* 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 [] out_of_memory+0x7f/0x19c [] __alloc_pages+0x208/0x292 [] __do_page_cache_readahead+0xcf/0x1fc [] io_schedule+0x22/0x2c [] __wait_on_bit_lock+0x4b/0x52 [] __lock_page+0x64/0x6b [] do_page_cache_readahead+0x41/0x4a [] filemap_nopage+0x159/0x304 [] __handle_mm_fault+0x170/0x85d [] common_interrupt+0x23/0x28 [] do_page_fault+0x231/0x543 [] read_tsc+0x6/0x7 [] do_page_fault+0x0/0x543 [] error_code+0x7c/0x84 [] 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 [] out_of_memory+0x7f/0x19c [] __alloc_pages+0x208/0x292 [] __do_page_cache_readahead+0xcf/0x1fc [] kmap_atomic+0x80/0x91 [] kunmap_atomic+0x54/0x61 [] get_page_from_freelist+0x26f/0x2f9 [] do_page_cache_readahead+0x41/0x4a [] filemap_nopage+0x159/0x304 [] __handle_mm_fault+0x170/0x85d [] vma_merge+0x168/0x178 [] do_brk+0x16e/0x202 [] do_page_fault+0x231/0x543 [] do_page_fault+0x0/0x543 [] error_code+0x7c/0x84 [] 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) }}}