Hi Mark,
Yes this is Linux. Debian 7.
Can try pulling off master of ADCore tonight. I have the defaults set and even wiped save/restore to set to defaults and it still segfaults.
If you get a specific tag or branch to work let me know, I can try this this end.
Best wishes,
Stuart
> On Mar 4, 2015, at 18:10, Mark Rivers <[email protected]> wrote:
>
> Hi Stuart,
>
> Is this on Linux?
>
> It looks like you are using HDF 1.8.8? I have been using 1.8.7, but I think the people at Diamond have been using more recent versions.
>
> ADCore R2-1 was a major re-write of the HDF5 plugin to allow the HDF5 file layout to be configured via an XML file. We have recently found some bugs in it, the most serious of which is that it is not possible to change the NDArray source after iocInit. R2-2 will be out soon, and will fix that bug and a number of others that we are actively working on.
>
> That being said, I think others have been using 2.0 without the problems you are describing. Are you using all of the default settings in terms of compression, chunking, etc?
>
> I'll try building 2-0 and see if I can reproduce your problem.
>
> Mark
>
> ________________________________________
> From: [email protected] [[email protected]] on behalf of Wilkins, Stuart [[email protected]]
> Sent: Wednesday, March 04, 2015 4:21 PM
> To: [email protected]
> Subject: Problem with HDF5 plugin for areaDetector
>
> Hi,
>
> I am having problems with the simdetector in Areadetector 2.0. I am running the HDF5 plugin and on trying to write a frame to disk, it segfaults. I have tried to start from a fresh state by taking away the save/restore files but nothing seems to fix it. Turning on traceback gives the errors below. Has anyone had this problem?
>
> Thanks,
> Stuart
>
> 2015/03/04 17:16:23.543 XF:23ID1-ES{Tst-Cam:1}HDF1:PoolFreeBuffers devAsynInt32 process value=0
> 2015/03/04 17:16:23.566 XF:23ID1-ES{Tst-Cam:1}HDF1:ArrayCounter_RBV devAsynInt32::interruptCallbackInput new value=1
> 2015/03/04 17:16:23.566 XF:23ID1-ES{Tst-Cam:1}HDF1:UniqueId_RBV devAsynInt32::interruptCallbackInput new value=4
> 2015/03/04 17:16:23.566 XF:23ID1-ES{Tst-Cam:1}HDF1:TimeStamp_RBV devAsynFloat64::interruptCallbackInput new value=794355383.558608
> 2015/03/04 17:16:23.566 XF:23ID1-ES{Tst-Cam:1}HDF1:EpicsTSSec_RBV devAsynInt32::interruptCallbackInput new value=794355383
> 2015/03/04 17:16:23.566 XF:23ID1-ES{Tst-Cam:1}HDF1:EpicsTSNsec_RBV devAsynInt32::interruptCallbackInput new value=565638532
> 2015/03/04 17:16:23.566 XF:23ID1-ES{Tst-Cam:1}HDF1:WriteStatus devAsynInt32::interruptCallbackInput new value=0
> 2015/03/04 17:16:23.566 XF:23ID1-ES{Tst-Cam:1}HDF1:ArrayCounter_RBV devAsynInt32::getCallbackValue from ringBuffer value=1
> 2015/03/04 17:16:23.566 XF:23ID1-ES{Tst-Cam:1}HDF1:UniqueId_RBV devAsynInt32::getCallbackValue from ringBuffer value=4
> 2015/03/04 17:16:23.566 XF:23ID1-ES{Tst-Cam:1}HDF1:WriteFile devAsynBusy::interruptCallback new value=1
> 2015/03/04 17:16:23.566 XF:23ID1-ES{Tst-Cam:1}HDF1:TimeStamp_RBV devAsynFloat64::getCallbackValue from ringBuffer value=794355383.558608
> 2015/03/04 17:16:23.566 XF:23ID1-ES{Tst-Cam:1}HDF1:EpicsTSSec_RBV devAsynInt32::getCallbackValue from ringBuffer value=794355383
> 2015/03/04 17:16:23.566 XF:23ID1-ES{Tst-Cam:1}HDF1:EpicsTSNsec_RBV devAsynInt32::getCallbackValue from ringBuffer value=565638532
> 2015/03/04 17:16:23.566 XF:23ID1-ES{Tst-Cam:1}HDF1:WriteStatus devAsynInt32::getCallbackValue from ringBuffer value=0
> 2015/03/04 17:16:23.566 XF:23ID1-ES{Tst-Cam:1}HDF1:WriteFile_RBV devAsynInt32::interruptCallbackInput new value=1
> 2015/03/04 17:16:23.566 XF:23ID1-ES{Tst-Cam:1}HDF1:WriteFile_RBV devAsynInt32::getCallbackValue from ringBuffer value=1
> 2015/03/04 17:16:23.566 NDFileHDF5::openFile Filename: /GPFS/xf23id/xf23id1/ccdtestdata/2015/3/4/4848c262-131d-49bb-b76a-db72c2ede134_000000.h5
> 2015/03/04 17:16:23.567 NDFileHDF5::openFile attribute list copied. num pArray attributes = 1 local copy = 1
> 2015/03/04 17:16:23.567 NDFileHDF5::configureDims NDArray: { 3, 1024, 1024, }
> 2015/03/04 17:16:23.567 NDFileHDF5::configureDims dimension report:
> framesize 1024, 1024, 3,
> chunkdims 1024, 1024, 3,
> maxdims 1024, 1024, 3,
> dims 1024, 1024, 3,
> offset 0, 0, 0,
> virtual 0,
> 2015/03/04 17:16:23.567 NDFileHDF5::createNewFile Setting istorek=1
> 2015/03/04 17:16:23.568 NDFileHDF5::createFileLayout Creating dataspace with given dimensions
> 2015/03/04 17:16:23.568 NDFileHDF5::createFileLayout Configuring chunking
> 2015/03/04 17:16:23.568 NDFileHDF5::createFileLayout Setting fillvalue
> 2015/03/04 17:16:23.568 NDFileHDF5::createFileLayout Empty layout file, use default layout
> 2015/03/04 17:16:23.569 NDFileHDF5::createXMLFileLayout Root tree: < Group: '' groups=1 dsets=0 attr=0>
> < Group: '/entry' groups=2 dsets=0 attr=1>
> < Group: '/entry/data' groups=0 dsets=0 attr=1>
> < Group: '/entry/instrument' groups=3 dsets=0 attr=1>
> < Group: '/entry/instrument/NDAttributes' groups=0 dsets=0 attr=1>
> < Group: '/entry/instrument/detector' groups=1 dsets=1 attr=1>
> < Group: '/entry/instrument/detector/NDAttributes' groups=0 dsets=1 attr=1>
> < Group: '/entry/instrument/performance' groups=0 dsets=1 attr=0>
> 2015/03/04 17:16:23.569 NDFileHDF5::writeH5attrStr name=NX_class value=NXentry
> 2015/03/04 17:16:23.569 NDFileHDF5::writeH5attrStr name=NX_class value=NXdata
> 2015/03/04 17:16:23.569 NDFileHDF5::writeH5attrStr name=NX_class value=NXinstrument
> 2015/03/04 17:16:23.569 NDFileHDF5::writeH5attrStr name=NX_class value=NXcollection
> 2015/03/04 17:16:23.569 NDFileHDF5::writeH5attrStr name=NX_class value=NXdetector
> 2015/03/04 17:16:23.569 NDFileHDF5::createDatasetDetector Setting cache size=3145728 slots=0
> 2015/03/04 17:16:23.569 NDFileHDF5::createDatasetDetector Creating first empty dataset called "data"
> 2015/03/04 17:16:23.570 NDFileHDF5::writeH5attrStr name=NX_class value=SDS
> 2015/03/04 17:16:23.570 NDFileHDF5::writeH5attrInt32 name=signal value=1
> 2015/03/04 17:16:23.570 NDFileHDF5::writeH5attrStr name=NX_class value=NXcollection
> 2015/03/04 17:16:23.570 NDFileHDF5::createXMLFileLayout Default dataset name: /entry/instrument/detector/data
> 2015/03/04 17:16:23.570 NDFileHDF5::createAttributeDataset Creating attribute datasets. extradims=0 attribute count=1
> 2015/03/04 17:16:23.570 NDFileHDF5::writeFile getting attribute list
> 2015/03/04 17:16:23.570 NDFileHDF5::writeFile copying attribute list
> 2015/03/04 17:16:23.570 NDFileHDF5::writeFile: set_extent dims={1024,1024,3}
> HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 139838595618560:
> #000: ../../../src/H5Dio.c line 245 in H5Dwrite(): file selection+offset not within extent
> major: Dataspace
> minor: Out of range
> Segmentation fault
>
>
- Replies:
- RE: Problem with HDF5 plugin for areaDetector Mark Rivers
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- Problem with HDF5 plugin for areaDetector Wilkins, Stuart
- RE: Problem with HDF5 plugin for areaDetector Mark Rivers
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