From ripley at stats.ox.ac.uk  Wed Mar 28 07:56:58 2012
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Wed, 28 Mar 2012 06:56:58 +0100
Subject: [Rd] serialization regression in 2.15.0 beta
In-Reply-To: <4F722A8D.6090105@columbia.edu>
References: <20120323191346.lmq6atwzhcgcsg00@cubmail.cc.columbia.edu>
	<4F722A8D.6090105@columbia.edu>
Message-ID: <4F72A82A.4080008@stats.ox.ac.uk>

On 27/03/2012 22:01, Ben Goodrich wrote:
> In case anyone is concerned that this regression will affect them, the
> code was reverted to the 2.14.x behavior by
>
> ------------------------------------------------------------------------
> r58842 | ripley | 2012-03-26 08:12:43 -0400 (Mon, 26 Mar 2012) | 1 line
> Changed paths:
>     M /branches/R-2-15-branch/doc/NEWS.Rd
>     M /branches/R-2-15-branch/src/library/parallel/R/unix/forkCluster.R
>     M /branches/R-2-15-branch/src/library/parallel/R/unix/mcfork.R
>
> revert to XDR serialization for 2.15.0
> ------------------------------------------------------------------------

But the underlying problem (in non-xdr binary unserialization) is AFAWK 
fixed: it was just that at this late stage there was too little time to 
test thoroughly before release.

Please test R-devel on your own problem (we haven't: the issue was found 
using a different example from elsewhere).

> Thanks,
> Ben
>
>
>> I am experiencing a problem related to serialization behavior in
>> 2.15.0 beta (binary installed from Debian unstable) and 2.16.0 (from
>> svn) that is not present in 2.14.2 (binary from Debian testing).
>>
>> I don't fully understand the problem. Also, I tried but have not yet
>> been able to create a small, self-contained example that reproduces
>> the problem. However, I do have a large, not self-contained example,
>> which requires an alpha version (not yet on CRAN) of the mi package
>> (the mi package on CRAN would not exhibit this issue). Anyone
>> interested in reproducing the problem can follow the readme.txt file
>> in this directory:
>>
>> http://www.columbia.edu/~bg2382/mi/serialization/
>>
>> I track r-devel with git-svn and was able to git bisect to svn commit r58219
>>
>> commit 799102bd9d0266fe89c3120981decf0b1f17ef11
>> Author: ripley<ripley at 00db46b3-68df-0310-9c12-caf00c1e9a41>
>> Date:   Sat Jan 28 15:02:34 2012 +0000
>>
>>       make use of non-xdr serialization;.
>>
>> although this commit could merely expose the problem rather than cause it.
>>
>> The problem occurs when the FUN called by mclapply() in the parallel
>> package returns a S4 object that contains a slot (called X) that is a
>> large matrix, specifically a "model matrix" similar to that produced
>> by glm(). Some columns of this matrix get corrupted with wrong values
>> (usually zero, but sometimes NaN or 10^300ish), which can be seen by
>> examining X right before FUN returns (to mclapply()'s environment) and
>> comparing to the "same" X after mclapply() returns to the calling
>> environment.
>>
>> Part of svn commit r58219 is this hunk
>>
>> diff --git a/src/library/parallel/R/unix/mcfork.R
>> b/src/library/parallel/R/unix/mcfork.R
>> index 8e27534..4f92193 100644
>> --- a/src/library/parallel/R/unix/mcfork.R
>> +++ b/src/library/parallel/R/unix/mcfork.R
>> @@ -82,7 +82,8 @@ mckill<- function(process, signal = 2L)
>>    ## used by mcparallel, mclapply
>>    sendMaster<- function(what)
>>    {
>> -    if (!is.raw(what)) what<- serialize(what, NULL, FALSE)
>> +    # This is talking to the same machine, so no point in using xdr.
>> +    if (!is.raw(what)) what<- serialize(what, NULL, xdr = FALSE)
>>        .Call(C_mc_send_master, what, PACKAGE = "parallel")
>>    }
>>
>> Contrary to the comment, I have found that if I specify xdr = TRUE, I
>> get the expected (non-corrupted X slot) behavior in 2.16.0, even
>> though it is forking locally on my 64bit Debian laptop with a little
>> endian i7 processor, whose specs are
>>
>> goodrich at CYBERPOWERPC:/tmp/serialization$ cat /proc/cpuinfo
>> processor       : 0
>> vendor_id       : GenuineIntel
>> cpu family      : 6
>> model           : 42
>> model name      : Intel(R) Core(TM) i7-2630QM CPU @ 2.00GHz
>> stepping        : 7
>> microcode       : 0x17
>> cpu MHz         : 800.000
>> cache size      : 6144 KB
>> physical id     : 0
>> siblings        : 8
>> core id         : 0
>> cpu cores       : 4
>> apicid          : 0
>> initial apicid  : 0
>> fpu             : yes
>> fpu_exception   : yes
>> cpuid level     : 13
>> wp              : yes
>> flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge
>> mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe
>> syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl
>> xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl
>> vmx est tm2 ssse3 cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic popcnt
>> tsc_deadline_timer xsave avx lahf_lm ida arat epb xsaveopt pln pts dts
>> tpr_shadow vnmi flexpriority ept vpid
>> bogomips        : 3990.83
>> clflush size    : 64
>> cache_alignment : 64
>> address sizes   : 36 bits physical, 48 bits virtual
>> power management:
>>
>> ...
>>
>> processor       : 7
>> [same as processor 0]
>>
>> So, to summarize I get the good behavior on R 2.14.2 when using
>> mclapply(), on 2.15.0 beta when using lapply(), and on 2.16.0 using
>> mclapply() iff I patch in xdr = TRUE in sendMaster(). I get the bad
>> behavior on 2.15.0 beta and unpatched 2.16.0 when using mclapply().
>>
>> My session info:
>>
>>> sessionInfo()
>> R version 2.15.0 beta (2012-03-16 r58769)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> locale:
>>    [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>    [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>    [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>    [7] LC_PAPER=C                 LC_NAME=C
>>    [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats4    stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>>    [1] mi_0.9-83        bigmemory_4.2.11 arm_1.5-03       foreign_0.8-49
>>    [5] abind_1.4-0      R2WinBUGS_2.1-18 coda_0.14-5      lme4_0.999375-42
>>    [9] Matrix_1.0-4     lattice_0.20-0   MASS_7.3-17
>>
>> loaded via a namespace (and not attached):
>> [1] grid_2.15.0  nlme_3.1-103
>>
>> Thanks,
>> Ben
>
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> https://stat.ethz.ch/mailman/listinfo/r-devel


-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] serialization regression in 2.15.0 beta
Prof Brian Ripley