Hi Christoph, h5check shouldn't give segmentation fault. We need to fix this and will need the file. Could you please upload it to ftp://ftp.hdfgroup.uiuc.edu/pub/incoming/epourmal/
Thank you! Elena ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Elena Pourmal The HDF Group http://hdfgroup.org 1800 So. Oak St., Suite 203, Champaign IL 61820 217.531.6112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Feb 5, 2014, at 6:42 AM, Dana Robinson <derob...@hdfgroup.org> wrote: > Hi Christoph, > > Did the software crash while writing the file? > > It looks like the file is missing an object header. Since we use a metadata > cache, this can happen if a program crashes while the cache contains > unflushed metadata. HDF5 is not (currently) journaled, so we don't order or > group metadata writes to avoid this situation (yet). > > Dana > > From: Hdf-forum [mailto:hdf-forum-boun...@lists.hdfgroup.org] On Behalf Of > Christoph Laimer > Sent: Wednesday, February 05, 2014 5:33 AM > To: HDF Users Discussion List > Subject: Re: [Hdf-forum] Hdf5 view crashes without error message when opening > a (corrupt) file > > Hi Elena > > Thanks for your quick response. > > H5check produces the output below. It ends with a segmentation fault. There > is also an error message, but I don’t know how to interpret this. Maybe an > indicator of the subsequent crash. I’ve tested also other files, which are > generated by our software, and “h5check” doesn’t tell errors there. > > ./h5check --verbose=2 > /Volumes/Data/tmp/Cropped_ferret182group2confocalalign.ims > VERBOSE is true:verbose # = 2 > > VALIDATING /Volumes/Data/tmp/Cropped_ferret182group2confocalalign.ims > according to library version 1.8.0 > > FOUND super block signature > VALIDATING the super block at physical address 0... > Validating version 2 superblock... > INITIALIZING filters ... > VALIDATING the object header at logical address 48... > VALIDATING version 2 object header ... > FOUND Version 2 object header signature > VALIDATING the object header at logical address 1382334217... > VALIDATING version 1 object header... > Version 1 object header encountered > VALIDATING the local heap at logical address 1382334801... > FOUND local heap signature. > VALIDATING version 1 btree at logical address 1382334257... > FOUND version 1 btree signature. > VALIDATING the Symbol table node at logical address 1382335675... > FOUND Symbol table node signature. > VALIDATING the object header at logical address 1382334971... > VALIDATING version 1 object header... > Version 1 object header encountered > VALIDATING the local heap at logical address 1382335555... > FOUND local heap signature. > VALIDATING version 1 btree at logical address 1382335011... > FOUND version 1 btree signature. > VALIDATING the Symbol table node at logical address 1382352746... > FOUND Symbol table node signature. > VALIDATING the object header at logical address 1382352042... > VALIDATING version 1 object header... > Version 1 object header encountered > VALIDATING the local heap at logical address 1382352626... > FOUND local heap signature. > VALIDATING version 1 btree at logical address 1382352082... > FOUND version 1 btree signature. > VALIDATING the object header at logical address 1382336003... > VALIDATING version 1 object header... > Version 1 object header encountered > VALIDATING version 1 btree at logical address 1382336275... > FOUND version 1 btree signature. > VALIDATING the object header at logical address 267213... > VALIDATING version 2 object header ... > FOUND Version 2 object header signature > ***Error*** > version 2 Object Header:Couldn't find CONT signature at addr 1351906296 > ***End of Error messages*** > VALIDATING the object header at logical address 267412... > VALIDATING version 1 object header... > ***Error*** > Object Header:Unable to read object header data at addr 267444 > Version 1 Object Header:Bad version number at addr 267412; Value decoded: 120 > ***End of Error messages*** > VALIDATING the object header at logical address 1096354995... > VALIDATING version 2 object header ... > FOUND Version 2 object header signature > VALIDATING the object header at logical address 1096355142... > VALIDATING version 2 object header ... > FOUND Version 2 object header signature > VALIDATING the object header at logical address 1096355289... > VALIDATING version 2 object header ... > FOUND Version 2 object header signature > VALIDATING the object header at logical address 1096355665... > VALIDATING version 2 object header ... > FOUND Version 2 object header signature > VALIDATING version 1 btree at logical address 1096358724... > Segmentation fault: 11 > > (I don’t expect, that our customer was storing a lot of hdf5-objects. In > situations, where our software potentially produces tons of “objects”, we > consequently use tables that contain these “objects” – and the file certainly > contains 4d-image-data) > > Cheers, > Christoph > > > > > > From: Hdf-forum [mailto:hdf-forum-boun...@lists.hdfgroup.org] On Behalf Of > Elena Pourmal > Sent: Mittwoch, 5. Februar 2014 02:38 > To: HDF Users Discussion List > Subject: Re: [Hdf-forum] Hdf5 view crashes without error message when opening > a (corrupt) file > > Hi Christoph, > > > > On Feb 3, 2014, at 7:50 AM, Christoph Laimer <christ...@bitplane.com> wrote: > > > Dear HDF-Forum > > I have a file, which causes an immediate crash of the HDF-viewer (no error > message, tested with newest versions on Windows and Mac OS X). > > HDFView cannot handle big files or files with a lot of objects. This is a > known limitation that we are trying to address in the next major release. You > will need to use other tools to confirm that the file is indeed corrupted. > > > I have to assume the file is corrupt. It was written with our Software > (Imaris) which uses regular calls from the official HDF-library (v1.8.6). > Loading the file with our Software causes a crash. In order to figure out, > what was last written into the file, I opened the file in the HDF-viewer, but > there it also crashes (Windows and Mac OS X). In the debugger on Windows it > crashes inside “H5Gopen”, but I don’t understand, what happens there in > detail. Try catch(…) doesn’t catch – it must be a severe memory violation. > > Could you please try to run h5check tool to see if HDF5 metadata in this file > is corrupted? If h5check doesn't find anything, try to run h5ls to see how > far you can traverse the file. Information about both tools can be found here > http://www.hdfgroup.org/HDF5/doc/RM/Tools.html > Hi > Obviously something went wrong when the file was written. Unfortunately I > can’t tell, what exactly was done there – it was a customer using our > software, and “save” was successful. I’d like to do two things: > > - Try to understand from the file content, what went wrong when the > file was written. HDF View would be helpful, if it would show the > non-corrupted parts of the file (instead of crashing). > - Show a more graceful message to the user, when he tries to open > such a file in our Software. Ideally “H5Gopen” would return some error code, > or at least do something catchable. > > Agree on both issues. > > > Is there a common place for the HDF-forum to upload my file? The zipped file > size is 1.3 GB. > > I'll check with our sysadmin people. Stay tuned. > > Elena > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Elena Pourmal The HDF Group http://hdfgroup.org > 1800 So. Oak St., Suite 203, Champaign IL 61820 > 217.531.6112 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > Please help! > > Cheers, > Christoph > This message is intended only for the use of the addressee and may contain > information that is confidential and/or subject to copyright. If you are not > the intended recipient, you are hereby notified that any dissemination, > copying, or redistribution of this message is strictly prohibited. If you > have received this message in error please delete all copies immediately. Any > views or opinions presented in this email are solely those of the author and > do not necessarily represent those of Andor Technology Plc Companies. Andor > Technology Plc has taken reasonable precautions to ensure that no viruses are > contained in this email, but does not accept any responsibility once this > email has been transmitted. Andor Technology PLC is a registered company in > Northern Ireland, registration number: NI022466. Registered Office: Andor > Technology, 7 Millennium Way, Springvale Business Park, Belfast, BT12 7AL. > _______________________________________________ > Hdf-forum is for HDF software users discussion. > Hdf-forum@lists.hdfgroup.org > http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > Hdf-forum@lists.hdfgroup.org > http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
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