"Derek Stephen Elmerick" <delmeric at gmail.com> writes:
Peter,
=20
I ran the memory limit function you mention below and both versions provi=
de
the same result:
=20
memory.limit(size=3D4095)
NULL
memory.limit(NA)
[1] 4293918720
I do have 4GB ram on my PC. As a more reproducible form of the test, I
have attached output that uses a randomly generated dataset after fixing =
the
seed. Same result as last time: works with 2.3.0 and not 2.4.0. I guess t=
he
one caveat here is that I just increased the dataset size until I got the
memory issue with at least one of the R versions. It's okay. No need to
spend more time on this. I really don't mind using the previous version.
Like you mentioned, probably just a function of the new version requiring
more memory.
Hmm, you might want to take a final look at the Windows FAQ 2.9. I am
still not quite convinced you're really getting more than the default
1.5 GB.
Also, how much can you increase the problem size on 2.3.0 before it
breaks? If you can only go to say 39 or 40 variables, then there's
probably not much we can do. If it is orders of magnitude, then we may
have a real bug (or not: sometimes we fix bugs resulting from things
not being duplicated when they should have been, the fixed code then
uses more memory than the unfixed code.)
=20
Thanks,
Derek
=20
=20
=20
On 06 Nov 2006 21:42:04 +0100, Peter Dalgaard <p.dalgaard at biostat.ku.dk>
wrote:
"Derek Stephen Elmerick" <delmeric at gmail.com> writes:
Thanks for the replies. Point taken regarding submission protocol. I
have
included a text file attachment that shows the R output with version
2.3.0and
2.4.0. A label distinguishing the version is included in the comments.
A quick background on the attached example. The dataset has 650,000
records
and 32 variables. the response is dichotomous (0/1) and i ran a logis=
tic
model (i previously mentioned multinomial, but decided to start simple
for
the example). Covariates in the model may be continuous or categorica=
l,
but
all are numeric. You'll notice that the code is the same for both
versions;
however, there is a memory error with the 2.3.0 version. i ran this
several
times and in different orders to make sure it was not some sort of
hardware
issue.
If there is some sort of additional output that would be helpful, I c=
an
provide as well. Or, if there is nothing I can do, that is fine also.
I don't think it was ever possible to request 4GB on XP. The version
difference might be caused by different response to invalid input in
memory.limit(). What does memory.limit(NA) tell you after the call to
memory.limit(4095) in the two versions?
If that is not the reason: What is the *real* restriction of memory on
your system? Do you actually have 4GB in your system (RAM+swap)?
Your design matrix is on the order of 160 MB, so shouldn't be a
problem with a GB-sized workspace. However, three copies of it will
brush against 512 MB, and it's not unlikely to have that many copies
around.
-Derek
On 11/6/06, Kasper Daniel Hansen < khansen at stat.berkeley.edu> wrote:
It would be helpful to produce a script that reproduces the error on
your system. And include details on the size of your data set and
what you are doing with it. It is unclear what function is actually
causing the error and such. Really, in order to do something about =
it
you need to show how to actually obtain the error.
To my knowledge nothing _major_ has happened with the memory
consumption, but of course R could use slightly more memory for
specific purposes.
But chances are that this is not really memory related but more
related to the functions your are using - perhaps a bug or perhaps a
user error.
Kasper
On Nov 6, 2006, at 10:20 AM, Derek Stephen Elmerick wrote:
thanks for the friendly reply. i think my description was fairly
clear: i
import a large dataset and run a model. using the same dataset, t=
he
process worked previously and it doesn't work now. if the new
version of R
requires more memory and this compromises some basic data analyse=
s,
i would
label this as a bug. if this memory issue was mentioned in the
documentation, then i apologize. this email was clearly not well
received,
so if there is a more appropriate place to post these sort of
questions,
that would be helpful.
-derek
On 06 Nov 2006 18:20:33 +0100, Peter Dalgaard
< p.dalgaard at biostat.ku.dk>
wrote:
delmeric at gmail.com writes:
Full_Name: Derek Elmerick
Version: 2.4.0
OS: Windows XP
Submission from: (NULL) ( 38.117.162.243 )
hello -
i have some code that i run regularly using R version 2.3.x . t=
he
final
step of
the code is to build a multinomial logit model. the dataset is
large;
however, i
have not had issues in the past. i just installed the 2.4.0
version of R
and now
have memory allocation issues. to verify, i ran the code again
against
the 2.3
version and no problems. since i have set the memory limit to t=
he
max
size, i
have no alternative but to downgrade to the 2.3 version. though=
ts?
And what do you expect the maintainers to do about it? ( I.e. why
are
you filing a bug report.)
You give absolutely no handle on what the cause of the problem
might
be, or even to reproduce it. It may be a bug, or maybe just R
requiring more memory to run than previously.
--
O__ ---- Peter Dalgaard =C3=98ster Farimagsgade 5=
, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+4=
5)
35327918
~~~~~~~~~~ - ( p.dalgaard at biostat.ku.dk) FAX: