Segmentation fault with view (random access) on Lustre FS #219
Description
Hi,
I should start by saying that our Lustre file system is new and we're only setting things up.
I'm running a samtools view command that randomly seg fault when the data is on our Lustre file system.
The command I'm using is
for i in {1..50};
do
echo $i
sambamba view -f bam -L test_10015AT.bed test_10015AT-sort.bam > /dev/null
doneWhen run on lustre I get this output
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Segmentation fault (core dumped)
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Segmentation fault (core dumped)
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Segmentation fault (core dumped)
Here is the gdb output backtrace if that helps:
#0 0x00002aaaab61330b in __memset_sse2 () from /lib64/libc.so.6
#1 0x000000000057ef15 in gc.gc.GC.malloc() ()
#2 0x0000000000433114 in bio.core.bgzf.inputstream.BgzfInputStream.__ctor() ()
#3 0x0000000000434f70 in bio.bam.randomaccessmanager.RandomAccessManager.__T15readsFromChunksS313bio3bam9readrange11withOffsetsTAS3bio4core4bgzf5chunk5ChunkZ.readsFromChunks() ()
#4 0x0000000000435632 in std.algorithm.iteration.__T9MapResultS1483bio3bam19randomaccessmanager19RandomAccessManager47__T8getReadsS313bio3bam9readrange11withOffsetsZ8getReadsMFAS3bio3bam6region9BamRegionZ9__lambda4TS3std5range121__T3ZipTAAS3bio3bam6region9BamRegionTS3std5range63__T6RepeatTC3bio3bam19randomaccessmanager19RandomAccessManagerZ6RepeatZ3ZipZ.MapResult.front() ()
#5 0x0000000000416d86 in std.algorithm.iteration.__T6joinerTS3std9algorithm9iteration306__T9MapResultS1483bio3bam19randomaccessmanager19RandomAccessManager47__T8getReadsS313bio3bam9readrange11withOffsetsZ8getReadsMFAS3bio3bam6region9BamRegionZ9__lambda4TS3std5range121__T3ZipTAAS3bio3bam6region9BamRegionTS3std5range63__T6RepeatTC3bio3bam19randomaccessmanager19RandomAccessManagerZ6RepeatZ3ZipZ9MapResultZ.joiner() ()
#6 0x00000000004b8332 in sambamba.utils.view.alignmentrangeprocessor.BamSerializer.__T7processTS3std9algorithm9iteration356__T6joinerTS3std9algorithm9iteration306__T9MapResultS1483bio3bam19randomaccessmanager19RandomAccessManager47__T8getReadsS313bio3bam9readrange11withOffsetsZ8getReadsMFAS3bio3bam6region9BamRegionZ9__lambda4TS3std5range121__T3ZipTAAS3bio3bam6region9BamRegionTS3std5range63__T6RepeatTC3bio3bam19randomaccessmanager19RandomAccessManagerZ6RepeatZ3ZipZ9MapResultZ6joinerFS3std9algorithm9iteration306__T9MapResultS1483bio3bam19randomaccessmanager19RandomAccessManager47__T8getReadsS313bio3bam9readrange11withOffsetsZ8getReadsMFAS3bio3bam6region9BamRegionZ9__lambda4TS3std5range121__T3ZipTAAS3bio3bam6region9BamRegionTS3std5range63__T6RepeatTC3bio3bam19randomaccessmanager19RandomAccessManagerZ6RepeatZ3ZipZ9MapResultZ6ResultTC3bio3bam6reader9BamReaderZ.process() ()
#7 0x00000000004dd76c in sambamba.view.__T12sambambaMainTC3bio3bam6reader9BamReaderZ.sambambaMain() ()
#8 0x00000000004cb955 in sambamba.view.__T12sambambaMainTC3bio3bam6reader9BamReaderZ.sambambaMain() ()
#9 0x00000000004054e3 in sambamba.view.view_main() ()
#10 0x0000000000588924 in _d_run_main ()
#11 0x00002aaaab5add5d in __libc_start_main () from /lib64/libc.so.6
#12 0x0000000000404969 in _start ()
When I run the same command on the local filesystem there are no segmentation faults.
Is there any known problem with Lustre file system?
I also ran the equivalent samtools view command but that did not results in segfaults.