February 19, 2013

System Information on Cyberstar

funes Linux

Number of Processors

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[yuy121@cyberstar231: ~]# grep "^processor" /proc/cpuinfo
processor   : 0
processor   : 1
processor   : 2
processor   : 3
processor   : 4
processor   : 5
processor   : 6
processor   : 7
processor   : 8
processor   : 9
processor   : 10
processor   : 11
processor   : 12
processor   : 13
processor   : 14
processor   : 15
processor   : 16
processor   : 17
processor   : 18
processor   : 19
processor   : 20
processor   : 21
processor   : 22
processor   : 23
processor   : 24
processor   : 25
processor   : 26
processor   : 27
processor   : 28
processor   : 29
processor   : 30
processor   : 31

Memory Information

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[yuy121@cyberstar231: ~]# cat /proc/meminfo
MemTotal:     528642176 kB
MemFree:      524562356 kB
Buffers:        461100 kB
Cached:        2118892 kB
SwapCached:          0 kB
Active:        1672396 kB
Inactive:      1595732 kB
HighTotal:           0 kB
HighFree:            0 kB
LowTotal:     528642176 kB
LowFree:      524562356 kB
SwapTotal:     2096472 kB
SwapFree:      2096472 kB
Dirty:             120 kB
Writeback:           0 kB
AnonPages:      688120 kB
Mapped:         118552 kB
Slab:           427984 kB
PageTables:       6836 kB
NFS_Unstable:        0 kB
Bounce:              0 kB
CommitLimit:  504306536 kB
Committed_AS:  1280648 kB
VmallocTotal: 34359738367 kB
VmallocUsed:    371456 kB
VmallocChunk: 34359366851 kB
HugePages_Total:     0
HugePages_Free:      0
HugePages_Rsvd:      0
Hugepagesize:     2048 kB
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February 1, 2013

Bio at Cyberstar

funes bio, Linux

The data is at 

/gpfs/scratch/yuy121/Bio

The program is at 

/gpfs/work/yuy121
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Last login: Fri Feb  1 03:11:02 2013 from *.cse.psu.edu
[yuy121@cyberstar: ~]# cd /gpfs/work/yuy121/samtools/
[yuy121@cyberstar: /gpfs/work/yuy121/samtools]# ls
AUTHORS          bam_reheader.c  faidx.c         misc
bam2bcf.c        bam_rmdup.c     faidx.h         NEWS
bam2bcf.h        bam_rmdupse.c   INSTALL         padding.c
bam2bcf_indel.c  bam_sort.c      kaln.c          phase.c
bam2depth.c      bam_stat.c      kaln.h          razf.c
bam_aux.c        bamtk.c         khash.h         razf.h
bam.c            bam_tview.c     klist.h         razip.c
bam_cat.c        bcftools        knetfile.c      sam.c
bam_color.c      bedidx.c        knetfile.h      sam.h
bam_endian.h     bgzf.c          kprobaln.c      sam_header.c
bam.h            bgzf.h          kprobaln.h      sam_header.h
bam_import.c     bgzip.c         kseq.h          sample.c
bam_index.c      ChangeLog.old   ksort.h         sample.h
bam_lpileup.c    COPYING         kstring.c       samtools
bam_mate.c       cut_target.c    kstring.h       samtools.1
bam_md.c         errmod.c        libbam.a        sam_view.c
bam_pileup.c     errmod.h        Makefile        win32
bam_plcmd.c      examples        Makefile.mingw
[yuy121@cyberstar: /gpfs/work/yuy121/samtools]# ls /gpfs/scratch/yuy121/Bio/
NA19240_GAIIx_100_chr21.bam
[yuy121@cyberstar: /gpfs/work/yuy121/samtools]# ./samtools view -H /gpfs/scratch/yuy121/Bio/NA19240_GAIIx_100_chr21.bam
[yuy121@cyberstar: /gpfs/work/yuy121/samtools]# ./samtools view /gpfs/scratch/yuy121/Bio/NA19240_GAIIx_100_chr21.bam
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