> Hello NONMEM Users,
> We have a computer with 4 processors. When I try to run more
> than 3 NONMEM7 jobs, I am getting the following message:
> Starting nonmem execution ...
> The system cannot execute the specified program.
> KP9022.OUT
> newline
> 1 file(s) copied.
> Could Not Find H:\4\output
>
> The message is code and directory independent. It always
> appears when I try to run more than 3 codes. When I test
> nonmem7 using a laptop, which also has 4 processors, I can
> execute 4 programs. Also, when I had NONMEM6, I did not have
> this problem on the same machine.
> Do you familiar with this problem? Thanks.
> Pavel
>
The system cannot execute the specified program
Pavel,
Do you have enough RAM? I had something similar once when I used large size nonmem 7 installation (I do not remember the exact message, but this part: "The system cannot execute the specified program" was there for sure).
Leonid
--------------------------------------
Leonid Gibiansky, Ph.D.
President, QuantPharm LLC
web: www.quantpharm.com
e-mail: LGibiansky at quantpharm.com
tel: (301) 767 5566
[email protected] wrote:
> > Hello NONMEM Users,
> > We have a computer with 4 processors. When I try to run more
> > than 3 NONMEM7 jobs, I am getting the following message:
> > Starting nonmem execution ...
> > The system cannot execute the specified program.
> > KP9022.OUT
> > newline
> > 1 file(s) copied.
> > Could Not Find H:\4\output
> >
> > The message is code and directory independent. It always
> > appears when I try to run more than 3 codes. When I test
> > nonmem7 using a laptop, which also has 4 processors, I can
> > execute 4 programs. Also, when I had NONMEM6, I did not have
> > this problem on the same machine.
> > Do you familiar with this problem? Thanks.
> > Pavel
> >
According to ICON, this is due to the size of the RAM on your PC. If you
have less than 3 GB of RAM and running the 'big' nm7 job, it will not allow
you to run more than 2 jobs at once. You may need to increase your RAM to
6GB to solve this problem.
Best regards,
Sam Liao
Pharmax Research
Quoted reply history
From: [email protected] [mailto:[email protected]] On
Behalf Of [email protected]
Sent: Friday, October 16, 2009 2:02 PM
To: [email protected]
Cc: [email protected]
Subject: [NMusers] The system cannot execute the specified program
> Hello NONMEM Users,
> We have a computer with 4 processors. When I try to run more
> than 3 NONMEM7 jobs, I am getting the following message:
> Starting nonmem execution ...
> The system cannot execute the specified program.
> KP9022.OUT
> newline
> 1 file(s) copied.
> Could Not Find H:\4\output
>
> The message is code and directory independent. It always
> appears when I try to run more than 3 codes. When I test
> nonmem7 using a laptop, which also has 4 processors, I can
> execute 4 programs. Also, when I had NONMEM6, I did not have
> this problem on the same machine.
> Do you familiar with this problem? Thanks.
> Pavel
>
Pavel,
The message you describe is usually the result of not having enough
memory available for the NONMEM 7 memory image. If you are using the
"big" version of SIZES you may need about 1.6-2 GB of available memory
for each job. For the efficient use of NONMEM 7's new methods more
variables are now stored in memory than was the case for NONMEM VI. The
memory image is larger even if one is not using the new methods.
When using NONMEM 7 and the "reg" SIZES, I have been able to run 8 jobs
simultaneously on a dual processor dual core machine, but only 3-4 jobs
when using the "big" version of SIZES depending upon what else is
running. I have 3 GB of memory and the task manager indicates a maximum
of about 7.4 GB via paging.
Tom
Thomas M. Ludden Ph.D.
Vice-President, Pharmacometrics R&D
ICON Development Solutions
Tel: + 1 410 696 3040
Mob: + 1 410 258 2411
Fax: + 1 410 480 0776
Email: [email protected]
Web: www.icondevsolutions.com
http://emailsignature/stationary/Icon_Development_Solutions.gif
Quoted reply history
________________________________
From: [email protected] [mailto:[email protected]]
On Behalf Of [email protected]
Sent: Friday, October 16, 2009 2:02 PM
To: [email protected]
Cc: [email protected]
Subject: [NMusers] The system cannot execute the specified program
> Hello NONMEM Users,
> We have a computer with 4 processors. When I try to run more
> than 3 NONMEM7 jobs, I am getting the following message:
> Starting nonmem execution ...
> The system cannot execute the specified program.
> KP9022.OUT
> newline
> 1 file(s) copied.
> Could Not Find H:\4\output
>
> The message is code and directory independent. It always
> appears when I try to run more than 3 codes. When I test
> nonmem7 using a laptop, which also has 4 processors, I can
> execute 4 programs. Also, when I had NONMEM6, I did not have
> this problem on the same machine.
> Do you familiar with this problem? Thanks.
> Pavel
>
For 32 bit Windows systems with 4GB of RAM then only 2GB of RAM is
accessible to applications. The other 2 GB is taken by the Windows
Kernel. It is possible to give more RAM to applications using the
boot.ini /3GB switch but this is only effective if the applications (eg.
NONMEM) are specifically enabled to take advantage of this:
"Executables that can use the 3-GB address space are required to have
the bit IMAGE_FILE_LARGE_ADDRESS_AWARE set in their image header. To set
this bit, you must use Microsoft Visual Studio Version 6.0 or later and
the Editbin.exe utility, which has the ability to modify the image
header (/LARGEADDRESSAWARE) flag."
http://www.microsoft.com/whdc/system/platform/server/PAE/PAEmem.mspx
It should be possible to run editbin after you have created a NONMEM.exe
but before you run it. This might allow more NONMEM runs to work on the
same machine. But I cannot find a clear statement that LAA is helpful to
run several instances of an application or if it only helps for one
instance.
http://bilbroblog.com/wow64/hidden-secrets-of-w0w64-ndash-large-address-space/
My limited comparisons of NONMEM 6 and NONMEM 7 indicate that NONMEM 7
is usually slower and may take a lot more RAM. So unless you really need
to use a NONMEM 7 feature you will get more work done using NONMEM 6.
Nick
Leonid Gibiansky wrote:
> > You may need to increase your RAM to 6GB to solve this problem.
>
> but keep in mind that on a 32-bit Windows machine it makes no sense to
> go beyond 4 GB (computer will not be able to work with it any way).
> Leonid
>
> --------------------------------------
> Leonid Gibiansky, Ph.D.
> President, QuantPharm LLC
> web: www.quantpharm.com
> e-mail: LGibiansky at quantpharm.com
> tel: (301) 767 5566
>
>
>
>
> Sam Liao wrote:
>> According to ICON, this is due to the size of the RAM on your PC. If
>> you have less than 3 GB of RAM and running the big nm7 job, it will
>> not allow you to run more than 2 jobs at once. You may need to
>> increase your RAM to 6GB to solve this problem.
>>
>>
>>
>> Best regards,
>>
>> Sam Liao
>>
>> Pharmax Research
>>
>>
>>
>> *From:* owner-nmusers
>> [mailto:owner-nmusers
>> *nonmem
>> *Sent:* Friday, October 16, 2009 2:02 PM
>> *To:* nonmem
>> *Cc:* nmusers
>> *Subject:* [NMusers] The system cannot execute the specified program
>>
>>
>>
>> > Hello NONMEM Users,
>> > We have a computer with 4 processors. When I try to run more
>> > than 3 NONMEM7 jobs, I am getting the following message:
>> > Starting nonmem execution ...
>> > The system cannot execute the specified program.
>> > KP9022.OUT
>> > newline
>> > 1 file(s) copied.
>> > Could Not Find H:\4\output
>> >
>> > The message is code and directory independent. It always
>> > appears when I try to run more than 3 codes. When I test
>> > nonmem7 using a laptop, which also has 4 processors, I can
>> > execute 4 programs. Also, when I had NONMEM6, I did not have
>> > this problem on the same machine.
>> > Do you familiar with this problem? Thanks.
>> > Pavel
>> >
>>
--
Nick Holford, Professor Clinical Pharmacology
Dept Pharmacology & Clinical Pharmacology
University of Auckland, 85 Park Rd, Private Bag 92019, Auckland, New Zealand
n.holford
mobile: +64 21 46 23 53
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
For 32 bit Windows systems with 4GB of RAM then only 2GB of RAM is accessible to applications. The other 2 GB is taken by the Windows Kernel. It is possible to give more RAM to applications using the boot.ini /3GB switch but this is only effective if the applications (eg. NONMEM) are specifically enabled to take advantage of this:
"Executables that can use the 3-GB address space are required to have the bit IMAGE_FILE_LARGE_ADDRESS_AWARE set in their image header. To set this bit, you must use Microsoft Visual Studio Version 6.0 or later and the Editbin.exe utility, which has the ability to modify the image header (/LARGEADDRESSAWARE) flag."
http://www.microsoft.com/whdc/system/platform/server/PAE/PAEmem.mspx
It should be possible to run editbin after you have created a NONMEM.exe but before you run it. This might allow more NONMEM runs to work on the same machine. But I cannot find a clear statement that LAA is helpful to run several instances of an application or if it only helps for one instance.
http://bilbroblog.com/wow64/hidden-secrets-of-w0w64-ndash-large-address-space/
My limited comparisons of NONMEM 6 and NONMEM 7 indicate that NONMEM 7 is usually slower and may take a lot more RAM. So unless you really need to use a NONMEM 7 feature you will get more work done using NONMEM 6.
Nick
Leonid Gibiansky wrote:
> > You may need to increase your RAM to 6GB to solve this problem.
>
> but keep in mind that on a 32-bit Windows machine it makes no sense to go beyond 4 GB (computer will not be able to work with it any way).
>
> Leonid
>
> --------------------------------------
> Leonid Gibiansky, Ph.D.
> President, QuantPharm LLC
> web: www.quantpharm.com
> e-mail: LGibiansky at quantpharm.com
> tel: (301) 767 5566
>
> Sam Liao wrote:
>
> > According to ICON, this is due to the size of the RAM on your PC. If you have less than 3 GB of RAM and running the ‘big’ nm7 job, it will not allow you to run more than 2 jobs at once. You may need to increase your RAM to 6GB to solve this problem.
> >
> > Best regards,
> >
> > Sam Liao
> >
> > Pharmax Research
> >
> > *From:* [email protected] [ mailto: [email protected] ] *On Behalf Of * [email protected]
> >
> > *Sent:* Friday, October 16, 2009 2:02 PM
> > *To:* [email protected]
> > *Cc:* [email protected]
> > *Subject:* [NMusers] The system cannot execute the specified program
> >
> > > Hello NONMEM Users,
> > > We have a computer with 4 processors. When I try to run more
> > > than 3 NONMEM7 jobs, I am getting the following message:
> > > Starting nonmem execution ...
> > > The system cannot execute the specified program.
> > > KP9022.OUT
> > > newline
> > > 1 file(s) copied.
> > > Could Not Find H:\4\output
> > >
> > > The message is code and directory independent. It always
> > > appears when I try to run more than 3 codes. When I test
> > > nonmem7 using a laptop, which also has 4 processors, I can
> > > execute 4 programs. Also, when I had NONMEM6, I did not have
> > > this problem on the same machine.
> > > Do you familiar with this problem? Thanks.
> > > Pavel
> > >
--
Nick Holford, Professor Clinical Pharmacology
Dept Pharmacology & Clinical Pharmacology
University of Auckland, 85 Park Rd, Private Bag 92019, Auckland, New Zealand
[email protected] tel:+64(9)923-6730 fax:+64(9)373-7090
mobile: +64 21 46 23 53
http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
Hello Everyone,
Thenk you for your help. It sounds about right. I have difficulties with
32-bit server (4 processors, Total Physical Memory 3,327.30 MB, Available
Physical Memory 2.68 GB, Total Virtual Memory 6.73 GB, Available Virtual Memory
839.90 MB) and do not have problems with 64-bit laptop (4 processors, 8GB ram).
It looks like the execution slows down a little when I use more than 3
processors, but othervise evetrything is fine. I guess it is a good time to
switch to 64-bit computers.
Thanks,
Pavel
Quoted reply history
----- Original Message -----
From: Nick Holford
Date: Friday, October 16, 2009 11:55 pm
Subject: Re: [NMusers] The system cannot execute the specified program
To: nmusers
> For 32 bit Windows systems with 4GB of RAM then only 2GB of RAM
> is
> accessible to applications. The other 2 GB is taken by the
> Windows
> Kernel. It is possible to give more RAM to applications using
> the
> boot.ini /3GB switch but this is only effective if the
> applications (eg.
> NONMEM) are specifically enabled to take advantage of this:
>
> "Executables that can use the 3-GB address space are required to
> have
> the bit IMAGE_FILE_LARGE_ADDRESS_AWARE set in their image
> header. To set
> this bit, you must use Microsoft Visual Studio Version 6.0 or
> later and
> the Editbin.exe utility, which has the ability to modify the
> image
> header (/LARGEADDRESSAWARE) flag."
>
> http://www.microsoft.com/whdc/system/platform/server/PAE/PAEmem.mspx
>
> It should be possible to run editbin after you have created a
> NONMEM.exe
> but before you run it. This might allow more NONMEM runs to work
> on the
> same machine. But I cannot find a clear statement that LAA is
> helpful to
> run several instances of an application or if it only helps for
> one
> instance.
>
> http://bilbroblog.com/wow64/hidden-secrets-of-w0w64-ndash-large-
> address-space/
>
> My limited comparisons of NONMEM 6 and NONMEM 7 indicate that
> NONMEM 7
> is usually slower and may take a lot more RAM. So unless you
> really need
> to use a NONMEM 7 feature you will get more work done using
> NONMEM 6.
>
> Nick
>
> Leonid Gibiansky wrote:
> > > You may need to increase your RAM to 6GB to solve this problem.
> >
> > but keep in mind that on a 32-bit Windows machine it makes no
> sense to
> > go beyond 4 GB (computer will not be able to work with it any way).
> > Leonid
> >
> > --------------------------------------
> > Leonid Gibiansky, Ph.D.
> > President, QuantPharm LLC
> > web: www.quantpharm.com
> > e-mail: LGibiansky at quantpharm.com
> > tel: (301) 767 5566
> >
> >
> >
> >
> > Sam Liao wrote:
> >> According to ICON, this is due to the size of the RAM on your
> PC. If
> >> you have less than 3 GB of RAM and running the ‘big’ nm7 job,
> it will
> >> not allow you to run more than 2 jobs at once. You may need
> to
> >> increase your RAM to 6GB to solve this problem.
> >>
> >>
> >>
> >> Best regards,
> >>
> >> Sam Liao
> >>
> >> Pharmax Research
> >>
> >>
> >>
> >> *From:* [email protected]
> >> [mailto:[email protected]] *On Behalf Of
> >> *[email protected]
> >> *Sent:* Friday, October 16, 2009 2:02 PM
> >> *To:* [email protected]
> >> *Cc:* [email protected]
> >> *Subject:* [NMusers] The system cannot execute the specified
> program>>
> >>
> >>
> >> > Hello NONMEM Users,
> >> > We have a computer with 4 processors. When I try to run more
> >> > than 3 NONMEM7 jobs, I am getting the following message:
> >> > Starting nonmem execution ...
> >> > The system cannot execute the specified program.
> >> > KP9022.OUT
> >> > newline
> >> > 1 file(s) copied.
> >> > Could Not Find H:\4\output
> >> >
> >> > The message is code and directory independent. It always
> >> > appears when I try to run more than 3 codes. When I test
> >> > nonmem7 using a laptop, which also has 4 processors, I can
> >> > execute 4 programs. Also, when I had NONMEM6, I did not have
> >> > this problem on the same machine.
> >> > Do you familiar with this problem? Thanks.
> >> > Pavel
> >> >
> >>
>
> --
> Nick Holford, Professor Clinical Pharmacology
> Dept Pharmacology & Clinical Pharmacology
> University of Auckland, 85 Park Rd, Private Bag 92019, Auckland,
> New Zealand
> [email protected] tel:+64(9)923-6730 fax:+64(9)373-7090
> mobile: +64 21 46 23 53
> http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford
>
>
Dear Tom,
Dear All,
For those of us who prefer project specific NONMEM installations to save estimation time,
it might be helpful, if ICON can provide some rough guidance on the main contributor
to the RAM needs of NONMEM 7.
I.e. is it primarily the number of observations, compartments, thetas, omegas, or
another variable or some function of these variables?
The following might be very cumbersome: Would it be possible to include a switch
during the installation which disables certain NONMEM 7 features to save RAM.
(I recognize that this might cause a lot of unpredictable software issues.)
Dual CPU servers currently have around 8-18 RAM slots. 2 and 4 GB RAM chips are
reasonably priced. Thus, on the 64-bit server side, this is probably a minor issue.
Best wishes
Juergen
Quoted reply history
From: owner-nmusers
Behalf Of Ludden, Thomas
Sent: Friday, October 16, 2009 3:14 PM
To: nonmem
Cc: nmusers
Subject: RE: [NMusers] The system cannot execute the specified program
Pavel,
The message you describe is usually the result of not having enough memory available for the NONMEM 7 memory image. If you are using the "big" version of SIZES you may need about 1.6-2 GB of available memory for each job. For the efficient use of NONMEM 7's new methods more variables are now stored in memory than was the case for NONMEM VI. The memory image is larger even if one is not using the new methods.
When using NONMEM 7 and the "reg" SIZES, I have been able to run 8 jobs simultaneously on a dual processor dual core machine, but only 3-4 jobs when using the "big" version of SIZES depending upon what else is running. I have 3 GB of memory and the task manager indicates a maximum of about 7.4 GB via paging.
Tom
Thomas M. Ludden Ph.D.
Vice-President, Pharmacometrics R&D
ICON Development Solutions
Tel: + 1 410 696 3040
Mob: + 1 410 258 2411
Fax: + 1 410 480 0776
Email: thomas.ludden
Web: www.icondevsolutions.com
[cid:image001.jpg
________________________________
From: owner-nmusers
Behalf Of nonmem
Sent: Friday, October 16, 2009 2:02 PM
To: nonmem
Cc: nmusers
Subject: [NMusers] The system cannot execute the specified program
> Hello NONMEM Users,
> We have a computer with 4 processors. When I try to run more
> than 3 NONMEM7 jobs, I am getting the following message:
> Starting nonmem execution ...
> The system cannot execute the specified program.
> KP9022.OUT
> newline
> 1 file(s) copied.
> Could Not Find H:\4\output
>
> The message is code and directory independent. It always
> appears when I try to run more than 3 codes. When I test
> nonmem7 using a laptop, which also has 4 processors, I can
> execute 4 programs. Also, when I had NONMEM6, I did not have
> this problem on the same machine.
> Do you familiar with this problem? Thanks.
> Pavel
>
Dear Tom,
Dear All,
For those of us who prefer project specific NONMEM installations to save
estimation time,
it might be helpful, if ICON can provide some rough guidance on the main
contributor
to the RAM needs of NONMEM 7.
I.e. is it primarily the number of observations, compartments, thetas, omegas,
or
another variable or some function of these variables?
The following might be very cumbersome: Would it be possible to include a switch
during the installation which disables certain NONMEM 7 features to save RAM.
(I recognize that this might cause a lot of unpredictable software issues.)
Dual CPU servers currently have around 8-18 RAM slots. 2 and 4 GB RAM chips are
reasonably priced. Thus, on the 64-bit server side, this is probably a minor
issue.
Best wishes
Juergen
Quoted reply history
From: [email protected] [mailto:[email protected]] On
Behalf Of Ludden, Thomas
Sent: Friday, October 16, 2009 3:14 PM
To: [email protected]
Cc: [email protected]
Subject: RE: [NMusers] The system cannot execute the specified program
Pavel,
The message you describe is usually the result of not having enough memory
available for the NONMEM 7 memory image. If you are using the "big" version of
SIZES you may need about 1.6-2 GB of available memory for each job. For the
efficient use of NONMEM 7's new methods more variables are now stored in
memory than was the case for NONMEM VI. The memory image is larger even if one
is not using the new methods.
When using NONMEM 7 and the "reg" SIZES, I have been able to run 8 jobs
simultaneously on a dual processor dual core machine, but only 3-4 jobs when
using the "big" version of SIZES depending upon what else is running. I have 3
GB of memory and the task manager indicates a maximum of about 7.4 GB via
paging.
Tom
Thomas M. Ludden Ph.D.
Vice-President, Pharmacometrics R&D
ICON Development Solutions
Tel: + 1 410 696 3040
Mob: + 1 410 258 2411
Fax: + 1 410 480 0776
Email: [email protected]<mailto:[email protected]>
Web: www.icondevsolutions.com
[cid:[email protected]]
________________________________
From: [email protected] [mailto:[email protected]] On
Behalf Of [email protected]
Sent: Friday, October 16, 2009 2:02 PM
To: [email protected]
Cc: [email protected]
Subject: [NMusers] The system cannot execute the specified program
> Hello NONMEM Users,
> We have a computer with 4 processors. When I try to run more
> than 3 NONMEM7 jobs, I am getting the following message:
> Starting nonmem execution ...
> The system cannot execute the specified program.
> KP9022.OUT
> newline
> 1 file(s) copied.
> Could Not Find H:\4\output
>
> The message is code and directory independent. It always
> appears when I try to run more than 3 codes. When I test
> nonmem7 using a laptop, which also has 4 processors, I can
> execute 4 programs. Also, when I had NONMEM6, I did not have
> this problem on the same machine.
> Do you familiar with this problem? Thanks.
> Pavel
>
Juergen,
I'd be interested to know of your experience of how much estimation
time you save by making project specific installations. Given that you
must take additional time to setup SIZES and recompile NONMEM for each
project (say 10-15 minutes) how much time do you save per run compared
with having regular and big installations of NONMEM?
Nick
Jurgen Bulitta wrote:
Dear
Tom,
Dear
All,
For
those of us who prefer project specific NONMEM installations to save
estimation
time,
it
might be helpful, if ICON can provide some rough guidance on the main
contributor
to
the RAM needs of NONMEM 7.
I.e.
is it primarily the number of observations, compartments, thetas,
omegas, or
another
variable or some function of these variables?
The
following might be very cumbersome: Would it be possible to include a
switch
during
the installation which disables certain NONMEM 7 features to save RAM.
(I
recognize that this might cause a lot of unpredictable software issues.)
Dual
CPU servers currently have around 8-18 RAM slots. 2 and 4 GB RAM chips
are
reasonably
priced. Thus, on the 64-bit server side, this is probably a minor issue.
Best
wishes
Juergen
Quoted reply history
From:
[email protected] [ mailto: [email protected] ] On
Behalf
Of Ludden, Thomas
Sent: Friday, October 16, 2009 3:14 PM
To: [email protected]
Cc: [email protected]
Subject: RE: [NMusers] The system cannot execute the specified
program
Pavel,
The
message you describe is usually the result of not having enough
memory available for the NONMEM 7 memory image. If you are using the
"big" version of SIZES you may need about 1.6-2 GB of
available memory for each job. For the efficient use
of NONMEM 7's new methods more variables are now stored in
memory than was the case for NONMEM VI. The memory image is larger
even
if one is not using the new methods.
When
using NONMEM 7 and the "reg" SIZES, I have been able
to run 8 jobs simultaneously on a dual processor dual core machine, but
only
3-4 jobs when using the "big" version of SIZES depending upon what
else is running. I have 3 GB of memory and the task manager indicates
a
maximum of about 7.4 GB via paging.
Tom
Thomas
M. Ludden Ph.D .
Vice-President,
Pharmacometrics
R&D
ICON
Development
Solutions
Tel:
+ 1
410 696 3040
Mob: + 1 410 258 2411
Fax: + 1 410
480 0776
Email: [email protected]
Web:
www.icondevsolutions.com
From:
[email protected]
[ mailto: [email protected] ] On Behalf Of [email protected]
Sent: Friday, October 16, 2009 2:02 PM
To: [email protected]
Cc: [email protected]
Subject: [NMusers] The system cannot execute the specified
program
> Hello NONMEM Users,
> We have a computer with 4 processors. When I try to run more
> than 3 NONMEM7 jobs, I am getting the following message:
> Starting nonmem execution ...
> The system cannot execute the specified program.
> KP9022.OUT
> newline
> 1 file(s) copied.
> Could Not Find H:\4\output
>
> The message is code and directory independent. It always
> appears when I try to run more than 3 codes. When I test
> nonmem7 using a laptop, which also has 4 processors, I can
> execute 4 programs. Also, when I had NONMEM6, I did not have
> this problem on the same machine.
> Do you familiar with this problem? Thanks.
> Pavel
>
Based on limited experience with the sizing of variables in SIZES for
NONMEM 7.1.0, some known determinants of memory usage are the maximum
number of observations per individual, NO, the maximum number of
individuals, MAXIDS, and the maximum number of estimated parameters,
LPAR. The dimensions of many arrays are determined by these values.
There are likely to be other important determinants as well.
For the "reg" version of SIZES:
NO: 250
MAXIDS: 10000
LPAR: 70
For the "big" version:
NO: 500
MAXIDS: 15000
LPAR: 195
We will do a more systematic investigation of this issue and will report
the results when they are available.
Bob Bauer is working with Nous Infosystems to explore the practicality
of allocating memory for selected variables at the beginning of a
problem based on the specific needs of the problem. A future version
may incorporate this capability.
Tom
Thomas M. Ludden Ph.D.
Vice-President, Pharmacometrics R&D
ICON Development Solutions
Tel: + 1 410 696 3040
Mob: + 1 410 258 2411
Fax: + 1 410 480 0776
Email: [email protected]
Web: www.icondevsolutions.com
http://emailsignature/stationary/Icon_Development_Solutions.gif
Quoted reply history
________________________________
From: Jurgen Bulitta [mailto:[email protected]]
Sent: Saturday, October 17, 2009 10:59 PM
To: Ludden, Thomas; [email protected]
Cc: [email protected]
Subject: RE: [NMusers] The system cannot execute the specified program
Dear Tom,
Dear All,
For those of us who prefer project specific NONMEM installations to save
estimation time,
it might be helpful, if ICON can provide some rough guidance on the main
contributor
to the RAM needs of NONMEM 7.
I.e. is it primarily the number of observations, compartments, thetas,
omegas, or
another variable or some function of these variables?
The following might be very cumbersome: Would it be possible to include
a switch
during the installation which disables certain NONMEM 7 features to save
RAM.
(I recognize that this might cause a lot of unpredictable software
issues.)
Dual CPU servers currently have around 8-18 RAM slots. 2 and 4 GB RAM
chips are
reasonably priced. Thus, on the 64-bit server side, this is probably a
minor issue.
Best wishes
Juergen
From: [email protected] [mailto:[email protected]]
On Behalf Of Ludden, Thomas
Sent: Friday, October 16, 2009 3:14 PM
To: [email protected]
Cc: [email protected]
Subject: RE: [NMusers] The system cannot execute the specified program
Pavel,
The message you describe is usually the result of not having enough
memory available for the NONMEM 7 memory image. If you are using the
"big" version of SIZES you may need about 1.6-2 GB of available memory
for each job. For the efficient use of NONMEM 7's new methods more
variables are now stored in memory than was the case for NONMEM VI. The
memory image is larger even if one is not using the new methods.
When using NONMEM 7 and the "reg" SIZES, I have been able to run 8 jobs
simultaneously on a dual processor dual core machine, but only 3-4 jobs
when using the "big" version of SIZES depending upon what else is
running. I have 3 GB of memory and the task manager indicates a maximum
of about 7.4 GB via paging.
Tom
Thomas M. Ludden Ph.D.
Vice-President, Pharmacometrics R&D
ICON Development Solutions
Tel: + 1 410 696 3040
Mob: + 1 410 258 2411
Fax: + 1 410 480 0776
Email: [email protected]
Web: www.icondevsolutions.com
________________________________
From: [email protected] [mailto:[email protected]]
On Behalf Of [email protected]
Sent: Friday, October 16, 2009 2:02 PM
To: [email protected]
Cc: [email protected]
Subject: [NMusers] The system cannot execute the specified program
> Hello NONMEM Users,
> We have a computer with 4 processors. When I try to run more
> than 3 NONMEM7 jobs, I am getting the following message:
> Starting nonmem execution ...
> The system cannot execute the specified program.
> KP9022.OUT
> newline
> 1 file(s) copied.
> Could Not Find H:\4\output
>
> The message is code and directory independent. It always
> appears when I try to run more than 3 codes. When I test
> nonmem7 using a laptop, which also has 4 processors, I can
> execute 4 programs. Also, when I had NONMEM6, I did not have
> this problem on the same machine.
> Do you familiar with this problem? Thanks.
> Pavel
>
Tom,
The SIZES for 'big' NM7 show that the max number of THETA is 70, max
number of ETA+EPS is 70 and LPAR is 195. Can you explain why LPAR is
195 and not simply the sum of LTH + LVR? Is this to allow for
estimation of off-diagonal elements of OMEGA and SIGMA?
Can you confirm that one can set LTH and LVR to values greater than 70
to accommodate problems with more parameters?
Nick
! LTH: MAX. NO. OF
THETA'S
! IF LTH IS CHANGED, ALSO RECOMPILE PREDPP, NM-TRAN, NM-TRAN LIBRARY
PARAMETER (LTH=70) ! TL 4/22/09
! LVR: MAX. NO. OF ETA'S + EPS'S
! IF LVR IS CHANGED, ALSO RECOMPILE PREDPP, NM-TRAN, NM-TRAN LIBRARY
PARAMETER (LVR=70) ! TL 4/22/09
! LVR2: MAX. NO. OF ETA'S PERMITTED WHEN LAPLACIAN METHOD IS USED
! IF LVR2 IS CHANGED, ALSO RECOMPILE NMTRAN
PARAMETER (LVR2=70) ! TL 4/22/09
! LPAR: MAX. NO. OF PARAMETERS THAT MAY BE ESTIMATED
PARAMETER (LVRM=MAX(LVR,LVR2)) ! Bauer
! PARAMETER (LPAR=LTH+((LVRM+1)*LVRM)/2)
PARAMETER (LPAR=195) ! TL 4/22/09
Ludden, Thomas wrote:
Based on limited experience
with the sizing of variables in SIZES for NONMEM 7.1.0, some known
determinants of memory usage are the maximum number of observations per
individual, NO, the maximum number of individuals, MAXIDS, and
the maximum number of estimated parameters, LPAR. The dimensions of
many arrays are determined by these values. There are likely to be
other important determinants as well.
For the "reg" version of
SIZES:
NO: 250
MAXIDS: 10000
LPAR: 70
For the "big" version:
NO: 500
MAXIDS: 15000
LPAR: 195
We will do a more systematic
investigation of this issue and will report the results when they are
available.
Bob Bauer is working with
Nous Infosystems to explore the practicality of allocating memory
for selected variables at the beginning of a problem based on the
specific needs of the problem. A future version may incorporate this
capability.
Tom
Thomas
M. Ludden Ph.D .
Vice-President, Pharmacometrics R&D
ICON Development Solutions
Tel:
+ 1 410 696 3040
Mob: + 1 410
258 2411
Fax: +
1 410 480 0776
Email: [email protected]
Web:
www.icondevsolutions.com
Quoted reply history
From: Jurgen
Bulitta [ mailto: [email protected] ]
Sent: Saturday, October 17, 2009 10:59 PM
To: Ludden, Thomas; [email protected]
Cc: [email protected]
Subject: RE: [NMusers] The system cannot execute the specified
program
Dear
Tom,
Dear
All,
For
those of us who prefer project specific NONMEM installations to save
estimation time,
it
might be helpful, if ICON can provide some rough guidance on the main
contributor
to
the RAM needs of NONMEM 7.
I.e.
is it primarily the number of observations, compartments, thetas,
omegas, or
another
variable or some function of these variables?
The
following might be very cumbersome: Would it be possible to include a
switch
during
the installation which disables certain NONMEM 7 features to save RAM.
(I
recognize that this might cause a lot of unpredictable software issues.)
Dual
CPU servers currently have around 8-18 RAM slots. 2 and 4 GB RAM chips
are
reasonably
priced. Thus, on the 64-bit server side, this is probably a minor issue.
Best
wishes
Juergen
From:
[email protected] [ mailto: [email protected] ] On
Behalf Of Ludden, Thomas
Sent: Friday, October 16, 2009 3:14 PM
To: [email protected]
Cc: [email protected]
Subject: RE: [NMusers] The system cannot execute the specified
program
Pavel,
The
message you describe is usually the result of not having enough memory
available for the NONMEM 7 memory image. If you are using the "big"
version of SIZES you may need about 1.6-2 GB of available memory for
each job. For the efficient use of NONMEM 7's new methods more
variables are now stored in memory than was the case for NONMEM VI.
The memory image is larger even if one is not using the new methods.
When
using NONMEM 7 and the "reg" SIZES, I have been able to run 8 jobs
simultaneously on a dual processor dual core machine, but only 3-4 jobs
when using the "big" version of SIZES depending upon what else is
running. I have 3 GB of memory and the task manager indicates a
maximum of about 7.4 GB via paging.
Tom
Thomas
M. Ludden Ph.D .
Vice-President,
Pharmacometrics R&D
ICON
Development Solutions
Tel:
+ 1 410 696 3040
Mob: + 1 410 258 2411
Fax: + 1 410
480 0776
Email: [email protected]
Web:
www.icondevsolutions.com
From:
[email protected] [ mailto: [email protected] ] On
Behalf Of [email protected]
Sent: Friday, October 16, 2009 2:02 PM
To: [email protected]
Cc: [email protected]
Subject: [NMusers] The system cannot execute the specified
program
> Hello NONMEM Users,
> We have a computer with 4 processors. When I try to run more
> than 3 NONMEM7 jobs, I am getting the following message:
> Starting nonmem execution ...
> The system cannot execute the specified program.
> KP9022.OUT
> newline
> 1 file(s) copied.
> Could Not Find H:\4\output
>
> The message is code and directory independent. It always
> appears when I try to run more than 3 codes. When I test
> nonmem7 using a laptop, which also has 4 processors, I can
> execute 4 programs. Also, when I had NONMEM6, I did not have
> this problem on the same machine.
> Do you familiar with this problem? Thanks.
> Pavel
>
Dear Nick,
Dear All,
Please find below the results of some benchmarking with a customized installation
(i.e. std installation with no. of observations and no. of compartments set to the smallest
values for the respective dataset) vs. the big installation with additionally no. of compartments
increased to 50 and no. of observations increased to 1001.
I did not test any intermediately sized installations, since the results were reasonably
surprising, at least to me.
The bottom line is that, memory use did not seem to be the bottleneck, at least not on this
test system. The benefit of the small installation was biggest for ADVAN1 and ADVAN3.
However, one will probably only notice this benefit during bootstrapping.
I would interpret these differences in the benefit of the customized installation vs. the big
installation that some parts of NONMEM are memory dependent whereas others (especially
solving of differential equations) are not. As long as NONMEM does not return a memory
overflow error and runs the job, I would not worry much about the size of the NONMEM
installation.
Best wishes
Juergen
Cases 1, 2, and 3:
Customized installation: Virtual memory size: 84 MB
BIG installation: Virtual memory size: 828 MB
(nothing else ran on the server other than this one NONMEM VI version 6.2 run)
Case 1: Linear 1-Cmt model, ADVAN1, 15 observations, 50 subjects,
100 bootstrap resplicates with nmbs (in WFN):
Customized installation finished 100 replicates
BIG installation finished 61 replicates in the same time (run on a different, but identical computer)
--> 64% advantage for the customized installation
Case 2: Linear 2-Cmt model, ADVAN3, 15 observations, 50 subjects,
100 bootstrap resplicates with nmbs (in WFN):
Customized installation finished 100 replicates
BIG installation finished 76 replicates in the same time (run on a different, but identical computer)
--> 32% advantage for the customized installation
Case 3: Linear 3-Cmt model, ADVAN11, 15 observations, 50 subjects,
100 bootstrap resplicates with nmbs (in WFN):
Customized installation finished 100 replicates
BIG installation finished 89 replicates in the same time (run on a different, but identical computer)
--> 12% advantage for the customized installation
Case 4: Population PK model, 5 compartments, ADVAN6, run as a single job
Customized installation: 131 min, peak memory use: 75 MB, virtual memory size: 86 MB
BIG installation: 140 min, peak memory use: 225 MB, virtual memory size: 724 MB
--> 7% advantage for the customized installation
Case 5: same as 4, but with overloading of my laptop by running too many programs simultaneously
--> 7% advantage for the customized installation (i.e. exactly the same benefit as in case 4)
Case 6: Population PK/PD model, ADVAN6, about 40 compartments, 15 observations, run as a single job
Customized installation: 330.77 min
BIG installation: 331.12 min
--> 0.11% advantage for the customized installation
Quoted reply history
From: owner-nmusers
Behalf Of Nick Holford
Sent: Sunday, October 18, 2009 12:04 AM
To: nmusers
Subject: Re: [NMusers] The system cannot execute the specified program
Juergen,
I'd be interested to know of your experience of how much estimation time you save by making project specific installations. Given that you must take additional time to setup SIZES and recompile NONMEM for each project (say 10-15 minutes) how much time do you save per run compared with having regular and big installations of NONMEM?
Nick
Jurgen Bulitta wrote:
Dear Tom,
Dear All,
For those of us who prefer project specific NONMEM installations to save estimation time,
it might be helpful, if ICON can provide some rough guidance on the main contributor
to the RAM needs of NONMEM 7.
I.e. is it primarily the number of observations, compartments, thetas, omegas, or
another variable or some function of these variables?
The following might be very cumbersome: Would it be possible to include a switch
during the installation which disables certain NONMEM 7 features to save RAM.
(I recognize that this might cause a lot of unpredictable software issues.)
Dual CPU servers currently have around 8-18 RAM slots. 2 and 4 GB RAM chips are
reasonably priced. Thus, on the 64-bit server side, this is probably a minor issue.
Best wishes
Juergen
From: owner-nmusers
ilto:owner-nmusers
Sent: Friday, October 16, 2009 3:14 PM
To: nonmem
Cc: nmusers
Subject: RE: [NMusers] The system cannot execute the specified program
Pavel,
The message you describe is usually the result of not having enough memory available for the NONMEM 7 memory image. If you are using the "big" version of SIZES you may need about 1.6-2 GB of available memory for each job. For the efficient use of NONMEM 7's new methods more variables are now stored in memory than was the case for NONMEM VI. The memory image is larger even if one is not using the new methods.
When using NONMEM 7 and the "reg" SIZES, I have been able to run 8 jobs simultaneously on a dual processor dual core machine, but only 3-4 jobs when using the "big" version of SIZES depending upon what else is running. I have 3 GB of memory and the task manager indicates a maximum of about 7.4 GB via paging.
Tom
Thomas M. Ludden Ph.D.
Vice-President, Pharmacometrics R&D
ICON Development Solutions
Tel: + 1 410 696 3040
Mob: + 1 410 258 2411
Fax: + 1 410 480 0776
Email: thomas.ludden
Web: http://www.icondevsolutions.com
[cid:image001.jpg
________________________________
From: owner-nmusers
ilto:owner-nmusers
:nonmem
Sent: Friday, October 16, 2009 2:02 PM
To: nonmem
Cc: nmusers
Subject: [NMusers] The system cannot execute the specified program
> Hello NONMEM Users,
> We have a computer with 4 processors. When I try to run more
> than 3 NONMEM7 jobs, I am getting the following message:
> Starting nonmem execution ...
> The system cannot execute the specified program.
> KP9022.OUT
> newline
> 1 file(s) copied.
> Could Not Find H:\4\output
>
> The message is code and directory independent. It always
> appears when I try to run more than 3 codes. When I test
> nonmem7 using a laptop, which also has 4 processors, I can
> execute 4 programs. Also, when I had NONMEM6, I did not have
> this problem on the same machine.
> Do you familiar with this problem? Thanks.
> Pavel
>
Juergen,
Thanks for these benchmark results. One thing that is missing from the
results is the actual time to do each test and the additional time for
a customized installation of figuring out what parameters are needed
for SIZES and the time to recompile the customized NONMEM. This
customization overhead should be considered when the only criterion for
success is total runtime.
Best wishes,
Nick
Jurgen Bulitta wrote:
Dear
Nick,
Dear
All,
Please
find below the results of some benchmarking with a customized
installation
(i.e.
std installation with no. of observations and no. of compartments set
to the
smallest
values
for the respective dataset) vs. the big installation with additionally
no. of
compartments
increased
to 50 and no. of observations increased to 1001.
I
did not test any intermediately sized installations, since the results
were
reasonably
surprising,
at least to me.
The
bottom line is that, memory use did not seem to be the bottleneck, at
least not
on this
test
system. The benefit of the small installation was biggest for ADVAN1
and
ADVAN3.
However,
one will probably only notice this benefit during bootstrapping.
I
would interpret these differences in the benefit of the customized
installation
vs. the big
installation
that some parts of NONMEM are memory dependent whereas others
(especially
solving
of differential equations) are not. As long as NONMEM does not return a
memory
overflow
error and runs the job, I would not worry much about the size of the
NONMEM
installation.
Best
wishes
Juergen
Cases
1, 2, and 3:
Customized
installation: Virtual memory size: 84 MB
BIG
installation: Virtual memory size: 828 MB
(nothing
else ran on the server other than this one NONMEM VI version 6.2 run)
Case
1: Linear 1-Cmt model, ADVAN1, 15 observations, 50 subjects,
100
bootstrap resplicates with nmbs (in WFN):
Customized
installation finished 100 replicates
BIG
installation finished 61 replicates in the same time (run on a
different, but
identical computer)
-->
64% advantage for the customized installation
Case
2: Linear 2-Cmt model, ADVAN3, 15 observations, 50 subjects,
100
bootstrap resplicates with nmbs (in WFN):
Customized
installation finished 100 replicates
BIG
installation finished 76 replicates in the same time (run on a
different, but
identical computer)
-->
32% advantage for the customized installation
Case
3: Linear 3-Cmt model, ADVAN11, 15 observations, 50 subjects,
100
bootstrap resplicates with nmbs (in WFN):
Customized
installation finished 100 replicates
BIG
installation finished 89 replicates in the same time (run on a
different, but
identical computer)
-->
12% advantage for the customized installation
Case
4: Population PK model, 5 compartments, ADVAN6, run as a single job
Customized
installation: 131 min, peak memory use: 75 MB, virtual memory size: 86
MB
BIG
installation: 140 min, peak memory use: 225 MB, virtual memory size:
724 MB
-->
7% advantage for the customized installation
Case
5: same as 4, but with overloading of my laptop by running too many
programs
simultaneously
-->
7% advantage for the customized installation (i.e. exactly the same
benefit as
in case 4)
Case
6: Population PK/PD model, ADVAN6, about 40 compartments, 15
observations, run
as a single job
Customized
installation: 330.77 min
BIG
installation: 331.12 min
-->
0.11% advantage for the customized installation
Quoted reply history
From:
[email protected]
[ mailto: [email protected] ] On Behalf Of Nick Holford
Sent: Sunday, October 18, 2009 12:04 AM
To: nmusers
Subject: Re: [NMusers] The system cannot execute the specified
program
Juergen,
I'd be interested to know of your experience of how much estimation
time you
save by making project specific installations. Given that you must take
additional time to setup SIZES and recompile NONMEM for each project
(say 10-15
minutes) how much time do you save per run compared with having regular
and big
installations of NONMEM?
Nick
Jurgen Bulitta wrote:
Dear
Tom,
Dear
All,
For
those of us who prefer project specific NONMEM installations to save
estimation
time,
it
might be helpful, if ICON can provide some rough guidance on the main
contributor
to
the RAM needs of NONMEM 7.
I.e.
is it primarily the number of observations, compartments, thetas,
omegas, or
another
variable or some function of these variables?
The
following might be very cumbersome: Would it be possible to include a
switch
during
the installation which disables certain NONMEM 7 features to save RAM.
(I
recognize that this might cause a lot of unpredictable software issues.)
Dual
CPU servers currently have around 8-18 RAM slots. 2 and 4 GB RAM chips
are
reasonably
priced. Thus, on the 64-bit server side, this is probably a minor issue.
Best
wishes
Juergen
From: [email protected]
[ mailto: [email protected] ]
On Behalf Of Ludden, Thomas
Sent: Friday, October 16, 2009 3:14 PM
To: [email protected]
Cc: [email protected]
Subject: RE: [NMusers] The system cannot execute the specified
program
Pavel,
The
message you describe is usually the result of not having enough
memory available for the NONMEM 7 memory image. If you are using the
"big" version of SIZES you may need about 1.6-2 GB of
available memory for each job. For the efficient use
of NONMEM 7's new methods more variables are now stored in memory
than was the case for NONMEM VI. The memory image is larger even if
one
is not using the new methods.
When
using NONMEM 7 and the "reg" SIZES, I have been able
to run 8 jobs simultaneously on a dual processor dual core machine, but
only
3-4 jobs when using the "big" version of SIZES depending upon what
else is running. I have 3 GB of memory and the task manager indicates
a
maximum of about 7.4 GB via paging.
Tom
Thomas
M. Ludden Ph.D .
Vice-President,
Pharmacometrics
R&D
ICON
Development
Solutions
Tel:
+ 1 410 696 3040
Mob: + 1 410 258 2411
Fax: + 1 410
480 0776
Email: [email protected]
Web:
www.icondevsolutions.com
From: [email protected]
[ mailto: [email protected] ]
On Behalf Of [email protected]
Sent: Friday, October 16, 2009 2:02 PM
To: [email protected]
Cc: [email protected]
Subject: [NMusers] The system cannot execute the specified
program
> Hello NONMEM Users,
> We have a computer with 4 processors. When I try to run more
> than 3 NONMEM7 jobs, I am getting the following message:
> Starting nonmem execution ...
> The system cannot execute the specified program.
> KP9022.OUT
> newline
> 1 file(s) copied.
> Could Not Find H:\4\output
>
> The message is code and directory independent. It always
> appears when I try to run more than 3 codes. When I test
> nonmem7 using a laptop, which also has 4 processors, I can
> execute 4 programs. Also, when I had NONMEM6, I did not have
> this problem on the same machine.
> Do you familiar with this problem? Thanks.
> Pavel
>