[R-sig-hpc] doMC and RWeka
Max Kuhn
mxkuhn at gmail.com
Mon Sep 26 18:20:25 CEST 2011
Everyone,
I recently converted the caret package do use foreach for
parallelizing resampling computations, such as cross-validation.
Below is an example that approximates what caret does. When using
foreach with dopar and no parallelization, things work fine. For
example, if I run the code below without doMC loaded it, works fine.
If I run the code below (Rweka model and multicore), the workers start
but do not appear to use any CPU time.
If I run first without doMC then load doMC and 2 workers, I get ‘#
fatal error: mach_msg (send) failed: 0x10000003’ (much more
information is below) .
The code below with doMPI also works without error.
Any ideas?
Thanks,
Max
> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] doMC_1.2.2 multicore_0.1-5 RWeka_0.4-8 mlbench_2.1-0
[5] foreach_1.3.2 codetools_0.2-8 iterators_1.0.5
loaded via a namespace (and not attached):
[1] compiler_2.13.1 grid_2.13.1 rJava_0.9-1 RWekajars_3.7.3-1
[5] tools_2.13.1
###############################################################
## code
library(foreach)
library(mlbench)
library(doMC)
registerDoMC(2)
if(FALSE)
{
## this worked
library(doMPI)
cl <- startMPIcluster(2)
registerDoMPI(cl)
}
data(BostonHousing)
resampleIndex <- vector(mode = "list", length = 5)
set.seed(1)
resampleIndex <- lapply(resampleIndex,
function(x, y) sample(1:nrow(y), replace = TRUE),
y = BostonHousing)
parameters <- data.frame(pruning = c(TRUE, FALSE))
result <- foreach(iter = seq(along = resampleIndex), .combine =
"rbind", .verbose = FALSE, .errorhandling = "stop") %:%
foreach(parm = 1:nrow(parameters), .combine = "rbind", .verbose =
FALSE, .errorhandling = "stop") %dopar%
{
library(RWeka)
dataSubset <- BostonHousing[resampleIndex[[iter]],]
holdOut <- unique(resampleIndex[[iter]])
model <- M5Rules(medv ~ ., data = dataSubset,
control = Weka_control(N = parameters$pruning[parm]))
## test non-Weka models using lm:
## model <- lm(medv ~ ., data = dataSubset)
pred <- predict(model, BostonHousing[-holdOut, -14])
data.frame(obs = BostonHousing$medv[-holdOut],
pred = pred,
prune = parameters$pruning[parm],
subset = iter)
}
###############################################################
Process: R [1481]
Path: /Applications/R64.app/Contents/MacOS/R
Identifier: R
Version: ??? (???)
Code Type: X86-64 (Native)
Parent Process: R [1314]
Date/Time: 2011-09-26 12:01:10.930 -0400
OS Version: Mac OS X 10.6.8 (10K549)
Report Version: 6
Anonymous UUID: EAD58366-FAFB-444E-84A2-CEEC1CBD7E82
Exception Type: EXC_BREAKPOINT (SIGTRAP)
Exception Codes: 0x0000000000000002, 0x0000000000000000
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Application Specific Information:
*** multi-threaded process forked ***
Java information:
Exception type: Internal Error
(/SourceCache/JavaJDK16/JavaJDK16-384/hotspot/src/os/macosx/vm/os_macosx.cpp,
line 2798)
# fatal error: mach_msg (send) failed: 0x10000003
Java VM: Java HotSpot(TM) 64-Bit Server VM (20.1-b02-384 mixed mode
macosx-amd64)
Current thread (123001800): JavaThread "main" [_thread_in_vm,
id=1893948608, stack(7fff5f400000,7fff5fc00000)]
Stack: [7fff5f400000,7fff5fc00000]
Java frames: (J=compiled Java code, j=interpreted, Vv=VM code)
v ~RuntimeStub::_new_array_Java
J weka.filters.Filter.setOutputFormat(Lweka/core/Instances;)V
J weka.filters.unsupervised.attribute.Remove.setInputFormat(Lweka/core/Instances;)Z
J weka.classifiers.trees.m5.RuleNode.buildLinearModel([I)V
J weka.classifiers.trees.m5.RuleNode.prune()V
J weka.classifiers.trees.m5.RuleNode.prune()V
J weka.classifiers.trees.m5.RuleNode.prune()V
J weka.classifiers.trees.m5.RuleNode.prune()V
J weka.classifiers.trees.m5.RuleNode.prune()V
J weka.classifiers.trees.m5.RuleNode.prune()V
J weka.classifiers.trees.m5.RuleNode.prune()V
J weka.classifiers.trees.m5.RuleNode.prune()V
J weka.classifiers.trees.m5.RuleNode.prune()V
J weka.classifiers.trees.m5.RuleNode.prune()V
J weka.classifiers.trees.m5.RuleNode.prune()V
j weka.classifiers.trees.m5.Rule.buildClassifier(Lweka/core/Instances;)V+188
j weka.classifiers.trees.m5.M5Base.buildClassifier(Lweka/core/Instances;)V+240
v ~StubRoutines::call_stub
Java Threads: ( => current thread )
12310b800 JavaThread "Low Memory Detector" daemon [_thread_blocked,
id=722472960, stack(12b001000,12b101000)]
12310b000 JavaThread "C2 CompilerThread1" daemon [_thread_blocked,
id=719978496, stack(12ada0000,12aea0000)]
12310a000 JavaThread "C2 CompilerThread0" daemon [_thread_blocked,
id=718917632, stack(12ac9d000,12ad9d000)]
123109800 JavaThread "Signal Dispatcher" daemon [_thread_blocked,
id=717856768, stack(12ab9a000,12ac9a000)]
123108800 JavaThread "Surrogate Locker Thread (Concurrent GC)"
daemon [_thread_blocked, id=716795904, stack(12aa97000,12ab97000)]
1230f1000 JavaThread "Finalizer" daemon [_thread_blocked,
id=715735040, stack(12a994000,12aa94000)]
1230f0000 JavaThread "Reference Handler" daemon [_thread_blocked,
id=714674176, stack(12a891000,12a991000)]
=>123001800 JavaThread "main" [_thread_in_vm, id=1893948608,
stack(7fff5f400000,7fff5fc00000)]
Other Threads:
1230eb800 VMThread [stack: 12a78e000,12a88e000] [id=713613312]
12311d800 WatcherThread [stack: 12b104000,12b204000] [id=723533824]
VM state:not at safepoint (normal execution)
VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event])
[11d1027a0] Heap_lock - owner thread: 123001800
Heap
par new generation total 19136K, used 17081K [7dae00000, 7dc2c0000,
7dee00000)
eden space 17024K, 100% used [7dae00000, 7dbea0000, 7dbea0000)
from space 2112K, 2% used [7dbea0000, 7dbeae560, 7dc0b0000)
to space 2112K, 0% used [7dc0b0000, 7dc0b0000, 7dc2c0000)
concurrent mark-sweep generation total 63872K, used 29717K
[7dee00000, 7e2c60000, 7fae00000)
concurrent-mark-sweep perm gen total 21248K, used 6499K [7fae00000,
7fc2c0000, 800000000)
Code Cache [123801000, 123a72000, 126801000)
total_blobs=546 nmethods=338 adapters=170 free_code_cache=48470144
largest_free_block=57920
Virtual Machine Arguments:
JVM Args: -Dr.arch=/x86_64 -Xmx512m vfprintf exit
Java Command: <unknown>
Launcher Type: generic
Physical Memory: Page Size = 4k, Total = 8192M, Free = 5435M
Thread 0 Crashed: Dispatch queue: com.apple.main-thread
0 libclient64.dylib 0x0000000116cd6364
JVM_RaiseSignal + 574914
1 libclient64.dylib 0x00000001168cba9a jio_snprintf + 38228
2 libclient64.dylib 0x0000000116a5b443
JVM_MonitorNotifyAll + 4747
3 libclient64.dylib 0x000000011694a1a1 JVM_Lseek + 91023
4 libclient64.dylib 0x0000000116949bb7 JVM_Lseek + 89509
5 libclient64.dylib 0x0000000116949a38 JVM_Lseek + 89126
6 libclient64.dylib 0x000000011694f6be JVM_Lseek + 112812
7 libclient64.dylib 0x0000000116aad7cf JVM_NanoTime + 108795
8 ??? 0x000000012385e289 0 + 4890944137
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000116f7c20a rbx: 0x00007fff5fbf2718 rcx:
0x00007fff877ba47a rdx: 0x0000000000000008
rdi: 0x00007fff7117ae40 rsi: 0x0000000000000000 rbp:
0x00007fff5fbf26d0 rsp: 0x00007fff5fbf26d0
r8: 0x00007fff711777f8 r9: 0x0000000000000000 r10:
0x00007fff5fbf2650 r11: 0x0000000000000206
r12: 0x0000000000000b1b r13: 0x0000000116f85298 r14:
0x0000000123001800 r15: 0x0000000000000000
rip: 0x0000000116cd6364 rfl: 0x0000000000000202 cr2: 0x0000000116fa4c7f
Binary Images:
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(55002) <4419AFFC-DAE7-873E-6A7D-5C9A5A4497A6>
/System/Library/Frameworks/Security.framework/Versions/A/Security
0x7fff89be1000 - 0x7fff89c36ff7
com.apple.framework.familycontrols 2.0.2 (2020)
<F09541B6-5E28-1C01-C1AE-F6A2508670C7>
/System/Library/PrivateFrameworks/FamilyControls.framework/Versions/A/FamilyControls
0x7fff89c37000 - 0x7fff89c5afff com.apple.opencl 12.3.6
(12.3.6) <42FA5783-EB80-1168-4015-B8C68F55842F>
/System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL
0x7fff89c5b000 - 0x7fff89d7afe7 libcrypto.0.9.8.dylib 0.9.8
(compatibility 0.9.8) <14115D29-432B-CF02-6B24-A60CC533A09E>
/usr/lib/libcrypto.0.9.8.dylib
0x7fff89d7b000 - 0x7fff89d90ff7 com.apple.LangAnalysis 1.6.6
(1.6.6) <DC999B32-BF41-94C8-0583-27D9AB463E8B>
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/LangAnalysis.framework/Versions/A/LangAnalysis
0x7fff89dd0000 - 0x7fff89dd3ff7 com.apple.securityhi 4.0
(36638) <38935851-09E4-DDAB-DB1D-30ADC39F7ED0>
/System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/SecurityHI
0x7fff89dd4000 - 0x7fff89e20fff libauto.dylib ??? (???)
<F7221B46-DC4F-3153-CE61-7F52C8C293CF> /usr/lib/libauto.dylib
0x7fff89e21000 - 0x7fff8a51dff7 com.apple.CoreGraphics
1.545.0 (???) <58D597B1-EB3B-710E-0B8C-EC114D54E11B>
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
0x7fff8a51e000 - 0x7fff8a52dfef com.apple.opengl 1.6.13
(1.6.13) <516098B3-4517-8A55-64BB-195CDAA5334D>
/System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
0x7fff8a536000 - 0x7fff8a570fff libcups.2.dylib 2.8.0
(compatibility 2.0.0) <7982734A-B66B-44AA-DEEC-364D2C10009B>
/usr/lib/libcups.2.dylib
0x7fff8a571000 - 0x7fff8a5b8ff7 com.apple.coreui 2 (114)
<D7645B59-0431-6283-7322-957D944DAB21>
/System/Library/PrivateFrameworks/CoreUI.framework/Versions/A/CoreUI
0x7fff8a5b9000 - 0x7fff8a6c3ff7 com.apple.MeshKitIO 1.1
(49.2) <F296E151-80AE-7764-B969-C2050DF26BFE>
/System/Library/PrivateFrameworks/MeshKit.framework/Versions/A/Frameworks/MeshKitIO.framework/Versions/A/MeshKitIO
0x7fffffe00000 - 0x7fffffe01fff libSystem.B.dylib ??? (???)
<9AB4F1D1-89DC-0E8A-DC8E-A4FE4D69DB69> /usr/lib/libSystem.B.dylib
Model: MacBookPro6,1, BootROM MBP61.0057.B0C, 2 processors, Intel Core
i7, 2.66 GHz, 8 GB, SMC 1.57f17
Graphics: NVIDIA GeForce GT 330M, NVIDIA GeForce GT 330M, PCIe, 512 MB
Graphics: Intel HD Graphics, Intel HD Graphics, Built-In, 288 MB
Memory Module: global_name
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x93),
Broadcom BCM43xx 1.0 (5.10.131.42.4)
Bluetooth: Version 2.4.5f3, 2 service, 19 devices, 1 incoming serial ports
Network Service: Ethernet, Ethernet, en0
Network Service: AirPort, AirPort, en1
Serial ATA Device: Hitachi HTS725050A9A362, 465.76 GB
Serial ATA Device: HL-DT-ST DVDRW GS23N
USB Device: Hub, 0x0424 (SMSC), 0x2514, 0xfa100000 / 2
USB Device: Apple Internal Keyboard / Trackpad, 0x05ac (Apple Inc.),
0x0236, 0xfa120000 / 4
USB Device: BRCM2070 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0xfa110000 / 3
USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.),
0x8218, 0xfa113000 / 6
USB Device: Hub, 0x0424 (SMSC), 0x2514, 0xfd100000 / 2
USB Device: Hub, 0x05ac (Apple Inc.), 0x9136, 0xfd140000 / 5
USB Device: Keyboard Hub, 0x05ac (Apple Inc.), 0x1006, 0xfd141000 / 11
USB Device: Trackball, 0x046d (Logitech Inc.), 0xc404, 0xfd141300 / 13
USB Device: Apple Keyboard, 0x05ac (Apple Inc.), 0x0220, 0xfd141200 / 12
USB Device: USB Audio DAC, 0x08bb (Texas Instruments Japan), 0x2704,
0xfd142000 / 7
USB Device: Hub, 0x05ac (Apple Inc.), 0x9137, 0xfd144000 / 6
USB Device: Display Audio, 0x05ac (Apple Inc.), 0x2912, 0xfd144100 / 10
USB Device: Apple LED Cinema Display, 0x05ac (Apple Inc.), 0x9236,
0xfd144300 / 9
USB Device: Display iSight, 0x05ac (Apple Inc.), 0x8508, 0xfd144200 / 8
USB Device: IR Receiver, 0x05ac (Apple Inc.), 0x8242, 0xfd120000 / 4
USB Device: Built-in iSight, 0x05ac (Apple Inc.), 0x8507, 0xfd110000 / 3
FireWire Device: unknown_device, Unknown
--
Max
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