Re: areaDetector and HDF5 file saving segafaults

[Hinko Kocevar <hinkocevar@gmail.com>]

Hi Mark,

Image size is 1936 x 1216, data type is uint16 (~2.3MB). Camera is AlliedVision Manta G-235B, controlled with aravis+aravisGigE.

I'm saving some attributes - see the attached XML file.

I'm using Single saving mode, saving one image per acquisition at ~10 images per second.

It happens quite often, if I leave if running for couple of minutes I get the segfault.

I have not yet tried reproducing with simDetector - will do.

I'm using HDF5 ver 1.10.1 that comes with ADSupport.

The thing is that I have not noticed this problems before, this now happens on a remote machine at an experiment we are conducting. It could be the hardware..

Thank you,

Hinko

On Tue, Nov 7, 2017 at 2:59 PM, Mark Rivers <rivers@cars.uchicago.edu> wrote:

Hi Hinko,


Also, what version of HDF5 are you using, the one from ADSupport (and if so what version) or a system library version?


Mark



________________________________
From: tech-talk-bounces@aps.anl.gov <tech-talk-bounces@aps.anl.gov> on behalf of Hinko Kocevar <hinkocevar@gmail.com>
Sent: Tuesday, November 7, 2017 3:58 AM
To: tech-talk@aps.anl.gov
Subject: areaDetector and HDF5 file saving segafaults

Hi,

I'm experiencing segmentation faults that trace to HDF5 file saving plugin. This is with ADAravis camera, 10 images per second.

EPICS base is 3.15.4, AreaDetector is 3-1.

epics>
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7fffed55a700 (LWP 27283)]
0x00007ffff35d7d89 in __memcpy_ssse3_back () from /lib64/libc.so.6
(gdb) bt
#0  0x00007ffff35d7d89 in __memcpy_ssse3_back () at /lib64/libc.so.6
#1  0x00007ffff6371211 in H5Pset_fill_value (plist_id=<optimized out>, type_id=216172782117023038, value=0x7ffd67ff2fb0) at ../H5Pdcpl.c:3217
#2  0x00007ffff776bff7 in NDFileHDF5AttributeDataset::createHDF5Dataset() (this=this@entry=0x7ffd5c007460) at ../NDFileHDF5AttributeDataset.cpp:99
#3  0x00007ffff776c648 in NDFileHDF5AttributeDataset::createDataset(int) (this=this@entry=0x7ffd5c007460, user_chunking=<optimized out>)
    at ../NDFileHDF5AttributeDataset.cpp:75
#4  0x00007ffff776529e in NDFileHDF5::createAttributeDataset(NDArray*) (this=this@entry=0x939530, pArray=pArray@entry=0x7fff10968800)
    at ../NDFileHDF5.cpp:2535
#5  0x00007ffff776717f in NDFileHDF5::openFile(char const*, int, NDArray*) (this=0x939530, fileName=0x7fffed5595d0 "/home/dev/DTUdata/image1_20896.h5", openMode=<optimized out>, pArray=0x7fff10968800) at ../NDFileHDF5.cpp:268
#6  0x00007ffff775820d in NDPluginFile::openFileBase(int, NDArray*) (this=this@entry=0x939530, openMode=openMode@entry=2, pArray=pArray@entry=0x7fff10968800) at ../NDPluginFile.cpp:73
#7  0x00007ffff7758ee4 in NDPluginFile::writeFileBase() (this=this@entry=0x939530) at ../NDPluginFile.cpp:230
#8  0x00007ffff77597f8 in NDPluginFile::processCallbacks(NDArray*) (this=0x939530, pArray=0x7fff10968800) at ../NDPluginFile.cpp:751
#9  0x00007ffff770871e in NDPluginDriver::processTask() (this=0x939530) at ../NDPluginDriver.cpp:467
#10 0x00007ffff48d44c9 in epicsThreadCallEntryPoint(void*) (pPvt=0x7fffd4001400) at ../../../src/libCom/osi/epicsThread.cpp:85
#11 0x00007ffff48d9f6c in start_routine (arg=0x7fffd4001310) at ../../../src/libCom/osi/os/posix/osdThread.c:403
#12 0x00007ffff2f66e25 in start_thread () at /lib64/libpthread.so.0
#13 0x00007ffff358534d in clone () at /lib64/libc.so.6

Thanks,
Hinko

--
.. the more I see the less I believe.., AE AoR

--

.. the more I see the less I believe.., AE AoR

<?xml version="1.0" standalone="no" ?>
<!-- Attributes -->
<Attributes
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
    xsi:noNamespaceSchemaLocation="NDAttributes.xsd"
    >
    <Attribute name="CameraManufacturer"  type="EPICS_PV" source="CAM1:det1:Manufacturer_RBV"     dbrtype="DBR_NATIVE"  description="Camera manufacturer"/>
    <Attribute name="CameraModel"         type="EPICS_PV" source="CAM1:det1:Model_RBV"            dbrtype="DBR_NATIVE"  description="Camera model"/>
    <Attribute name="ImageCounter"        type="EPICS_PV" source="CAM1:det1:ArrayCounter_RBV"     dbrtype="DBR_NATIVE"  description="Array counter"/>
    <Attribute name="MaxSizeX"            type="EPICS_PV" source="CAM1:det1:MaxSizeX_RBV"         dbrtype="DBR_NATIVE"  description="Detector X size"/>
    <Attribute name="MaxSizeY"            type="EPICS_PV" source="CAM1:det1:MaxSizeY_RBV"         dbrtype="DBR_NATIVE"  description="Detector Y size"/>
    <Attribute name="BinX"                type="EPICS_PV" source="CAM1:det1:BinX_RBV"             dbrtype="DBR_NATIVE"  description="Binning in X"/>
    <Attribute name="BinY"                type="EPICS_PV" source="CAM1:det1:BinY_RBV"             dbrtype="DBR_NATIVE"  description="Binning in Y"/>
    <Attribute name="AcquireTimePV"       type="EPICS_PV" source="CAM1:det1:AcquireTime_RBV"      dbrtype="DBR_NATIVE"  description="Camera acquire time"/>
    <Attribute name="AcquirePeriod"       type="EPICS_PV" source="CAM1:det1:AcquirePeriod_RBV"    dbrtype="DBR_NATIVE"  description="Acquire period"/>
    <Attribute name="ImageMode"           type="EPICS_PV" source="CAM1:det1:ImageMode_RBV"        dbrtype="DBR_NATIVE"  description="Image mode"/>
    <Attribute name="TriggerMode"         type="EPICS_PV" source="CAM1:det1:TriggerMode_RBV"      dbrtype="DBR_NATIVE"  description="Trigger mode"/>
    <Attribute name="DeviceTemperature"   type="EPICS_PV" source="CAM1:det1:DeviceTemperatu0_RBV" dbrtype="DBR_NATIVE"  description="Device temperature"/>
    <Attribute name="Gain"                type="EPICS_PV" source="CAM1:det1:Gain_RBV"             dbrtype="DBR_NATIVE"  description="Gain"/>
    
    <Attribute name="Current"             type="EPICS_PV" source="DTU:Current"                    dbrtype="DBR_NATIVE"  description="Current"/>
    <Attribute name="Temperature"         type="EPICS_PV" source="DTU:Temperature"                dbrtype="DBR_NATIVE"  description="Temperature"/>
    <Attribute name="GaussParam1"         type="EPICS_PV" source="DTU:GaussParam1"                dbrtype="DBR_NATIVE"  description="Gauss param 1"/>
    <Attribute name="GaussParam2"         type="EPICS_PV" source="DTU:GaussParam2"                dbrtype="DBR_NATIVE"  description="Gauss param 2"/>
    <Attribute name="GaussParam3"         type="EPICS_PV" source="DTU:GaussParam3"                dbrtype="DBR_NATIVE"  description="Gauss param 3"/>
    <Attribute name="GaussParam4"         type="EPICS_PV" source="DTU:GaussParam4"                dbrtype="DBR_NATIVE"  description="Gauss param 4"/>
    <Attribute name="GaussParam5"         type="EPICS_PV" source="DTU:GaussParam5"                dbrtype="DBR_NATIVE"  description="Gauss param 5"/>
    <Attribute name="GaussParam6"         type="EPICS_PV" source="DTU:GaussParam6"                dbrtype="DBR_NATIVE"  description="Gauss param 6"/>
    <Attribute name="GaussParam7"         type="EPICS_PV" source="DTU:GaussParam7"                dbrtype="DBR_NATIVE"  description="Gauss param 7"/>
    <Attribute name="GaussParam8"         type="EPICS_PV" source="DTU:GaussParam8"                dbrtype="DBR_NATIVE"  description="Gauss param 8"/>
    <Attribute name="GaussParam9"         type="EPICS_PV" source="DTU:GaussParam9"                dbrtype="DBR_NATIVE"  description="Gauss param 9"/>
    <Attribute name="GaussParam10"        type="EPICS_PV" source="DTU:GaussParam10"               dbrtype="DBR_NATIVE"  description="Gauss param 10"/>
    <Attribute name="Sample"              type="EPICS_PV" source="DTU:Sample"                     dbrtype="DBR_STRING"  description="Sample"/>
    <Attribute name="Comment"             type="EPICS_PV" source="DTU:Comment"                    dbrtype="DBR_STRING"  description="Comment"/>

<!--
    <Attribute name="ID_Energy"           type="EPICS_PV" source="ID34:Energy"                  dbrtype="DBR_NATIVE"  description="Undulator energy"/>
    <Attribute name="AttributesFileParam"  type="PARAM"   source="ND_ATTRIBUTES_FILE"            datatype="STRING"     description="Attributes file param"/>
-->
</Attributes>