Hi all,
Is it possible to get some more informative error from H5Fopen than
"it failed"? E.g. if it was a permission problem, nonexistent file,
corrupted file, ...? Or must I try to deduce the reason for the
failure myself? (always risky to do such checks pre- or post-mortem so
to speak..).
Thanks in advance,
Elvis
Hi all,
Is it possible to get some more informative error from H5Fopen than
"it failed"? E.g. if it was a permission problem, nonexistent file,
corrupted file, ...? Or must I try to deduce the reason for the
failure myself? (always risky to do such checks pre- or post-mortem so
to speak..).
I think you are going to have to share your output with the list. Whenever *I* run hdf5 and get an error I get screenfuls of information.
For example, here's a simple hdf5 program trying to open a file for which I have removed all read and write permissions:
HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
#000: ../../../hdf5-1.8.16/src/H5F.c line 604 in H5Fopen(): unable to open file
major: File accessibilty
minor: Unable to open file
#001: ../../../hdf5-1.8.16/src/H5Fint.c line 992 in H5F_open(): unable to open file: time = Mon Nov 28 14:41:40 2016
, name = 'try.h5', tent_flags = 1
major: File accessibilty
minor: Unable to open file
#002: ../../../hdf5-1.8.16/src/H5FD.c line 993 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#003: ../../../hdf5-1.8.16/src/H5FDsec2.c line 339 in H5FD_sec2_open(): unable to open file: name = 'try.h5', errno = 13, error message = 'Permission denied', flags = 1, o_flags = 2
major: File accessibilty
minor: Unable to open file
On 11/08/2016 01:18 PM, Elvis Stansvik wrote:
Thanks in advance,
Elvis_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
"Hdf-forum on behalf of Rob Latham" wrote:
I think you are going to have to share your output with the list.
Whenever *I* run hdf5 and get an error I get screenfuls of information.
For example, here's a simple hdf5 program trying to open a file for
which I have removed all read and write permissions:
HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
#000: ../../../hdf5-1.8.16/src/H5F.c line 604 in H5Fopen(): unable to
open file
major: File accessibilty
minor: Unable to open file
#001: ../../../hdf5-1.8.16/src/H5Fint.c line 992 in H5F_open():
unable to open file: time = Mon Nov 28 14:41:40 2016
, name = 'try.h5', tent_flags = 1
major: File accessibilty
minor: Unable to open file
#002: ../../../hdf5-1.8.16/src/H5FD.c line 993 in H5FD_open(): open
failed
major: Virtual File Layer
minor: Unable to initialize object
#003: ../../../hdf5-1.8.16/src/H5FDsec2.c line 339 in
H5FD_sec2_open(): unable to open file: name = 'try.h5', errno = 13,
error message = 'Permission denied', flags = 1, o_flags = 2
major: File accessibilty
minor: Unable to open file
I am not sure how other users feel about this and it may not even be the original poster's ( Elvis Stansvik) complaint but a big challenge I have with interpreting HDF5 errors *is* the "...screenfuls of information".
It is challenging to paw through it to discover the root cause.
For example, in the above error stack, we get information about why sec2 VFD failed..."errno=13 ("Permission enied") but what are 'flags' and 'o_flags' there? Are these params to sec2 open call? That has only an 'oflag' argument and not an additional 'flags' argument. And, their numeric values, '1' and '2' are too informatvie either. What about similar info at the HDF5 public interface (e.g. H5Fopen)? What was passed for 'flags' there. Oh, maybe 'flags' in the #003 trace *is* the 'flags' argument caller passed to H5Fopen and 'o_flags' is what HDF5 lib passed to sec2 open call? I could see having 'flags' emitted in the #000 trace if that is indeed the argument passed as 'flags' to H5Fopen. and 'oflags' not 'o_flags' emitted in the #003 trace. Finally, it would be *much* more helpful to see the symbolic constants for the flags and not their numerics.
So, I personally find grocking HDF5 error stack output very awkward.
It may be that it is awkward enough for others that no one really is able to find the information they needed in it (e.g. the signal to noise ratio is just way too low).
My two cents.
Mark
--
Mark C. Miller, LLNL
"In the end, we will remember not the words of
our enemies but the silence of our friends" - MLK
Hi Rob,
Hi all,
Is it possible to get some more informative error from H5Fopen than
"it failed"? E.g. if it was a permission problem, nonexistent file,
corrupted file, ...? Or must I try to deduce the reason for the
failure myself? (always risky to do such checks pre- or post-mortem so
to speak..).I think you are going to have to share your output with the list. Whenever
*I* run hdf5 and get an error I get screenfuls of information.For example, here's a simple hdf5 program trying to open a file for which
I have removed all read and write permissions:
Yes, and I'm sorry. I should have replied to myself quite soon after I sent
my message, but somehow forgot about it.
When I first wrote my message, I was
1. working through the C++ API, and
2. building my program in release mode.
Working through the C++ API meant I was using
H5::Exception::getDetailMsg(), hoping to get some detailed message, but it
was giving me something like "H5Fopen failed" (which is why I mentioned the
H5Fopen C function in my post). Building my program in release mode also
meant I did not get the detailed error stack printout that the C layer does
by default in debug mode (like you showed below). That's why I was a little
puzzled.
Since I wrote my message, I have
1. switched to working with the C API (through a simple HDF5File C++
class of my own),
2. learned all about the gory details of the H5E API [1] and error
handling in chapter 9 of the User Guide.
So I'm all good now 
Though I must say the error handling API is quite
complicated (I still haven't written my custom error walking/formatting
functions, so only relying on the default printouts I get in debug mode).
One thing that I would wish for is
1. an API similar to H5Eprint that would take an output char* parameter
instead of a FILE*,
2. a simpler API to just get the human readable message (if any) for the
most likely "root cause" for the latest error.
1 because if you're interested in getting the error trace into a string
(for e.g. showing it in the UI), then setting up an in-memory FILE* is not
something that can be easily done in a portable way (I know about
fmemopen/open_memstream, but they are POSIX). I know this can be done by
setting up your own error stack walking function, but it's quite awkward to
have to do that, especially if you're happy with the formatting that HDF5
does by default, and you just want the result as a string instead.
2 because like others have mentioned, sometimes you're not interested in
the full trace, but only the likely root cause (which is probably somewhere
at the bottom of the stack).
Anyway, thanks for chiming in, and sorry again for not following up on my
own post earlier.
Elvis
2016-11-28 21:43 GMT+01:00 Rob Latham <robl@mcs.anl.gov>:
On 11/08/2016 01:18 PM, Elvis Stansvik wrote:
HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
#000: ../../../hdf5-1.8.16/src/H5F.c line 604 in H5Fopen(): unable to
open file
major: File accessibilty
minor: Unable to open file
#001: ../../../hdf5-1.8.16/src/H5Fint.c line 992 in H5F_open(): unable
to open file: time = Mon Nov 28 14:41:40 2016
, name = 'try.h5', tent_flags = 1
major: File accessibilty
minor: Unable to open file
#002: ../../../hdf5-1.8.16/src/H5FD.c line 993 in H5FD_open(): open
failed
major: Virtual File Layer
minor: Unable to initialize object
#003: ../../../hdf5-1.8.16/src/H5FDsec2.c line 339 in H5FD_sec2_open():
unable to open file: name = 'try.h5', errno = 13, error message =
'Permission denied', flags = 1, o_flags = 2
major: File accessibilty
minor: Unable to open fileThanks in advance,
Elvis_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
Mark,
I get what you mean. I have rarely found the error output of HDF5 to be of
much use, although sometimes it can be helpful. For instance just off the
top of my head, I've been getting errors about HDF attributes. I've called
H5Aclose and I get errors about the argument not being an attribute. Turns
out the variable I passed was never initialized. So in that case it's
helpful.
One thing to realize is that the error is most likely NOT reading in the
library itself. I recommend that you use a debugger like GDB to find
exactly what you are passing into the function and to see if every value
you're passing in makes sense. That's really the only way to go about it.
It all comes down to this: H5Fopen is failing and there are a finite number
of issues we can address.
1. Does the file exist, and if so are you providing the correct path to it
(relative or absolute)? Do you have read/write permission for the file?
2. Have you misspelled the file?
3. Are you providing either DF_ACC_RDWR or DF_ACC_RDONLY to the second
argument? Only those two arguments are valid.
4. What file access property list are you providing? You should be able to
rule out providing a buggy access property by just passing in the default
parameter.
I guarantee that your error lies in one of these issues. I recommend you
make the second and third arguments the read only and default respectively.
That will isolate the problem to your first argument and whether or not you
have appropriate file permissions.
Regards,
Landon
On Nov 28, 2016 3:33 PM, "Miller, Mark C." <miller86@llnl.gov> wrote:
"Hdf-forum on behalf of Rob Latham" wrote:
I think you are going to have to share your output with the list.
Whenever *I* run hdf5 and get an error I get screenfuls of information.For example, here's a simple hdf5 program trying to open a file for
which I have removed all read and write permissions:HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
#000: ../../../hdf5-1.8.16/src/H5F.c line 604 in H5Fopen(): unable to
open file
major: File accessibilty
minor: Unable to open file
#001: ../../../hdf5-1.8.16/src/H5Fint.c line 992 in H5F_open():
unable to open file: time = Mon Nov 28 14:41:40 2016
, name = 'try.h5', tent_flags = 1
major: File accessibilty
minor: Unable to open file
#002: ../../../hdf5-1.8.16/src/H5FD.c line 993 in H5FD_open(): open
failed
major: Virtual File Layer
minor: Unable to initialize object
#003: ../../../hdf5-1.8.16/src/H5FDsec2.c line 339 in
H5FD_sec2_open(): unable to open file: name = 'try.h5', errno = 13,
error message = 'Permission denied', flags = 1, o_flags = 2
major: File accessibilty
minor: Unable to open fileI am not sure how other users feel about this and it may not even be the
original poster's ( Elvis Stansvik) complaint but a big challenge I have
with interpreting HDF5 errors *is* the "...screenfuls of information".It is challenging to paw through it to discover the root cause.
For example, in the above error stack, we get information about why sec2
VFD failed..."errno=13 ("Permission enied") but what are 'flags' and
'o_flags' there? Are these params to sec2 open call? That has only an
'oflag' argument and not an additional 'flags' argument. And, their numeric
values, '1' and '2' are too informatvie either. What about similar info at
the HDF5 public interface (e.g. H5Fopen)? What was passed for 'flags'
there. Oh, maybe 'flags' in the #003 trace *is* the 'flags' argument caller
passed to H5Fopen and 'o_flags' is what HDF5 lib passed to sec2 open call?
I could see having 'flags' emitted in the #000 trace if that is indeed the
argument passed as 'flags' to H5Fopen. and 'oflags' not 'o_flags' emitted
in the #003 trace. Finally, it would be *much* more helpful to see the
symbolic constants for the flags and not their numerics.So, I personally find grocking HDF5 error stack output very awkward.
It may be that it is awkward enough for others that no one really is able
to find the information they needed in it (e.g. the signal to noise ratio
is just way too low).My two cents.
Mark
--
Mark C. Miller, LLNL"In the end, we will remember not the words of
our enemies but the silence of our friends" - MLK_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
Also one more possible issue I'd add onto my list there: it is possible
that the file is corrupt. So try ruling that out by making an empty HDF5
file in the same directory as the one you're trying to access and run the
same functions, only opening this new file instead.
Regards,
Landon
On Nov 28, 2016 4:26 PM, "Landon Clipp" <clipp2@illinois.edu> wrote:
Mark,
I get what you mean. I have rarely found the error output of HDF5 to be of
much use, although sometimes it can be helpful. For instance just off the
top of my head, I've been getting errors about HDF attributes. I've called
H5Aclose and I get errors about the argument not being an attribute. Turns
out the variable I passed was never initialized. So in that case it's
helpful.One thing to realize is that the error is most likely NOT reading in the
library itself. I recommend that you use a debugger like GDB to find
exactly what you are passing into the function and to see if every value
you're passing in makes sense. That's really the only way to go about it.It all comes down to this: H5Fopen is failing and there are a finite
number of issues we can address.1. Does the file exist, and if so are you providing the correct path to it
(relative or absolute)? Do you have read/write permission for the file?
2. Have you misspelled the file?
3. Are you providing either DF_ACC_RDWR or DF_ACC_RDONLY to the second
argument? Only those two arguments are valid.
4. What file access property list are you providing? You should be able to
rule out providing a buggy access property by just passing in the default
parameter.I guarantee that your error lies in one of these issues. I recommend you
make the second and third arguments the read only and default respectively.
That will isolate the problem to your first argument and whether or not you
have appropriate file permissions.Regards,
LandonOn Nov 28, 2016 3:33 PM, "Miller, Mark C." <miller86@llnl.gov> wrote:
"Hdf-forum on behalf of Rob Latham" wrote:
I think you are going to have to share your output with the list.
Whenever *I* run hdf5 and get an error I get screenfuls of information.For example, here's a simple hdf5 program trying to open a file for
which I have removed all read and write permissions:HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
#000: ../../../hdf5-1.8.16/src/H5F.c line 604 in H5Fopen(): unable to
open file
major: File accessibilty
minor: Unable to open file
#001: ../../../hdf5-1.8.16/src/H5Fint.c line 992 in H5F_open():
unable to open file: time = Mon Nov 28 14:41:40 2016
, name = 'try.h5', tent_flags = 1
major: File accessibilty
minor: Unable to open file
#002: ../../../hdf5-1.8.16/src/H5FD.c line 993 in H5FD_open(): open
failed
major: Virtual File Layer
minor: Unable to initialize object
#003: ../../../hdf5-1.8.16/src/H5FDsec2.c line 339 in
H5FD_sec2_open(): unable to open file: name = 'try.h5', errno = 13,
error message = 'Permission denied', flags = 1, o_flags = 2
major: File accessibilty
minor: Unable to open fileI am not sure how other users feel about this and it may not even be the
original poster's ( Elvis Stansvik) complaint but a big challenge I have
with interpreting HDF5 errors *is* the "...screenfuls of information".It is challenging to paw through it to discover the root cause.
For example, in the above error stack, we get information about why sec2
VFD failed..."errno=13 ("Permission enied") but what are 'flags' and
'o_flags' there? Are these params to sec2 open call? That has only an
'oflag' argument and not an additional 'flags' argument. And, their numeric
values, '1' and '2' are too informatvie either. What about similar info at
the HDF5 public interface (e.g. H5Fopen)? What was passed for 'flags'
there. Oh, maybe 'flags' in the #003 trace *is* the 'flags' argument caller
passed to H5Fopen and 'o_flags' is what HDF5 lib passed to sec2 open call?
I could see having 'flags' emitted in the #000 trace if that is indeed the
argument passed as 'flags' to H5Fopen. and 'oflags' not 'o_flags' emitted
in the #003 trace. Finally, it would be *much* more helpful to see the
symbolic constants for the flags and not their numerics.So, I personally find grocking HDF5 error stack output very awkward.
It may be that it is awkward enough for others that no one really is able
to find the information they needed in it (e.g. the signal to noise ratio
is just way too low).My two cents.
Mark
--
Mark C. Miller, LLNL"In the end, we will remember not the words of
our enemies but the silence of our friends" - MLK_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
Also one more possible issue I'd add onto my list there: it is possible
that the file is corrupt. So try ruling that out by making an empty HDF5
file in the same directory as the one you're trying to access and run
the same functions, only opening this new file instead.
I think Mark and Landon are saying the same things here, but in different ways.
The 300-some HDF5 user-facing interfaces should return something helpful. The internal interfaces between, say, H5Fopen and lowest-level posix open(2) system call are not helpful for users. The probably aren't all that helpful for developers at this point in the HDF5 life cycle, either.
==rob
On 11/28/2016 04:28 PM, Landon Clipp wrote:
Regards,
LandonOn Nov 28, 2016 4:26 PM, "Landon Clipp" <clipp2@illinois.edu > <mailto:clipp2@illinois.edu>> wrote:
Mark,
I get what you mean. I have rarely found the error output of HDF5 to
be of much use, although sometimes it can be helpful. For instance
just off the top of my head, I've been getting errors about HDF
attributes. I've called H5Aclose and I get errors about the argument
not being an attribute. Turns out the variable I passed was never
initialized. So in that case it's helpful.One thing to realize is that the error is most likely NOT reading in
the library itself. I recommend that you use a debugger like GDB to
find exactly what you are passing into the function and to see if
every value you're passing in makes sense. That's really the only
way to go about it.It all comes down to this: H5Fopen is failing and there are a finite
number of issues we can address.1. Does the file exist, and if so are you providing the correct path
to it (relative or absolute)? Do you have read/write permission for
the file?
2. Have you misspelled the file?
3. Are you providing either DF_ACC_RDWR or DF_ACC_RDONLY to the
second argument? Only those two arguments are valid.
4. What file access property list are you providing? You should be
able to rule out providing a buggy access property by just passing
in the default parameter.I guarantee that your error lies in one of these issues. I recommend
you make the second and third arguments the read only and default
respectively. That will isolate the problem to your first argument
and whether or not you have appropriate file permissions.Regards,
LandonOn Nov 28, 2016 3:33 PM, "Miller, Mark C." <miller86@llnl.gov > <mailto:miller86@llnl.gov>> wrote:
"Hdf-forum on behalf of Rob Latham" wrote:
I think you are going to have to share your output with the
list.
Whenever *I* run hdf5 and get an error I get screenfuls of
information.For example, here's a simple hdf5 program trying to open a
file for
which I have removed all read and write permissions:HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
#000: ../../../hdf5-1.8.16/src/H5F.c line 604 in
H5Fopen(): unable to
open file
major: File accessibilty
minor: Unable to open file
#001: ../../../hdf5-1.8.16/src/H5Fint.c line 992 in
H5F_open():
unable to open file: time = Mon Nov 28 14:41:40 2016
, name = 'try.h5', tent_flags = 1
major: File accessibilty
minor: Unable to open file
#002: ../../../hdf5-1.8.16/src/H5FD.c line 993 in
H5FD_open(): open
failed
major: Virtual File Layer
minor: Unable to initialize object
#003: ../../../hdf5-1.8.16/src/H5FDsec2.c line 339 in
H5FD_sec2_open(): unable to open file: name = 'try.h5',
errno = 13,
error message = 'Permission denied', flags = 1, o_flags = 2
major: File accessibilty
minor: Unable to open fileI am not sure how other users feel about this and it may not
even be the original poster's ( Elvis Stansvik) complaint but a
big challenge I have with interpreting HDF5 errors *is* the
"...screenfuls of information".It is challenging to paw through it to discover the root cause.
For example, in the above error stack, we get information about
why sec2 VFD failed..."errno=13 ("Permission enied") but what
are 'flags' and 'o_flags' there? Are these params to sec2 open
call? That has only an 'oflag' argument and not an additional
'flags' argument. And, their numeric values, '1' and '2' are too
informatvie either. What about similar info at the HDF5 public
interface (e.g. H5Fopen)? What was passed for 'flags' there. Oh,
maybe 'flags' in the #003 trace *is* the 'flags' argument caller
passed to H5Fopen and 'o_flags' is what HDF5 lib passed to sec2
open call? I could see having 'flags' emitted in the #000 trace
if that is indeed the argument passed as 'flags' to H5Fopen. and
'oflags' not 'o_flags' emitted in the #003 trace. Finally, it
would be *much* more helpful to see the symbolic constants for
the flags and not their numerics.So, I personally find grocking HDF5 error stack output very
awkward.It may be that it is awkward enough for others that no one
really is able to find the information they needed in it (e.g.
the signal to noise ratio is just way too low).My two cents.
Mark
--
Mark C. Miller, LLNL"In the end, we will remember not the words of
our enemies but the silence of our friends" - MLK_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org <mailto:Hdf-forum@lists.hdfgroup.org>
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
<http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org>
Twitter: https://twitter.com/hdf5_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
If you download the latest source, with the Java API, or the hdf-java 3.2.1 source - you can inspect the JNI code for exceptions in the native hdf5 exceptionImp.c file.
Another source of using the exception API for custom error reporting is the tools library and h5dump.
Allen
On Tuesday, November 29, 2016 9:20:03 AM CST Elvis Stansvik wrote:
Hi Rob,
2016-11-28 21:43 GMT+01:00 Rob Latham <robl@mcs.anl.gov>:
>
>
> On 11/08/2016 01:18 PM, Elvis Stansvik wrote:
>
>> Hi all,
>>
>> Is it possible to get some more informative error from H5Fopen than
>> "it failed"? E.g. if it was a permission problem, nonexistent file,
>> corrupted file, ...? Or must I try to deduce the reason for the
>> failure myself? (always risky to do such checks pre- or post-mortem so
>> to speak..).
>>
>
> I think you are going to have to share your output with the list. Whenever
> *I* run hdf5 and get an error I get screenfuls of information.
>
> For example, here's a simple hdf5 program trying to open a file for which
> I have removed all read and write permissions:
>Yes, and I'm sorry. I should have replied to myself quite soon after I sent
my message, but somehow forgot about it.When I first wrote my message, I was
1. working through the C++ API, and
2. building my program in release mode.Working through the C++ API meant I was using
H5::Exception::getDetailMsg(), hoping to get some detailed message, but it
was giving me something like "H5Fopen failed" (which is why I mentioned the
H5Fopen C function in my post). Building my program in release mode also
meant I did not get the detailed error stack printout that the C layer does
by default in debug mode (like you showed below). That's why I was a little
puzzled.Since I wrote my message, I have
1. switched to working with the C API (through a simple HDF5File C++
class of my own),
2. learned all about the gory details of the H5E API [1] and error
handling in chapter 9 of the User Guide.So I'm all good now
complicated (I still haven't written my custom error walking/formatting
functions, so only relying on the default printouts I get in debug mode).One thing that I would wish for is
1. an API similar to H5Eprint that would take an output char* parameter
instead of a FILE*,
2. a simpler API to just get the human readable message (if any) for the
most likely "root cause" for the latest error.1 because if you're interested in getting the error trace into a string
(for e.g. showing it in the UI), then setting up an in-memory FILE* is not
something that can be easily done in a portable way (I know about
fmemopen/open_memstream, but they are POSIX). I know this can be done by
setting up your own error stack walking function, but it's quite awkward to
have to do that, especially if you're happy with the formatting that HDF5
does by default, and you just want the result as a string instead.2 because like others have mentioned, sometimes you're not interested in
the full trace, but only the likely root cause (which is probably somewhere
at the bottom of the stack).Anyway, thanks for chiming in, and sorry again for not following up on my
own post earlier.Elvis
>
> HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
> #000: ../../../hdf5-1.8.16/src/H5F.c line 604 in H5Fopen(): unable to
> open file
> major: File accessibilty
> minor: Unable to open file
> #001: ../../../hdf5-1.8.16/src/H5Fint.c line 992 in H5F_open(): unable
> to open file: time = Mon Nov 28 14:41:40 2016
> , name = 'try.h5', tent_flags = 1
> major: File accessibilty
> minor: Unable to open file
> #002: ../../../hdf5-1.8.16/src/H5FD.c line 993 in H5FD_open(): open
> failed
> major: Virtual File Layer
> minor: Unable to initialize object
> #003: ../../../hdf5-1.8.16/src/H5FDsec2.c line 339 in H5FD_sec2_open():
> unable to open file: name = 'try.h5', errno = 13, error message =
> 'Permission denied', flags = 1, o_flags = 2
> major: File accessibilty
> minor: Unable to open file
>
>
>> Thanks in advance,
>> Elvis
>>
>> _______________________________________________
>> Hdf-forum is for HDF software users discussion.
>> Hdf-forum@lists.hdfgroup.org
>> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
>> Twitter: https://twitter.com/hdf5
>>
>>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@lists.hdfgroup.org
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> Twitter: https://twitter.com/hdf5
>
Also one more possible issue I'd add onto my list there: it is possible
that the file is corrupt. So try ruling that out by making an empty HDF5
file in the same directory as the one you're trying to access and run the
same functions, only opening this new file instead.
Ah yes, sorry I should have been more clear: In my case I wasn't debugging
a particular failure, just looking for a way to get as much info out of
HDF5 as possible to present together with an error message to the user
(it's a GUI application) (see also my response to Rob just now).
Thanks for this suggestion and the ones below as well though. They will
surely help when things truly hit the fan
Elvis
2016-11-28 23:28 GMT+01:00 Landon Clipp <clipp2@illinois.edu>:
Regards,
LandonOn Nov 28, 2016 4:26 PM, "Landon Clipp" <clipp2@illinois.edu> wrote:
Mark,
I get what you mean. I have rarely found the error output of HDF5 to be
of much use, although sometimes it can be helpful. For instance just off
the top of my head, I've been getting errors about HDF attributes. I've
called H5Aclose and I get errors about the argument not being an attribute.
Turns out the variable I passed was never initialized. So in that case it's
helpful.One thing to realize is that the error is most likely NOT reading in the
library itself. I recommend that you use a debugger like GDB to find
exactly what you are passing into the function and to see if every value
you're passing in makes sense. That's really the only way to go about it.It all comes down to this: H5Fopen is failing and there are a finite
number of issues we can address.1. Does the file exist, and if so are you providing the correct path to
it (relative or absolute)? Do you have read/write permission for the file?
2. Have you misspelled the file?
3. Are you providing either DF_ACC_RDWR or DF_ACC_RDONLY to the second
argument? Only those two arguments are valid.
4. What file access property list are you providing? You should be able
to rule out providing a buggy access property by just passing in the
default parameter.I guarantee that your error lies in one of these issues. I recommend you
make the second and third arguments the read only and default respectively.
That will isolate the problem to your first argument and whether or not you
have appropriate file permissions.Regards,
LandonOn Nov 28, 2016 3:33 PM, "Miller, Mark C." <miller86@llnl.gov> wrote:
"Hdf-forum on behalf of Rob Latham" wrote:
I think you are going to have to share your output with the list.
Whenever *I* run hdf5 and get an error I get screenfuls of information.For example, here's a simple hdf5 program trying to open a file for
which I have removed all read and write permissions:HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
#000: ../../../hdf5-1.8.16/src/H5F.c line 604 in H5Fopen(): unable to
open file
major: File accessibilty
minor: Unable to open file
#001: ../../../hdf5-1.8.16/src/H5Fint.c line 992 in H5F_open():
unable to open file: time = Mon Nov 28 14:41:40 2016
, name = 'try.h5', tent_flags = 1
major: File accessibilty
minor: Unable to open file
#002: ../../../hdf5-1.8.16/src/H5FD.c line 993 in H5FD_open(): open
failed
major: Virtual File Layer
minor: Unable to initialize object
#003: ../../../hdf5-1.8.16/src/H5FDsec2.c line 339 in
H5FD_sec2_open(): unable to open file: name = 'try.h5', errno = 13,
error message = 'Permission denied', flags = 1, o_flags = 2
major: File accessibilty
minor: Unable to open fileI am not sure how other users feel about this and it may not even be the
original poster's ( Elvis Stansvik) complaint but a big challenge I have
with interpreting HDF5 errors *is* the "...screenfuls of information".It is challenging to paw through it to discover the root cause.
For example, in the above error stack, we get information about why sec2
VFD failed..."errno=13 ("Permission enied") but what are 'flags' and
'o_flags' there? Are these params to sec2 open call? That has only an
'oflag' argument and not an additional 'flags' argument. And, their numeric
values, '1' and '2' are too informatvie either. What about similar info at
the HDF5 public interface (e.g. H5Fopen)? What was passed for 'flags'
there. Oh, maybe 'flags' in the #003 trace *is* the 'flags' argument caller
passed to H5Fopen and 'o_flags' is what HDF5 lib passed to sec2 open call?
I could see having 'flags' emitted in the #000 trace if that is indeed the
argument passed as 'flags' to H5Fopen. and 'oflags' not 'o_flags' emitted
in the #003 trace. Finally, it would be *much* more helpful to see the
symbolic constants for the flags and not their numerics.So, I personally find grocking HDF5 error stack output very awkward.
It may be that it is awkward enough for others that no one really is
able to find the information they needed in it (e.g. the signal to noise
ratio is just way too low).My two cents.
Mark
--
Mark C. Miller, LLNL"In the end, we will remember not the words of
our enemies but the silence of our friends" - MLK_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
If you download the latest source, with the Java API, or the hdf-java
3.2.1 source - you can inspect the JNI code for exceptions in the native
hdf5 exceptionImp.c file.
Another source of using the exception API for custom error reporting is
the tools library and h5dump.
Ah, thanks for the pointers Allen. I actually think I came across the JNI
code during my googlings, but didn't look closer at it before I got busy
with other things. I'll take a look when I'm back at it.
Elvis
Allen
> Hi Rob,
>
>
> >
> >
> >
> >> Hi all,
> >>
> >> Is it possible to get some more informative error from H5Fopen than
> >> "it failed"? E.g. if it was a permission problem, nonexistent file,
> >> corrupted file, ...? Or must I try to deduce the reason for the
> >> failure myself? (always risky to do such checks pre- or post-mortem
so
> >> to speak..).
> >>
> >
> > I think you are going to have to share your output with the list.
Whenever
> > *I* run hdf5 and get an error I get screenfuls of information.
> >
> > For example, here's a simple hdf5 program trying to open a file for
which
> > I have removed all read and write permissions:
> >
>
> Yes, and I'm sorry. I should have replied to myself quite soon after I
sent
> my message, but somehow forgot about it.
>
> When I first wrote my message, I was
>
> 1. working through the C++ API, and
> 2. building my program in release mode.
>
> Working through the C++ API meant I was using
> H5::Exception::getDetailMsg(), hoping to get some detailed message, but
it
> was giving me something like "H5Fopen failed" (which is why I mentioned
the
> H5Fopen C function in my post). Building my program in release mode also
> meant I did not get the detailed error stack printout that the C layer
does
> by default in debug mode (like you showed below). That's why I was a
little
> puzzled.
>
> Since I wrote my message, I have
>
> 1. switched to working with the C API (through a simple HDF5File C++
> class of my own),
> 2. learned all about the gory details of the H5E API [1] and error
> handling in chapter 9 of the User Guide.
>
> So I'm all good nowThough I must say the error handling API is quite
> complicated (I still haven't written my custom error walking/formatting
> functions, so only relying on the default printouts I get in debug
mode).
>
> One thing that I would wish for is
>
> 1. an API similar to H5Eprint that would take an output char*
parameter
> instead of a FILE*,
> 2. a simpler API to just get the human readable message (if any) for
the
> most likely "root cause" for the latest error.
>
> 1 because if you're interested in getting the error trace into a string
> (for e.g. showing it in the UI), then setting up an in-memory FILE* is
not
> something that can be easily done in a portable way (I know about
> fmemopen/open_memstream, but they are POSIX). I know this can be done by
> setting up your own error stack walking function, but it's quite
awkward to
> have to do that, especially if you're happy with the formatting that
HDF5
> does by default, and you just want the result as a string instead.
>
> 2 because like others have mentioned, sometimes you're not interested in
> the full trace, but only the likely root cause (which is probably
somewhere
> at the bottom of the stack).
>
> Anyway, thanks for chiming in, and sorry again for not following up on
my
> own post earlier.
>
> Elvis
>
>
> >
> > HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
> > #000: ../../../hdf5-1.8.16/src/H5F.c line 604 in H5Fopen(): unable
to
> > open file
> > major: File accessibilty
> > minor: Unable to open file
> > #001: ../../../hdf5-1.8.16/src/H5Fint.c line 992 in H5F_open():
unable
> > to open file: time = Mon Nov 28 14:41:40 2016
> > , name = 'try.h5', tent_flags = 1
> > major: File accessibilty
> > minor: Unable to open file
> > #002: ../../../hdf5-1.8.16/src/H5FD.c line 993 in H5FD_open(): open
> > failed
> > major: Virtual File Layer
> > minor: Unable to initialize object
> > #003: ../../../hdf5-1.8.16/src/H5FDsec2.c line 339 in
H5FD_sec2_open():
> > unable to open file: name = 'try.h5', errno = 13, error message =
> > 'Permission denied', flags = 1, o_flags = 2
> > major: File accessibilty
> > minor: Unable to open file
> >
> >
> >> Thanks in advance,
> >> Elvis
> >>
> >> _______________________________________________
> >> Hdf-forum is for HDF software users discussion.
> >> Hdf-forum@lists.hdfgroup.org
> >>
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> >> Twitter: https://twitter.com/hdf5
> >>
> >>
> > _______________________________________________
> > Hdf-forum is for HDF software users discussion.
> > Hdf-forum@lists.hdfgroup.org
> >
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Den 29 nov. 2016 3:32 em skrev "Allen Byrne" <byrn@hdfgroup.org>:
On Tuesday, November 29, 2016 9:20:03 AM CST Elvis Stansvik wrote:
> 2016-11-28 21:43 GMT+01:00 Rob Latham <robl@mcs.anl.gov>:
> > On 11/08/2016 01:18 PM, Elvis Stansvik wrote:
> > Twitter: https://twitter.com/hdf5
> >
>
>
> If you download the latest source, with the Java API, or the hdf-java
3.2.1 source - you can inspect the JNI code for exceptions in the native
hdf5 exceptionImp.c file.
> Another source of using the exception API for custom error reporting is
the tools library and h5dump.
Ah, thanks for the pointers Allen. I actually think I came across the JNI
code during my googlings, but didn't look closer at it before I got busy
with other things. I'll take a look when I'm back at it.
I looked at it briefly again, and the JNI code looks like it's doing
exactly what I want (a custom walker + H5E_walk2 to just get the top error,
and then H5E_get_msg to get the corresponding message). Many thanks.
I think when I was trying to figure it out on my own, I didn't realize it's
the minor error code I should feed to H5E_get_msg.
Elvis
Elvis
>
> Allen
>
> > Hi Rob,
> >
> >
> > >
> > >
> > >
> > >> Hi all,
> > >>
> > >> Is it possible to get some more informative error from H5Fopen than
> > >> "it failed"? E.g. if it was a permission problem, nonexistent file,
> > >> corrupted file, ...? Or must I try to deduce the reason for the
> > >> failure myself? (always risky to do such checks pre- or
post-mortem so
> > >> to speak..).
> > >>
> > >
> > > I think you are going to have to share your output with the list.
Whenever
> > > *I* run hdf5 and get an error I get screenfuls of information.
> > >
> > > For example, here's a simple hdf5 program trying to open a file for
which
> > > I have removed all read and write permissions:
> > >
> >
> > Yes, and I'm sorry. I should have replied to myself quite soon after
I sent
> > my message, but somehow forgot about it.
> >
> > When I first wrote my message, I was
> >
> > 1. working through the C++ API, and
> > 2. building my program in release mode.
> >
> > Working through the C++ API meant I was using
> > H5::Exception::getDetailMsg(), hoping to get some detailed message,
but it
> > was giving me something like "H5Fopen failed" (which is why I
mentioned the
> > H5Fopen C function in my post). Building my program in release mode
also
> > meant I did not get the detailed error stack printout that the C
layer does
> > by default in debug mode (like you showed below). That's why I was a
little
> > puzzled.
> >
> > Since I wrote my message, I have
> >
> > 1. switched to working with the C API (through a simple HDF5File C++
> > class of my own),
> > 2. learned all about the gory details of the H5E API [1] and error
> > handling in chapter 9 of the User Guide.
> >
> > So I'm all good now
quite
> > complicated (I still haven't written my custom error
walking/formatting
> > functions, so only relying on the default printouts I get in debug
mode).
> >
> > One thing that I would wish for is
> >
> > 1. an API similar to H5Eprint that would take an output char*
parameter
> > instead of a FILE*,
> > 2. a simpler API to just get the human readable message (if any)
for the
> > most likely "root cause" for the latest error.
> >
> > 1 because if you're interested in getting the error trace into a
string
> > (for e.g. showing it in the UI), then setting up an in-memory FILE*
is not
> > something that can be easily done in a portable way (I know about
> > fmemopen/open_memstream, but they are POSIX). I know this can be done
by
> > setting up your own error stack walking function, but it's quite
awkward to
> > have to do that, especially if you're happy with the formatting that
HDF5
> > does by default, and you just want the result as a string instead.
> >
> > 2 because like others have mentioned, sometimes you're not interested
in
> > the full trace, but only the likely root cause (which is probably
somewhere
> > at the bottom of the stack).
> >
> > Anyway, thanks for chiming in, and sorry again for not following up
on my
> > own post earlier.
> >
> > Elvis
> >
> >
> > >
> > > HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
> > > #000: ../../../hdf5-1.8.16/src/H5F.c line 604 in H5Fopen():
unable to
> > > open file
> > > major: File accessibilty
> > > minor: Unable to open file
> > > #001: ../../../hdf5-1.8.16/src/H5Fint.c line 992 in H5F_open():
unable
> > > to open file: time = Mon Nov 28 14:41:40 2016
> > > , name = 'try.h5', tent_flags = 1
> > > major: File accessibilty
> > > minor: Unable to open file
> > > #002: ../../../hdf5-1.8.16/src/H5FD.c line 993 in H5FD_open():
open
> > > failed
> > > major: Virtual File Layer
> > > minor: Unable to initialize object
> > > #003: ../../../hdf5-1.8.16/src/H5FDsec2.c line 339 in
H5FD_sec2_open():
> > > unable to open file: name = 'try.h5', errno = 13, error message =
> > > 'Permission denied', flags = 1, o_flags = 2
> > > major: File accessibilty
> > > minor: Unable to open file
> > >
> > >
> > >> Thanks in advance,
> > >> Elvis
> > >>
> > >> _______________________________________________
> > >> Hdf-forum is for HDF software users discussion.
> > >> Hdf-forum@lists.hdfgroup.org
> > >>
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> > >> Twitter: https://twitter.com/hdf5
> > >>
> > >>
> > > _______________________________________________
> > > Hdf-forum is for HDF software users discussion.
> > > Hdf-forum@lists.hdfgroup.org
> > >
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Den 29 nov. 2016 5:41 em skrev "Elvis Stansvik" < elvis.stansvik@orexplore.com>:
Den 29 nov. 2016 3:32 em skrev "Allen Byrne" <byrn@hdfgroup.org>:
> On Tuesday, November 29, 2016 9:20:03 AM CST Elvis Stansvik wrote:
> > 2016-11-28 21:43 GMT+01:00 Rob Latham <robl@mcs.anl.gov>:
> > > On 11/08/2016 01:18 PM, Elvis Stansvik wrote:
> > > Twitter: https://twitter.com/hdf5
> > >
> >
>
>
One thing to keep in mind, and the JNI code does, is that you clear the error stack when you use certain H5E APIs.
Allen
On Tuesday, November 29, 2016 6:07:22 PM CST Elvis Stansvik wrote:
Den 29 nov. 2016 5:41 em skrev "Elvis Stansvik" <
elvis.stansvik@orexplore.com>:
>
> Den 29 nov. 2016 3:32 em skrev "Allen Byrne" <byrn@hdfgroup.org>:
> >
> > If you download the latest source, with the Java API, or the hdf-java
3.2.1 source - you can inspect the JNI code for exceptions in the native
hdf5 exceptionImp.c file.
> > Another source of using the exception API for custom error reporting is
the tools library and h5dump.
>
> Ah, thanks for the pointers Allen. I actually think I came across the JNI
code during my googlings, but didn't look closer at it before I got busy
with other things. I'll take a look when I'm back at it.I looked at it briefly again, and the JNI code looks like it's doing
exactly what I want (a custom walker + H5E_walk2 to just get the top error,
and then H5E_get_msg to get the corresponding message). Many thanks.I think when I was trying to figure it out on my own, I didn't realize it's
the minor error code I should feed to H5E_get_msg.Elvis
> Elvis
>
> >
> > Allen
> >
> > On Tuesday, November 29, 2016 9:20:03 AM CST Elvis Stansvik wrote:
> > > Hi Rob,
> > >
> > > 2016-11-28 21:43 GMT+01:00 Rob Latham <robl@mcs.anl.gov>:
> > >
> > > >
> > > >
> > > > On 11/08/2016 01:18 PM, Elvis Stansvik wrote:
> > > >
> > > >> Hi all,
> > > >>
> > > >> Is it possible to get some more informative error from H5Fopen than
> > > >> "it failed"? E.g. if it was a permission problem, nonexistent file,
> > > >> corrupted file, ...? Or must I try to deduce the reason for the
> > > >> failure myself? (always risky to do such checks pre- or
post-mortem so
> > > >> to speak..).
> > > >>
> > > >
> > > > I think you are going to have to share your output with the list.
Whenever
> > > > *I* run hdf5 and get an error I get screenfuls of information.
> > > >
> > > > For example, here's a simple hdf5 program trying to open a file for
which
> > > > I have removed all read and write permissions:
> > > >
> > >
> > > Yes, and I'm sorry. I should have replied to myself quite soon after
I sent
> > > my message, but somehow forgot about it.
> > >
> > > When I first wrote my message, I was
> > >
> > > 1. working through the C++ API, and
> > > 2. building my program in release mode.
> > >
> > > Working through the C++ API meant I was using
> > > H5::Exception::getDetailMsg(), hoping to get some detailed message,
but it
> > > was giving me something like "H5Fopen failed" (which is why I
mentioned the
> > > H5Fopen C function in my post). Building my program in release mode
also
> > > meant I did not get the detailed error stack printout that the C
layer does
> > > by default in debug mode (like you showed below). That's why I was a
little
> > > puzzled.
> > >
> > > Since I wrote my message, I have
> > >
> > > 1. switched to working with the C API (through a simple HDF5File C++
> > > class of my own),
> > > 2. learned all about the gory details of the H5E API [1] and error
> > > handling in chapter 9 of the User Guide.
> > >
> > > So I'm all good now
quite
> > > complicated (I still haven't written my custom error
walking/formatting
> > > functions, so only relying on the default printouts I get in debug
mode).
> > >
> > > One thing that I would wish for is
> > >
> > > 1. an API similar to H5Eprint that would take an output char*
parameter
> > > instead of a FILE*,
> > > 2. a simpler API to just get the human readable message (if any)
for the
> > > most likely "root cause" for the latest error.
> > >
> > > 1 because if you're interested in getting the error trace into a
string
> > > (for e.g. showing it in the UI), then setting up an in-memory FILE*
is not
> > > something that can be easily done in a portable way (I know about
> > > fmemopen/open_memstream, but they are POSIX). I know this can be done
by
> > > setting up your own error stack walking function, but it's quite
awkward to
> > > have to do that, especially if you're happy with the formatting that
HDF5
> > > does by default, and you just want the result as a string instead.
> > >
> > > 2 because like others have mentioned, sometimes you're not interested
in
> > > the full trace, but only the likely root cause (which is probably
somewhere
> > > at the bottom of the stack).
> > >
> > > Anyway, thanks for chiming in, and sorry again for not following up
on my
> > > own post earlier.
> > >
> > > Elvis
> > >
> > >
> > > >
> > > > HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
> > > > #000: ../../../hdf5-1.8.16/src/H5F.c line 604 in H5Fopen():
unable to
> > > > open file
> > > > major: File accessibilty
> > > > minor: Unable to open file
> > > > #001: ../../../hdf5-1.8.16/src/H5Fint.c line 992 in H5F_open():
unable
> > > > to open file: time = Mon Nov 28 14:41:40 2016
> > > > , name = 'try.h5', tent_flags = 1
> > > > major: File accessibilty
> > > > minor: Unable to open file
> > > > #002: ../../../hdf5-1.8.16/src/H5FD.c line 993 in H5FD_open():
open
> > > > failed
> > > > major: Virtual File Layer
> > > > minor: Unable to initialize object
> > > > #003: ../../../hdf5-1.8.16/src/H5FDsec2.c line 339 in
H5FD_sec2_open():
> > > > unable to open file: name = 'try.h5', errno = 13, error message =
> > > > 'Permission denied', flags = 1, o_flags = 2
> > > > major: File accessibilty
> > > > minor: Unable to open file
> > > >
> > > >
> > > >> Thanks in advance,
> > > >> Elvis
> > > >>
> > > >> _______________________________________________
> > > >> Hdf-forum is for HDF software users discussion.
> > > >> Hdf-forum@lists.hdfgroup.org
> > > >>
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> > > >> Twitter: https://twitter.com/hdf5
> > > >>
> > > >>
> > > > _______________________________________________
> > > > Hdf-forum is for HDF software users discussion.
> > > > Hdf-forum@lists.hdfgroup.org
> > > >
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> > > > Twitter: https://twitter.com/hdf5
> > > >
> > >
> >
> >
One thing to keep in mind, and the JNI code does, is that you clear the
error stack when you use certain H5E APIs.
Thanks for the heads up. Will proceed with care.
Elvis
Allen
> Den 29 nov. 2016 5:41 em skrev "Elvis Stansvik" <
> elvis.stansvik@orexplore.com>:
> >
> > >
> > > If you download the latest source, with the Java API, or the
hdf-java
> 3.2.1 source - you can inspect the JNI code for exceptions in the native
> hdf5 exceptionImp.c file.
> > > Another source of using the exception API for custom error
reporting is
> the tools library and h5dump.
> >
> > Ah, thanks for the pointers Allen. I actually think I came across the
JNI
> code during my googlings, but didn't look closer at it before I got busy
> with other things. I'll take a look when I'm back at it.
>
> I looked at it briefly again, and the JNI code looks like it's doing
> exactly what I want (a custom walker + H5E_walk2 to just get the top
error,
> and then H5E_get_msg to get the corresponding message). Many thanks.
>
> I think when I was trying to figure it out on my own, I didn't realize
it's
> the minor error code I should feed to H5E_get_msg.
>
> Elvis
>
> > Elvis
> >
> > >
> > > Allen
> > >
> > > > Hi Rob,
> > > >
> > > >
> > > > >
> > > > >
> > > > >
> > > > >> Hi all,
> > > > >>
> > > > >> Is it possible to get some more informative error from H5Fopen
than
> > > > >> "it failed"? E.g. if it was a permission problem, nonexistent
file,
> > > > >> corrupted file, ...? Or must I try to deduce the reason for the
> > > > >> failure myself? (always risky to do such checks pre- or
> post-mortem so
> > > > >> to speak..).
> > > > >>
> > > > >
> > > > > I think you are going to have to share your output with the
list.
> Whenever
> > > > > *I* run hdf5 and get an error I get screenfuls of information.
> > > > >
> > > > > For example, here's a simple hdf5 program trying to open a file
for
> which
> > > > > I have removed all read and write permissions:
> > > > >
> > > >
> > > > Yes, and I'm sorry. I should have replied to myself quite soon
after
> I sent
> > > > my message, but somehow forgot about it.
> > > >
> > > > When I first wrote my message, I was
> > > >
> > > > 1. working through the C++ API, and
> > > > 2. building my program in release mode.
> > > >
> > > > Working through the C++ API meant I was using
> > > > H5::Exception::getDetailMsg(), hoping to get some detailed
message,
> but it
> > > > was giving me something like "H5Fopen failed" (which is why I
> mentioned the
> > > > H5Fopen C function in my post). Building my program in release
mode
> also
> > > > meant I did not get the detailed error stack printout that the C
> layer does
> > > > by default in debug mode (like you showed below). That's why I
was a
> little
> > > > puzzled.
> > > >
> > > > Since I wrote my message, I have
> > > >
> > > > 1. switched to working with the C API (through a simple
HDF5File C++
> > > > class of my own),
> > > > 2. learned all about the gory details of the H5E API [1] and
error
> > > > handling in chapter 9 of the User Guide.
> > > >
> > > > So I'm all good now
> quite
> > > > complicated (I still haven't written my custom error
> walking/formatting
> > > > functions, so only relying on the default printouts I get in debug
> mode).
> > > >
> > > > One thing that I would wish for is
> > > >
> > > > 1. an API similar to H5Eprint that would take an output char*
> parameter
> > > > instead of a FILE*,
> > > > 2. a simpler API to just get the human readable message (if any)
> for the
> > > > most likely "root cause" for the latest error.
> > > >
> > > > 1 because if you're interested in getting the error trace into a
> string
> > > > (for e.g. showing it in the UI), then setting up an in-memory
FILE*
> is not
> > > > something that can be easily done in a portable way (I know about
> > > > fmemopen/open_memstream, but they are POSIX). I know this can be
done
> by
> > > > setting up your own error stack walking function, but it's quite
> awkward to
> > > > have to do that, especially if you're happy with the formatting
that
> HDF5
> > > > does by default, and you just want the result as a string instead.
> > > >
> > > > 2 because like others have mentioned, sometimes you're not
interested
> in
> > > > the full trace, but only the likely root cause (which is probably
> somewhere
> > > > at the bottom of the stack).
> > > >
> > > > Anyway, thanks for chiming in, and sorry again for not following
up
> on my
> > > > own post earlier.
> > > >
> > > > Elvis
> > > >
> > > >
> > > > >
> > > > > HDF5-DIAG: Error detected in HDF5 (1.8.16) thread 0:
> > > > > #000: ../../../hdf5-1.8.16/src/H5F.c line 604 in H5Fopen():
> unable to
> > > > > open file
> > > > > major: File accessibilty
> > > > > minor: Unable to open file
> > > > > #001: ../../../hdf5-1.8.16/src/H5Fint.c line 992 in
H5F_open():
Den 29 nov. 2016 10:45 em skrev "Allen Byrne" <byrn@hdfgroup.org>:
On Tuesday, November 29, 2016 6:07:22 PM CST Elvis Stansvik wrote:
> > Den 29 nov. 2016 3:32 em skrev "Allen Byrne" <byrn@hdfgroup.org>:
> > > On Tuesday, November 29, 2016 9:20:03 AM CST Elvis Stansvik wrote:
> > > > 2016-11-28 21:43 GMT+01:00 Rob Latham <robl@mcs.anl.gov>:
> > > > > On 11/08/2016 01:18 PM, Elvis Stansvik wrote:
> unable
> > > > > to open file: time = Mon Nov 28 14:41:40 2016
> > > > > , name = 'try.h5', tent_flags = 1
> > > > > major: File accessibilty
> > > > > minor: Unable to open file
> > > > > #002: ../../../hdf5-1.8.16/src/H5FD.c line 993 in H5FD_open():
> open
> > > > > failed
> > > > > major: Virtual File Layer
> > > > > minor: Unable to initialize object
> > > > > #003: ../../../hdf5-1.8.16/src/H5FDsec2.c line 339 in
> H5FD_sec2_open():
> > > > > unable to open file: name = 'try.h5', errno = 13, error message
=
> > > > > 'Permission denied', flags = 1, o_flags = 2
> > > > > major: File accessibilty
> > > > > minor: Unable to open file
> > > > >
> > > > >
> > > > >> Thanks in advance,
> > > > >> Elvis
> > > > >>
> > > > >> _______________________________________________
> > > > >> Hdf-forum is for HDF software users discussion.
> > > > >> Hdf-forum@lists.hdfgroup.org
> > > > >>
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> > > > >> Twitter: https://twitter.com/hdf5
> > > > >>
> > > > >>
> > > > > _______________________________________________
> > > > > Hdf-forum is for HDF software users discussion.
> > > > > Hdf-forum@lists.hdfgroup.org
> > > > >
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> > > > > Twitter: https://twitter.com/hdf5
> > > > >
> > > >
> > >
> > >
>
