"Christoph Höger" <christoph.hoeger@tu-berlin.de> a écrit :

>Dear all,

Hi Christoph,

>
>I am currently working with the DerivativeStructure-based AD framework
>integrated into math 3.2.
>
>Calculating the n-th order partial derivatives works fine, but I am
>facing some trouble calculating the n-th order total derivative of a
>MultivariateVectorFunction.
>
>My Idea was to have a class Derivative (implementing
>MultivariateVectorFunction) that delegates to its base
>MultivariateVectorFunction and returns the first order total derivative
>of that function. Chaining many such classes should create the n-th
>order total derivative (direct creation would be an optimization).
>
>The class looks like this:
>
>public final class Derivative implements
>MultivariateDifferentiableFunction {
>
>    private final MultivariateDifferentiableFunction base;
>
>    @Override
>    public double value(double[] point) {
>        final int dim = 1 + point.length / 2;
>
>     final DerivativeStructure[] dpoint = new DerivativeStructure[dim];
>        for (int i = 0; i < dim; i++)
>            dpoint[i] = new DerivativeStructure(dim, 1, i, point[i]);
>
>        final double[] dvalue = base.value(dpoint).getAllDerivatives();
>
>        double ret = dvalue[0]; // 𝛿base/𝛿t
>
>        for (int i = 1; i < dvalue.length; i++)
>            ret = dvalue[i] * point[i + dim]; // 𝛿base/𝛿point[i] *
>                                              // dpoint[i]/dt
>
>        return ret;
>    }
>
>    @Override
>    public DerivativeStructure value(DerivativeStructure[] point)
>            throws MathIllegalArgumentException {
>       //??
>        return null;
>    }
>
>}
>
>As you can see, the Derivative takes _more_ parameters than the base
>function. Those additional parameters are the total derivatives of the
>original parameters. The first parameter is the independent variable.
>
>This function is highly regular, and I can probably just calculate the
>partial derivatives directly:
>
>The partial derivative of a parameter from 1 to (dim-1) is the second
>order partial derivative of that parameter in base. The partial
>derivative of a parameter from dim upwards is the corresponding partial
>derivative of base.
>
>
>My problem is: What shall I do with the DerivativeStructure[] point I
>am
>handed from the outside? How to get them into the equation?

I am not sure I understood your use case properly. I'll look at it further in the next few
days.

A first very quick answer is that the interface as it is defined does not seem to correspond
to your needs.
In the current interface, the meaning of the two "value" method is the same. So the various
elements in
The point array should be the same. In your case, I think you already use the array to represent
derivatives
of the first element, so I think you expanded the content of what should be a single DerivativeStructure
instance as a double array.

Are you sure you should not use a univariate function ? The DerivativeStructure argument you
would get
would contain all the partial derivatives already.

Once again, I'm not sure I understood your example properly as I did not find the time to
think about it for now.

Best regards,
Luc

-- 
Envoyé de mon téléphone Android avec K-9 Mail. Excusez la brièveté.

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For the records: Please exchange MultivariateVectorFunction with
MultivariateDifferentiableFunction in my mail below.

Am 22.05.2013 13:52, schrieb Christoph Höger:
> Dear all,
> 
> I am currently working with the DerivativeStructure-based AD framework
> integrated into math 3.2.
> 
> Calculating the n-th order partial derivatives works fine, but I am
> facing some trouble calculating the n-th order total derivative of a
> MultivariateVectorFunction.
> 
> My Idea was to have a class Derivative (implementing
> MultivariateVectorFunction) that delegates to its base
> MultivariateVectorFunction and returns the first order total derivative
> of that function. Chaining many such classes should create the n-th
> order total derivative (direct creation would be an optimization).
> 
> The class looks like this:
> 
> public final class Derivative implements
> MultivariateDifferentiableFunction {
> 
>     private final MultivariateDifferentiableFunction base;
> 
>     @Override
>     public double value(double[] point) {
>         final int dim = 1 + point.length / 2;
> 
>         final DerivativeStructure[] dpoint = new DerivativeStructure[dim];
>         for (int i = 0; i < dim; i++)
>             dpoint[i] = new DerivativeStructure(dim, 1, i, point[i]);
> 
>         final double[] dvalue = base.value(dpoint).getAllDerivatives();
> 
>         double ret = dvalue[0]; // 𝛿base/𝛿t
> 
>         for (int i = 1; i < dvalue.length; i++)
>             ret = dvalue[i] * point[i + dim]; // 𝛿base/𝛿point[i] *
>                                               // dpoint[i]/dt
> 
>         return ret;
>     }
> 
>     @Override
>     public DerivativeStructure value(DerivativeStructure[] point)
>             throws MathIllegalArgumentException {
>        //??
>         return null;
>     }
> 
> }
> 
> As you can see, the Derivative takes _more_ parameters than the base
> function. Those additional parameters are the total derivatives of the
> original parameters. The first parameter is the independent variable.
> 
> This function is highly regular, and I can probably just calculate the
> partial derivatives directly:
> 
> The partial derivative of a parameter from 1 to (dim-1) is the second
> order partial derivative of that parameter in base. The partial
> derivative of a parameter from dim upwards is the corresponding partial
> derivative of base.
> 
> 
> My problem is: What shall I do with the DerivativeStructure[] point I am
> handed from the outside? How to get them into the equation?
> 
> 


-- 
Christoph Höger

Technische Universität Berlin
Fakultät IV - Elektrotechnik und Informatik
Übersetzerbau und Programmiersprachen

Sekr. TEL12-2, Ernst-Reuter-Platz 7, 10587 Berlin

Tel.: +49 (30) 314-24890
E-Mail: christoph.hoeger@tu-berlin.de

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Hi Thomas,

great, it works that way! Thank you very much! It is nice that I don't
have to do the derivation myself anymore! Is there any perfomance
drawback if the derivation is done internally?

Best regards,
Franz



Am Mittwoch, den 22.05.2013, 14:51 +0200 schrieb Thomas Neidhart:
> Hi Franz,
> 
> you can take a look at the following class which is used for the unit tests:
> 
> public class QuinticFunction implements UnivariateDifferentiableFunction {
> 
>     /* Evaluate quintic.
>      * @see org.apache.commons.math3.UnivariateFunction#value(double)
>      */
>     public double value(double x) {
>         return (x-1)*(x-0.5)*x*(x+0.5)*(x+1);
>     }
> 
>     public DerivativeStructure value(DerivativeStructure t) {
>         return
> t.subtract(1).multiply(t.subtract(0.5)).multiply(t).multiply(t.add(0.5)).multiply(t.add(1));
>     }
> 
> }
> 
> The DerivativeStructure provides the standard arithmetic operations which
> you can use.
> So in your case the value method would look like this imho:
> 
>     public DerivativeStructure value(DerivativeStructure t) {
>         return t.multiply(t);
>     }
> 
> This just a quick help from myside, Luc (Maisonobe) will surely give you
> more infos on how to use the DerivativeStructure.
> 
> Thomas
> 
> 
> 
> On Tue, May 21, 2013 at 4:21 PM, Franz Simons <
> franz.simons@wahyd.tu-berlin.de> wrote:
> 
> > Dear all,
> >
> > I don't understand the usage of the new DerivativeStructure in version 3
> > of the commons math.
> >
> > In the old version I had the following function, which was then used in
> > the Newton solver:
> >
> > public class MyFunction implements
> >          DifferentiableUnivariateRealFunction {
> >
> >
> >         public double value(double x) {
> >                 // example value
> >                 return x*x;
> >         }
> >
> >         public UnivariateRealFunction derivative() {
> >                 return new UnivariateRealFunction() {
> >                         public double value(double x) {
> >                                 // example derivative
> >                                 return 2.*x;
> >                         }
> >                 }
> >         }
> > }
> >
> > To use the Newton Raphson solver in version 3, I have to implement the
> > new UnivariateDifferentiableFunction interface:
> >
> > public class MyFunctionNew implements
> >          UnivariateDifferentiableFunction {
> >
> >         public double value(double x) {
> >                 // example value
> >                 return x*x;
> >         }
> >
> >         public DerivativeStructure value(DerivativeStructure t) {
> >
> >                 // What do I have to do here??
> >                 // return what?
> >         }
> > }
> >
> > I don't know how to use the DerivativeStructure. What do I have to do,
> > to get the same functionality like in the the previous function? How can
> > I define the derivative of my function?
> > I tried to understand from the user guide, but it wasn't clear for me.
> >
> > It would be great if someone could give me a hint or further explanation
> > on this.
> >
> > Thank you very much in advance!
> >
> > Best regards,
> > Franz
> >
> >
> > ---------------------------------------------------------------------
> > To unsubscribe, e-mail: user-unsubscribe@commons.apache.org
> > For additional commands, e-mail: user-help@commons.apache.org
> >
> >

-- 
Dipl.-Ing. Franz Simons
Fachgebiet Wasserwirtschaft und Hydrosystemmodellierung
Chair of Water Resources Management and Modeling of Hydrosystems

Institut für Bauingenieurwesen
Technische Universität Berlin | Sekr. TIB 1-B14
Gustav-Meyer-Allee 25 | 13355 Berlin | Germany
Tel.: +49 30 314-72429 | Fax: +49 30 314-72430
franz.simons@wahyd.tu-berlin.de | www.wahyd.tu-berlin.de




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Hi Franz,

you can take a look at the following class which is used for the unit tests:

public class QuinticFunction implements UnivariateDifferentiableFunction {

    /* Evaluate quintic.
     * @see org.apache.commons.math3.UnivariateFunction#value(double)
     */
    public double value(double x) {
        return (x-1)*(x-0.5)*x*(x+0.5)*(x+1);
    }

    public DerivativeStructure value(DerivativeStructure t) {
        return
t.subtract(1).multiply(t.subtract(0.5)).multiply(t).multiply(t.add(0.5)).multiply(t.add(1));
    }

}

The DerivativeStructure provides the standard arithmetic operations which
you can use.
So in your case the value method would look like this imho:

    public DerivativeStructure value(DerivativeStructure t) {
        return t.multiply(t);
    }

This just a quick help from myside, Luc (Maisonobe) will surely give you
more infos on how to use the DerivativeStructure.

Thomas



On Tue, May 21, 2013 at 4:21 PM, Franz Simons <
franz.simons@wahyd.tu-berlin.de> wrote:

> Dear all,
>
> I don't understand the usage of the new DerivativeStructure in version 3
> of the commons math.
>
> In the old version I had the following function, which was then used in
> the Newton solver:
>
> public class MyFunction implements
>          DifferentiableUnivariateRealFunction {
>
>
>         public double value(double x) {
>                 // example value
>                 return x*x;
>         }
>
>         public UnivariateRealFunction derivative() {
>                 return new UnivariateRealFunction() {
>                         public double value(double x) {
>                                 // example derivative
>                                 return 2.*x;
>                         }
>                 }
>         }
> }
>
> To use the Newton Raphson solver in version 3, I have to implement the
> new UnivariateDifferentiableFunction interface:
>
> public class MyFunctionNew implements
>          UnivariateDifferentiableFunction {
>
>         public double value(double x) {
>                 // example value
>                 return x*x;
>         }
>
>         public DerivativeStructure value(DerivativeStructure t) {
>
>                 // What do I have to do here??
>                 // return what?
>         }
> }
>
> I don't know how to use the DerivativeStructure. What do I have to do,
> to get the same functionality like in the the previous function? How can
> I define the derivative of my function?
> I tried to understand from the user guide, but it wasn't clear for me.
>
> It would be great if someone could give me a hint or further explanation
> on this.
>
> Thank you very much in advance!
>
> Best regards,
> Franz
>
>
> ---------------------------------------------------------------------
> To unsubscribe, e-mail: user-unsubscribe@commons.apache.org
> For additional commands, e-mail: user-help@commons.apache.org
>
>

Dear all,

I am currently working with the DerivativeStructure-based AD framework
integrated into math 3.2.

Calculating the n-th order partial derivatives works fine, but I am
facing some trouble calculating the n-th order total derivative of a
MultivariateVectorFunction.

My Idea was to have a class Derivative (implementing
MultivariateVectorFunction) that delegates to its base
MultivariateVectorFunction and returns the first order total derivative
of that function. Chaining many such classes should create the n-th
order total derivative (direct creation would be an optimization).

The class looks like this:

public final class Derivative implements
MultivariateDifferentiableFunction {

    private final MultivariateDifferentiableFunction base;

    @Override
    public double value(double[] point) {
        final int dim = 1 + point.length / 2;

        final DerivativeStructure[] dpoint = new DerivativeStructure[dim];
        for (int i = 0; i < dim; i++)
            dpoint[i] = new DerivativeStructure(dim, 1, i, point[i]);

        final double[] dvalue = base.value(dpoint).getAllDerivatives();

        double ret = dvalue[0]; // 𝛿base/𝛿t

        for (int i = 1; i < dvalue.length; i++)
            ret = dvalue[i] * point[i + dim]; // 𝛿base/𝛿point[i] *
                                              // dpoint[i]/dt

        return ret;
    }

    @Override
    public DerivativeStructure value(DerivativeStructure[] point)
            throws MathIllegalArgumentException {
       //??
        return null;
    }

}

As you can see, the Derivative takes _more_ parameters than the base
function. Those additional parameters are the total derivatives of the
original parameters. The first parameter is the independent variable.

This function is highly regular, and I can probably just calculate the
partial derivatives directly:

The partial derivative of a parameter from 1 to (dim-1) is the second
order partial derivative of that parameter in base. The partial
derivative of a parameter from dim upwards is the corresponding partial
derivative of base.


My problem is: What shall I do with the DerivativeStructure[] point I am
handed from the outside? How to get them into the equation?


-- 
Christoph Höger

Technische Universität Berlin
Fakultät IV - Elektrotechnik und Informatik
Übersetzerbau und Programmiersprachen

Sekr. TEL12-2, Ernst-Reuter-Platz 7, 10587 Berlin

Tel.: +49 (30) 314-24890
E-Mail: christoph.hoeger@tu-berlin.de

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I'll take a look tonight. It would speed things up for you if attached
a patch with a unit test that reproduces the problem.

Gary

On May 21, 2013, at 16:42, Sarvesh Sakalanaga
<Sarvesh.Sakalanaga@microsoft.com> wrote:

> Hi,
>
> Is there any work around for https://issues.apache.org/jira/browse/DBCP-398? This is
stalling our production Hadoop clusters.
>
> Thanks,
> Sarvesh

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Hi,

Is there any work around for https://issues.apache.org/jira/browse/DBCP-398? This is stalling
our production Hadoop clusters.

Thanks,
Sarvesh

Hello.

The Apache Commons team is pleased to announce the release of
commons-logging-1.1.3.

Commons Logging is a thin adapter allowing configurable bridging to
other, well known logging systems.

Source and binary distributions are available for download
from the Apache Commons download site:

http://commons.apache.org/proper/commons-logging/download_logging.cgi

For information on Commons Logging, please visit our website:

http://commons.apache.org/logging/

Details of the changes and bug fixes in this release can be found in the
release notes or change-report:

http://www.apache.org/dist/commons/logging/RELEASE-NOTES.txt
http://commons.apache.org/proper/commons-logging/changes-report.html

This release only changes the Bundle-SymbolicName in the manifest to
"org.apache.commons.logging" to simplify the packaging for certain
distributions.

Best regards,

Thomas, on behalf of the Apache Commons community

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Dear all,

I don't understand the usage of the new DerivativeStructure in version 3
of the commons math. 

In the old version I had the following function, which was then used in
the Newton solver:

public class MyFunction implements
         DifferentiableUnivariateRealFunction {


	public double value(double x) {
		// example value
		return x*x;
	}

	public UnivariateRealFunction derivative() {
        	return new UnivariateRealFunction() {          		
            		public double value(double x) {
				// example derivative	
				return 2.*x;
			}
		}
	}
}

To use the Newton Raphson solver in version 3, I have to implement the
new UnivariateDifferentiableFunction interface:

public class MyFunctionNew implements
         UnivariateDifferentiableFunction {

	public double value(double x) {
		// example value
		return x*x;
	}

	public DerivativeStructure value(DerivativeStructure t) {

		// What do I have to do here??
		// return what?
	}
}

I don't know how to use the DerivativeStructure. What do I have to do,
to get the same functionality like in the the previous function? How can
I define the derivative of my function? 
I tried to understand from the user guide, but it wasn't clear for me.

It would be great if someone could give me a hint or further explanation
on this.

Thank you very much in advance!

Best regards,
Franz


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Hi.

>
> I am, I am a seasonned java developper and I am developping some
> personal research project in DSP.
>
> I need to assess different optim methods for a familly of numerically
> differntiable functions in R^n.
> So far I implemented a few of them on my own (gradient descent,
> Newton, quasi-Newton).
>
> I just discovered that commons-maths 3.2 provide a framework for
> multivariables function. So I would be very happy to use the existing
> optim classes as is, and also, as a base for form own development.
>
> Unfortunately, neither the online dev guide, nor the the javadoc is
> sufficient to use, for instance GradientMultivariateOptimizer : it 
> has
> no specific javadoc for the key methods optimise and
> parseOptimisationData.
>
> Is there some documentation somewher to help me?

The developer's guide needs updating.

But in that page:
   
http://commons.apache.org/proper/commons-math/javadocs/api-3.2/org/apache/commons/math3/optim/nonlinear/scalar/GradientMultivariateOptimizer.html
you can follow the link to the parent class's documentation
in order to find out all the parameters used by the class.

However, before you start writing code that rely on this API,
be sure to read that recent thread:
   http://markmail.org/thread/3fjvucyz7rax4cyi
What is your opinion on the proposed change?


Regards,
Gilles


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Hello,

I am, I am a seasonned java developper and I am developping some personal research project
in DSP.

I need to assess different optim methods for a familly of numerically differntiable functions
in R^n.
So far I implemented a few of them on my own (gradient descent, Newton, quasi-Newton).

I just discovered that commons-maths 3.2 provide a framework for multivariables function.
So I would be very happy to use the existing optim classes as is, and also, as a base for
form own development.

Unfortunately, neither the online dev guide, nor the the javadoc is sufficient to use, for
instance GradientMultivariateOptimizer : it has no specific javadoc for the key methods optimise
and parseOptimisationData.

Is there some documentation somewher to help me?

thanks advance

François Laferrière

Hello,

I've successfully set up a Java application using procrun (using
Oracle Java 6 u45, on Windows 7, 64-bit), and I'd like it to enable
the JMX Attach API, as described in:
http://docs.oracle.com/javase/6/docs/technotes/guides/management/agent.html

When I run the application standalone, it just works (none of the
"com.sun.management" system properties are required), because of the
Attach API.  I could probably get things working using other
properties, such as other remote protocols using port numbers and so
on.  The advantage of the Attach API is that it's limited to the local
machine, so I don't need to worry about remote access.  So I'd like to
continue this approach, and get it working.

The Java process running as a service (as Local System, the default)
works fine.  But it's not visible to either "jps" or "jconsole".  I
*have* ensured that :
C:\Users\[USERNAME]\AppData\Local\Temp\hsperfdata_USERNAME

...is accessible to "Everyone" with "Full Control" when running as a
user.  Maybe it's because I need to locate the equivalent folder for
"Local System" ?  I'm not sure if it's that, or if it is, where to
look?

The other possibility (but for which I can't find information to
explain it or resolve it) is the perhaps "java.exe" starts the Attach
API, and so it's short-circuited by calling directly into "jvm.dll"
(as procrun does).  Or maybe a CLASSPATH error to a specific
JDK-bundled JAR file?

Any ideas ?

Thanks,
Christopher

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Hi Thomas,

Thanks for the hints.

> thanks for the sample code.
> 
> Something that may be helpful for you:
> 
> You compute the relative action frequencies for each resource and then add
> a constraint that they have to be equal to the expected probabilities for
> this action in total. This is quite a hard constraint, try to relax it like
> that:

I tried that out and it leads to the same solution, but also the runtime doesn't change.


> Another observation that I have made, the resources array does contain a
> lot of zeros, but when creating the constraint that each resource must have
> one action assigned this is not taken into account (my understanding is
> that when in the resource array the corresponding entry is 0, this action
> can not be assigned to this resource), so I added also this:
> 
>        if (resources[bucket][action] != 0.0) {
>          constraintValuesAction[currentIndex] = 1;
>        }
> 
> this means only the actions that are available for this resource are used.

This is rather a matter of data representation - the assumption that the action cannot be
assigned to a resource if the value is 0 is not true, so I cannot do this optimization.

Thanks anyway for the help and I guess I just wait for the 4.0 release to be able to get the
result after x iterations. One minor remark as I think you are part of the developing team:

The type "GoalType" is currently in the package nonlinear.scalar, but also used by linear
optimizations. Maybe its a bit cleaner to move it to the optim package. 

Cheers,

Thorsten
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Hello list,

I'd like to customise fileupload to save one file according to a specific form 
name to a specific location, and just ignore any other information in the 
request. Am I right in thinking a custom FileItemFactory is the way to do 
this? Is it easy?

I saw this page, but, well, in its current form it doesn't help much:
http://commons.apache.org/proper/commons-fileupload/customizing.html

Please CC/reply; I don't really want to join another list.

Best regards,
Diggory

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I think you need to discover why the error is occuring and fix that.
I doubt it will be possible to reuse the existing connection once an
error occurs.

However if that proves impossible the FTP protocol does support the
REST command which tells the server where to start uploading.
Obviously you have to skip the same portion of the file when you then
do the transfer.

On 8 May 2013 17:58, G E <empaingeo@hotmail.com> wrote:
> Alright, so I tried the last algorithme I sent you, and now I get this ^^ :
>
> 68 %
> java.net.SocketException: Connection reset
>     at java.net.SocketInputStream.read(SocketInputStream.java:168)
>     at sun.nio.cs.StreamDecoder$CharsetSD.readBytes(StreamDecoder.java:411)
>     at sun.nio.cs.StreamDecoder$CharsetSD.implRead(StreamDecoder.java:453)
>     at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:183)
>     at java.io.InputStreamReader.read(InputStreamReader.java:167)
>     at java.io.BufferedReader.fill(BufferedReader.java:136)
>     at java.io.BufferedReader.read(BufferedReader.java:157)
>     at org.apache.commons.net.io.CRLFLineReader.readLine(CRLFLineReader.java:58)
>     at org.apache.commons.net.ftp.FTP.__getReply(FTP.java:314)
>     at org.apache.commons.net.ftp.FTP.__getReply(FTP.java:294)
>     at org.apache.commons.net.ftp.FTP.sendCommand(FTP.java:483)
>     at org.apache.commons.net.ftp.FTP.sendCommand(FTP.java:556)
>     at org.apache.commons.net.ftp.FTP.sendCommand(FTP.java:605)
>     at org.apache.commons.net.ftp.FTP.pasv(FTP.java:956)
>     at org.apache.commons.net.ftp.FTPClient._openDataConnection_(FTPClient.java:806)
>     at org.apache.commons.net.ftp.FTPClient._storeFileStream(FTPClient.java:657)
>     at org.apache.commons.net.ftp.FTPClient.__storeFileStream(FTPClient.java:648)
>     at org.apache.commons.net.ftp.FTPClient.appendFileStream(FTPClient.java:1995)
>     at Main.startUpload(Main.java:356)
>     at Main.uploadFiles(Main.java:240)
>     at Main$2.actionPerformed(Main.java:154)
>     at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
>     at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
>     at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
>     at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
>     at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:246)
>     at java.awt.Component.processMouseEvent(Component.java:5617)
>     at javax.swing.JComponent.processMouseEvent(JComponent.java:3129)
>     at java.awt.Component.processEvent(Component.java:5382)
>     at java.awt.Container.processEvent(Container.java:2010)
>     at java.awt.Component.dispatchEventImpl(Component.java:4083)
>     at java.awt.Container.dispatchEventImpl(Container.java:2068)
>     at java.awt.Component.dispatchEvent(Component.java:3918)
>     at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
>     at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
>     at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
>     at java.awt.Container.dispatchEventImpl(Container.java:2054)
>     at java.awt.Window.dispatchEventImpl(Window.java:1801)
>     at java.awt.Component.dispatchEvent(Component.java:3918)
>     at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:501)
>     at java.awt.EventQueue.access$000(EventQueue.java:80)
>     at java.awt.EventQueue$1.run(EventQueue.java:462)
>     at java.awt.EventQueue$1.run(EventQueue.java:461)
>     at java.security.AccessController.doPrivileged(Native Method)
>     at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:84)
>     at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:95)
>     at java.awt.EventQueue$2.run(EventQueue.java:476)
>     at java.awt.EventQueue$2.run(EventQueue.java:475)
>     at java.security.AccessController.doPrivileged(Native Method)
>     at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:84)
>     at java.awt.EventQueue.dispatchEvent(EventQueue.java:473)
>     at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:269)
>     at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
>     at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)
>     at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)
>     at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>
> So it sounds like it's not the write methode that thrws the exception :/
>
> Any idea?
>
> Best regards, G. E.
>

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On 05/08/2013 07:54 PM, luca.marchetti@univr.it wrote:
> 
> Dear all,
> I would like to know if in math commons is implemented an algorithm that can be used
for cleaning a noisy time series.
> I have the following problem: in my Java application I need to run some calculations
on a set of time series of experimental data. Before applying my algorithms, I would like
to apply a suitable smoothing technique for reducing the noise in the data.
> Usually, when I work with Matlab, I solve the problem by means of the fitting toolbox
and, more specifically, by substituting the noisy time series with those obtained by applying
the Smoothing spline fitting algorithm (which is, more or less, the same of the smooth.spline
algorithm implemented in R).
> Is there something similar implemented in math commons?

Hi Luca,

to smooth the output of a stochastic linear process, you can use the
KalmanFilter implementation (see
http://commons.apache.org/proper/commons-math/userguide/filter.html).
You may need to setup your process model and define the estimated
(gaussian) noise to get good results, just ask if you need help.

There are also several (polynomial) fitters in the fitter package, which
may do what you have in mind.

Thomas

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Dear all,
I would like to know if in math commons is implemented an algorithm that can be used for cleaning
a noisy time series.
I have the following problem: in my Java application I need to run some calculations on a
set of time series of experimental data. Before applying my algorithms, I would like to apply
a suitable smoothing technique for reducing the noise in the data.
Usually, when I work with Matlab, I solve the problem by means of the fitting toolbox and,
more specifically, by substituting the noisy time series with those obtained by applying the
Smoothing spline fitting algorithm (which is, more or less, the same of the smooth.spline algorithm
implemented in R).
Is there something similar implemented in math commons?


Thank you very much for the support,


Luca

Alright, so I tried the last algorithme I sent you, and now I get this ^^ :

68 %
java.net.SocketException: Connection reset
    at java.net.SocketInputStream.read(SocketInputStream.java:168)
    at sun.nio.cs.StreamDecoder$CharsetSD.readBytes(StreamDecoder.java:411)
    at sun.nio.cs.StreamDecoder$CharsetSD.implRead(StreamDecoder.java:453)
    at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:183)
    at java.io.InputStreamReader.read(InputStreamReader.java:167)
    at java.io.BufferedReader.fill(BufferedReader.java:136)
    at java.io.BufferedReader.read(BufferedReader.java:157)
    at org.apache.commons.net.io.CRLFLineReader.readLine(CRLFLineReader.java:58)
    at org.apache.commons.net.ftp.FTP.__getReply(FTP.java:314)
    at org.apache.commons.net.ftp.FTP.__getReply(FTP.java:294)
    at org.apache.commons.net.ftp.FTP.sendCommand(FTP.java:483)
    at org.apache.commons.net.ftp.FTP.sendCommand(FTP.java:556)
    at org.apache.commons.net.ftp.FTP.sendCommand(FTP.java:605)
    at org.apache.commons.net.ftp.FTP.pasv(FTP.java:956)
    at org.apache.commons.net.ftp.FTPClient._openDataConnection_(FTPClient.java:806)
    at org.apache.commons.net.ftp.FTPClient._storeFileStream(FTPClient.java:657)
    at org.apache.commons.net.ftp.FTPClient.__storeFileStream(FTPClient.java:648)
    at org.apache.commons.net.ftp.FTPClient.appendFileStream(FTPClient.java:1995)
    at Main.startUpload(Main.java:356)
    at Main.uploadFiles(Main.java:240)
    at Main$2.actionPerformed(Main.java:154)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:246)
    at java.awt.Component.processMouseEvent(Component.java:5617)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3129)
    at java.awt.Component.processEvent(Component.java:5382)
    at java.awt.Container.processEvent(Container.java:2010)
    at java.awt.Component.dispatchEventImpl(Component.java:4083)
    at java.awt.Container.dispatchEventImpl(Container.java:2068)
    at java.awt.Component.dispatchEvent(Component.java:3918)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
    at java.awt.Container.dispatchEventImpl(Container.java:2054)
    at java.awt.Window.dispatchEventImpl(Window.java:1801)
    at java.awt.Component.dispatchEvent(Component.java:3918)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:501)
    at java.awt.EventQueue.access$000(EventQueue.java:80)
    at java.awt.EventQueue$1.run(EventQueue.java:462)
    at java.awt.EventQueue$1.run(EventQueue.java:461)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:84)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:95)
    at java.awt.EventQueue$2.run(EventQueue.java:476)
    at java.awt.EventQueue$2.run(EventQueue.java:475)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:84)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:473)
    at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:269)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)

So it sounds like it's not the write methode that thrws the exception :/

Any idea?

Best regards, G. E.
 		 	   		  

Hi and thank you for the reply. Is this what you mean : (?)

OutputStream outputStream = ftpClient.storeFileStream(remoteFile);                 
while ((read = inputStream.read(bytesIn)) != -1) {
    try {
        outputStream.write(bytesIn, 0, read);
    } catch (Exception e) {
        OutputStream os = ftpClient.appendFileStream(remoteFile);
        os.write(bytesIn, 0, read);
        os.close;
    }       
}
Best regards.

> From: mcucchiara@apache.org
> Date: Tue, 7 May 2013 12:34:07 +0200
> Subject: Re: FTPClient, resume an interrupted upload?
> To: user@commons.apache.org
> 
> Since the exception is probably thrown on outputStream.write method, you should:
> * create a new outputStream using appendFileStream method [1].
> * try to append the previously read bytesIn value
> 
> > OutputStream outputStream = ftpClient.storeFileStream(remoteFile);
> >
> >         // Transfer
> >         while ((read = inputStream.read(bytesIn)) != -1) {
> >             outputStream.write(bytesIn, 0, read);
> >             transfered += read;
> >         }
> 
> [1] http://commons.apache.org/proper/commons-net/apidocs/org/apache/commons/net/ftp/FTPClient.html#appendFileStream(java.lang.String)
> Twitter     :http://www.twitter.com/m_cucchiara
> G+          :https://plus.google.com/107903711540963855921
> Linkedin    :http://www.linkedin.com/in/mauriziocucchiara
> VisualizeMe: http://vizualize.me/maurizio.cucchiara?r=maurizio.cucchiara
> 
> Maurizio Cucchiara
> 
> ---------------------------------------------------------------------
> To unsubscribe, e-mail: user-unsubscribe@commons.apache.org
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> 
 		 	   		  

Since the exception is probably thrown on outputStream.write method, you should:
* create a new outputStream using appendFileStream method [1].
* try to append the previously read bytesIn value

> OutputStream outputStream = ftpClient.storeFileStream(remoteFile);
>
>         // Transfer
>         while ((read = inputStream.read(bytesIn)) != -1) {
>             outputStream.write(bytesIn, 0, read);
>             transfered += read;
>         }

[1] http://commons.apache.org/proper/commons-net/apidocs/org/apache/commons/net/ftp/FTPClient.html#appendFileStream(java.lang.String)
Twitter     :http://www.twitter.com/m_cucchiara
G+          :https://plus.google.com/107903711540963855921
Linkedin    :http://www.linkedin.com/in/mauriziocucchiara
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Maurizio Cucchiara

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Hello there,

thanks a lot for the reply. I set the keep alive timeout with "setControlKeepAliveTimeout(300)"
but it did not work, here is the exception thrown :
java.net.SocketException: Broken pipe
    at java.net.SocketOutputStream.socketWrite0(Native Method)
    at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:92)
    at java.net.SocketOutputStream.write(SocketOutputStream.java:136)
    at org.apache.commons.net.io.SocketOutputStream.write(SocketOutputStream.java:71)
    at Main.startUpload(Main.java:349)
    at Main.uploadFiles(Main.java:239)
    at Main$2.actionPerformed(Main.java:153)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:246)
    at java.awt.Component.processMouseEvent(Component.java:5617)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3129)
    at java.awt.Component.processEvent(Component.java:5382)
    at java.awt.Container.processEvent(Container.java:2010)
    at java.awt.Component.dispatchEventImpl(Component.java:4083)
    at java.awt.Container.dispatchEventImpl(Container.java:2068)
    at java.awt.Component.dispatchEvent(Component.java:3918)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
    at java.awt.Container.dispatchEventImpl(Container.java:2054)
    at java.awt.Window.dispatchEventImpl(Window.java:1801)
    at java.awt.Component.dispatchEvent(Component.java:3918)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:501)
    at java.awt.EventQueue.access$000(EventQueue.java:80)
    at java.awt.EventQueue$1.run(EventQueue.java:462)
    at java.awt.EventQueue$1.run(EventQueue.java:461)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:84)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:95)
    at java.awt.EventQueue$2.run(EventQueue.java:476)
    at java.awt.EventQueue$2.run(EventQueue.java:475)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:84)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:473)
    at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:269)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)

The upload always fails when I ge to either 65% or 69% of the upload.

Thanks for the support!
Best regards,
G.E.

> Date: Sun, 5 May 2013 18:10:05 +0200
> Subject: Re: FTPClient, resume an interrupted upload?
> From: mcucchiara@apache.org
> To: user@commons.apache.org
> 
> By incrementing the keep alive timeout you should fix the issue.
> Anyway the code you posted could not work:
> * the output stream doesn't append to the file (there is a method for it)
> * the exception is probably thrown on outputStream.write, so you should try
> to write again the sa me byte array

 		 	   		  

Hi Oliver,

great to get some feedback on the new re-designed trunk!

Am 05.05.2013 01:17, schrieb Oliver Kopp:
> Hi,
>
> I'm working with the trunk version of apache.commons.configuration. There,
> FileHandler allows to have passed a "FileBased" object in the constructor.
> I thought, I could implement that interface to provide an abstraction to
> the underlying file system. However, if I do it htat way, there is an
> exception "No file name has been set!". When going through the code, it
> seems that this object is the internal data storage for the configuration
> and not the external file storage.
>
> Possibly, just the header comments of this constructor should be updated.
> Like sort of saying "this constructor is for internal use only".

The purpose of FileHandler is to manage a file description in various 
formats (File, URL, file name, etc.). It can be associated with a 
FileBased object which has a read() and a write() method and thus more 
or less defines the content of the file.

The typical usage scenario is that you create a FileHandler and 
associate it with a FileBased object (all file-based configurations now 
implement this interface). Then you use some of the set() methods to 
define the file name. Finally, you can call load() to get the FileBased 
object loaded. Alternatively, you can use one of the load() methods 
expecting a parameter (again various parameter types are supported).

There is still the FileSystem class which provides an abstraction over 
concrete file operations. So this is probably the class you are after. 
(Note: I plan to move this class also into the io package. And maybe it 
can be a bit simplified.)

HTH
Oliver

>
> Cheers,
>
> Oliver
>


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By incrementing the keep alive timeout you should fix the issue.
Anyway the code you posted could not work:
* the output stream doesn't append to the file (there is a method for it)
* the exception is probably thrown on outputStream.write, so you should try
to write again the sa me byte array

Hello everyone,

I'm currently working on an App that uploads large PDFs to a server. The app works fine, but
everytime, since the PDFs are so large (25MB), the upload takes a while, and usually after
let's say 30 or 40 minutes, I get a "socketException : broken pipe". I believe that this is
due to a timeout or disconnect from the server (the server cuts the connection I guess), so
I moved the upload routine in a loop that has a try / catch. When an exception is thrown,
I try to reconnect. It works fine. The upload starts where it stopped and completes.

Problem? Well, since the upload is "broken" in two parts (or more if any other connection
loss occurs), the file uploaded is broken too! I mean that's definatley normal and I unerstand
why that happens, but what I'd like to know is how you can keep the upload on "hold" while
trying to reconnect. I just want to be able to do a complete upload even if there are reconnections.
I want my PDF to uploaded completely. Here is the code I have :

// In
inputStream = new FileInputStream(localFile); 

// For upload loop
byte[] bytesIn = new byte[4096];
int read = 0;

// Loop until job is not completed (will try to reconnect if any exception is thrown)
boolean completed = false;
while (!completed){
    try{

        // Out
        OutputStream outputStream = ftpClient.storeFileStream(remoteFile);

        // Transfer                    
        while ((read = inputStream.read(bytesIn)) != -1) {
            outputStream.write(bytesIn, 0, read);
            transfered += read;
        }

        // Closing streams
        inputStream.close();
        outputStream.close();

        // Final information
        completed = ftpClient.completePendingCommand();
        if (completed) System.out.println("Done");
        else System.out.println("Failure.");
        completed = true;

    } // end try 
    catch (Exception e) {

        // Telling the user
        System.out.println("Trying to reconnect...");
        Thread.sleep(1000);

        // Try to reconnect
        ftpClient.connect(server, port);
        success = ftpClient.login(user, pass);
        if (success) {
            System.out.println("Connection : OK");
            Thread.sleep(1000);
        } else {
            System.out.println("Failed to connect");
        }

        // Set passive mode and file type to binary
        ftpClient.enterLocalPassiveMode();
        ftpClient.setFileType(FTPClient.BINARY_FILE_TYPE);

    } // end catch
} // end loop

Any help will be greatly apreciated! Thanks to the community!

Best regards;

Geoffrey
 		 	   		  

Hi,

I'm working with the trunk version of apache.commons.configuration. There,
FileHandler allows to have passed a "FileBased" object in the constructor.
I thought, I could implement that interface to provide an abstraction to
the underlying file system. However, if I do it htat way, there is an
exception "No file name has been set!". When going through the code, it
seems that this object is the internal data storage for the configuration
and not the external file storage.

Possibly, just the header comments of this constructor should be updated.
Like sort of saying "this constructor is for internal use only".

Cheers,

Oliver

I re-opened this issue because the previous fix didn't work.  I also attached a patch to the
issue that (I believe) fixes it correctly.
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Hello Keith,

Are you looking at the latest code from trunk?

I do not see a call to createTempFile in DefaultFileReplicatorin trunk.

Gary


On Wed, May 1, 2013 at 12:36 PM, Keith Turner <keith@deenlo.com> wrote:

> I was looking at the code to see if collisions could occur and if it would
> retry in the case where collisions did occur.  It seems that collisions can
> occur, since the name is based on a random 16 bit in.  It seems like the
> code will throw an error if a collision occurs, but I am not sure.
>
> Why doesn't org.apache.commons.vfs2.impl.DefaultFileReplicator use
> File.createTempFile(String, String, File)?  I was thinking of
> subclassing DefaultFileReplicator and overriding to use
> File.createTempFile().  But I was wondering if there was an issue with this
> approach.
>



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Hi Thorsten,

thanks for the sample code.

Something that may be helpful for you:

You compute the relative action frequencies for each resource and then add
a constraint that they have to be equal to the expected probabilities for
this action in total. This is quite a hard constraint, try to relax it like
that:

    // add constraints for action frequencies
    for (int action=0; action<numberOfActions; action++) {
      constraints.add(new
LinearConstraint(coefficientActionFrequencies[action], Relationship.LEQ,
actionProbabilities[action] + 0.01));
      constraints.add(new
LinearConstraint(coefficientActionFrequencies[action], Relationship.GEQ,
actionProbabilities[action] - 0.01));
    }

Another observation that I have made, the resources array does contain a
lot of zeros, but when creating the constraint that each resource must have
one action assigned this is not taken into account (my understanding is
that when in the resource array the corresponding entry is 0, this action
can not be assigned to this resource), so I added also this:

        if (resources[bucket][action] != 0.0) {
          constraintValuesAction[currentIndex] = 1;
        }

this means only the actions that are available for this resource are used.

With these changes it runs a bit faster on my machine, but the absolute
values are of course not comparable.

Thomas



On Thu, May 2, 2013 at 8:09 PM, Thorsten Schaefer <email@thorstenschaefer.de
> wrote:

> Thanks Thomas for the information so far. It took me some time to create
> an example w/o dependencies, but here is one smaller problem which is
> self-contained:
> http://pastebin.com/7QVMMBpA
>
> Solving it on my laptop takes around 400ms, but as said, there are several
> hundred similar problems to solve and that in many iterations as the input
> (resources and payoffs) change. Note that I first solve the problem
> regularly using simplex, and then round the values to booleans to get a
> heuristic - even though it might not be conform exactly to the restrictions
> its a good enough heuristic for me; if there are faster heuristics for such
> a problem structure I'd be happy to hear them, but as far as I know Integer
> programming is considered harder in general.
> One observation I also made is: if I calculate the problem and then do it
> again with the same input value, giving the optimal solution as an initial
> guess, the runtime doesn't change at all. I suspect that the initial guess
> does not have any impacts on the simplex solver, but it might make sense to
> warn the user about it.
>
> Cheers,
>
> Thorsten
>
>
> On Apr 30, 2013, at 2:43 AM, Thomas Neidhart <thomas.neidhart@gmail.com>
> wrote:
>
> > On 04/28/2013 11:14 PM, Thorsten Schaefer wrote:
> >> Hello,
> >>
> >> I just started using common math and have a performance issue with the
> optimization algorithm, hoping to be able to speed it up in some way, even
> if this reduces the accuracy of the results.
> >>
> >> My problem is as follows:
> >> There are n resources and m actions that can be performed for each
> resource. Each combination of action/resource has a specific payoff, which
> I want to maximize. I linearized the data into rows of size (n*m). An index
> i has the semantics of resource=n/i and action=n%i. Each entry in a row
> must be non-negative, so I added a the respective constraint to the
> Optimization data. Furthermore, the sum of all actions for any resource
> needs to be 1, which are n additional constraints I have. Also, any type of
> action needs to be performed with a relative frequency of x% (additional
> constraint). And finally there are constraints for the limited number of
> resources.
> >> I used the SimplexSolver and can find a working solution within about
> half a second (the size of the problem n*m is somewhere about 2500). The
> problem is, that I need to perform the calculation very frequently and its
> currently too slow. I wonder if there is a way to restrict the number of
> iterations for example or tell the solver to return a solution even if
> there might be way better after a certain number of iterations? I tried the
> MaxIter constraint, which leads only to a TooManyIterations exception
> without being able to retrieve the result found so far. I also tried to
> initialize the solver with different epsilon values, but either it took the
> same amount of iterations (and time) or it finished with a
> NoFeasableSolutionException.
> >> So my question is if there is a way to get non-optimal solutions, but
> those quicker?
> >> If it would speed up the solution finding process, I could live with a
> solution where we restrict the possible results to booleans, i.e., an
> action for any resource is either performed never or always.
> >
> > Hi Thorsten,
> >
> > at the moment there is no way to get the best solution so far, if the
> > maximum number of iterations has been reached.
> >
> > We could add a feature like this (as already several other people have
> > requested it).
> >
> > Could you also attach your example somewhere, so I can take a look at it
> > and maybe provide some more optimization tips?
> >
> > Thanks,
> >
> > Thomas
> >
> > ---------------------------------------------------------------------
> > To unsubscribe, e-mail: user-unsubscribe@commons.apache.org
> > For additional commands, e-mail: user-help@commons.apache.org
> >
>
>

Thanks Thomas for the information so far. It took me some time to create an example w/o dependencies,
but here is one smaller problem which is self-contained:
http://pastebin.com/7QVMMBpA

Solving it on my laptop takes around 400ms, but as said, there are several hundred similar
problems to solve and that in many iterations as the input (resources and payoffs) change.
Note that I first solve the problem regularly using simplex, and then round the values to
booleans to get a heuristic - even though it might not be conform exactly to the restrictions
its a good enough heuristic for me; if there are faster heuristics for such a problem structure
I'd be happy to hear them, but as far as I know Integer programming is considered harder in
general. 
One observation I also made is: if I calculate the problem and then do it again with the same
input value, giving the optimal solution as an initial guess, the runtime doesn't change at
all. I suspect that the initial guess does not have any impacts on the simplex solver, but
it might make sense to warn the user about it.

Cheers,

Thorsten


On Apr 30, 2013, at 2:43 AM, Thomas Neidhart <thomas.neidhart@gmail.com> wrote:

> On 04/28/2013 11:14 PM, Thorsten Schaefer wrote:
>> Hello, 
>> 
>> I just started using common math and have a performance issue with the optimization
algorithm, hoping to be able to speed it up in some way, even if this reduces the accuracy
of the results.
>> 
>> My problem is as follows:
>> There are n resources and m actions that can be performed for each resource. Each
combination of action/resource has a specific payoff, which I want to maximize. I linearized
the data into rows of size (n*m). An index i has the semantics of resource=n/i and action=n%i.
Each entry in a row must be non-negative, so I added a the respective constraint to the Optimization
data. Furthermore, the sum of all actions for any resource needs to be 1, which are n additional
constraints I have. Also, any type of action needs to be performed with a relative frequency
of x% (additional constraint). And finally there are constraints for the limited number of
resources.
>> I used the SimplexSolver and can find a working solution within about half a second
(the size of the problem n*m is somewhere about 2500). The problem is, that I need to perform
the calculation very frequently and its currently too slow. I wonder if there is a way to
restrict the number of iterations for example or tell the solver to return a solution even
if there might be way better after a certain number of iterations? I tried the MaxIter constraint,
which leads only to a TooManyIterations exception without being able to retrieve the result
found so far. I also tried to initialize the solver with different epsilon values, but either
it took the same amount of iterations (and time) or it finished with a NoFeasableSolutionException.
>> So my question is if there is a way to get non-optimal solutions, but those quicker?
>> If it would speed up the solution finding process, I could live with a solution where
we restrict the possible results to booleans, i.e., an action for any resource is either performed
never or always. 
> 
> Hi Thorsten,
> 
> at the moment there is no way to get the best solution so far, if the
> maximum number of iterations has been reached.
> 
> We could add a feature like this (as already several other people have
> requested it).
> 
> Could you also attach your example somewhere, so I can take a look at it
> and maybe provide some more optimization tips?
> 
> Thanks,
> 
> Thomas
> 
> ---------------------------------------------------------------------
> To unsubscribe, e-mail: user-unsubscribe@commons.apache.org
> For additional commands, e-mail: user-help@commons.apache.org
> 

I was looking at the code to see if collisions could occur and if it would
retry in the case where collisions did occur.  It seems that collisions can
occur, since the name is based on a random 16 bit in.  It seems like the
code will throw an error if a collision occurs, but I am not sure.

Why doesn't org.apache.commons.vfs2.impl.DefaultFileReplicator use
File.createTempFile(String, String, File)?  I was thinking of
subclassing DefaultFileReplicator and overriding to use
File.createTempFile().  But I was wondering if there was an issue with this
approach.

On 04/30/2013 07:43 AM, Thomas Neidhart wrote:
> On 04/28/2013 11:14 PM, Thorsten Schaefer wrote:
>> Hello, 
>>
>> I just started using common math and have a performance issue with the optimization
algorithm, hoping to be able to speed it up in some way, even if this reduces the accuracy
of the results.
>>
>> My problem is as follows:
>> There are n resources and m actions that can be performed for each resource. Each
combination of action/resource has a specific payoff, which I want to maximize. I linearized
the data into rows of size (n*m). An index i has the semantics of resource=n/i and action=n%i.
Each entry in a row must be non-negative, so I added a the respective constraint to the Optimization
data. Furthermore, the sum of all actions for any resource needs to be 1, which are n additional
constraints I have. Also, any type of action needs to be performed with a relative frequency
of x% (additional constraint). And finally there are constraints for the limited number of
resources.
>> I used the SimplexSolver and can find a working solution within about half a second
(the size of the problem n*m is somewhere about 2500). The problem is, that I need to perform
the calculation very frequently and its currently too slow. I wonder if there is a way to
restrict the number of iterations for example or tell the solver to return a solution even
if there might be way better after a certain number of iterations? I tried the MaxIter constraint,
which leads only to a TooManyIterations exception without being able to retrieve the result
found so far. I also tried to initialize the solver with different epsilon values, but either
it took the same amount of iterations (and time) or it finished with a NoFeasableSolutionException.
>> So my question is if there is a way to get non-optimal solutions, but those quicker?
>> If it would speed up the solution finding process, I could live with a solution where
we restrict the possible results to booleans, i.e., an action for any resource is either performed
never or always. 
> 
> Hi Thorsten,
> 
> at the moment there is no way to get the best solution so far, if the
> maximum number of iterations has been reached.
> 
> We could add a feature like this (as already several other people have
> requested it).

btw. I have created an issue for this:

https://issues.apache.org/jira/browse/MATH-970

Thomas

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Hi,

I'm using the Digester Annotations and everything works pretty well
(looking forward to 3.3 for DIGESTER-174).

We have a model where we share a "contact" class and have that
annotated with an @ObjectCreate.List because it can live under
multiple different elements and a tree-like structure where the top
level element contains other elements that in turn have "contacts".

Here's a simplified version of the schema:
A(/a) has B(/a/b)
A(/a) has C(/a/c)

B has D(/a/b/d + /a/c/d)
C has D(/a/b/d + /a/c/d)

The problem now is that the AnnotationHandler processes the D element
multiple times because it's being reached through multiple branches of
the "tree", thus creating multiple instances of the ObjectCreateRule
which are all fired and obviously screw up the stack.

To me this seems like a bug and the AnnotationHandlers should check if
they have already visited an element. I'm happy to file a JIRA but I
wasn't sure if this might not be intended behavior for some reason I
don't understand yet. Also: I might be completely wrong in my
diagnosis of this problem.

Any help is greatly appreciated.

Cheers,
Lars

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On 04/30/2013 12:47 AM, John Boyer wrote:
> Hi:
>
> UPDATE:
> The UNIX error message is referring to the absolute path of the jsvc executable. When
I invoked the executable with its absolute path it worked. I assume it's the same problem
on Mac OS X.
>
> /usr/local/bin/jsvc -jvm server -debug -home /usr/lib/jvm/java-6-openjdk -cp /usr/local/bin/commons-daemon-1.0.15.jar:myjar.jar
MyDaemonClass
>
> I'm really happy it's working now.
>

Yeah. Sorry, forgot that this message is for jsvc not classpath.
You should either call ./jsvc or /absolute/path/jsvc
The reason is again security so that child does not pick up different
executable in case users and root environment PATH mismatch and both
have jsvc in PATH directories in different places.
Eg. a typical would be systems with jsvc inside /usr/sbin/ and you
wish to start your own from /foo/bar/. It would be hard to determine
which one would be called (depends on PATH)

So, just use either relative or absolute paths.
Actually we just test if the executable has '/' inside invocation
since this prevents PATH search.


Regards
-- 
^TM

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'Mornin John
 
so to recap

prepend /usr/local/bin/jsvc to $PATH
 
put "-jvm server -debug -home /usr/lib/jvm/java-6-openjdk" ON $JAVA_OPTS

prepend /usr/local/bin/commons-daemon-1.0.15.jar to $CLASSPATH
 
then automate the process with 
https://github.com/jeroenr/Maven-Jsvc-Plugin

glad you're on your way to a solution!

Martin 
______________________________________________ 
Verzicht und Vertraulichkeitanmerkung/Note de déni et de confidentialité

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Ce message est confidentiel et peut être privilégié. Si vous n'êtes pas le destinataire
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> Subject: Re: [daemon] JSVC re-exec requires execution with an absolute or relative path
> From: johnboyer99@gmail.com
> Date: Mon, 29 Apr 2013 15:47:57 -0700
> To: user@commons.apache.org
> 
> Hi:
> 
> UPDATE: 
> The UNIX error message is referring to the absolute path of the jsvc executable. When
I invoked the executable with its absolute path it worked. I assume it's the same problem
on Mac OS X.
> 
> /usr/local/bin/jsvc -jvm server -debug -home /usr/lib/jvm/java-6-openjdk -cp /usr/local/bin/commons-daemon-1.0.15.jar:myjar.jar
MyDaemonClass
> 
> I'm really happy it's working now.
> 
> Regards,
> 
> John
> 
> On Apr 29, 2013, at 9:10 AM, John Boyer <johnboyer99@gmail.com> wrote:
> 
> > UPDATE: Unfortunately, using the absolute and relative classpaths results in the
same error.
> > 
> > We haven't been able to get this to work on UNIX or Mac OS X. I think we'll need
to look at other alternatives such as the Java Service Wrapper.
> > 
> > UNIX Error: "JSVC re-exec requires execution with an absolute or relative path"
> > 
> > Mac OS X: "Cannot find daemon loader org/apache/commons/daemon/support/DaemonLoader"
> > 
> > Regards,
> > 
> > John
> > 
> > 
> > On Apr 29, 2013, at 8:46 AM, John Boyer <johnboyer99@gmail.com> wrote:
> > 
> >> Hi TM:
> >> 
> >> Thanks, I will try this. In any case, I believe if the log message mentioned
the "classpath" explicitly it would have saved me a lot of time. It's unclear what the real
object of the sentence is or what path it's referring to. Just spitting out the classpath
in the log message would've given me a clue as to what it was complaining about.
> >> 
> >> JSVC re-exec requires execution with an absolute or relative path
> >> 
> >> Thanks again,
> >> 
> >> John 
> >> 
> >> On Apr 28, 2013, at 9:42 PM, Mladen Turk <mturk@apache.org> wrote:
> >> 
> >>> On 04/28/2013 11:05 PM, John Boyer wrote:
> >>>> Hello:
> >>>> 
> >>>> I'm trying to run jsvc on Ubuntu Linux (10.04.4). I'm getting a re-exec
path error. I've sunk a lot of hours into this. I'm beginning to think I should have used
the Java Service Wrapper Community Edition instead.
> >>>> 
> >>>> Anyway, can anyone help me with this problem? Thank you for your time.
John
> >>>> 
> >>> 
> >>> Like the log says. Use either absolute or relative paths.
> >>> I presume you know what those concepts are.
> >>> 
> >>> Reason for that is security. Having just 'commons-daemon-1.0.15.jar' in
the classpath
> >>> means it can come from anywhere in the PATH.
> >>> So use
> >>> -cp ./commons-daemon-1.0.15.jar:./api-monitor.jar
> >>> (That's relative path)
> >>> or
> >>> -cp `pwd`/commons-daemon-1.0.15.jar:`pwd`/api-monitor.jar
> >>> (That's absolute path)
> >>> 
> >>> 
> >>> 
> >>> Regards
> >>> -- 
> >>> ^TM
> >>> 
> >>> ---------------------------------------------------------------------
> >>> To unsubscribe, e-mail: user-unsubscribe@commons.apache.org
> >>> For additional commands, e-mail: user-help@commons.apache.org
> >>> 
> >> 
> >> 
> >> ---------------------------------------------------------------------
> >> To unsubscribe, e-mail: user-unsubscribe@commons.apache.org
> >> For additional commands, e-mail: user-help@commons.apache.org
> >> 
> > 
> 
> 
> ---------------------------------------------------------------------
> To unsubscribe, e-mail: user-unsubscribe@commons.apache.org
> For additional commands, e-mail: user-help@commons.apache.org
> 
 		 	   		  

On 04/28/2013 11:14 PM, Thorsten Schaefer wrote:
> Hello, 
> 
> I just started using common math and have a performance issue with the optimization algorithm,
hoping to be able to speed it up in some way, even if this reduces the accuracy of the results.
> 
> My problem is as follows:
> There are n resources and m actions that can be performed for each resource. Each combination
of action/resource has a specific payoff, which I want to maximize. I linearized the data
into rows of size (n*m). An index i has the semantics of resource=n/i and action=n%i. Each
entry in a row must be non-negative, so I added a the respective constraint to the Optimization
data. Furthermore, the sum of all actions for any resource needs to be 1, which are n additional
constraints I have. Also, any type of action needs to be performed with a relative frequency
of x% (additional constraint). And finally there are constraints for the limited number of
resources.
> I used the SimplexSolver and can find a working solution within about half a second (the
size of the problem n*m is somewhere about 2500). The problem is, that I need to perform the
calculation very frequently and its currently too slow. I wonder if there is a way to restrict
the number of iterations for example or tell the solver to return a solution even if there
might be way better after a certain number of iterations? I tried the MaxIter constraint,
which leads only to a TooManyIterations exception without being able to retrieve the result
found so far. I also tried to initialize the solver with different epsilon values, but either
it took the same amount of iterations (and time) or it finished with a NoFeasableSolutionException.
> So my question is if there is a way to get non-optimal solutions, but those quicker?
> If it would speed up the solution finding process, I could live with a solution where
we restrict the possible results to booleans, i.e., an action for any resource is either performed
never or always. 

Hi Thorsten,

at the moment there is no way to get the best solution so far, if the
maximum number of iterations has been reached.

We could add a feature like this (as already several other people have
requested it).

Could you also attach your example somewhere, so I can take a look at it
and maybe provide some more optimization tips?

Thanks,

Thomas

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Hi:

UPDATE: 
The UNIX error message is referring to the absolute path of the jsvc executable. When I invoked
the executable with its absolute path it worked. I assume it's the same problem on Mac OS
X.

/usr/local/bin/jsvc -jvm server -debug -home /usr/lib/jvm/java-6-openjdk -cp /usr/local/bin/commons-daemon-1.0.15.jar:myjar.jar
MyDaemonClass

I'm really happy it's working now.

Regards,

John

On Apr 29, 2013, at 9:10 AM, John Boyer <johnboyer99@gmail.com> wrote:

> UPDATE: Unfortunately, using the absolute and relative classpaths results in the same
error.
> 
> We haven't been able to get this to work on UNIX or Mac OS X. I think we'll need to look
at other alternatives such as the Java Service Wrapper.
> 
> UNIX Error: "JSVC re-exec requires execution with an absolute or relative path"
> 
> Mac OS X: "Cannot find daemon loader org/apache/commons/daemon/support/DaemonLoader"
> 
> Regards,
> 
> John
> 
> 
> On Apr 29, 2013, at 8:46 AM, John Boyer <johnboyer99@gmail.com> wrote:
> 
>> Hi TM:
>> 
>> Thanks, I will try this. In any case, I believe if the log message mentioned the
"classpath" explicitly it would have saved me a lot of time. It's unclear what the real object
of the sentence is or what path it's referring to. Just spitting out the classpath in the
log message would've given me a clue as to what it was complaining about.
>> 
>> JSVC re-exec requires execution with an absolute or relative path
>> 
>> Thanks again,
>> 
>> John 
>> 
>> On Apr 28, 2013, at 9:42 PM, Mladen Turk <mturk@apache.org> wrote:
>> 
>>> On 04/28/2013 11:05 PM, John Boyer wrote:
>>>> Hello:
>>>> 
>>>> I'm trying to run jsvc on Ubuntu Linux (10.04.4). I'm getting a re-exec path
error. I've sunk a lot of hours into this. I'm beginning to think I should have used the Java
Service Wrapper Community Edition instead.
>>>> 
>>>> Anyway, can anyone help me with this problem? Thank you for your time. John
>>>> 
>>> 
>>> Like the log says. Use either absolute or relative paths.
>>> I presume you know what those concepts are.
>>> 
>>> Reason for that is security. Having just 'commons-daemon-1.0.15.jar' in the classpath
>>> means it can come from anywhere in the PATH.
>>> So use
>>> -cp ./commons-daemon-1.0.15.jar:./api-monitor.jar
>>> (That's relative path)
>>> or
>>> -cp `pwd`/commons-daemon-1.0.15.jar:`pwd`/api-monitor.jar
>>> (That's absolute path)
>>> 
>>> 
>>> 
>>> Regards
>>> -- 
>>> ^TM
>>> 
>>> ---------------------------------------------------------------------
>>> To unsubscribe, e-mail: user-unsubscribe@commons.apache.org
>>> For additional commands, e-mail: user-help@commons.apache.org
>>> 
>> 
>> 
>> ---------------------------------------------------------------------
>> To unsubscribe, e-mail: user-unsubscribe@commons.apache.org
>> For additional commands, e-mail: user-help@commons.apache.org
>> 
> 


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UPDATE: Unfortunately, using the absolute and relative classpaths results in the same error.

We haven't been able to get this to work on UNIX or Mac OS X. I think we'll need to look at
other alternatives such as the Java Service Wrapper.

UNIX Error: "JSVC re-exec requires execution with an absolute or relative path"

Mac OS X: "Cannot find daemon loader org/apache/commons/daemon/support/DaemonLoader"

Regards,

John


On Apr 29, 2013, at 8:46 AM, John Boyer <johnboyer99@gmail.com> wrote:

> Hi TM:
> 
> Thanks, I will try this. In any case, I believe if the log message mentioned the "classpath"
explicitly it would have saved me a lot of time. It's unclear what the real object of the
sentence is or what path it's referring to. Just spitting out the classpath in the log message
would've given me a clue as to what it was complaining about.
> 
> JSVC re-exec requires execution with an absolute or relative path
> 
> Thanks again,
> 
> John 
> 
> On Apr 28, 2013, at 9:42 PM, Mladen Turk <mturk@apache.org> wrote:
> 
>> On 04/28/2013 11:05 PM, John Boyer wrote:
>>> Hello:
>>> 
>>> I'm trying to run jsvc on Ubuntu Linux (10.04.4). I'm getting a re-exec path
error. I've sunk a lot of hours into this. I'm beginning to think I should have used the Java
Service Wrapper Community Edition instead.
>>> 
>>> Anyway, can anyone help me with this problem? Thank you for your time. John
>>> 
>> 
>> Like the log says. Use either absolute or relative paths.
>> I presume you know what those concepts are.
>> 
>> Reason for that is security. Having just 'commons-daemon-1.0.15.jar' in the classpath
>> means it can come from anywhere in the PATH.
>> So use
>> -cp ./commons-daemon-1.0.15.jar:./api-monitor.jar
>> (That's relative path)
>> or
>> -cp `pwd`/commons-daemon-1.0.15.jar:`pwd`/api-monitor.jar
>> (That's absolute path)
>> 
>> 
>> 
>> Regards
>> -- 
>> ^TM
>> 
>> ---------------------------------------------------------------------
>> To unsubscribe, e-mail: user-unsubscribe@commons.apache.org
>> For additional commands, e-mail: user-help@commons.apache.org
>> 
> 
> 
> ---------------------------------------------------------------------
> To unsubscribe, e-mail: user-unsubscribe@commons.apache.org
> For additional commands, e-mail: user-help@commons.apache.org
> 


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Hi TM:

Thanks, I will try this. In any case, I believe if the log message mentioned the "classpath"
explicitly it would have saved me a lot of time. It's unclear what the real object of the
sentence is or what path it's referring to. Just spitting out the classpath in the log message
would've given me a clue as to what it was complaining about.

JSVC re-exec requires execution with an absolute or relative path

Thanks again,

John 

On Apr 28, 2013, at 9:42 PM, Mladen Turk <mturk@apache.org> wrote:

> On 04/28/2013 11:05 PM, John Boyer wrote:
>> Hello:
>> 
>> I'm trying to run jsvc on Ubuntu Linux (10.04.4). I'm getting a re-exec path error.
I've sunk a lot of hours into this. I'm beginning to think I should have used the Java Service
Wrapper Community Edition instead.
>> 
>> Anyway, can anyone help me with this problem? Thank you for your time. John
>> 
> 
> Like the log says. Use either absolute or relative paths.
> I presume you know what those concepts are.
> 
> Reason for that is security. Having just 'commons-daemon-1.0.15.jar' in the classpath
> means it can come from anywhere in the PATH.
> So use
> -cp ./commons-daemon-1.0.15.jar:./api-monitor.jar
> (That's relative path)
> or
> -cp `pwd`/commons-daemon-1.0.15.jar:`pwd`/api-monitor.jar
> (That's absolute path)
> 
> 
> 
> Regards
> -- 
> ^TM
> 
> ---------------------------------------------------------------------
> To unsubscribe, e-mail: user-unsubscribe@commons.apache.org
> For additional commands, e-mail: user-help@commons.apache.org
> 


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>>> [...]
>>> Very hard to guess that this parameter (Bound) is not required
>>> according to the documentation.
>>
>> Excerpt from
>> 
>> http://commons.apache.org/proper/commons-math/javadocs/api-3.2/org/apache/commons/math3/optim/nonlinear/vector/jacobian/LevenbergMarquardtOptimizer.html
>>
>> "Constraints are not supported: the call to optimize will throw
>> MathUnsupportedOperationException if bounds are passed to it."
>>
>> Would you suggest a better alternative?
>
> I didn't see that. It is clear enough. But,
> my starting point was:
>
>
> 
> http://commons.apache.org/proper/commons-math///javadocs/api-3.2/org/apache/commons/math3/optim/nonlinear/vector/jacobian/LevenbergMarquardtOptimizer.html
>
> where there is no such comment (the sentence "Constraints are not
> supported:  ... " has disappeared). I dont' remember where
> I took this link on the web ...

The link is the same (and the comment is there, now; until a few days
ago it pointed to the Javadoc of release 3.1.1).

Regards,
Gilles


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Le 29 avr. 2013 à 13:31, Gilles a écrit :

> Hi.
> 
>>>> Thanks Luc for your help.
>>>> 
>>>> I modified my code as you recommend (it is given below), but it
>>>> doesn't work either.
>>>> 
>>>> The error message (at running) is :
>>>> 
>>>> Exception in thread "main"
>>>> org.apache.commons.math3.exception.MathUnsupportedOperationException: contrainte
>>>> [...]
>>>> 
>>>> It is about a contraint ...
>>> 
>>> Indeed.
>>> 
>>>> [...]
>>>> 
>>>> Do you any idea about what goes wrong ?
>>> 
>>> Yes. The "SimpleBounds" (constraint) is not a parameter of "LevenbergMarquardtOptimizer";
>>> hence an exception is thrown. Just try to remove this parameter.
>> 
>> That works !
>> Very hard to guess that this parameter (Bound) is not required
>> according to the documentation.
> 
> Excerpt from
> http://commons.apache.org/proper/commons-math/javadocs/api-3.2/org/apache/commons/math3/optim/nonlinear/vector/jacobian/LevenbergMarquardtOptimizer.html
> 
> "Constraints are not supported: the call to optimize will throw
> MathUnsupportedOperationException if bounds are passed to it."
> 
> Would you suggest a better alternative?

I didn't see that. It is clear enough. But,
my starting point was:

  http://commons.apache.org/proper/commons-math///javadocs/api-3.2/org/apache/commons/math3/optim/nonlinear/vector/jacobian/LevenbergMarquardtOptimizer.html

where there is no such comment (the sentence "Constraints are not supported:  ... " has disappeared).
I dont' remember where
I took this link on the web ...

Thanks again.
Eric




> 
>> Thank you very much Gilles.
>> I give below the code that works well.
>> Have a nice week.
> 
> Thanks,
> Gilles
> 
> 
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