Hi all
First of all, sorry for the kind on newbie question.
I'm running some memory-heavy statistical analyses using R, which
require more memory than what's physically available. I.e. the machine
(a x201, which is running -current amd64) has 4Gb of physical mem, but R
needs at least 6Gb. If I understand correctly, this is what virtual mem
is there for, but -- and here's the newbie part -- I'm not quite sure on
how to make it work.
Steps taken so far:
1. Raise datasize-cur and datasize-max to 3G.
Everything runs OK, but R complains about not being able to allocate
enough mem (expected).
2. datasize-cur=3G + datasize-max=3G + vmemoryuse=4G (swap partition has
5G).
Everything runs OK, but R complains about not being able to allocate
enough mem. systat swap shows absolutely no change.
3. vmemoryuse=3G + datasize-max=infinity
Admittedly not knowing what I was doing. Big time SNAFU.
Everything slows to a crawl when memory usage goes past the available
phys mem (about 3.6G). And by a crawl I mean unusable if using X,
requiring great patience if on virtual consoles.
top shows R using over 1000% (not a typo) CPU although the CPU summary
lines say they're all idling. "state" is "run/3", "wait" column says
"pagerse". Swap usage increases, though. R never gets back to a usable
state.
Clue bat required. Is there anything else that needs to be done to
enable R to (properly) use some of the virtual memory?
Thanks in advance
Zé
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OpenBSD 5.4-current (GENERIC.MP) #185: Thu Dec 5 17:02:54 MST 2013
dera...@amd64.openbsd.org:/usr/src/sys/arch/amd64/compile/GENERIC.MP
real mem = 4062691328 (3874MB)
avail mem = 3946405888 (3763MB)
mainbus0 at root
bios0 at mainbus0: SMBIOS rev. 2.6 @ 0xe0010 (78 entries)
bios0: vendor LENOVO version "6QET69WW (1.39 )" date 04/26/2012
bios0: LENOVO 3680WE9
acpi0 at bios0: rev 2
acpi0: sleep states S0 S3 S4 S5
acpi0: tables DSDT FACP SSDT ECDT APIC MCFG HPET ASF! BOOT SSDT TCPA SSDT SSDT
SSDT
acpi0: wakeup devices LID_(S3) SLPB(S3) IGBE(S4) EXP1(S4) EXP2(S4) EXP3(S4)
EXP4(S4) EXP5(S4) EHC1(S3) EHC2(S3) HDEF(S4)
acpitimer0 at acpi0: 3579545 Hz, 24 bits
acpiec0 at acpi0
acpimadt0 at acpi0 addr 0xfee00000: PC-AT compat
cpu0 at mainbus0: apid 0 (boot processor)
cpu0: Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz, 2660.46 MHz
cpu0:
FPU,VME,DE,PSE,TSC,MSR,PAE,MCE,CX8,APIC,SEP,MTRR,PGE,MCA,CMOV,PAT,PSE36,CFLUSH,DS,ACPI,MMX,FXSR,SSE,SSE2,SS,HTT,TM,PBE,SSE3,PCLMUL,DTES64,MWAIT,DS-CPL,VMX,SMX,EST,TM2,SSSE3,CX16,xTPR,PDCM,SSE4.1,SSE4.2,POPCNT,AES,NXE,LONG,LAHF,PERF,ITSC
cpu0: 256KB 64b/line 8-way L2 cache
cpu0: smt 0, core 0, package 0
cpu0: apic clock running at 133MHz
cpu0: mwait min=64, max=64, C-substates=0.2.1.1.0, IBE
cpu1 at mainbus0: apid 1 (application processor)
cpu1: Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz, 2660.02 MHz
cpu1:
FPU,VME,DE,PSE,TSC,MSR,PAE,MCE,CX8,APIC,SEP,MTRR,PGE,MCA,CMOV,PAT,PSE36,CFLUSH,DS,ACPI,MMX,FXSR,SSE,SSE2,SS,HTT,TM,PBE,SSE3,PCLMUL,DTES64,MWAIT,DS-CPL,VMX,SMX,EST,TM2,SSSE3,CX16,xTPR,PDCM,SSE4.1,SSE4.2,POPCNT,AES,NXE,LONG,LAHF,PERF,ITSC
cpu1: 256KB 64b/line 8-way L2 cache
cpu1: smt 1, core 0, package 0
cpu2 at mainbus0: apid 4 (application processor)
cpu2: Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz, 2660.02 MHz
cpu2:
FPU,VME,DE,PSE,TSC,MSR,PAE,MCE,CX8,APIC,SEP,MTRR,PGE,MCA,CMOV,PAT,PSE36,CFLUSH,DS,ACPI,MMX,FXSR,SSE,SSE2,SS,HTT,TM,PBE,SSE3,PCLMUL,DTES64,MWAIT,DS-CPL,VMX,SMX,EST,TM2,SSSE3,CX16,xTPR,PDCM,SSE4.1,SSE4.2,POPCNT,AES,NXE,LONG,LAHF,PERF,ITSC
cpu2: 256KB 64b/line 8-way L2 cache
cpu2: smt 0, core 2, package 0
cpu3 at mainbus0: apid 5 (application processor)
cpu3: Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz, 2660.02 MHz
cpu3:
FPU,VME,DE,PSE,TSC,MSR,PAE,MCE,CX8,APIC,SEP,MTRR,PGE,MCA,CMOV,PAT,PSE36,CFLUSH,DS,ACPI,MMX,FXSR,SSE,SSE2,SS,HTT,TM,PBE,SSE3,PCLMUL,DTES64,MWAIT,DS-CPL,VMX,SMX,EST,TM2,SSSE3,CX16,xTPR,PDCM,SSE4.1,SSE4.2,POPCNT,AES,NXE,LONG,LAHF,PERF,ITSC
cpu3: 256KB 64b/line 8-way L2 cache
cpu3: smt 1, core 2, package 0
ioapic0 at mainbus0: apid 1 pa 0xfec00000, version 20, 24 pins
ioapic0: misconfigured as apic 2, remapped to apid 1
acpimcfg0 at acpi0 addr 0xe0000000, bus 0-255
acpihpet0 at acpi0: 14318179 Hz
acpiprt0 at acpi0: bus 0 (PCI0)
acpiprt1 at acpi0: bus -1 (PEG_)
acpiprt2 at acpi0: bus 13 (EXP1)
acpiprt3 at acpi0: bus -1 (EXP2)
acpiprt4 at acpi0: bus -1 (EXP3)
acpiprt5 at acpi0: bus 5 (EXP4)
acpiprt6 at acpi0: bus 2 (EXP5)
acpicpu0 at acpi0: C3, C1, PSS
acpicpu1 at acpi0: C3, C1, PSS
acpicpu2 at acpi0: C3, C1, PSS
acpicpu3 at acpi0: C3, C1, PSS
acpipwrres0 at acpi0: PUBS: resource for EHC1, EHC2
acpitz0 at acpi0: critical temperature is 100 degC
acpibtn0 at acpi0: LID_
acpibtn1 at acpi0: SLPB
acpibat0 at acpi0: BAT0 not present
acpibat1 at acpi0: BAT1 not present
acpiac0 at acpi0: AC unit online
acpithinkpad0 at acpi0
acpidock0 at acpi0: GDCK docked (15)
cpu0: Enhanced SpeedStep 2660 MHz: speeds: 2400, 2399, 2266, 2133, 1999, 1866,
1733, 1599, 1466, 1333, 1199 MHz
pci0 at mainbus0 bus 0
pchb0 at pci0 dev 0 function 0 "Intel Core Host" rev 0x02
vga1 at pci0 dev 2 function 0 "Intel HD Graphics" rev 0x02
intagp0 at vga1
agp0 at intagp0: aperture at 0xd0000000, size 0x10000000
inteldrm0 at vga1
drm0 at inteldrm0
inteldrm0: 1280x800
wsdisplay0 at vga1 mux 1: console (std, vt100 emulation)
wsdisplay0: screen 1-5 added (std, vt100 emulation)
"Intel 3400 MEI" rev 0x06 at pci0 dev 22 function 0 not configured
"Intel 3400 KT" rev 0x06 at pci0 dev 22 function 3 not configured
em0 at pci0 dev 25 function 0 "Intel 82577LM" rev 0x06: msi, address
00:26:2d:fb:7c:63
ehci0 at pci0 dev 26 function 0 "Intel 3400 USB" rev 0x06: apic 1 int 23
usb0 at ehci0: USB revision 2.0
uhub0 at usb0 "Intel EHCI root hub" rev 2.00/1.00 addr 1
azalia0 at pci0 dev 27 function 0 "Intel 3400 HD Audio" rev 0x06: msi
azalia0: codecs: Conexant/0x5069, Intel/0x2804, using Conexant/0x5069
audio0 at azalia0
ppb0 at pci0 dev 28 function 0 "Intel 3400 PCIE" rev 0x06: msi
pci1 at ppb0 bus 13
ppb1 at pci0 dev 28 function 3 "Intel 3400 PCIE" rev 0x06: msi
pci2 at ppb1 bus 5
ppb2 at pci0 dev 28 function 4 "Intel 3400 PCIE" rev 0x06: msi
pci3 at ppb2 bus 2
iwn0 at pci3 dev 0 function 0 "Intel Centrino Advanced-N 6200" rev 0x35: msi,
MIMO 2T2R, MoW, address 00:23:14:5d:af:e4
ehci1 at pci0 dev 29 function 0 "Intel 3400 USB" rev 0x06: apic 1 int 19
usb1 at ehci1: USB revision 2.0
uhub1 at usb1 "Intel EHCI root hub" rev 2.00/1.00 addr 1
ppb3 at pci0 dev 30 function 0 "Intel 82801BAM Hub-to-PCI" rev 0xa6
pci4 at ppb3 bus 14
pcib0 at pci0 dev 31 function 0 "Intel QM57 LPC" rev 0x06
ahci0 at pci0 dev 31 function 2 "Intel 3400 AHCI" rev 0x06: msi, AHCI 1.3
scsibus0 at ahci0: 32 targets
sd0 at scsibus0 targ 0 lun 0: <ATA, HITACHI HTS72503, PC3Z> SCSI3 0/direct
fixed naa.5000cca645c68684
sd0: 305245MB, 512 bytes/sector, 625142448 sectors
cd0 at scsibus0 targ 1 lun 0: <HL-DT-ST, DVDRAM GU10N, MX05> ATAPI 5/cdrom
removable
ichiic0 at pci0 dev 31 function 3 "Intel 3400 SMBus" rev 0x06: apic 1 int 23
iic0 at ichiic0
spdmem0 at iic0 addr 0x50: 2GB DDR3 SDRAM PC3-10600 SO-DIMM
spdmem1 at iic0 addr 0x51: 2GB DDR3 SDRAM PC3-10600 SO-DIMM
itherm0 at pci0 dev 31 function 6 "Intel 3400 Thermal" rev 0x06
isa0 at pcib0
isadma0 at isa0
pckbc0 at isa0 port 0x60/5
pckbd0 at pckbc0 (kbd slot)
pckbc0: using irq 1 for kbd slot
wskbd0 at pckbd0: console keyboard, using wsdisplay0
pms0 at pckbc0 (aux slot)
pckbc0: using irq 12 for aux slot
wsmouse0 at pms0 mux 0
wsmouse1 at pms0 mux 0
pms0: Synaptics touchpad, firmware 7.4
pcppi0 at isa0 port 0x61
spkr0 at pcppi0
aps0 at isa0 port 0x1600/31
pci5 at mainbus0 bus 255
pchb1 at pci5 dev 0 function 0 "Intel QuickPath" rev 0x02
pchb2 at pci5 dev 0 function 1 "Intel QuickPath" rev 0x02
pchb3 at pci5 dev 2 function 0 "Intel QPI Link" rev 0x02
pchb4 at pci5 dev 2 function 1 "Intel QPI Physical" rev 0x02
pchb5 at pci5 dev 2 function 2 "Intel Reserved" rev 0x02
pchb6 at pci5 dev 2 function 3 "Intel Reserved" rev 0x02
mtrr: Pentium Pro MTRR support, 8 var ranges, 88 fixed ranges
uhub2 at uhub0 port 1 "Intel Rate Matching Hub" rev 2.00/0.00 addr 2
uhub3 at uhub2 port 5 "Lenovo product 0x1005" rev 2.00/0.01 addr 3
uhub4 at uhub3 port 2 "NEC hub" rev 2.00/1.00 addr 4
uhub5 at uhub4 port 4 "NEC hub" rev 2.00/1.00 addr 5
uhub6 at uhub1 port 1 "Intel Rate Matching Hub" rev 2.00/0.00 addr 2
vscsi0 at root
scsibus1 at vscsi0: 256 targets
softraid0 at root
scsibus2 at softraid0: 256 targets
sd1 at scsibus2 targ 1 lun 0: <OPENBSD, SR CRYPTO, 005> SCSI2 0/direct fixed
sd1: 305242MB, 512 bytes/sector, 625135808 sectors
root on sd1a (40b8b4a2a7e90f03.a) swap on sd1b dump on sd1b
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