Appion

Reported by Tom Houweling

appion svn r18192 topologyAlignment script fail

This has occurred with two separate data sets with two separate experienced users.

Command:

topologyAlignment.py --projectid=86 --rundir=/k2data/appion/taylor/14may08a/align/topol4 --description="test" --runname=topol4 --stack=1 --lowpass=10 --highpass=2000 --num-part=340 --start=5 --end=19 --bin=2 --mask=70 --iter=5 --itermul=10 --learn=0.01 --ilearn=0.0005 --age=25 --mramethod=imagic --msamethod=can --nproc=8 --msaproc=8 --commit --expid=2403 --jobtype=partalign

Error log leading up to buffer overflow:

calculating class average : 0
total number of node images = 19
outputing average images to : classes_avg.hed
total number of avg images = 19
executing IMAGIC command: /opt/qb3/imagic-110817e/stand/arithm.e
!!! WARNING: removing stack: classes.hed
!!! WARNING: removing stack: classes.img
executing IMAGIC command: /opt/qb3/imagic-110817e/stand/pretreat.e
!!! WARNING: removing stack: classes_mask.hed
!!! WARNING: removing stack: classes_mask.img
finished alignment in 9.03 sec
EMAN: proc2d classes_mask_norm.hed /k2data/appion/taylor/14may08a/align/topol4/classes05.hed
!!! WARNING: removing stack: classes_mask_norm.hed
!!! WARNING: removing stack: classes_mask_norm.img
... Alignment time: 2 min 24 sec
... Sorting final class averages
!!! WARNING: replacing stack file '/k2data/appion/taylor/14may08a/align/topol4/classes05.hed' with 'sortedcls.hed'
!!! WARNING: replacing stack file '/k2data/appion/taylor/14may08a/align/topol4/classes05.img' with 'sortedcls.img'
executing IMAGIC command: /opt/qb3/imagic-110817e/stand/testim.e
... replacing 'mrastack.hed' with 'tempimg.hed'

• buffer overflow detected ***: python terminated ======= Backtrace: =========
  /lib/libc.so.6(_fortify_fail+0x37)[0x7fe783be9cd7]
  /lib/libc.so.6(+0x101b90)[0x7fe783be8b90]
  /lib/libc.so.6(+0x100ff9)[0x7fe783be7ff9]
  /lib/libc.so.6(_IO_default_xsputn+0xcc)[0x7fe783b5e35c]
  /lib/libc.so.6(_IO_vfprintf+0x3b96)[0x7fe783b31286]
  /lib/libc.so.6(_vsprintf_chk+0x99)[0x7fe783be8099]
  /lib/libc.so.6(_sprintf_chk+0x7f)[0x7fe783be7fdf]
  /opt/qb3/eman-2.05/lib/libEM2.so(_ZN4EMAN9ImagicIO212write_headerERKNS_4DictEiPKNS_6RegionENS_6EMUtil10EMDataTypeEb+0x84f)[0x7fe7831d8fef]
  /opt/qb3/eman-2.05/lib/libEM2.so(_ZN4EMAN6EMData11write_imageERKSsiNS_6EMUtil9ImageTypeEbPKNS_6RegionENS3_10EMDataTypeEb+0x6d5)[0x7fe78313b555]
  /opt/qb3/eman-2.05/lib/libpyEMData2.so(+0xb4360)[0x7fe77fc6e360]
  /opt/qb3/eman-2.05/lib/libpyEMData2.so(_ZN5boost6python7objects23caller_py_function_implINS0_6detail6callerIPFvRN4EMAN6EMDataERKSsiENS0_21default_call_policiesENS_3mpl7vector4IvS7_S9_iEEEEEclEP7_objectSJ+0x128)[0x7fe77ff48da8]