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