I stumbled over some error in yt while executing a script that used to work on an older version of yt. Here is the traceback: File "start_SGE.py", line 28, in <module> File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 58, in get_snapshots File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 43, in get_redshift File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 218, in __init__ File "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 165, in __init__ File "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 57, in make_fid File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1626) IOError: unable to open file (File accessability: Unable to open file) Exception AttributeError: "'NoneType' object has no attribute 'close'" in ignored I'd be very thankful if somebody got any idea how to fix this! Best wishes, Patrick
Hi Patrick, What happens if you do $ h5ls <filename> where <filename> is the file you're trying to open? This looks like it could be an error outside of yt. Also, can you load() any other snapshots? Jeff On Mon, Jan 7, 2013 at 10:49 AM, Patrick Rieser <patrick.rieser@uibk.ac.at>wrote:
I stumbled over some error in yt while executing a script that used to work on an older version of yt. Here is the traceback:
File "start_SGE.py", line 28, in <module> File "/home/patrick/Auswertung/yt-**run/Find_Clumps/get_name.py", line 58, in get_snapshots File "/home/patrick/Auswertung/yt-**run/Find_Clumps/get_name.py", line 43, in get_redshift File "/home/patrick/Programme/yt-**x86_64/src/yt-hg/yt/**convenience.py", line 71, in load File "/home/patrick/Programme/yt-**x86_64/src/yt-hg/yt/frontends/**flash/data_structures.py", line 218, in __init__ File "/home/patrick/Programme/yt-**x86_64/lib/python2.7/site-**packages/h5py/_hl/files.py", line 165, in __init__ File "/home/patrick/Programme/yt-**x86_64/lib/python2.7/site-**packages/h5py/_hl/files.py", line 57, in make_fid File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1626) IOError: unable to open file (File accessability: Unable to open file) Exception AttributeError: "'NoneType' object has no attribute 'close'" in ignored
I'd be very thankful if somebody got any idea how to fix this!
Best wishes, Patrick
______________________________**_________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/**listinfo.cgi/yt-users-**spacepope.org<http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
In iyt I can load a snapshot just fine. It could be a problem using the Sun Grid Engine then. Here is my python submit script if you need it (it sources the yt environment, does some things on the data set and then submits a yt job for a subset): http://paste.yt-project.org/show/3045/ h5ls output seems ok: bflags Dataset {2633, 1} block\ size Dataset {2633, 3} bounding\ box Dataset {2633, 3, 2} coordinates Dataset {2633, 3} dens Dataset {2633, 16, 16, 16} gid Dataset {2633, 15} integer\ runtime\ parameters Dataset {46} integer\ scalars Dataset {14} logical\ runtime\ parameters Dataset {53} logical\ scalars Dataset {2} magp Dataset {2633, 16, 16, 16} magx Dataset {2633, 16, 16, 16} magy Dataset {2633, 16, 16, 16} magz Dataset {2633, 16, 16, 16} node\ type Dataset {2633} pden Dataset {2633, 16, 16, 16} pres Dataset {2633, 16, 16, 16} processor\ number Dataset {2633} real\ runtime\ parameters Dataset {76} real\ scalars Dataset {15} refine\ level Dataset {2633} sim\ info Dataset {1} string\ runtime\ parameters Dataset {78} string\ scalars Dataset {1} temp Dataset {2633, 16, 16, 16} unknown\ names Dataset {11, 1} velx Dataset {2633, 16, 16, 16} vely Dataset {2633, 16, 16, 16} velz Dataset {2633, 16, 16, 16} which\ child Dataset {2633} Could the problem be caused by a defunct snapshot that got mixed in? Best wishes, Patrick Am 2013-01-07 16:54, schrieb j s oishi:
Hi Patrick,
What happens if you do
$ h5ls <filename>
where <filename> is the file you're trying to open? This looks like it could be an error outside of yt.
Also, can you load() any other snapshots?
Jeff
On Mon, Jan 7, 2013 at 10:49 AM, Patrick Rieser <patrick.rieser@uibk.ac.at <mailto:patrick.rieser@uibk.ac.at>> wrote:
I stumbled over some error in yt while executing a script that used to work on an older version of yt. Here is the traceback:
File "start_SGE.py", line 28, in <module> File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 58, in get_snapshots File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 43, in get_redshift File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 218, in __init__ File "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 165, in __init__ File "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 57, in make_fid File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1626) IOError: unable to open file (File accessability: Unable to open file) Exception AttributeError: "'NoneType' object has no attribute 'close'" in ignored
I'd be very thankful if somebody got any idea how to fix this!
Best wishes, Patrick
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Patrick, This could also be related to a critical bug fix identified not too long ago. One tricky thing about HDF5 is that once in a while depending on the order of operations, errors can accumulate without being flushed. What may have happened is that the file was left open at a different juncture and then never closed; this could result in a non-intuitive error message. What we identified was that the GridDataFormat frontend was in fact leaving the files open, which then left the handle around and caused non-intuitive errors later on during the process. Could you send the output of: yt instinfo This will help us determine how the error is occurring. Best, Matt On Mon, Jan 7, 2013 at 11:02 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
In iyt I can load a snapshot just fine.
It could be a problem using the Sun Grid Engine then. Here is my python submit script if you need it (it sources the yt environment, does some things on the data set and then submits a yt job for a subset): http://paste.yt-project.org/show/3045/
h5ls output seems ok: bflags Dataset {2633, 1} block\ size Dataset {2633, 3} bounding\ box Dataset {2633, 3, 2} coordinates Dataset {2633, 3} dens Dataset {2633, 16, 16, 16} gid Dataset {2633, 15} integer\ runtime\ parameters Dataset {46} integer\ scalars Dataset {14} logical\ runtime\ parameters Dataset {53} logical\ scalars Dataset {2} magp Dataset {2633, 16, 16, 16} magx Dataset {2633, 16, 16, 16} magy Dataset {2633, 16, 16, 16} magz Dataset {2633, 16, 16, 16} node\ type Dataset {2633} pden Dataset {2633, 16, 16, 16} pres Dataset {2633, 16, 16, 16} processor\ number Dataset {2633} real\ runtime\ parameters Dataset {76} real\ scalars Dataset {15} refine\ level Dataset {2633} sim\ info Dataset {1} string\ runtime\ parameters Dataset {78} string\ scalars Dataset {1} temp Dataset {2633, 16, 16, 16} unknown\ names Dataset {11, 1} velx Dataset {2633, 16, 16, 16} vely Dataset {2633, 16, 16, 16} velz Dataset {2633, 16, 16, 16} which\ child Dataset {2633}
Could the problem be caused by a defunct snapshot that got mixed in?
Best wishes, Patrick
Am 2013-01-07 16:54, schrieb j s oishi:
Hi Patrick,
What happens if you do
$ h5ls <filename>
where <filename> is the file you're trying to open? This looks like it could be an error outside of yt.
Also, can you load() any other snapshots?
Jeff
On Mon, Jan 7, 2013 at 10:49 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
I stumbled over some error in yt while executing a script that used to work on an older version of yt. Here is the traceback:
File "start_SGE.py", line 28, in <module> File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 58, in get_snapshots File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 43, in get_redshift File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 218, in __init__ File "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 165, in __init__ File "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 57, in make_fid File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1626) IOError: unable to open file (File accessability: Unable to open file) Exception AttributeError: "'NoneType' object has no attribute 'close'" in ignored
I'd be very thankful if somebody got any idea how to fix this!
Best wishes, Patrick
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Here you go: yt module located at: /home/patrick/Programme/yt-x86_64/src/yt-hg The supplemental repositories are located at: /home/patrick/Programme/yt-x86_64/src/yt-supplemental The current version of the code is: --- 9d5b945ee428+ (yt) tip --- This installation CAN be automatically updated. Updated successfully. Best wishes, Patrick Am 2013-01-07 17:04, schrieb Matthew Turk:
Hi Patrick,
This could also be related to a critical bug fix identified not too long ago. One tricky thing about HDF5 is that once in a while depending on the order of operations, errors can accumulate without being flushed. What may have happened is that the file was left open at a different juncture and then never closed; this could result in a non-intuitive error message. What we identified was that the GridDataFormat frontend was in fact leaving the files open, which then left the handle around and caused non-intuitive errors later on during the process. Could you send the output of:
yt instinfo
This will help us determine how the error is occurring.
Best,
Matt
On Mon, Jan 7, 2013 at 11:02 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
In iyt I can load a snapshot just fine.
It could be a problem using the Sun Grid Engine then. Here is my python submit script if you need it (it sources the yt environment, does some things on the data set and then submits a yt job for a subset): http://paste.yt-project.org/show/3045/
h5ls output seems ok: bflags Dataset {2633, 1} block\ size Dataset {2633, 3} bounding\ box Dataset {2633, 3, 2} coordinates Dataset {2633, 3} dens Dataset {2633, 16, 16, 16} gid Dataset {2633, 15} integer\ runtime\ parameters Dataset {46} integer\ scalars Dataset {14} logical\ runtime\ parameters Dataset {53} logical\ scalars Dataset {2} magp Dataset {2633, 16, 16, 16} magx Dataset {2633, 16, 16, 16} magy Dataset {2633, 16, 16, 16} magz Dataset {2633, 16, 16, 16} node\ type Dataset {2633} pden Dataset {2633, 16, 16, 16} pres Dataset {2633, 16, 16, 16} processor\ number Dataset {2633} real\ runtime\ parameters Dataset {76} real\ scalars Dataset {15} refine\ level Dataset {2633} sim\ info Dataset {1} string\ runtime\ parameters Dataset {78} string\ scalars Dataset {1} temp Dataset {2633, 16, 16, 16} unknown\ names Dataset {11, 1} velx Dataset {2633, 16, 16, 16} vely Dataset {2633, 16, 16, 16} velz Dataset {2633, 16, 16, 16} which\ child Dataset {2633}
Could the problem be caused by a defunct snapshot that got mixed in?
Best wishes, Patrick
Am 2013-01-07 16:54, schrieb j s oishi:
Hi Patrick,
What happens if you do
$ h5ls <filename>
where <filename> is the file you're trying to open? This looks like it could be an error outside of yt.
Also, can you load() any other snapshots?
Jeff
On Mon, Jan 7, 2013 at 10:49 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
I stumbled over some error in yt while executing a script that used to work on an older version of yt. Here is the traceback:
File "start_SGE.py", line 28, in <module> File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 58, in get_snapshots File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 43, in get_redshift File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 218, in __init__ File "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 165, in __init__ File "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 57, in make_fid File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1626) IOError: unable to open file (File accessability: Unable to open file) Exception AttributeError: "'NoneType' object has no attribute 'close'" in ignored
I'd be very thankful if somebody got any idea how to fix this!
Best wishes, Patrick
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Patrick, Ah, interesting -- this is before the fix to the GDF frontend. A couple things -- it looks like you've made some changes to the source code (the + at the end of the hash indicates this.) If this isn't a big deal, or you don't need those changes, I'd recommend you update to the latest version manually: cd /home/patrick/Programme/yt-x86_64/src/yt-hg hg pull hg up -C python2.7 setup.py build_ext -i If you want to retain those changes, you can be a bit safer about it: cd /home/patrick/Programme/yt-x86_64/src/yt-hg hg diff > backup.patch hg pull hg up python2.7 setup.py build_ext -i This will prompt you to merge your changes into the tip of the development repository. If the merge fails, you can use the contents of "backup.patch" to restore your changes later. Can you try updating and see if that fixes the issue? -Matt On Mon, Jan 7, 2013 at 11:16 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
Here you go:
yt module located at: /home/patrick/Programme/yt-x86_64/src/yt-hg The supplemental repositories are located at: /home/patrick/Programme/yt-x86_64/src/yt-supplemental
The current version of the code is:
--- 9d5b945ee428+ (yt) tip ---
This installation CAN be automatically updated. Updated successfully.
Best wishes, Patrick
Am 2013-01-07 17:04, schrieb Matthew Turk:
Hi Patrick,
This could also be related to a critical bug fix identified not too long ago. One tricky thing about HDF5 is that once in a while depending on the order of operations, errors can accumulate without being flushed. What may have happened is that the file was left open at a different juncture and then never closed; this could result in a non-intuitive error message. What we identified was that the GridDataFormat frontend was in fact leaving the files open, which then left the handle around and caused non-intuitive errors later on during the process. Could you send the output of:
yt instinfo
This will help us determine how the error is occurring.
Best,
Matt
On Mon, Jan 7, 2013 at 11:02 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
In iyt I can load a snapshot just fine.
It could be a problem using the Sun Grid Engine then. Here is my python submit script if you need it (it sources the yt environment, does some things on the data set and then submits a yt job for a subset): http://paste.yt-project.org/show/3045/
h5ls output seems ok: bflags Dataset {2633, 1} block\ size Dataset {2633, 3} bounding\ box Dataset {2633, 3, 2} coordinates Dataset {2633, 3} dens Dataset {2633, 16, 16, 16} gid Dataset {2633, 15} integer\ runtime\ parameters Dataset {46} integer\ scalars Dataset {14} logical\ runtime\ parameters Dataset {53} logical\ scalars Dataset {2} magp Dataset {2633, 16, 16, 16} magx Dataset {2633, 16, 16, 16} magy Dataset {2633, 16, 16, 16} magz Dataset {2633, 16, 16, 16} node\ type Dataset {2633} pden Dataset {2633, 16, 16, 16} pres Dataset {2633, 16, 16, 16} processor\ number Dataset {2633} real\ runtime\ parameters Dataset {76} real\ scalars Dataset {15} refine\ level Dataset {2633} sim\ info Dataset {1} string\ runtime\ parameters Dataset {78} string\ scalars Dataset {1} temp Dataset {2633, 16, 16, 16} unknown\ names Dataset {11, 1} velx Dataset {2633, 16, 16, 16} vely Dataset {2633, 16, 16, 16} velz Dataset {2633, 16, 16, 16} which\ child Dataset {2633}
Could the problem be caused by a defunct snapshot that got mixed in?
Best wishes, Patrick
Am 2013-01-07 16:54, schrieb j s oishi:
Hi Patrick,
What happens if you do
$ h5ls <filename>
where <filename> is the file you're trying to open? This looks like it could be an error outside of yt.
Also, can you load() any other snapshots?
Jeff
On Mon, Jan 7, 2013 at 10:49 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
I stumbled over some error in yt while executing a script that used to work on an older version of yt. Here is the traceback:
File "start_SGE.py", line 28, in <module> File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 58, in get_snapshots File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 43, in get_redshift File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 218, in __init__ File
"/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 165, in __init__ File
"/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 57, in make_fid File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1626) IOError: unable to open file (File accessability: Unable to open file) Exception AttributeError: "'NoneType' object has no attribute 'close'" in ignored
I'd be very thankful if somebody got any idea how to fix this!
Best wishes, Patrick
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Thanks a lot, it seems to be working now! By the way, I did only change the fields.py in frontends/flash to include some more stuff. Best wishes, Patrick Am 2013-01-07 17:19, schrieb Matthew Turk:
Hi Patrick,
Ah, interesting -- this is before the fix to the GDF frontend. A couple things -- it looks like you've made some changes to the source code (the + at the end of the hash indicates this.) If this isn't a big deal, or you don't need those changes, I'd recommend you update to the latest version manually:
cd /home/patrick/Programme/yt-x86_64/src/yt-hg hg pull hg up -C python2.7 setup.py build_ext -i
If you want to retain those changes, you can be a bit safer about it:
cd /home/patrick/Programme/yt-x86_64/src/yt-hg hg diff > backup.patch hg pull hg up python2.7 setup.py build_ext -i
This will prompt you to merge your changes into the tip of the development repository. If the merge fails, you can use the contents of "backup.patch" to restore your changes later.
Can you try updating and see if that fixes the issue?
-Matt
On Mon, Jan 7, 2013 at 11:16 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
Here you go:
yt module located at: /home/patrick/Programme/yt-x86_64/src/yt-hg The supplemental repositories are located at: /home/patrick/Programme/yt-x86_64/src/yt-supplemental
The current version of the code is:
--- 9d5b945ee428+ (yt) tip ---
This installation CAN be automatically updated. Updated successfully.
Best wishes, Patrick
Am 2013-01-07 17:04, schrieb Matthew Turk:
Hi Patrick,
This could also be related to a critical bug fix identified not too long ago. One tricky thing about HDF5 is that once in a while depending on the order of operations, errors can accumulate without being flushed. What may have happened is that the file was left open at a different juncture and then never closed; this could result in a non-intuitive error message. What we identified was that the GridDataFormat frontend was in fact leaving the files open, which then left the handle around and caused non-intuitive errors later on during the process. Could you send the output of:
yt instinfo
This will help us determine how the error is occurring.
Best,
Matt
On Mon, Jan 7, 2013 at 11:02 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
In iyt I can load a snapshot just fine.
It could be a problem using the Sun Grid Engine then. Here is my python submit script if you need it (it sources the yt environment, does some things on the data set and then submits a yt job for a subset): http://paste.yt-project.org/show/3045/
h5ls output seems ok: bflags Dataset {2633, 1} block\ size Dataset {2633, 3} bounding\ box Dataset {2633, 3, 2} coordinates Dataset {2633, 3} dens Dataset {2633, 16, 16, 16} gid Dataset {2633, 15} integer\ runtime\ parameters Dataset {46} integer\ scalars Dataset {14} logical\ runtime\ parameters Dataset {53} logical\ scalars Dataset {2} magp Dataset {2633, 16, 16, 16} magx Dataset {2633, 16, 16, 16} magy Dataset {2633, 16, 16, 16} magz Dataset {2633, 16, 16, 16} node\ type Dataset {2633} pden Dataset {2633, 16, 16, 16} pres Dataset {2633, 16, 16, 16} processor\ number Dataset {2633} real\ runtime\ parameters Dataset {76} real\ scalars Dataset {15} refine\ level Dataset {2633} sim\ info Dataset {1} string\ runtime\ parameters Dataset {78} string\ scalars Dataset {1} temp Dataset {2633, 16, 16, 16} unknown\ names Dataset {11, 1} velx Dataset {2633, 16, 16, 16} vely Dataset {2633, 16, 16, 16} velz Dataset {2633, 16, 16, 16} which\ child Dataset {2633}
Could the problem be caused by a defunct snapshot that got mixed in?
Best wishes, Patrick
Am 2013-01-07 16:54, schrieb j s oishi:
Hi Patrick,
What happens if you do
$ h5ls <filename>
where <filename> is the file you're trying to open? This looks like it could be an error outside of yt.
Also, can you load() any other snapshots?
Jeff
On Mon, Jan 7, 2013 at 10:49 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
I stumbled over some error in yt while executing a script that used to work on an older version of yt. Here is the traceback:
File "start_SGE.py", line 28, in <module> File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 58, in get_snapshots File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 43, in get_redshift File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 218, in __init__ File
"/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 165, in __init__ File
"/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 57, in make_fid File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1626) IOError: unable to open file (File accessability: Unable to open file) Exception AttributeError: "'NoneType' object has no attribute 'close'" in ignored
I'd be very thankful if somebody got any idea how to fix this!
Best wishes, Patrick
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Patrick, On Mon, Jan 7, 2013 at 11:38 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
Thanks a lot, it seems to be working now!
Awesome, I'm glad to hear it!
By the way, I did only change the fields.py in frontends/flash to include some more stuff.
If you think these are of general use, please feel free to submit a pull request. The "yt bootstrap_dev" command will get you bitbucket and hg usernames. You can then do this by forking on BitBucket: https://bitbucket.org/yt_analysis/yt/fork then pushing to your new repository: cd /home/patrick/Programme/yt-x86_64/src/yt-hg hg commit hg push https://bitbucket.org/your_username/yt and issuing a pull request: https://bitbucket.org/your_username/yt/pull-request/new But if you'd rather not, of course that's okay too. :) Best, Matt
Best wishes, Patrick
Am 2013-01-07 17:19, schrieb Matthew Turk:
Hi Patrick,
Ah, interesting -- this is before the fix to the GDF frontend. A couple things -- it looks like you've made some changes to the source code (the + at the end of the hash indicates this.) If this isn't a big deal, or you don't need those changes, I'd recommend you update to the latest version manually:
cd /home/patrick/Programme/yt-x86_64/src/yt-hg hg pull hg up -C python2.7 setup.py build_ext -i
If you want to retain those changes, you can be a bit safer about it:
cd /home/patrick/Programme/yt-x86_64/src/yt-hg hg diff > backup.patch hg pull hg up python2.7 setup.py build_ext -i
This will prompt you to merge your changes into the tip of the development repository. If the merge fails, you can use the contents of "backup.patch" to restore your changes later.
Can you try updating and see if that fixes the issue?
-Matt
On Mon, Jan 7, 2013 at 11:16 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
Here you go:
yt module located at: /home/patrick/Programme/yt-x86_64/src/yt-hg The supplemental repositories are located at: /home/patrick/Programme/yt-x86_64/src/yt-supplemental
The current version of the code is:
--- 9d5b945ee428+ (yt) tip ---
This installation CAN be automatically updated. Updated successfully.
Best wishes, Patrick
Am 2013-01-07 17:04, schrieb Matthew Turk:
Hi Patrick,
This could also be related to a critical bug fix identified not too long ago. One tricky thing about HDF5 is that once in a while depending on the order of operations, errors can accumulate without being flushed. What may have happened is that the file was left open at a different juncture and then never closed; this could result in a non-intuitive error message. What we identified was that the GridDataFormat frontend was in fact leaving the files open, which then left the handle around and caused non-intuitive errors later on during the process. Could you send the output of:
yt instinfo
This will help us determine how the error is occurring.
Best,
Matt
On Mon, Jan 7, 2013 at 11:02 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
In iyt I can load a snapshot just fine.
It could be a problem using the Sun Grid Engine then. Here is my python submit script if you need it (it sources the yt environment, does some things on the data set and then submits a yt job for a subset): http://paste.yt-project.org/show/3045/
h5ls output seems ok: bflags Dataset {2633, 1} block\ size Dataset {2633, 3} bounding\ box Dataset {2633, 3, 2} coordinates Dataset {2633, 3} dens Dataset {2633, 16, 16, 16} gid Dataset {2633, 15} integer\ runtime\ parameters Dataset {46} integer\ scalars Dataset {14} logical\ runtime\ parameters Dataset {53} logical\ scalars Dataset {2} magp Dataset {2633, 16, 16, 16} magx Dataset {2633, 16, 16, 16} magy Dataset {2633, 16, 16, 16} magz Dataset {2633, 16, 16, 16} node\ type Dataset {2633} pden Dataset {2633, 16, 16, 16} pres Dataset {2633, 16, 16, 16} processor\ number Dataset {2633} real\ runtime\ parameters Dataset {76} real\ scalars Dataset {15} refine\ level Dataset {2633} sim\ info Dataset {1} string\ runtime\ parameters Dataset {78} string\ scalars Dataset {1} temp Dataset {2633, 16, 16, 16} unknown\ names Dataset {11, 1} velx Dataset {2633, 16, 16, 16} vely Dataset {2633, 16, 16, 16} velz Dataset {2633, 16, 16, 16} which\ child Dataset {2633}
Could the problem be caused by a defunct snapshot that got mixed in?
Best wishes, Patrick
Am 2013-01-07 16:54, schrieb j s oishi:
Hi Patrick,
What happens if you do
$ h5ls <filename>
where <filename> is the file you're trying to open? This looks like it could be an error outside of yt.
Also, can you load() any other snapshots?
Jeff
On Mon, Jan 7, 2013 at 10:49 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
I stumbled over some error in yt while executing a script that used to work on an older version of yt. Here is the traceback:
File "start_SGE.py", line 28, in <module> File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 58, in get_snapshots File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", line 43, in get_redshift File "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load File
"/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 218, in __init__ File
"/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 165, in __init__ File
"/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", line 57, in make_fid File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1626) IOError: unable to open file (File accessability: Unable to open file) Exception AttributeError: "'NoneType' object has no attribute 'close'" in ignored
I'd be very thankful if somebody got any idea how to fix this!
Best wishes, Patrick
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
You can also create a my_plugins.py file in the .yt directory in your home directory. This can contain supplementary functions and field definitions outside of yt source control. Cheers, Nathan On Jan 7, 2013, at 6:42 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Patrick,
On Mon, Jan 7, 2013 at 11:38 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
Thanks a lot, it seems to be working now!
Awesome, I'm glad to hear it!
By the way, I did only change the fields.py in frontends/flash to include some more stuff.
If you think these are of general use, please feel free to submit a pull request. The "yt bootstrap_dev" command will get you bitbucket and hg usernames. You can then do this by forking on BitBucket:
https://bitbucket.org/yt_analysis/yt/fork
then pushing to your new repository:
cd /home/patrick/Programme/yt-x86_64/src/yt-hg hg commit hg push https://bitbucket.org/your_username/yt
and issuing a pull request:
https://bitbucket.org/your_username/yt/pull-request/new
But if you'd rather not, of course that's okay too. :)
Best,
Matt
Best wishes, Patrick
Am 2013-01-07 17:19, schrieb Matthew Turk:
Hi Patrick,
Ah, interesting -- this is before the fix to the GDF frontend. A couple things -- it looks like you've made some changes to the source code (the + at the end of the hash indicates this.) If this isn't a big deal, or you don't need those changes, I'd recommend you update to the latest version manually:
cd /home/patrick/Programme/yt-x86_64/src/yt-hg hg pull hg up -C python2.7 setup.py build_ext -i
If you want to retain those changes, you can be a bit safer about it:
cd /home/patrick/Programme/yt-x86_64/src/yt-hg hg diff > backup.patch hg pull hg up python2.7 setup.py build_ext -i
This will prompt you to merge your changes into the tip of the development repository. If the merge fails, you can use the contents of "backup.patch" to restore your changes later.
Can you try updating and see if that fixes the issue?
-Matt
On Mon, Jan 7, 2013 at 11:16 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
Here you go:
yt module located at: /home/patrick/Programme/yt-x86_64/src/yt-hg The supplemental repositories are located at: /home/patrick/Programme/yt-x86_64/src/yt-supplemental
The current version of the code is:
--- 9d5b945ee428+ (yt) tip ---
This installation CAN be automatically updated. Updated successfully.
Best wishes, Patrick
Am 2013-01-07 17:04, schrieb Matthew Turk:
Hi Patrick,
This could also be related to a critical bug fix identified not too long ago. One tricky thing about HDF5 is that once in a while depending on the order of operations, errors can accumulate without being flushed. What may have happened is that the file was left open at a different juncture and then never closed; this could result in a non-intuitive error message. What we identified was that the GridDataFormat frontend was in fact leaving the files open, which then left the handle around and caused non-intuitive errors later on during the process. Could you send the output of:
yt instinfo
This will help us determine how the error is occurring.
Best,
Matt
On Mon, Jan 7, 2013 at 11:02 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
In iyt I can load a snapshot just fine.
It could be a problem using the Sun Grid Engine then. Here is my python submit script if you need it (it sources the yt environment, does some things on the data set and then submits a yt job for a subset): http://paste.yt-project.org/show/3045/
h5ls output seems ok: bflags Dataset {2633, 1} block\ size Dataset {2633, 3} bounding\ box Dataset {2633, 3, 2} coordinates Dataset {2633, 3} dens Dataset {2633, 16, 16, 16} gid Dataset {2633, 15} integer\ runtime\ parameters Dataset {46} integer\ scalars Dataset {14} logical\ runtime\ parameters Dataset {53} logical\ scalars Dataset {2} magp Dataset {2633, 16, 16, 16} magx Dataset {2633, 16, 16, 16} magy Dataset {2633, 16, 16, 16} magz Dataset {2633, 16, 16, 16} node\ type Dataset {2633} pden Dataset {2633, 16, 16, 16} pres Dataset {2633, 16, 16, 16} processor\ number Dataset {2633} real\ runtime\ parameters Dataset {76} real\ scalars Dataset {15} refine\ level Dataset {2633} sim\ info Dataset {1} string\ runtime\ parameters Dataset {78} string\ scalars Dataset {1} temp Dataset {2633, 16, 16, 16} unknown\ names Dataset {11, 1} velx Dataset {2633, 16, 16, 16} vely Dataset {2633, 16, 16, 16} velz Dataset {2633, 16, 16, 16} which\ child Dataset {2633}
Could the problem be caused by a defunct snapshot that got mixed in?
Best wishes, Patrick
Am 2013-01-07 16:54, schrieb j s oishi:
Hi Patrick,
What happens if you do
$ h5ls <filename>
where <filename> is the file you're trying to open? This looks like it could be an error outside of yt.
Also, can you load() any other snapshots?
Jeff
On Mon, Jan 7, 2013 at 10:49 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote: > > I stumbled over some error in yt while executing a script that used to > work on an older version of yt. Here is the traceback: > > File "start_SGE.py", line 28, in <module> > File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", > line > 58, > in get_snapshots > File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", > line > 43, > in get_redshift > File > "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/convenience.py", > line 71, in load > File > > > "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", > line 218, in __init__ > File > > > "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", > line 165, in __init__ > File > > > "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", > line 57, in make_fid > File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1626) > IOError: unable to open file (File accessability: Unable to open file) > Exception AttributeError: "'NoneType' object has no attribute 'close'" > in > ignored > > > I'd be very thankful if somebody got any idea how to fix this! > > Best wishes, > Patrick > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Ah it's basically just some diry hacks and some copy&paste to get some things going. But I'll take a look at it to see if there is something useful inside to commit! Best wishes, Patrick Am 2013-01-07 17:42, schrieb Matthew Turk:
Hi Patrick,
On Mon, Jan 7, 2013 at 11:38 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
Thanks a lot, it seems to be working now! Awesome, I'm glad to hear it!
By the way, I did only change the fields.py in frontends/flash to include some more stuff. If you think these are of general use, please feel free to submit a pull request. The "yt bootstrap_dev" command will get you bitbucket and hg usernames. You can then do this by forking on BitBucket:
https://bitbucket.org/yt_analysis/yt/fork
then pushing to your new repository:
cd /home/patrick/Programme/yt-x86_64/src/yt-hg hg commit hg push https://bitbucket.org/your_username/yt
and issuing a pull request:
https://bitbucket.org/your_username/yt/pull-request/new
But if you'd rather not, of course that's okay too. :)
Best,
Matt
Best wishes, Patrick
Am 2013-01-07 17:19, schrieb Matthew Turk:
Hi Patrick,
Ah, interesting -- this is before the fix to the GDF frontend. A couple things -- it looks like you've made some changes to the source code (the + at the end of the hash indicates this.) If this isn't a big deal, or you don't need those changes, I'd recommend you update to the latest version manually:
cd /home/patrick/Programme/yt-x86_64/src/yt-hg hg pull hg up -C python2.7 setup.py build_ext -i
If you want to retain those changes, you can be a bit safer about it:
cd /home/patrick/Programme/yt-x86_64/src/yt-hg hg diff > backup.patch hg pull hg up python2.7 setup.py build_ext -i
This will prompt you to merge your changes into the tip of the development repository. If the merge fails, you can use the contents of "backup.patch" to restore your changes later.
Can you try updating and see if that fixes the issue?
-Matt
On Mon, Jan 7, 2013 at 11:16 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
Here you go:
yt module located at: /home/patrick/Programme/yt-x86_64/src/yt-hg The supplemental repositories are located at: /home/patrick/Programme/yt-x86_64/src/yt-supplemental
The current version of the code is:
--- 9d5b945ee428+ (yt) tip ---
This installation CAN be automatically updated. Updated successfully.
Best wishes, Patrick
Am 2013-01-07 17:04, schrieb Matthew Turk:
Hi Patrick,
This could also be related to a critical bug fix identified not too long ago. One tricky thing about HDF5 is that once in a while depending on the order of operations, errors can accumulate without being flushed. What may have happened is that the file was left open at a different juncture and then never closed; this could result in a non-intuitive error message. What we identified was that the GridDataFormat frontend was in fact leaving the files open, which then left the handle around and caused non-intuitive errors later on during the process. Could you send the output of:
yt instinfo
This will help us determine how the error is occurring.
Best,
Matt
On Mon, Jan 7, 2013 at 11:02 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote:
In iyt I can load a snapshot just fine.
It could be a problem using the Sun Grid Engine then. Here is my python submit script if you need it (it sources the yt environment, does some things on the data set and then submits a yt job for a subset): http://paste.yt-project.org/show/3045/
h5ls output seems ok: bflags Dataset {2633, 1} block\ size Dataset {2633, 3} bounding\ box Dataset {2633, 3, 2} coordinates Dataset {2633, 3} dens Dataset {2633, 16, 16, 16} gid Dataset {2633, 15} integer\ runtime\ parameters Dataset {46} integer\ scalars Dataset {14} logical\ runtime\ parameters Dataset {53} logical\ scalars Dataset {2} magp Dataset {2633, 16, 16, 16} magx Dataset {2633, 16, 16, 16} magy Dataset {2633, 16, 16, 16} magz Dataset {2633, 16, 16, 16} node\ type Dataset {2633} pden Dataset {2633, 16, 16, 16} pres Dataset {2633, 16, 16, 16} processor\ number Dataset {2633} real\ runtime\ parameters Dataset {76} real\ scalars Dataset {15} refine\ level Dataset {2633} sim\ info Dataset {1} string\ runtime\ parameters Dataset {78} string\ scalars Dataset {1} temp Dataset {2633, 16, 16, 16} unknown\ names Dataset {11, 1} velx Dataset {2633, 16, 16, 16} vely Dataset {2633, 16, 16, 16} velz Dataset {2633, 16, 16, 16} which\ child Dataset {2633}
Could the problem be caused by a defunct snapshot that got mixed in?
Best wishes, Patrick
Am 2013-01-07 16:54, schrieb j s oishi:
Hi Patrick,
What happens if you do
$ h5ls <filename>
where <filename> is the file you're trying to open? This looks like it could be an error outside of yt.
Also, can you load() any other snapshots?
Jeff
On Mon, Jan 7, 2013 at 10:49 AM, Patrick Rieser <patrick.rieser@uibk.ac.at> wrote: > I stumbled over some error in yt while executing a script that used to > work on an older version of yt. Here is the traceback: > > File "start_SGE.py", line 28, in <module> > File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", > line > 58, > in get_snapshots > File "/home/patrick/Auswertung/yt-run/Find_Clumps/get_name.py", > line > 43, > in get_redshift > File > "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/convenience.py", > line 71, in load > File > > > "/home/patrick/Programme/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", > line 218, in __init__ > File > > > "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", > line 165, in __init__ > File > > > "/home/patrick/Programme/yt-x86_64/lib/python2.7/site-packages/h5py/_hl/files.py", > line 57, in make_fid > File "h5f.pyx", line 70, in h5py.h5f.open (h5py/h5f.c:1626) > IOError: unable to open file (File accessability: Unable to open file) > Exception AttributeError: "'NoneType' object has no attribute 'close'" > in > ignored > > > I'd be very thankful if somebody got any idea how to fix this! > > Best wishes, > Patrick > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
participants (4)
-
j s oishi -
Matthew Turk -
Nathan Goldbaum -
Patrick Rieser