I ran quip to compress a 78+ Gb bam file, and got a segmentation fault in the memory allocator:
$ qsub -I -V -l nodes=1,mem=128gb
-rw-r--r-- 1 sandor sandor 7862860454 Mar 28 03:00
accepted_hits_big.bam $ module load quip $ gdb quip
(gdb) run accepted_hits_big.bam
Starting program: /spin1/sys/i386/usrlocal/apps/quip/1.1.5/quip
accepted_hits_big.bam
warning: no loadable sections found in added symbol-file
system-supplied DSO at
0x2aaaaaac7000
[Thread debugging using libthread_db enabled]
Program received signal SIGSEGV, Segmentation fault.
0x00002aaaab37851b in malloc_consolidate () from /lib64/libc.so.6
(gdb)
This job was run with 128Gb memory.
This BAM file is derived from what I understand to be a typical state-of-the-art paired-end, mRNA data acquisition.
???
Sanford M. Orlow, Computer Engineer
Center for Information Technology, National Institutes of Health
12 South Dr. 12/2208 , Bethesda, MD 20892-5680
PHONE 301.496.5362 EMAIL sandor@mail.nih.gov
I ran quip to compress a 78+ Gb bam file, and got a segmentation fault in the memory allocator:
This job was run with 128Gb memory.
This BAM file is derived from what I understand to be a typical state-of-the-art paired-end, mRNA data acquisition.
???
Sanford M. Orlow, Computer Engineer Center for Information Technology, National Institutes of Health 12 South Dr. 12/2208 , Bethesda, MD 20892-5680 PHONE 301.496.5362 EMAIL sandor@mail.nih.gov