• Error: cannot allocate vector of size

  You have, presumably, a 32-bit computer with a 4GB-per-process memory limit. You have hit it (you get less than 4Gb as the OS services need some and there is some fragmentation). The last failed allocation may be small, as you see, if you are allocating lots of smallish pieces.
  
  The only way to overcome that is to use a 64-bit OS and version of R. 
  

• run in kerrighed, meet out of memory error message -> Guess that Kerrigthed MM module's scheduler not support R's operation
  • Enable Kerrighed USE_REMOTE_MEMORY

    $ R
    # justRMA original limit: 145 CELs
    setwd("/home/mnt/chris_rmpi/cel_data_mixed")
    rm(list=ls())
    dir()
    library(affy)
    CELNames<-dir(".", "[.]CEL")
    CELNames<-CELNames[1:305]
    data <- justRMA(filenames=CELNames)
    
    $ dmesg
    init.orig invoked oom-killer: gfp_mask=0x201d2, order=0, oomkilladj=0
     [<c013fd53>] out_of_memory+0x7f/0x19c
     [<c014124d>] __alloc_pages+0x208/0x292
     [<c0142742>] __do_page_cache_readahead+0xcf/0x1fc
     [<c03fe349>] io_schedule+0x22/0x2c
     [<c03fe5c4>] __wait_on_bit_lock+0x4b/0x52
     [<c013cf7a>] __lock_page+0x64/0x6b
     [<c0142b7d>] do_page_cache_readahead+0x41/0x4a
     [<c013f1ca>] filemap_nopage+0x159/0x304
     [<c0147ed6>] __handle_mm_fault+0x170/0x85d
     [<c01043af>] common_interrupt+0x23/0x28
     [<c0400e01>] do_page_fault+0x231/0x543
     [<c0108b13>] read_tsc+0x6/0x7
     [<c0400bd0>] do_page_fault+0x0/0x543
     [<c03ff81c>] error_code+0x7c/0x84
     [<c03f0033>] tipc_link_send_long_buf+0x2b/0x1eb
     =======================
    Mem-info:
    DMA per-cpu:
    CPU    0: Hot: hi:    0, btch:   1 usd:   0   Cold: hi:    0, btch:   1 usd:   0
    CPU    1: Hot: hi:    0, btch:   1 usd:   0   Cold: hi:    0, btch:   1 usd:   0
    CPU    2: Hot: hi:    0, btch:   1 usd:   0   Cold: hi:    0, btch:   1 usd:   0
    CPU    3: Hot: hi:    0, btch:   1 usd:   0   Cold: hi:    0, btch:   1 usd:   0
    Normal per-cpu:
    CPU    0: Hot: hi:  186, btch:  31 usd:  57   Cold: hi:   62, btch:  15 usd:  61
    CPU    1: Hot: hi:  186, btch:  31 usd:  44   Cold: hi:   62, btch:  15 usd:  50
    CPU    2: Hot: hi:  186, btch:  31 usd: 156   Cold: hi:   62, btch:  15 usd:  14
    CPU    3: Hot: hi:  186, btch:  31 usd: 163   Cold: hi:   62, btch:  15 usd:  25
    HighMem per-cpu:
    CPU    0: Hot: hi:  186, btch:  31 usd:  30   Cold: hi:   62, btch:  15 usd:  14
    CPU    1: Hot: hi:  186, btch:  31 usd:   9   Cold: hi:   62, btch:  15 usd:  17
    CPU    2: Hot: hi:  186, btch:  31 usd:  29   Cold: hi:   62, btch:  15 usd:  43
    CPU    3: Hot: hi:  186, btch:  31 usd: 149   Cold: hi:   62, btch:  15 usd:  56
    Active:493418 inactive:306 dirty:0 writeback:0 unstable:0 free:12001 slab:4191 mapped:2 pagetables:576
    DMA free:8032kB min:68kB low:84kB high:100kB active:2748kB inactive:0kB present:16256kB pages_scanned:13504 all_unreclaimable? yes
    lowmem_reserve[]: 0 873 1991
    Normal free:39508kB min:3744kB low:4680kB high:5616kB active:819348kB inactive:748kB present:894080kB pages_scanned:1380165 all_unreclaimable? yes
    lowmem_reserve[]: 0 0 8950
    HighMem free:464kB min:512kB low:1712kB high:2912kB active:1151464kB inactive:476kB present:1145604kB pages_scanned:3364854 all_unreclaimable? yes
    lowmem_reserve[]: 0 0 0
    DMA: 0*4kB 0*8kB 0*16kB 1*32kB 1*64kB 0*128kB 1*256kB 1*512kB 1*1024kB 1*2048kB 1*4096kB = 8032kB
    Normal: 1*4kB 0*8kB 1*16kB 0*32kB 1*64kB 0*128kB 0*256kB 1*512kB 0*1024kB 15*2048kB 2*4096kB = 39508kB
    HighMem: 0*4kB 2*8kB 2*16kB 1*32kB 0*64kB 1*128kB 1*256kB 0*512kB 0*1024kB 0*2048kB 0*4096kB = 464kB
    Swap cache: add 0, delete 0, find 0/0, race 0+0
    Free swap  = 0kB
    Total swap = 0kB
    Free swap:            0kB
    518032 pages of RAM
    288656 pages of HIGHMEM
    5714 reserved pages
    173 pages shared
    0 pages swap cached
    0 pages dirty
    0 pages writeback
    2 pages mapped
    4191 pages slab
    576 pages pagetables
    

  • Don't enable Kerrighed USE_REMOTE_MEMORY

    $ dmesg
    R invoked oom-killer: gfp_mask=0x201d2, order=0, oomkilladj=0
     [<c013fd53>] out_of_memory+0x7f/0x19c
     [<c014124d>] __alloc_pages+0x208/0x292
     [<c0142742>] __do_page_cache_readahead+0xcf/0x1fc
     [<c0115e3b>] kmap_atomic+0x80/0x91
     [<c0115ca4>] kunmap_atomic+0x54/0x61
     [<c0140fbb>] get_page_from_freelist+0x26f/0x2f9
     [<c0142b7d>] do_page_cache_readahead+0x41/0x4a
     [<c013f1ca>] filemap_nopage+0x159/0x304
     [<c0147ed6>] __handle_mm_fault+0x170/0x85d
     [<c014ac3a>] vma_merge+0x168/0x178
     [<c014b026>] do_brk+0x16e/0x202
     [<c0400e01>] do_page_fault+0x231/0x543
     [<c0400bd0>] do_page_fault+0x0/0x543
     [<c03ff81c>] error_code+0x7c/0x84
     [<c03f0033>] tipc_link_send_long_buf+0x2b/0x1eb
     =======================
    Mem-info:
    DMA per-cpu:
    CPU    0: Hot: hi:    0, btch:   1 usd:   0   Cold: hi:    0, btch:   1 usd:   0
    CPU    1: Hot: hi:    0, btch:   1 usd:   0   Cold: hi:    0, btch:   1 usd:   0
    CPU    2: Hot: hi:    0, btch:   1 usd:   0   Cold: hi:    0, btch:   1 usd:   0
    CPU    3: Hot: hi:    0, btch:   1 usd:   0   Cold: hi:    0, btch:   1 usd:   0
    Normal per-cpu:
    CPU    0: Hot: hi:  186, btch:  31 usd: 160   Cold: hi:   62, btch:  15 usd:  58
    CPU    1: Hot: hi:  186, btch:  31 usd:  28   Cold: hi:   62, btch:  15 usd:  47
    CPU    2: Hot: hi:  186, btch:  31 usd:  24   Cold: hi:   62, btch:  15 usd:  48
    CPU    3: Hot: hi:  186, btch:  31 usd:  11   Cold: hi:   62, btch:  15 usd:  55
    HighMem per-cpu:
    CPU    0: Hot: hi:  186, btch:  31 usd:  25   Cold: hi:   62, btch:  15 usd:  61
    CPU    1: Hot: hi:  186, btch:  31 usd:   0   Cold: hi:   62, btch:  15 usd:  58
    CPU    2: Hot: hi:  186, btch:  31 usd:  30   Cold: hi:   62, btch:  15 usd:  58
    CPU    3: Hot: hi:  186, btch:  31 usd:  15   Cold: hi:   62, btch:  15 usd:  45
    Active:493781 inactive:44 dirty:12 writeback:0 unstable:0 free:11999 slab:4305 mapped:64 pagetables:573
    DMA free:8032kB min:68kB low:84kB high:100kB active:2748kB inactive:0kB present:16256kB pages_scanned:12864 all_unreclaimable? yes
    lowmem_reserve[]: 0 873 1991
    Normal free:39488kB min:3744kB low:4680kB high:5616kB active:820280kB inactive:128kB present:894080kB pages_scanned:1280802 all_unreclaimable? yes
    lowmem_reserve[]: 0 0 8950
    HighMem free:476kB min:512kB low:1712kB high:2912kB active:1152096kB inactive:48kB present:1145604kB pages_scanned:2358173 all_unreclaimable? yes
    lowmem_reserve[]: 0 0 0
    DMA: 0*4kB 0*8kB 0*16kB 1*32kB 1*64kB 0*128kB 1*256kB 1*512kB 1*1024kB 1*2048kB 1*4096kB = 8032kB
    Normal: 2*4kB 1*8kB 3*16kB 0*32kB 0*64kB 0*128kB 0*256kB 1*512kB 0*1024kB 15*2048kB 2*4096kB = 39488kB
    HighMem: 1*4kB 5*8kB 3*16kB 0*32kB 0*64kB 1*128kB 1*256kB 0*512kB 0*1024kB 0*2048kB 0*4096kB = 476kB
    Swap cache: add 0, delete 0, find 0/0, race 0+0
    Free swap  = 0kB
    Total swap = 0kB
    Free swap:            0kB
    518032 pages of RAM
    288656 pages of HIGHMEM
    5714 reserved pages
    76 pages shared
    0 pages swap cached
    12 pages dirty
    0 pages writeback
    64 pages mapped
    4305 pages slab
    573 pages pagetables
    Out of memory: kill process 38507 (bash) score 15539 or a child
    Killed process 38515 (R)
    

  • Use swap to slove this problem or wait kerrighed memory stable functions (If your clinet' fs is nfs, must use client's physical disk to be swap parition)

    $ dd if=/dev/zero of=swap.img bs=1M count=8000
    $ mkswap swap.img
    $ swapon swap.img