Hi,
I am trying to plot model parameters vs. covariates suing Xpose. The data
file is rather large and I get the following message:
In initialize(value, ...) :
Reached total allocation of 1535Mb: see help(memory.size)
2: In initialize(value, ...) :
Reached total allocation of 1535Mb: see help(memory.size)
Error in print(parm.vs.cov(.cur.db)) :
error in evaluating the argument 'x' in selecting a method for function
'print': Error: cannot allocate vector of size 171 Kb
Can anybody offer a remedy?
Thanks!
Toufigh
Memory problems with Xpose
Hi Toufigh,
You could add more physical memory to your system if it is 64 bits, not sure if that would make sense on 32 bits.
Otherwise, if your dataset is large enough, you could draw several random subsamples of the dataset and do the graph on that. And/or use other ways of subsetting.
Hope this helps,
Jeroen
Quoted reply history
________________________________
From: owner-nmusers
Behalf Of Toufigh Gordi
Sent: Friday, January 13, 2012 09:29
To: nmusers
Subject: [NMusers] Memory problems with Xpose
Hi,
I am trying to plot model parameters vs. covariates suing Xpose. The data file is rather large and I get the following message:
In initialize(value, ...) :
Reached total allocation of 1535Mb: see help(memory.size)
2: In initialize(value, ...) :
Reached total allocation of 1535Mb: see help(memory.size)
Error in print(parm.vs.cov(.cur.db)) :
error in evaluating the argument 'x' in selecting a method for function 'print': Error: cannot allocate vector of size 171 Kb
Can anybody offer a remedy?
Thanks!
Toufigh
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Hi Toufigh,
You could add more physical memory to your system if it is 64 bits, not sure if
that would make sense on 32 bits.
Otherwise, if your dataset is large enough, you could draw several random
subsamples of the dataset and do the graph on that. And/or use other ways of
subsetting.
Hope this helps,
Jeroen
Quoted reply history
________________________________
From: [email protected] [mailto:[email protected]] On
Behalf Of Toufigh Gordi
Sent: Friday, January 13, 2012 09:29
To: [email protected]
Subject: [NMusers] Memory problems with Xpose
Hi,
I am trying to plot model parameters vs. covariates suing Xpose. The data file
is rather large and I get the following message:
In initialize(value, ...) :
Reached total allocation of 1535Mb: see help(memory.size)
2: In initialize(value, ...) :
Reached total allocation of 1535Mb: see help(memory.size)
Error in print(parm.vs.cov(.cur.db)) :
error in evaluating the argument 'x' in selecting a method for function
'print': Error: cannot allocate vector of size 171 Kb
Can anybody offer a remedy?
Thanks!
Toufigh
Notice: This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact information
for affiliates is available at
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended solely
for the use of the individual or entity named on this message. If you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from
your system.
Hi Toufigh,
R has updated its memory handling in recent updates, so if you are using an
older version of R then updating to the latest version may help. Otherwise
you might try subsetting the plot to reduce the number of plots created.
For example:
# Change the covariate scope
change.xvardef(xpdb,var="covariates") <- c("SEX","AGE","WT")
# then run the plot again:
parm.vs.cov(xpdb)
The scope can also be changed in the classic menu system.
Best regards
Andy
Andrew Hooker, Ph.D.
Associate Professor of Pharmacometrics
Dept. of Pharmaceutical Biosciences
Uppsala University
Box 591, 751 24, Uppsala, Sweden
Phone: +46 18 471 4355
http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/
www.farmbio.uu.se/research/researchgroups/pharmacometrics/
Quoted reply history
From: [email protected] [mailto:[email protected]] On
Behalf Of Toufigh Gordi
Sent: den 13 januari 2012 09:29
To: [email protected]
Subject: [NMusers] Memory problems with Xpose
Hi,
I am trying to plot model parameters vs. covariates suing Xpose. The data
file is rather large and I get the following message:
In initialize(value, ...) :
Reached total allocation of 1535Mb: see help(memory.size)
2: In initialize(value, ...) :
Reached total allocation of 1535Mb: see help(memory.size)
Error in print(parm.vs.cov(.cur.db)) :
error in evaluating the argument 'x' in selecting a method for function
'print': Error: cannot allocate vector of size 171 Kb
Can anybody offer a remedy?
Thanks!
Toufigh
Dear Toufigh,
I guess you've got a relatively large model and/or dataset - R has bumped up
against its memory limit under your version of Windows (which I'm assuming
you're using based on the error message). Which version are you using? 32-bit
or 64-bit?
To support what Andy and Jeroen have suggested, the solutions are typically to
get more RAM, upgrade R, upgrade to a 64-bit OS if you aren't already running
on one, or to reduce the scope of the problem. You could accomplish the latter
by running the parameter vs covariate comparisons by hand, or by doing them in
smaller batches. See help(xpose.prefs-class) for details related to changing
the definitions of the parameters and covariates in the Xvardef section of an
Xpose data object - shortening the vectors of parameters (parms) and covariates
will reduce the dimensionality or the problem.
You could also try upping the memory limit (using memory.limit), but this may
not work. There's a short discussion of Windows memory limits in R here:
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to-be-a-limit-on-the-memory-it-uses_0021
Hope this helps!
Best
Justin
Quoted reply history
On Jan 13, 2012, at 9:28 AM, Toufigh Gordi wrote:
> Hi,
>
> I am trying to plot model parameters vs. covariates suing Xpose. The data
> file is rather large and I get the following message:
>
> In initialize(value, ...) :
> Reached total allocation of 1535Mb: see help(memory.size)
> 2: In initialize(value, ...) :
> Reached total allocation of 1535Mb: see help(memory.size)
> Error in print(parm.vs.cov(.cur.db)) :
> error in evaluating the argument 'x' in selecting a method for function
> 'print': Error: cannot allocate vector of size 171 Kb
>
> Can anybody offer a remedy?
>
> Thanks!
>
> Toufigh
--
Justin Wilkins, PhD
Exprimo NV
Tel: +41 (0) 81 599 23 82
Mobile: +41 (0) 76 561 09 49
E-mail: [email protected]
Web: www.exprimo.com
This e-mail is confidential. It is also privileged or otherwise protected by
work product immunity or other legal rules. The information is intended to be
for use of the individual or entity named above. If you are not the intended
recipient, please be aware that any disclosure, copying, distribution or use of
the contents of this information is prohibited. You should therefore delete
this message from your computer system. If you have received the message in
error, please notify us by reply e-mail. The integrity and security of this
message cannot be guaranteed on the Internet.
Thank you for your co-operation.
Dear Toufigh,
Your comment "Interestingly, the whole folder with about 50 tested models and
associated files is only 360 MB..." suggests to me that Xpose worked before
for the previous run. I know that R load all the saved R objects in memory
from the current directory. Perhaps the solution to your issue would be to
delete the files ".RData" and ".Rhistory" from your "Star in" directory of
Xpose.
Jean
Quoted reply history
From: [email protected] [mailto:[email protected]] On
Behalf Of Toufigh Gordi
Sent: Friday, January 13, 2012 10:53 AM
To: 'Justin Wilkins'
Cc: [email protected]
Subject: RE: [NMusers] Memory problems with Xpose
Hi Justin (and others),
My computer has 3GB, running Windows 7 on a 32 bit machine. The interesting
thing is that this is happening in the middle of a modeling project and so far
there have been no issues. I have now tried it on an XP machine with 4GB of Ram
and get the same message there. Interestingly, the whole folder with about 50
tested models and associated files is only 360 MB, so my RAM is over 10 time
that. My R version is 2.14.0 (2011-10-31). I'll see if a newer version is
available.
Toufigh
From: Justin Wilkins [mailto:[email protected]]
Sent: Friday, January 13, 2012 1:23 AM
To: Toufigh Gordi
Cc: [email protected]<mailto:[email protected]>
Subject: Re: [NMusers] Memory problems with Xpose
Dear Toufigh,
I guess you've got a relatively large model and/or dataset - R has bumped up
against its memory limit under your version of Windows (which I'm assuming
you're using based on the error message). Which version are you using? 32-bit
or 64-bit?
To support what Andy and Jeroen have suggested, the solutions are typically to
get more RAM, upgrade R, upgrade to a 64-bit OS if you aren't already running
on one, or to reduce the scope of the problem. You could accomplish the latter
by running the parameter vs covariate comparisons by hand, or by doing them in
smaller batches. See help(xpose.prefs-class) for details related to changing
the definitions of the parameters and covariates in the Xvardef section of an
Xpose data object - shortening the vectors of parameters (parms) and covariates
will reduce the dimensionality or the problem.
You could also try upping the memory limit (using memory.limit), but this may
not work. There's a short discussion of Windows memory limits in R here:
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to-be-a-limit-on-the-memory-it-uses_0021
Hope this helps!
Best
Justin
On Jan 13, 2012, at 9:28 AM, Toufigh Gordi wrote:
Hi,
I am trying to plot model parameters vs. covariates suing Xpose. The data file
is rather large and I get the following message:
In initialize(value, ...) :
Reached total allocation of 1535Mb: see help(memory.size)
2: In initialize(value, ...) :
Reached total allocation of 1535Mb: see help(memory.size)
Error in print(parm.vs.cov(.cur.db)) :
error in evaluating the argument 'x' in selecting a method for function
'print': Error: cannot allocate vector of size 171 Kb
Can anybody offer a remedy?
Thanks!
Toufigh
--
Justin Wilkins, PhD
Exprimo NV
Tel:
+41 (0) 81 599 23 82
Mobile:
+41 (0) 76 561 09 49
E-mail:
[email protected]<mailto:[email protected]>
Web:
http://www.exprimo.com/
This e-mail is confidential. It is also privileged or otherwise protected by
work product immunity or other legal rules. The information is intended to be
for use of the individual or entity named above. If you are not the intended
recipient, please be aware that any disclosure, copying, distribution or use of
the contents of this information is prohibited. You should therefore delete
this message from your computer system. If you have received the message in
error, please notify us by reply e-mail. The integrity and security of this
message cannot be guaranteed on the Internet.
Thank you for your co-operation.
This electronic transmission may contain confidential and/or proprietary
information and is intended to be for the use of the individual or entity named
above. If you are not the intended recipient, be aware that any disclosure,
copying, distribution or use of the contents of this electronic transmission is
prohibited. If you have received this electronic transmission in error, please
destroy it and immediately notify us of the error. Thank you.
Toufigh,
In my experience, R on 32 bit system crashes when it reaches about 1.4 GB of memory (even on a 4 GB system). You can see it in the task manager (observe how memory use increases until R crashes). I was not able to do anything with it except to switch to a 64 bit system, where the limit is much-much larger.
Sometimes it helps to start from the fresh system (starting clean R run): if you you to save the work space and start from the saved one, this may explain why you had no problems in the earlier stages of the project when the work space was smaller.
Leonid
--------------------------------------
Leonid Gibiansky, Ph.D.
President, QuantPharm LLC
web: www.quantpharm.com
e-mail: LGibiansky at quantpharm.com
tel: (301) 767 5566
Quoted reply history
On 1/13/2012 10:53 AM, Toufigh Gordi wrote:
> Hi Justin (and others),
>
> My computer has 3GB, running Windows 7 on a 32 bit machine. The interesting thing is that this is happening in the middle of a modeling project and so far there have been no issues. I have now tried it on an XP machine with 4GB of Ram and get the same message there. Interestingly, the whole folder with about 50 tested models and associated files is only 360 MB, so my RAM is over 10 time that. My R version is 2.14.0 (2011-10-31). I'll see if a newer version is available.
>
> Toufigh
>
> *From:*Justin Wilkins [mailto:[email protected]]
> *Sent:* Friday, January 13, 2012 1:23 AM
> *To:* Toufigh Gordi
> *Cc:* [email protected]
> *Subject:* Re: [NMusers] Memory problems with Xpose
>
> Dear Toufigh,
>
> I guess you've got a relatively large model and/or dataset - R has bumped up against its memory limit under your version of Windows (which I'm assuming you're using based on the error message). Which version are you using? 32-bit or 64-bit?
>
> To support what Andy and Jeroen have suggested, the solutions are typically to get more RAM, upgrade R, upgrade to a 64-bit OS if you aren't already running on one, or to reduce the scope of the problem. You could accomplish the latter by running the parameter vs covariate comparisons by hand, or by doing them in smaller batches. See help(xpose.prefs-class) for details related to changing the definitions of the parameters and covariates in the Xvardef section of an Xpose data object - shortening the vectors of parameters (parms) and covariates will reduce the dimensionality or the problem.
>
> You could also try upping the memory limit (using memory.limit), but this may not work. There's a short discussion of Windows memory limits in R here: http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to-be-a-limit-on-the-memory-it-uses_0021
>
> Hope this helps!
>
> Best
>
> Justin
>
> On Jan 13, 2012, at 9:28 AM, Toufigh Gordi wrote:
>
> Hi,
>
> I am trying to plot model parameters vs. covariates suing Xpose. The data file is rather large and I get the following message:
>
> In initialize(value, ...) :
>
> Reached total allocation of 1535Mb: see help(memory.size)
>
> 2: In initialize(value, ...) :
>
> Reached total allocation of 1535Mb: see help(memory.size)
>
> Error in print(parm.vs.cov(.cur.db)) :
>
> error in evaluating the argument 'x' in selecting a method for function 'print': Error: cannot allocate vector of size 171 Kb
>
> Can anybody offer a remedy?
>
> Thanks!
>
> Toufigh
>
> --
>
> Justin Wilkins, PhD
>
> Exprimo NV
>
> Tel:
>
> +41 (0) 81 599 23 82
>
> Mobile:
>
> +41 (0) 76 561 09 49
>
> E-mail:
>
> [email protected] <mailto:[email protected]>
>
> Web:
>
> www.exprimo.com http://www.exprimo.com/
>
> This e-mail is confidential. It is also privileged or otherwise protected by work product immunity or other legal rules. The information is intended to be for use of the individual or entity named above. If you are not the intended recipient, please be aware that any disclosure, copying, distribution or use of the contents of this information is prohibited. You should therefore delete this message from your computer system. If you have received the message in error, please notify us by reply e-mail. The integrity and security of this message cannot be guaranteed on the Internet.
>
> Thank you for your co-operation.