.18-238.1.1.el5 #1 SMP Tue Jan 18 18:49:37 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
I attach the std out+err from my configure and make steps. And here is the detailed error
[mccssmb2@redqueen hdf5-1.8.7]$ /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5 -vv -o select 2>&1 | less
For help use: /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5 -help
Linked with hdf5 version 1.8 release 7
Testing -- Configure definitions (config)
Testing -- Encoding/decoding metadata (metadata)
Testing -- Checksum algorithm (checksum)
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 -- Generic Object Functions (objects)
Testing -- Dataspaces (h5s)
*** UNEXPECTED RETURN from H5Fopen is -1 line 188 in th5s.c
HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
#000: H5F.c line 1522 in H5Fopen(): unable to open file
major: File accessability
minor: Unable to open file
#001: H5F.c line 1211 in H5F_open(): unable to open file: time = Fri Jun 24 12:41:23 2011
, name = 'th5s.h5', tent_flags = 0
major: File accessability
minor: Unable to open file
#002: H5FD.c line 1086 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#003: H5FDsec2.c line 348 in H5FD_sec2_open(): unable to open file: name = 'th5s.h5', errno = 2, error mess
age = 'No such file or directory', flags = 0, o_flags = 0
major: File accessability
minor: Unable to open file
***cannot open the pre-created H5S_MAX_RANK test file (th5s.h5)
Testing -- Dataspace coordinates (coords)
Testing -- Shared Object Header Messages (sohm)
Testing -- Attributes (attr)
Testing -- Selections (select)
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
{& much more of same}
Many thanks, Michael
mkb_make.txt (69.8 KB)
mkb_configure.txt (22.5 KB)
Hi Michael,
My hdf5 1.8.7 appears to build okay but my make check fails.
Hmm, where are you running the 'make check'? You should be running it from the top level of the directory where you built the software (i.e. where you ran the 'make' command).
Quincey
···
On Jun 24, 2011, at 7:01 AM, michael bane wrote:
This is on a Sci Linux box:
uname -a
Linux redqueen.rcs.manchester.ac.uk 2.6.18-238.1.1.el5 #1 SMP Tue Jan 18 18:49:37 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
I attach the std out+err from my configure and make steps. And here is the detailed error
[mccssmb2@redqueen hdf5-1.8.7]$ /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5 -vv -o select 2>&1 | less
For help use: /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5 -help
Linked with hdf5 version 1.8 release 7
Testing -- Configure definitions (config)
Testing -- Encoding/decoding metadata (metadata)
Testing -- Checksum algorithm (checksum)
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 -- Generic Object Functions (objects)
Testing -- Dataspaces (h5s)
*** UNEXPECTED RETURN from H5Fopen is -1 line 188 in th5s.c
HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
#000: H5F.c line 1522 in H5Fopen(): unable to open file
major: File accessability
minor: Unable to open file
#001: H5F.c line 1211 in H5F_open(): unable to open file: time = Fri Jun 24 12:41:23 2011
, name = 'th5s.h5', tent_flags = 0
major: File accessability
minor: Unable to open file
#002: H5FD.c line 1086 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#003: H5FDsec2.c line 348 in H5FD_sec2_open(): unable to open file: name = 'th5s.h5', errno = 2, error mess
age = 'No such file or directory', flags = 0, o_flags = 0
major: File accessability
minor: Unable to open file
***cannot open the pre-created H5S_MAX_RANK test file (th5s.h5)
Testing -- Dataspace coordinates (coords)
Testing -- Shared Object Header Messages (sohm)
Testing -- Attributes (attr)
Testing -- Selections (select)
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
{& much more of same}
Many thanks, Michael
<mkb_make.txt><mkb_configure.txt>_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Quincey
Thanks for the reply. Yes I'm running it in the same dir as where I did
'make'
M
···
On Fri, 2011-06-24 at 12:53 -0500, Quincey Koziol wrote:
Hi Michael,
On Jun 24, 2011, at 7:01 AM, michael bane wrote:
> My hdf5 1.8.7 appears to build okay but my make check fails.
Hmm, where are you running the 'make check'? You should be running it from the top level of the directory where you built the software (i.e. where you ran the 'make' command).
Quincey
Michael,
In 1.8.7 we enabled -O3 optimization for C Intel compiler. May be the higher level of optimization doesn't work on your machine (errors sound familiar, but I may be wrong)
Could you please set CC to "icc -O2" and recompile the library, or fix the config/intel-flags file (search 1.8.7 string to find the right place).
Thank you!
Elena
···
On Jun 24, 2011, at 4:01 PM, michael bane wrote:
My hdf5 1.8.7 appears to build okay but my make check fails. This is on a Sci Linux box:
uname -a
Linux redqueen.rcs.manchester.ac.uk 2.6.18-238.1.1.el5 #1 SMP Tue Jan 18 18:49:37 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
I attach the std out+err from my configure and make steps. And here is the detailed error
[mccssmb2@redqueen hdf5-1.8.7]$ /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5 -vv -o select 2>&1 | less
For help use: /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5 -help
Linked with hdf5 version 1.8 release 7
Testing -- Configure definitions (config)
Testing -- Encoding/decoding metadata (metadata)
Testing -- Checksum algorithm (checksum)
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 -- Generic Object Functions (objects)
Testing -- Dataspaces (h5s)
*** UNEXPECTED RETURN from H5Fopen is -1 line 188 in th5s.c
HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
#000: H5F.c line 1522 in H5Fopen(): unable to open file
major: File accessability
minor: Unable to open file
#001: H5F.c line 1211 in H5F_open(): unable to open file: time = Fri Jun 24 12:41:23 2011
, name = 'th5s.h5', tent_flags = 0
major: File accessability
minor: Unable to open file
#002: H5FD.c line 1086 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#003: H5FDsec2.c line 348 in H5FD_sec2_open(): unable to open file: name = 'th5s.h5', errno = 2, error mess
age = 'No such file or directory', flags = 0, o_flags = 0
major: File accessability
minor: Unable to open file
***cannot open the pre-created H5S_MAX_RANK test file (th5s.h5)
Testing -- Dataspace coordinates (coords)
Testing -- Shared Object Header Messages (sohm)
Testing -- Attributes (attr)
Testing -- Selections (select)
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
{& much more of same}
Many thanks, Michael
<mkb_make.txt><mkb_configure.txt>_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
I've tried setting CC as you said but at 'make' stage it's being ignored it seems:
[mccssmb2@redqueen hdf5-1.8.7]$ make
Making all in src
make[1]: Entering directory `/software/hdf/5/1.8.7/hdf5-1.8.7/src'
make all-am
make[2]: Entering directory `/software/hdf/5/1.8.7/hdf5-1.8.7/src'
CC H5.lo
icc: command line warning #10120: overriding '-O2' with '-O3'
H5.c(532): (col. 3) remark: LOOP WAS VECTORIZED.
H5.c(532): (col. 3) remark: LOOP WAS VECTORIZED.
CC H5checksum.lo
icc: command line warning #10120: overriding '-O2' with '-O3'
CC H5dbg.lo
icc: command line warning #10120: overriding '-O2' with '-O3'
···
On 24 Jun 2011, at 19:43, Elena Pourmal wrote:
Michael,
In 1.8.7 we enabled -O3 optimization for C Intel compiler. May be the higher level of optimization doesn't work on your machine (errors sound familiar, but I may be wrong)
Could you please set CC to "icc -O2" and recompile the library, or fix the config/intel-flags file (search 1.8.7 string to find the right place).
Thank you!
Elena
On Jun 24, 2011, at 4:01 PM, michael bane wrote:
My hdf5 1.8.7 appears to build okay but my make check fails. This is on a Sci Linux box:
uname -a
Linux redqueen.rcs.manchester.ac.uk 2.6.18-238.1.1.el5 #1 SMP Tue Jan 18 18:49:37 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
I attach the std out+err from my configure and make steps. And here is the detailed error
[mccssmb2@redqueen hdf5-1.8.7]$ /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5 -vv -o select 2>&1 | less
For help use: /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5 -help
Linked with hdf5 version 1.8 release 7
Testing -- Configure definitions (config)
Testing -- Encoding/decoding metadata (metadata)
Testing -- Checksum algorithm (checksum)
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 -- Generic Object Functions (objects)
Testing -- Dataspaces (h5s)
*** UNEXPECTED RETURN from H5Fopen is -1 line 188 in th5s.c
HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
#000: H5F.c line 1522 in H5Fopen(): unable to open file
major: File accessability
minor: Unable to open file
#001: H5F.c line 1211 in H5F_open(): unable to open file: time = Fri Jun 24 12:41:23 2011
, name = 'th5s.h5', tent_flags = 0
major: File accessability
minor: Unable to open file
#002: H5FD.c line 1086 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#003: H5FDsec2.c line 348 in H5FD_sec2_open(): unable to open file: name = 'th5s.h5', errno = 2, error mess
age = 'No such file or directory', flags = 0, o_flags = 0
major: File accessability
minor: Unable to open file
***cannot open the pre-created H5S_MAX_RANK test file (th5s.h5)
Testing -- Dataspace coordinates (coords)
Testing -- Shared Object Header Messages (sohm)
Testing -- Attributes (attr)
Testing -- Selections (select)
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
{& much more of same}
Many thanks, Michael
<mkb_make.txt><mkb_configure.txt>_______________________________________________
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
Thanks to Elena and Barbara's patient help, it appears lowering (by
editting config/intel-flags) the optimisation to -O1 is required for icc
11.0 (Build 20081105 Package ID: l_cproc_p_11.0.074) running under
Scientific Linux:
$ cat /etc/redhat-release ; uname -a
Scientific Linux SL release 5.2 (Boron)
Linux redqueen.rcs.manchester.ac.uk 2.6.18-238.1.1.el5 #1 SMP Tue Jan 18
18:49:37 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
Many thanks, Michael
···
On Fri, 2011-06-24 at 22:43 +0400, Elena Pourmal wrote:
Michael,
In 1.8.7 we enabled -O3 optimization for C Intel compiler. May be the higher level of optimization doesn't work on your machine (errors sound familiar, but I may be wrong)
Could you please set CC to "icc -O2" and recompile the library, or fix the config/intel-flags file (search 1.8.7 string to find the right place).
Thank you!
Elena
On Jun 24, 2011, at 4:01 PM, michael bane wrote:
> My hdf5 1.8.7 appears to build okay but my make check fails. This is on a Sci Linux box:
> uname -a
> Linux redqueen.rcs.manchester.ac.uk 2.6.18-238.1.1.el5 #1 SMP Tue Jan 18 18:49:37 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
>
> I attach the std out+err from my configure and make steps. And here is the detailed error
>
> [mccssmb2@redqueen hdf5-1.8.7]$ /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5 -vv -o select 2>&1 | less
>
> For help use: /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5 -help
> Linked with hdf5 version 1.8 release 7
> Testing -- Configure definitions (config)
> Testing -- Encoding/decoding metadata (metadata)
> Testing -- Checksum algorithm (checksum)
> 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 -- Generic Object Functions (objects)
> Testing -- Dataspaces (h5s)
> *** UNEXPECTED RETURN from H5Fopen is -1 line 188 in th5s.c
> HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
> #000: H5F.c line 1522 in H5Fopen(): unable to open file
> major: File accessability
> minor: Unable to open file
> #001: H5F.c line 1211 in H5F_open(): unable to open file: time = Fri Jun 24 12:41:23 2011
> , name = 'th5s.h5', tent_flags = 0
> major: File accessability
> minor: Unable to open file
> #002: H5FD.c line 1086 in H5FD_open(): open failed
> major: Virtual File Layer
> minor: Unable to initialize object
> #003: H5FDsec2.c line 348 in H5FD_sec2_open(): unable to open file: name = 'th5s.h5', errno = 2, error mess
> age = 'No such file or directory', flags = 0, o_flags = 0
> major: File accessability
> minor: Unable to open file
> ***cannot open the pre-created H5S_MAX_RANK test file (th5s.h5)
> Testing -- Dataspace coordinates (coords)
> Testing -- Shared Object Header Messages (sohm)
> Testing -- Attributes (attr)
> Testing -- Selections (select)
> large cube read from small cube has bad data! Line=2015
> large cube read from small cube has bad data! Line=2015
> large cube read from small cube has bad data! Line=2015
> large cube read from small cube has bad data! Line=2015
> large cube read from small cube has bad data! Line=2015
> large cube written from small cube has bad data! Line=2256
> large cube written from small cube has bad data! Line=2256
> large cube written from small cube has bad data! Line=2256
> large cube written from small cube has bad data! Line=2256
> large cube written from small cube has bad data! Line=2256
> large cube read from small cube has bad data! Line=2015
> large cube read from small cube has bad data! Line=2015
> {& much more of same}
>
>
> Many thanks, Michael
> <mkb_make.txt><mkb_configure.txt>_______________________________________________
> 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
--
Dr. Michael K. Bane
Snr Research Apps & Collabs Consultant
IT Services for Research
Univ. of Manchester M13 9PL
http://www.rcs.manchester.ac.uk
http://www.twitter.com/mkbane_mcr
Michael,
Then you have to modify intel-flags file (or did you already ?)
Elena
···
On Jun 25, 2011, at 1:30 PM, Michael Bane wrote:
I've tried setting CC as you said but at 'make' stage it's being ignored it seems:
[mccssmb2@redqueen hdf5-1.8.7]$ make
Making all in src
make[1]: Entering directory `/software/hdf/5/1.8.7/hdf5-1.8.7/src'
make all-am
make[2]: Entering directory `/software/hdf/5/1.8.7/hdf5-1.8.7/src'
CC H5.lo
icc: command line warning #10120: overriding '-O2' with '-O3'
H5.c(532): (col. 3) remark: LOOP WAS VECTORIZED.
H5.c(532): (col. 3) remark: LOOP WAS VECTORIZED.
CC H5checksum.lo
icc: command line warning #10120: overriding '-O2' with '-O3'
CC H5dbg.lo
icc: command line warning #10120: overriding '-O2' with '-O3'
On 24 Jun 2011, at 19:43, Elena Pourmal wrote:
Michael,
In 1.8.7 we enabled -O3 optimization for C Intel compiler. May be the higher level of optimization doesn't work on your machine (errors sound familiar, but I may be wrong)
Could you please set CC to "icc -O2" and recompile the library, or fix the config/intel-flags file (search 1.8.7 string to find the right place).
Thank you!
Elena
On Jun 24, 2011, at 4:01 PM, michael bane wrote:
My hdf5 1.8.7 appears to build okay but my make check fails. This is on a Sci Linux box:
uname -a
Linux redqueen.rcs.manchester.ac.uk 2.6.18-238.1.1.el5 #1 SMP Tue Jan 18 18:49:37 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
I attach the std out+err from my configure and make steps. And here is the detailed error
[mccssmb2@redqueen hdf5-1.8.7]$ /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5 -vv -o select 2>&1 | less
For help use: /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5 -help
Linked with hdf5 version 1.8 release 7
Testing -- Configure definitions (config)
Testing -- Encoding/decoding metadata (metadata)
Testing -- Checksum algorithm (checksum)
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 -- Generic Object Functions (objects)
Testing -- Dataspaces (h5s)
*** UNEXPECTED RETURN from H5Fopen is -1 line 188 in th5s.c
HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
#000: H5F.c line 1522 in H5Fopen(): unable to open file
major: File accessability
minor: Unable to open file
#001: H5F.c line 1211 in H5F_open(): unable to open file: time = Fri Jun 24 12:41:23 2011
, name = 'th5s.h5', tent_flags = 0
major: File accessability
minor: Unable to open file
#002: H5FD.c line 1086 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#003: H5FDsec2.c line 348 in H5FD_sec2_open(): unable to open file: name = 'th5s.h5', errno = 2, error mess
age = 'No such file or directory', flags = 0, o_flags = 0
major: File accessability
minor: Unable to open file
***cannot open the pre-created H5S_MAX_RANK test file (th5s.h5)
Testing -- Dataspace coordinates (coords)
Testing -- Shared Object Header Messages (sohm)
Testing -- Attributes (attr)
Testing -- Selections (select)
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
{& much more of same}
Many thanks, Michael
<mkb_make.txt><mkb_configure.txt>_______________________________________________
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
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Editting config/intel-flags then a fresh ./configure sorted that, thanks.
Done a
make clean && make -j 12 && make test
but still see the problem...
Ta, M
config.log (213 KB)
ATT00001.txt (5.13 KB)
Could you please check that th5s.h5 is indeed in the test directory?
···
On Jun 25, 2011, at 2:35 PM, Michael Bane wrote:
Editting config/intel-flags then a fresh ./configure sorted that, thanks.
Done a
make clean && make -j 12 && make test
but still see the problem...
Ta, M
<config.log>
On 25 Jun 2011, at 11:13, Elena Pourmal wrote:
Michael,
Then you have to modify intel-flags file (or did you already ?)
Elena
On Jun 25, 2011, at 1:30 PM, Michael Bane wrote:
I've tried setting CC as you said but at 'make' stage it's being ignored it seems:
[mccssmb2@redqueen hdf5-1.8.7]$ make
Making all in src
make[1]: Entering directory `/software/hdf/5/1.8.7/hdf5-1.8.7/src'
make all-am
make[2]: Entering directory `/software/hdf/5/1.8.7/hdf5-1.8.7/src'
CC H5.lo
icc: command line warning #10120: overriding '-O2' with '-O3'
H5.c(532): (col. 3) remark: LOOP WAS VECTORIZED.
H5.c(532): (col. 3) remark: LOOP WAS VECTORIZED.
CC H5checksum.lo
icc: command line warning #10120: overriding '-O2' with '-O3'
CC H5dbg.lo
icc: command line warning #10120: overriding '-O2' with '-O3'
On 24 Jun 2011, at 19:43, Elena Pourmal wrote:
Michael,
In 1.8.7 we enabled -O3 optimization for C Intel compiler. May be the higher level of optimization doesn't work on your machine (errors sound familiar, but I may be wrong)
Could you please set CC to "icc -O2" and recompile the library, or fix the config/intel-flags file (search 1.8.7 string to find the right place).
Thank you!
Elena
On Jun 24, 2011, at 4:01 PM, michael bane wrote:
My hdf5 1.8.7 appears to build okay but my make check fails. This is on a Sci Linux box:
uname -a
Linux redqueen.rcs.manchester.ac.uk 2.6.18-238.1.1.el5 #1 SMP Tue Jan 18 18:49:37 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
I attach the std out+err from my configure and make steps. And here is the detailed error
[mccssmb2@redqueen hdf5-1.8.7]$ /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5 -vv -o select 2>&1 | less
For help use: /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5 -help
Linked with hdf5 version 1.8 release 7
Testing -- Configure definitions (config)
Testing -- Encoding/decoding metadata (metadata)
Testing -- Checksum algorithm (checksum)
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 -- Generic Object Functions (objects)
Testing -- Dataspaces (h5s)
*** UNEXPECTED RETURN from H5Fopen is -1 line 188 in th5s.c
HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
#000: H5F.c line 1522 in H5Fopen(): unable to open file
major: File accessability
minor: Unable to open file
#001: H5F.c line 1211 in H5F_open(): unable to open file: time = Fri Jun 24 12:41:23 2011
, name = 'th5s.h5', tent_flags = 0
major: File accessability
minor: Unable to open file
#002: H5FD.c line 1086 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#003: H5FDsec2.c line 348 in H5FD_sec2_open(): unable to open file: name = 'th5s.h5', errno = 2, error mess
age = 'No such file or directory', flags = 0, o_flags = 0
major: File accessability
minor: Unable to open file
***cannot open the pre-created H5S_MAX_RANK test file (th5s.h5)
Testing -- Dataspace coordinates (coords)
Testing -- Shared Object Header Messages (sohm)
Testing -- Attributes (attr)
Testing -- Selections (select)
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
{& much more of same}
Many thanks, Michael
<mkb_make.txt><mkb_configure.txt>_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
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_______________________________________________
Hdf-forum is for HDF software users discussion.
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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
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Elena, yes it's in the test directory:
[mccssmb2@redqueen hdf5-1.8.7]$ ls -alt test/th5s*
-rw-r--r-- 1 mccssmb2 users 253104 Jun 25 11:29 test/th5s.o
-rw-r--r-- 1 mccssmb2 users 86268 Apr 22 21:52 test/th5s.c
-rw-r--r-- 1 mccssmb2 users 2049 Apr 20 22:22 test/th5s.h5
[mccssmb2@redqueen hdf5-1.8.7]$
Thanks, Michael
···
On 25 Jun 2011, at 12:07, Elena Pourmal wrote:
Could you please check that th5s.h5 is indeed in the test directory?
On Jun 25, 2011, at 2:35 PM, Michael Bane wrote:
Editting config/intel-flags then a fresh ./configure sorted that, thanks.
Done a
make clean && make -j 12 && make test
but still see the problem...
Ta, M
<config.log>
On 25 Jun 2011, at 11:13, Elena Pourmal wrote:
Michael,
Then you have to modify intel-flags file (or did you already ?)
Elena
On Jun 25, 2011, at 1:30 PM, Michael Bane wrote:
I've tried setting CC as you said but at 'make' stage it's being ignored it seems:
[mccssmb2@redqueen hdf5-1.8.7]$ make
Making all in src
make[1]: Entering directory `/software/hdf/5/1.8.7/hdf5-1.8.7/src'
make all-am
make[2]: Entering directory `/software/hdf/5/1.8.7/hdf5-1.8.7/src'
CC H5.lo
icc: command line warning #10120: overriding '-O2' with '-O3'
H5.c(532): (col. 3) remark: LOOP WAS VECTORIZED.
H5.c(532): (col. 3) remark: LOOP WAS VECTORIZED.
CC H5checksum.lo
icc: command line warning #10120: overriding '-O2' with '-O3'
CC H5dbg.lo
icc: command line warning #10120: overriding '-O2' with '-O3'
On 24 Jun 2011, at 19:43, Elena Pourmal wrote:
Michael,
In 1.8.7 we enabled -O3 optimization for C Intel compiler. May be the higher level of optimization doesn't work on your machine (errors sound familiar, but I may be wrong)
Could you please set CC to "icc -O2" and recompile the library, or fix the config/intel-flags file (search 1.8.7 string to find the right place).
Thank you!
Elena
On Jun 24, 2011, at 4:01 PM, michael bane wrote:
My hdf5 1.8.7 appears to build okay but my make check fails. This is on a Sci Linux box:
uname -a
Linux redqueen.rcs.manchester.ac.uk 2.6.18-238.1.1.el5 #1 SMP Tue Jan 18 18:49:37 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
I attach the std out+err from my configure and make steps. And here is the detailed error
[mccssmb2@redqueen hdf5-1.8.7]$ /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5 -vv -o select 2>&1 | less
For help use: /software/hdf/5/1.8.7/hdf5-1.8.7/test/.libs/lt-testhdf5 -help
Linked with hdf5 version 1.8 release 7
Testing -- Configure definitions (config)
Testing -- Encoding/decoding metadata (metadata)
Testing -- Checksum algorithm (checksum)
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 -- Generic Object Functions (objects)
Testing -- Dataspaces (h5s)
*** UNEXPECTED RETURN from H5Fopen is -1 line 188 in th5s.c
HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
#000: H5F.c line 1522 in H5Fopen(): unable to open file
major: File accessability
minor: Unable to open file
#001: H5F.c line 1211 in H5F_open(): unable to open file: time = Fri Jun 24 12:41:23 2011
, name = 'th5s.h5', tent_flags = 0
major: File accessability
minor: Unable to open file
#002: H5FD.c line 1086 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#003: H5FDsec2.c line 348 in H5FD_sec2_open(): unable to open file: name = 'th5s.h5', errno = 2, error mess
age = 'No such file or directory', flags = 0, o_flags = 0
major: File accessability
minor: Unable to open file
***cannot open the pre-created H5S_MAX_RANK test file (th5s.h5)
Testing -- Dataspace coordinates (coords)
Testing -- Shared Object Header Messages (sohm)
Testing -- Attributes (attr)
Testing -- Selections (select)
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube written from small cube has bad data! Line=2256
large cube read from small cube has bad data! Line=2015
large cube read from small cube has bad data! Line=2015
{& much more of same}
Many thanks, Michael
<mkb_make.txt><mkb_configure.txt>_______________________________________________
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
_______________________________________________
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
_______________________________________________
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
