On Feb 14, 2012, at 1:35 PM, Rachele Nerattini wrote:

Dear Mr Troyer,

I'm using ALPS to run MC simulations of classical Ising, XY and Heisenberg models in three dimensions. I want to study how the critical values of some observables varies with L in a regular cubic lattice so I run the simulations at T_c (critical value of the temperature).

I know that at the phase transition you have strong correlation in the system and it is difficult to obtain values of the observables with convergence on the errors. For this reasons I have the following questions:

1. Errors on the observables are given with three different levels of 'accuracy': converged (white), check the convergence (yellow), not converged (red).

How does the program test if the convergence is achieved? I mean I see the program evaluate the errors dividing the total number of steps in groups of binning and then evaluating the errors group by group. I suppose that it says that the convergence is achieved if the errors in different groups vary less then some interval that is fixed...is it true? Which is the test that it does?

The best will be if you look at the details of the binning analysis, as explained in tutorial MC-01. If the errors converge as a function of the bin size we mark it as converged, if they still increase slightly (which might just be a statistical fluctuation) mark it as yellow, and if it is clearly not converged we mark it as red. Still, to be sure you should always look at it yourself.

2. I suppose Tau is the correlation time. Does the program take into account the value of Tau in the final valuation of the errors? I mean, are those errors already multiplied by the sqrt of tau as it must be in case of correlations, or must be corrected bye the value of tau that is given?

Indeed it is multiplied by sqrt(1+2tau). Well, actually, sqrt(1+2tau) and thus tau is determined from the ratio between converged and naive error. But, to answer your question, the error indeed includes autocorrelation effects.

3. Since the correlation is strong at T_c do you think that it could be easier to get to convergence if we change the initial configuration of the MC? For example we could run a simulation for a while then take the last configuration it uses to evaluate the values of observables and then use this last configuration as the input configuration for a new run...can it be done in some way?

Yes, that could be done, it however will not help much. The time needed to equilibrate is of the same order as the autocorrelation time, and if you cannot afford to equilibrate you will also not be able to get many uncorrelated measurements.

4. Some months ago I wrote to you to ask if it could be possible to run a classical MC simulation for an O(4) model. in the tutorials you say that it can be done simply editing the spin_factory.C file. I tried but still it doesn't work. I'm afraid I made some mistakes in the installation of the ALPS library on my PC. Did you add this option in the new version 2.0?

What did not work? it should be very easy to add it. Can you tell me what you tried to do and what the problem was?

I hope this helps

Matthias Troyer

Which version of ALPS are you using? O(4) models work for me in ALPS. Can you send your full input files? In your input below the following line should not work:

BOUNDARY type="periodic"

Matthias

On Feb 14, 2012, at 5:08 PM, Rachele Nerattini wrote:

Dear Mr Troyer,

thank you very much for the quick and helpfulness answer. For what concerns the last point:

...

4. Some months ago I wrote to you to ask if it could be possible to run a classical MC simulation for an O(4) model. in the tutorials you say that it can be done simply editing the spin_factory.C file. I tried but still it doesn't work. I'm afraid I made some mistakes in the installation of the ALPS library on my PC. Did you add this option in the new version 2.0?

What did not work? it should be very easy to add it. Can you tell me what you tried to do and what the problem was?

I modified the file spinmc_factory.C adding:

else if (parms["MODEL"]=="O(4)") return new SpinSim<ONMoment<4>,MIdMatrix<double,4> >(where,parms,node);

then I open a terminal, I went into the folder

alps-2.0.0-r5363-src-with-boost/alps/

then I wrote

make install

the program did the installation. Then I wrote the input file

LATTICE_LIBRARY="lattices.xml" LATTICE="simple cubic lattice" L=8 J=1 THERMALIZATION=10000 SWEEPS=50000 UPDATE="cluster" MODEL="O(4)" BOUNDARY type="periodic" S=1 {T=0.8;}

and it retrns the following error line:

O(4) model not implemented in file factory.C

I'm sorry I'm not expert in programming at all...

Thank you for you help,

with best regards

Rachele Nerattini

2012/2/14 Matthias Troyer troyer@phys.ethz.ch

On Feb 14, 2012, at 1:35 PM, Rachele Nerattini wrote:

...

Dear Mr Troyer,

I'm using ALPS to run MC simulations of classical Ising, XY and Heisenberg models in three dimensions. I want to study how the critical values of some observables varies with L in a regular cubic lattice so I run the simulations at T_c (critical value of the temperature).

I know that at the phase transition you have strong correlation in the system and it is difficult to obtain values of the observables with convergence on the errors. For this reasons I have the following questions:

1. Errors on the observables are given with three different levels of 'accuracy': converged (white), check the convergence (yellow), not converged (red).

How does the program test if the convergence is achieved? I mean I see the program evaluate the errors dividing the total number of steps in groups of binning and then evaluating the errors group by group. I suppose that it says that the convergence is achieved if the errors in different groups vary less then some interval that is fixed...is it true? Which is the test that it does?

The best will be if you look at the details of the binning analysis, as explained in tutorial MC-01. If the errors converge as a function of the bin size we mark it as converged, if they still increase slightly (which might just be a statistical fluctuation) mark it as yellow, and if it is clearly not converged we mark it as red. Still, to be sure you should always look at it yourself.

...

2. I suppose Tau is the correlation time. Does the program take into account the value of Tau in the final valuation of the errors? I mean, are those errors already multiplied by the sqrt of tau as it must be in case of correlations, or must be corrected bye the value of tau that is given?

Indeed it is multiplied by sqrt(1+2tau). Well, actually, sqrt(1+2tau) and thus tau is determined from the ratio between converged and naive error. But, to answer your question, the error indeed includes autocorrelation effects.

...

3. Since the correlation is strong at T_c do you think that it could be easier to get to convergence if we change the initial configuration of the MC? For example we could run a simulation for a while then take the last configuration it uses to evaluate the values of observables and then use this last configuration as the input configuration for a new run...can it be done in some way?

Yes, that could be done, it however will not help much. The time needed to equilibrate is of the same order as the autocorrelation time, and if you cannot afford to equilibrate you will also not be able to get many uncorrelated measurements.

...

4. Some months ago I wrote to you to ask if it could be possible to run a classical MC simulation for an O(4) model. in the tutorials you say that it can be done simply editing the spin_factory.C file. I tried but still it doesn't work. I'm afraid I made some mistakes in the installation of the ALPS library on my PC. Did you add this option in the new version 2.0?

What did not work? it should be very easy to add it. Can you tell me what you tried to do and what the problem was?

I hope this helps

Matthias Troyer

That file works for me, but I have ALPS 2.0.2. If you used ALPS 2.0.0 and did the change you made below it should also work - are you sure that you use the newly built version of spinmc. Try the following:

ls -l `which spinmc`

and compare the date of that executable to the sate when you changed the source file.

Also, the parameter BOUNDARY type does not exist and will be ignored.

Matthias

On Feb 15, 2012, at 11:02 AM, Rachele Nerattini wrote:

The one I wrote below is the complete input file that I use...is it incomplete?

I have installed the version of ALPS 2.0.0

Thank you

Rachele

2012/2/14 Matthias Troyer troyer@phys.ethz.ch Which version of ALPS are you using? O(4) models work for me in ALPS. Can you send your full input files? In your input below the following line should not work:

...

BOUNDARY type="periodic"

Matthias

On Feb 14, 2012, at 5:08 PM, Rachele Nerattini wrote:

...

Dear Mr Troyer,

thank you very much for the quick and helpfulness answer. For what concerns the last point:

...

4. Some months ago I wrote to you to ask if it could be possible to run a classical MC simulation for an O(4) model. in the tutorials you say that it can be done simply editing the spin_factory.C file. I tried but still it doesn't work. I'm afraid I made some mistakes in the installation of the ALPS library on my PC. Did you add this option in the new version 2.0?

What did not work? it should be very easy to add it. Can you tell me what you tried to do and what the problem was?

I modified the file spinmc_factory.C adding:

else if (parms["MODEL"]=="O(4)") return new SpinSim<ONMoment<4>,MIdMatrix<double,4> >(where,parms,node);

then I open a terminal, I went into the folder

alps-2.0.0-r5363-src-with-boost/alps/

then I wrote

make install

the program did the installation. Then I wrote the input file

LATTICE_LIBRARY="lattices.xml" LATTICE="simple cubic lattice" L=8 J=1 THERMALIZATION=10000 SWEEPS=50000 UPDATE="cluster" MODEL="O(4)" BOUNDARY type="periodic" S=1 {T=0.8;}

and it retrns the following error line:

O(4) model not implemented in file factory.C

I'm sorry I'm not expert in programming at all...

Thank you for you help,

with best regards

Rachele Nerattini

2012/2/14 Matthias Troyer troyer@phys.ethz.ch

On Feb 14, 2012, at 1:35 PM, Rachele Nerattini wrote:

...

Dear Mr Troyer,

I'm using ALPS to run MC simulations of classical Ising, XY and Heisenberg models in three dimensions. I want to study how the critical values of some observables varies with L in a regular cubic lattice so I run the simulations at T_c (critical value of the temperature).

I know that at the phase transition you have strong correlation in the system and it is difficult to obtain values of the observables with convergence on the errors. For this reasons I have the following questions:

1. Errors on the observables are given with three different levels of 'accuracy': converged (white), check the convergence (yellow), not converged (red).

How does the program test if the convergence is achieved? I mean I see the program evaluate the errors dividing the total number of steps in groups of binning and then evaluating the errors group by group. I suppose that it says that the convergence is achieved if the errors in different groups vary less then some interval that is fixed...is it true? Which is the test that it does?

The best will be if you look at the details of the binning analysis, as explained in tutorial MC-01. If the errors converge as a function of the bin size we mark it as converged, if they still increase slightly (which might just be a statistical fluctuation) mark it as yellow, and if it is clearly not converged we mark it as red. Still, to be sure you should always look at it yourself.

...

2. I suppose Tau is the correlation time. Does the program take into account the value of Tau in the final valuation of the errors? I mean, are those errors already multiplied by the sqrt of tau as it must be in case of correlations, or must be corrected bye the value of tau that is given?

Indeed it is multiplied by sqrt(1+2tau). Well, actually, sqrt(1+2tau) and thus tau is determined from the ratio between converged and naive error. But, to answer your question, the error indeed includes autocorrelation effects.

...

3. Since the correlation is strong at T_c do you think that it could be easier to get to convergence if we change the initial configuration of the MC? For example we could run a simulation for a while then take the last configuration it uses to evaluate the values of observables and then use this last configuration as the input configuration for a new run...can it be done in some way?

Yes, that could be done, it however will not help much. The time needed to equilibrate is of the same order as the autocorrelation time, and if you cannot afford to equilibrate you will also not be able to get many uncorrelated measurements.

...

4. Some months ago I wrote to you to ask if it could be possible to run a classical MC simulation for an O(4) model. in the tutorials you say that it can be done simply editing the spin_factory.C file. I tried but still it doesn't work. I'm afraid I made some mistakes in the installation of the ALPS library on my PC. Did you add this option in the new version 2.0?

What did not work? it should be very easy to add it. Can you tell me what you tried to do and what the problem was?

I hope this helps

Matthias Troyer

Ok I try to see it...anyway I also want to upgrade the version of ALPS i've installed with the newest one. I'll do it and I try to make O(4) simulations work...

Thank you for the help.

Rachele

2012/2/15 Matthias Troyer troyer@phys.ethz.ch

That file works for me, but I have ALPS 2.0.2. If you used ALPS 2.0.0 and did the change you made below it should also work - are you sure that you use the newly built version of spinmc. Try the following:

ls -l `which spinmc`

and compare the date of that executable to the sate when you changed the source file.

Also, the parameter BOUNDARY type does not exist and will be ignored.

Matthias

On Feb 15, 2012, at 11:02 AM, Rachele Nerattini wrote:

The one I wrote below is the complete input file that I use...is it incomplete?

I have installed the version of ALPS 2.0.0

Thank you

Rachele

2012/2/14 Matthias Troyer troyer@phys.ethz.ch

...

Which version of ALPS are you using? O(4) models work for me in ALPS. Can you send your full input files? In your input below the following line should not work:

BOUNDARY type="periodic"

Matthias

On Feb 14, 2012, at 5:08 PM, Rachele Nerattini wrote:

Dear Mr Troyer,

thank you very much for the quick and helpfulness answer. For what concerns the last point:

...

4. Some months ago I wrote to you to ask if it could be possible to run

a classical MC simulation for an O(4) model. in the tutorials you say that it can be done simply editing the spin_factory.C file. I tried but still it doesn't work. I'm afraid I made some mistakes in the installation of the ALPS library on my PC. Did you add this option in the new version 2.0?

What did not work? it should be very easy to add it. Can you tell me what you tried to do and what the problem was?

I modified the file spinmc_factory.C adding:

else if (parms["MODEL"]=="O(4)") return new SpinSim<ONMoment<4>,MIdMatrix<double,4>

...

(where,parms,node);

then I open a terminal, I went into the folder

alps-2.0.0-r5363-src-with-boost/alps/

then I wrote

make install

the program did the installation. Then I wrote the input file

LATTICE_LIBRARY="lattices.xml" LATTICE="simple cubic lattice" L=8 J=1 THERMALIZATION=10000 SWEEPS=50000 UPDATE="cluster" MODEL="O(4)" BOUNDARY type="periodic" S=1 {T=0.8;}

and it retrns the following error line:

O(4) model not implemented in file factory.C

I'm sorry I'm not expert in programming at all...

Thank you for you help,

with best regards

Rachele Nerattini

2012/2/14 Matthias Troyer troyer@phys.ethz.ch

...

On Feb 14, 2012, at 1:35 PM, Rachele Nerattini wrote:

...

Dear Mr Troyer,

I'm using ALPS to run MC simulations of classical Ising, XY and

Heisenberg models in three dimensions. I want to study how the critical values of some observables varies with L in a regular cubic lattice so I run the simulations at T_c (critical value of the temperature).

...

I know that at the phase transition you have strong correlation in the

system and it is difficult to obtain values of the observables with convergence on the errors. For this reasons I have the following questions:

...

1. Errors on the observables are given with three different levels of

'accuracy': converged (white), check the convergence (yellow), not converged (red).

...

How does the program test if the convergence is achieved? I mean I see

the program evaluate the errors dividing the total number of steps in groups of binning and then evaluating the errors group by group. I suppose that it says that the convergence is achieved if the errors in different groups vary less then some interval that is fixed...is it true? Which is the test that it does?

The best will be if you look at the details of the binning analysis, as explained in tutorial MC-01. If the errors converge as a function of the bin size we mark it as converged, if they still increase slightly (which might just be a statistical fluctuation) mark it as yellow, and if it is clearly not converged we mark it as red. Still, to be sure you should always look at it yourself.

...

2. I suppose Tau is the correlation time. Does the program take into

account the value of Tau in the final valuation of the errors? I mean, are those errors already multiplied by the sqrt of tau as it must be in case of correlations, or must be corrected bye the value of tau that is given?

Indeed it is multiplied by sqrt(1+2tau). Well, actually, sqrt(1+2tau) and thus tau is determined from the ratio between converged and naive error. But, to answer your question, the error indeed includes autocorrelation effects.

...

3. Since the correlation is strong at T_c do you think that it could

be easier to get to convergence if we change the initial configuration of the MC? For example we could run a simulation for a while then take the last configuration it uses to evaluate the values of observables and then use this last configuration as the input configuration for a new run...can it be done in some way?

Yes, that could be done, it however will not help much. The time needed to equilibrate is of the same order as the autocorrelation time, and if you cannot afford to equilibrate you will also not be able to get many uncorrelated measurements.

...

4. Some months ago I wrote to you to ask if it could be possible to

run a classical MC simulation for an O(4) model. in the tutorials you say that it can be done simply editing the spin_factory.C file. I tried but still it doesn't work. I'm afraid I made some mistakes in the installation of the ALPS library on my PC. Did you add this option in the new version 2.0?

What did not work? it should be very easy to add it. Can you tell me what you tried to do and what the problem was?

I hope this helps

Matthias Troyer

I don't think that a Debian package has been created for the version that includes the O(4) model. You will have to build spinmc from source.

On Apr 4, 2012, at 4:47 PM, Rachele Nerattini wrote:

Dear Mr Troyer,

I'm writing to you because I have some problems in the installation of ALPS on Ubuntu GNU/Linux 10.04 lucid.

Following the instructions in the guide at

http://alps.comp-phys.org/mediawiki/index.php/Download_and_install_ALPS_2#Do...

I proceeded in the following manner:

I openend a terminal and I typed

curl http://www.cpht.polytechnique.fr/ubuntu/gpg_key / sudo apt-key add-

I then added the two debs : deb http://www.cpht.polytechnique.fr/ubuntu lucid alps deb-src http://www.cpht.polytechnique.fr/ubuntu lucid alps to the file etc/apt/source.list

then I typed

sudo aptitude update sudo aptitude install alps2-all sudo aptitude upgrade sudo reboot

I need to run classical MC simulations for Ising, XY, Heisenberg and O(4) model. I can do the simulations for the Ising, XY and Heisenberg models with the command

spinmc --Tmin 100 --write-xml parm.in.xml

and it seems to work...but I cannot run the simulation for the O(4) model that I know is already included in the newest version.

Which mistake I made in the installation? It seems that I missed some steps also because I have some problems in other commands. For example the command convert2xml works but the command convert2text doesn't exist.

can you tell me what I have to do ti install ALPS 2.0 on Ubuntu 10.04 lucid?

Thank you very much for the help, with best regards

Rachele Nerattini

Dear Mr.Troyer,

I'm running some simulations using ALPS at the CINECA cluster in Bologna. I will have to run really long simulations which go well beyond the walltime limit of the machine.

To do that I have to divide the whole run in several subsections and then run all the processes in cascade.

Can you tell me how can I do that with ALPS? Which are the commands of stop/restart that I have to use?

Thank you for your help,

Rachele Nerattini

Dear Mr.Troyer,

I'm using Monte Carlo simulations for classical O(n) spin models. To be more precise I'm using the spinmc algorithm for Ising, XY and Heisenberg models.

Thank you for the help,

all the best

Rachele Nerattini

2012/6/28 Matthias Troyer troyer@phys.ethz.ch

Dear Rachele Nerattini,

Are you using Monte Carlo simulations or one of the other codes?

With best regards

Matthias Troyer

On 28 Jun 2012, at 16:59, Rachele Nerattini wrote:

...

Dear Mr.Troyer,

I'm running some simulations using ALPS at the CINECA cluster in

Bologna. I will have to run really long simulations which go well beyond the walltime limit of the machine.

...

To do that I have to divide the whole run in several subsections and

then run all the processes in cascade.

...

Can you tell me how can I do that with ALPS? Which are the commands of

stop/restart that I have to use?

...

Thank you for your help,

Rachele Nerattini

Thank you very much for the help! I'll do it immediately. All the best Rachele Nerattini

2012/7/1 Matthias Troyer troyer@phys.ethz.ch

It is explained here:

http://alps.comp-phys.org/mediawiki/index.php/Documentation:Running

Best regards

Matthias Troyer

On Jul 1, 2012, at 12:18 PM, Rachele Nerattini wrote:

Dear Mr.Troyer,

I'm using Monte Carlo simulations for classical O(n) spin models. To be more precise I'm using the spinmc algorithm for Ising, XY and Heisenberg models.

Thank you for the help,

all the best

Rachele Nerattini

2012/6/28 Matthias Troyer troyer@phys.ethz.ch

...

Dear Rachele Nerattini,

Are you using Monte Carlo simulations or one of the other codes?

With best regards

Matthias Troyer

On 28 Jun 2012, at 16:59, Rachele Nerattini wrote:

...

Dear Mr.Troyer,

I'm running some simulations using ALPS at the CINECA cluster in

Bologna. I will have to run really long simulations which go well beyond the walltime limit of the machine.

...

To do that I have to divide the whole run in several subsections and

then run all the processes in cascade.

...

Can you tell me how can I do that with ALPS? Which are the commands of

stop/restart that I have to use?

...

Thank you for your help,

Rachele Nerattini

What is your walltime limit? Is 1:00:00 24 hours or 1 hour?

On 1 Jul 2012, at 14:40, Rachele Nerattini wrote:

Dear Mr. Troyer,

I read the page you suggested me but I still don't understand. It says how to restart a simulation stopped because the computer shut down or how to make it stop before its natural end in case you achieved the required error but I don't understad how to stop it in a controlled way.

For istance, let's suppose I have to run a simulation which is 24 hours long. I want to divide the long run in 10 runs of 2.4 hours each. The output of the first run must be the input of the following and I want to do all the runs in cascade.

What do I have to write in the input file to do that? Sorry but I didn't find it in the page

http://alps.comp-phys.org/mediawiki/index.php/Documentation:Running

certeinly because I'm not an expert in these kind of things.

I copy and paste here in the following an example of input file I've wrote for the CINECA and an example of script I had to write to run a tet job.... Can you tell me what I have to change to make it stop after a certain numeber of seconds? Then I'll ask to CINECA assistence how to make all the block run in cascade.

Thank you and all the best,

Rachele Nerattini

input file = Ising3DL10mpiprocs10

LATTICE="simple cubic lattice" LATTICE_LIBRARY="lattices.xml" T=4.511441614 J=1 THERMALIZATION=200000 SWEEPS=1000000 UPDATE="cluster" MODEL="Ising" {L=10;}

script = Ising3DL10mpiprocs10.sh

#!/bin/bash #PBS -A name_of_the_project #PBS -l walltime=1:00:00 #PBS -l select=1:ncpus=10:mpiprocs=10:mem=40GB #PBS -q parallel #PBS -o Ising3DL10mpiprocs10.out #PBS -e Ising3DL10mpiprocs10.err # put the executable in the PATH module load autoload alps # cd in the directory where you have input e job.sh cd $PBS_O_WORKDIR # prep gli input parameter2xml Ising3DL10mpiprocs10

# it mounts openmpi to have mpirun in the PATH

module load profile/advanced openmpi/1.4.4--intel--co-2011.6.233--binary

mpirun -np 10 spinmc --mpi --Tmin 100 --write-xml Ising3DL10mpiprocs10.in.xml

qsub Ising3DL10mpiprocs10.sh

What do I have to add to have what I need?

Thank you again for the help,

I whish you all the best

Rachele Nerattini

2012/7/1 Rachele Nerattini r.nerattini@gmail.com Thank you very much for the help! I'll do it immediately. All the best Rachele Nerattini

2012/7/1 Matthias Troyer troyer@phys.ethz.ch It is explained here:

http://alps.comp-phys.org/mediawiki/index.php/Documentation:Running

Best regards

Matthias Troyer

On Jul 1, 2012, at 12:18 PM, Rachele Nerattini wrote:

...

Dear Mr.Troyer,

I'm using Monte Carlo simulations for classical O(n) spin models. To be more precise I'm using the spinmc algorithm for Ising, XY and Heisenberg models.

Thank you for the help,

all the best

Rachele Nerattini

2012/6/28 Matthias Troyer troyer@phys.ethz.ch Dear Rachele Nerattini,

Are you using Monte Carlo simulations or one of the other codes?

With best regards

Matthias Troyer

On 28 Jun 2012, at 16:59, Rachele Nerattini wrote:

...

Dear Mr.Troyer,

I'm running some simulations using ALPS at the CINECA cluster in Bologna. I will have to run really long simulations which go well beyond the walltime limit of the machine.

To do that I have to divide the whole run in several subsections and then run all the processes in cascade.

Can you tell me how can I do that with ALPS? Which are the commands of stop/restart that I have to use?

Thank you for your help,

Rachele Nerattini

Thank you all very much! Yes, I think this could help. I'll send your mail to the CINECA-help-desk so that they will tell me if this is all we need and how to concatenate jobs.

In any case, if I understand well, all I have to do is:

0) to generate the file .out.xml;

1) to run the first block inserting the flag ' --time-limit #sec ' in the command line wich tells the program to stop after #sec seconds;

2) to run the second block using again the flag ' --time-limit #sec ' in the command line and the file .out.xml as input file;

3) to go on with this till the end of the simulations.

Is that ok? For what concerns the walltime limit I think it is 24 hours (24:00:00)... Thnak you again I'll let you know if everything works. Bye for now Rachele

2012/7/1 Fabien Alet alet@irsamc.ups-tlse.fr

Dear Rachele,

if I understood correctly, what you need to do is to : 0) run for 10 seconds or so your job locally on the main server such that file Ising3DL10mpiprocs10.out.xml gets generated (e.g. something like spinmc --time-limit 10 --write-xml Ising3DL10mpiprocs10.in.xml, alternatively just stop the job with CTRL-C)

1. add the time limit of 2.4 hours in the command line where you execute

your observable, such as e.g. mpirun -np 10 spinmc --mpi --Tmin 100 --time-limit 9000 --write-xml Ising3DL10mpiprocs10.out.xml [actually you should give slightly less than 2.4 hours such that files have the time to be written to disk, this is why I used 9000 seconds]

Remark that I used .out.xml , and not .in.xml such that your script really continues your ongoing jobs, and does not restart from scratch every time.

I hope this can help, Best Fabien

Le 1 juil. 2012 à 14:40, Rachele Nerattini a écrit :

Dear Mr. Troyer,

I read the page you suggested me but I still don't understand. It says how to restart a simulation stopped because the computer shut down or how to make it stop before its natural end in case you achieved the required error but I don't understad how to stop it in a controlled way.

For istance, let's suppose I have to run a simulation which is 24 hours long. I want to divide the long run in 10 runs of 2.4 hours each. The output of the first run must be the input of the following and I want to do all the runs in cascade.

What do I have to write in the input file to do that? Sorry but I didn't find it in the page

http://alps.comp-phys.org/mediawiki/index.php/Documentation:Running

certeinly because I'm not an expert in these kind of things.

I copy and paste here in the following an example of input file I've wrote for the CINECA and an example of script I had to write to run a tet job.... Can you tell me what I have to change to make it stop after a certain numeber of seconds? Then I'll ask to CINECA assistence how to make all the block run in cascade.

Thank you and all the best,

Rachele Nerattini

input file = Ising3DL10mpiprocs10

LATTICE="simple cubic lattice" LATTICE_LIBRARY="lattices.xml" T=4.511441614 J=1 THERMALIZATION=200000 SWEEPS=1000000 UPDATE="cluster" MODEL="Ising" {L=10;}

script = Ising3DL10mpiprocs10.sh

#!/bin/bash #PBS -A name_of_the_project #PBS -l walltime=1:00:00 #PBS -l select=1:ncpus=10:mpiprocs=10:mem=40GB #PBS -q parallel #PBS -o Ising3DL10mpiprocs10.out #PBS -e Ising3DL10mpiprocs10.err # put the executable in the PATH module load autoload alps # cd in the directory where you have input e job.sh cd $PBS_O_WORKDIR # prep gli input parameter2xml Ising3DL10mpiprocs10

# it mounts openmpi to have mpirun in the PATH

module load profile/advanced openmpi/1.4.4--intel--co-2011.6.233--binary

mpirun -np 10 spinmc --mpi --Tmin 100 --write-xml Ising3DL10mpiprocs10.in.xml

qsub Ising3DL10mpiprocs10.sh

What do I have to add to have what I need?

Thank you again for the help,

I whish you all the best

Rachele Nerattini

2012/7/1 Rachele Nerattini r.nerattini@gmail.com

...

Thank you very much for the help! I'll do it immediately. All the best Rachele Nerattini

2012/7/1 Matthias Troyer troyer@phys.ethz.ch

...

It is explained here:

http://alps.comp-phys.org/mediawiki/index.php/Documentation:Running

Best regards

Matthias Troyer

On Jul 1, 2012, at 12:18 PM, Rachele Nerattini wrote:

Dear Mr.Troyer,

I'm using Monte Carlo simulations for classical O(n) spin models. To be more precise I'm using the spinmc algorithm for Ising, XY and Heisenberg models.

Thank you for the help,

all the best

Rachele Nerattini

2012/6/28 Matthias Troyer troyer@phys.ethz.ch

...

Dear Rachele Nerattini,

Are you using Monte Carlo simulations or one of the other codes?

With best regards

Matthias Troyer

On 28 Jun 2012, at 16:59, Rachele Nerattini wrote:

...

Dear Mr.Troyer,

I'm running some simulations using ALPS at the CINECA cluster in

Bologna. I will have to run really long simulations which go well beyond the walltime limit of the machine.

...

To do that I have to divide the whole run in several subsections and

then run all the processes in cascade.

...

Can you tell me how can I do that with ALPS? Which are the commands

of stop/restart that I have to use?

...

Thank you for your help,

Rachele Nerattini

ok, I'll try to run it on CINECA and I'll tell you if it works.

2012/7/1 Matthias Troyer troyer@phys.ethz.ch

On 1 Jul 2012, at 15:25, Rachele Nerattini wrote:

Thank you all very much! Yes, I think this could help. I'll send your mail to the CINECA-help-desk so that they will tell me if this is all we need and how to concatenate jobs.

In any case, if I understand well, all I have to do is:

Nearly

0)use parameter2xml to generate the file .*.in.xml;

1. to run the first block inserting the flag ' --time-limit #sec ' in the

command line wich tells the program to stop after #sec seconds;

2. to run the second block using again the flag ' --time-limit #sec ' in

the command line and the file .out.xml as input file;

3. to go on with this till the end of the simulations.

Yes

Is that ok? For what concerns the walltime limit I think it is 24 hours (24:00:00)...

24 ho0urs will be 86400 seconds, but the code will need time to write the checkpoints, thus specify about 1000 seconds less to be on the safe side.

Thnak you again I'll let you know if everything works. Bye for now Rachele

2012/7/1 Fabien Alet alet@irsamc.ups-tlse.fr

...

Dear Rachele,

if I understood correctly, what you need to do is to : 0) run for 10 seconds or so your job locally on the main server such that file Ising3DL10mpiprocs10.out.xml gets generated (e.g. something like spinmc --time-limit 10 --write-xml Ising3DL10mpiprocs10.in.xml, alternatively just stop the job with CTRL-C)

1. add the time limit of 2.4 hours in the command line where you execute

your observable, such as e.g. mpirun -np 10 spinmc --mpi --Tmin 100 --time-limit 9000 --write-xml Ising3DL10mpiprocs10.out.xml [actually you should give slightly less than 2.4 hours such that files have the time to be written to disk, this is why I used 9000 seconds]

Remark that I used .out.xml , and not .in.xml such that your script really continues your ongoing jobs, and does not restart from scratch every time.

I hope this can help, Best Fabien

Le 1 juil. 2012 à 14:40, Rachele Nerattini a écrit :

Dear Mr. Troyer,

I read the page you suggested me but I still don't understand. It says how to restart a simulation stopped because the computer shut down or how to make it stop before its natural end in case you achieved the required error but I don't understad how to stop it in a controlled way.

For istance, let's suppose I have to run a simulation which is 24 hours long. I want to divide the long run in 10 runs of 2.4 hours each. The output of the first run must be the input of the following and I want to do all the runs in cascade.

What do I have to write in the input file to do that? Sorry but I didn't find it in the page

http://alps.comp-phys.org/mediawiki/index.php/Documentation:Running

certeinly because I'm not an expert in these kind of things.

I copy and paste here in the following an example of input file I've wrote for the CINECA and an example of script I had to write to run a tet job.... Can you tell me what I have to change to make it stop after a certain numeber of seconds? Then I'll ask to CINECA assistence how to make all the block run in cascade.

Thank you and all the best,

Rachele Nerattini

input file = Ising3DL10mpiprocs10

LATTICE="simple cubic lattice" LATTICE_LIBRARY="lattices.xml" T=4.511441614 J=1 THERMALIZATION=200000 SWEEPS=1000000 UPDATE="cluster" MODEL="Ising" {L=10;}

script = Ising3DL10mpiprocs10.sh

#!/bin/bash #PBS -A name_of_the_project #PBS -l walltime=1:00:00 #PBS -l select=1:ncpus=10:mpiprocs=10:mem=40GB #PBS -q parallel #PBS -o Ising3DL10mpiprocs10.out #PBS -e Ising3DL10mpiprocs10.err # put the executable in the PATH module load autoload alps # cd in the directory where you have input e job.sh cd $PBS_O_WORKDIR # prep gli input parameter2xml Ising3DL10mpiprocs10

# it mounts openmpi to have mpirun in the PATH

module load profile/advanced openmpi/1.4.4--intel--co-2011.6.233--binary

mpirun -np 10 spinmc --mpi --Tmin 100 --write-xml Ising3DL10mpiprocs10.in.xml

qsub Ising3DL10mpiprocs10.sh

What do I have to add to have what I need?

Thank you again for the help,

I whish you all the best

Rachele Nerattini

2012/7/1 Rachele Nerattini r.nerattini@gmail.com

...

Thank you very much for the help! I'll do it immediately. All the best Rachele Nerattini

2012/7/1 Matthias Troyer troyer@phys.ethz.ch

...

It is explained here:

http://alps.comp-phys.org/mediawiki/index.php/Documentation:Running

Best regards

Matthias Troyer

On Jul 1, 2012, at 12:18 PM, Rachele Nerattini wrote:

Dear Mr.Troyer,

I'm using Monte Carlo simulations for classical O(n) spin models. To be more precise I'm using the spinmc algorithm for Ising, XY and Heisenberg models.

Thank you for the help,

all the best

Rachele Nerattini

2012/6/28 Matthias Troyer troyer@phys.ethz.ch

...

Dear Rachele Nerattini,

Are you using Monte Carlo simulations or one of the other codes?

With best regards

Matthias Troyer

On 28 Jun 2012, at 16:59, Rachele Nerattini wrote:

...

Dear Mr.Troyer,

I'm running some simulations using ALPS at the CINECA cluster in

Bologna. I will have to run really long simulations which go well beyond the walltime limit of the machine.

...

To do that I have to divide the whole run in several subsections and

then run all the processes in cascade.

...

Can you tell me how can I do that with ALPS? Which are the commands

of stop/restart that I have to use?

...

Thank you for your help,

Rachele Nerattini

Dear Mr. Troyer,

I have to run very long simulations of classical O(n) model in three spatial dimensions. In particular I study the Ising model, the XY model, the Heisenberg model and the O(4) model at the critical value of the temperature. To gain time I wanted to run the simulations in parallel.

An example of the input file I used is:

============================ LATTICE="simple cubic lattice" LATTICE_LIBRARY="lattices.xml" T=4.511441614 J=1 THERMALIZATION=200000 SWEEPS=1000000 UPDATE="cluster" MODEL="Ising" {L=32;} ============================

And the command I used to run the simulation on 4 processors is

mpirun -np 4 spinmc --mpi --Tmin 300 --time-limit 2400 --write-xml Ising3DL32mpiprocs4.out.xml (1)

------------------------------------------------------------------------------------------- To run the same simulation in a serial manner I use the command

spinmc --Tmin 300 --time-limit 2400 --write-xml Ising3DL32serial.out.xml (2) -------------------------------------------------------------------------------------------- In both cases the simulation runs properly BUT I the gain, in terms of time, of the parallel run with respect to the serial run is almost zero. This is true independentely on the number of processors that I used (2,4,8,12).

Am I doing some mistakes in the command line (1) ? Am I missing any flags or something like that? Or the parallelization of the program is done only at a compliler level (In the sense that the program spinmc can run on different processors but as a matter of fact it is not really optimized in this sense...)?

Thank you for your attention and for your answer.

With best regards,

Rachele

2012/7/1 Rachele Nerattini r.nerattini@gmail.com

Thank you again for the quick and precise help.

2012/7/1 Rachele Nerattini r.nerattini@gmail.com

...

ok, I'll try to run it on CINECA and I'll tell you if it works.

2012/7/1 Matthias Troyer troyer@phys.ethz.ch

...

On 1 Jul 2012, at 15:25, Rachele Nerattini wrote:

Thank you all very much! Yes, I think this could help. I'll send your mail to the CINECA-help-desk so that they will tell me if this is all we need and how to concatenate jobs.

In any case, if I understand well, all I have to do is:

Nearly

0)use parameter2xml to generate the file .*.in.xml;

1. to run the first block inserting the flag ' --time-limit #sec ' in

the command line wich tells the program to stop after #sec seconds;

2. to run the second block using again the flag ' --time-limit #sec ' in

the command line and the file .out.xml as input file;

3. to go on with this till the end of the simulations.

Yes

Is that ok? For what concerns the walltime limit I think it is 24 hours (24:00:00)...

24 ho0urs will be 86400 seconds, but the code will need time to write the checkpoints, thus specify about 1000 seconds less to be on the safe side.

Thnak you again I'll let you know if everything works. Bye for now Rachele

2012/7/1 Fabien Alet alet@irsamc.ups-tlse.fr

...

Dear Rachele,

if I understood correctly, what you need to do is to : 0) run for 10 seconds or so your job locally on the main server such that file Ising3DL10mpiprocs10.out.xml gets generated (e.g. something like spinmc --time-limit 10 --write-xml Ising3DL10mpiprocs10.in.xml, alternatively just stop the job with CTRL-C)

1. add the time limit of 2.4 hours in the command line where you

execute your observable, such as e.g. mpirun -np 10 spinmc --mpi --Tmin 100 --time-limit 9000 --write-xml Ising3DL10mpiprocs10.out.xml [actually you should give slightly less than 2.4 hours such that files have the time to be written to disk, this is why I used 9000 seconds]

Remark that I used .out.xml , and not .in.xml such that your script really continues your ongoing jobs, and does not restart from scratch every time.

I hope this can help, Best Fabien

Le 1 juil. 2012 à 14:40, Rachele Nerattini a écrit :

Dear Mr. Troyer,

I read the page you suggested me but I still don't understand. It says how to restart a simulation stopped because the computer shut down or how to make it stop before its natural end in case you achieved the required error but I don't understad how to stop it in a controlled way.

For istance, let's suppose I have to run a simulation which is 24 hours long. I want to divide the long run in 10 runs of 2.4 hours each. The output of the first run must be the input of the following and I want to do all the runs in cascade.

What do I have to write in the input file to do that? Sorry but I didn't find it in the page

http://alps.comp-phys.org/mediawiki/index.php/Documentation:Running

certeinly because I'm not an expert in these kind of things.

I copy and paste here in the following an example of input file I've wrote for the CINECA and an example of script I had to write to run a tet job.... Can you tell me what I have to change to make it stop after a certain numeber of seconds? Then I'll ask to CINECA assistence how to make all the block run in cascade.

Thank you and all the best,

Rachele Nerattini

input file = Ising3DL10mpiprocs10

LATTICE="simple cubic lattice" LATTICE_LIBRARY="lattices.xml" T=4.511441614 J=1 THERMALIZATION=200000 SWEEPS=1000000 UPDATE="cluster" MODEL="Ising" {L=10;}

script = Ising3DL10mpiprocs10.sh

#!/bin/bash #PBS -A name_of_the_project #PBS -l walltime=1:00:00 #PBS -l select=1:ncpus=10:mpiprocs=10:mem=40GB #PBS -q parallel #PBS -o Ising3DL10mpiprocs10.out #PBS -e Ising3DL10mpiprocs10.err # put the executable in the PATH module load autoload alps # cd in the directory where you have input e job.sh cd $PBS_O_WORKDIR # prep gli input parameter2xml Ising3DL10mpiprocs10

# it mounts openmpi to have mpirun in the PATH

module load profile/advanced openmpi/1.4.4--intel--co-2011.6.233--binary

mpirun -np 10 spinmc --mpi --Tmin 100 --write-xml Ising3DL10mpiprocs10.in.xml

qsub Ising3DL10mpiprocs10.sh

What do I have to add to have what I need?

Thank you again for the help,

I whish you all the best

Rachele Nerattini

2012/7/1 Rachele Nerattini r.nerattini@gmail.com

...

Thank you very much for the help! I'll do it immediately. All the best Rachele Nerattini

2012/7/1 Matthias Troyer troyer@phys.ethz.ch

...

It is explained here:

http://alps.comp-phys.org/mediawiki/index.php/Documentation:Running

Best regards

Matthias Troyer

On Jul 1, 2012, at 12:18 PM, Rachele Nerattini wrote:

Dear Mr.Troyer,

I'm using Monte Carlo simulations for classical O(n) spin models. To be more precise I'm using the spinmc algorithm for Ising, XY and Heisenberg models.

Thank you for the help,

all the best

Rachele Nerattini

2012/6/28 Matthias Troyer troyer@phys.ethz.ch

> Dear Rachele Nerattini, > > Are you using Monte Carlo simulations or one of the other codes? > > With best regards > > Matthias Troyer > > On 28 Jun 2012, at 16:59, Rachele Nerattini wrote: > > > Dear Mr.Troyer, > > > > I'm running some simulations using ALPS at the CINECA cluster in > Bologna. I will have to run really long simulations which go well beyond > the walltime limit of the machine. > > > > To do that I have to divide the whole run in several subsections > and then run all the processes in cascade. > > > > Can you tell me how can I do that with ALPS? Which are the > commands of stop/restart that I have to use? > > > > Thank you for your help, > > > > Rachele Nerattini > >

Dear Rachele,

if I understand correctly your situation, the fact that each simulation on 2,4,8,12.. processors takes exactly the same computational time means that the total number of Monte Carlo iterations on each processor is always the same. In other words, on each processor you make a certain number of iterations which is **independent** on the total number of processors.

The advantage of using more processors is that the statistical error you will have with say 8 processors should be about a factor 2 smaller than the statistical error you have when running with 2 processor.

You might verify if this is the case.

Regards,

Giuseppe

Dear Mr Troyer,

sorry if I write again is only that I didn't hear anything from you and I'm not sure you received my mail. I have to run MC simulations for classical O(n) spin model in parallel.

I used the command

mpirun -np 4 spinmc --mpi --Tmin 300 --time-limit 2400 --write-xml Ising3DL32mpiprocs4.out.xml

to mean that I want to run it on 4 processors. The simulation goes fine and in the end I have these output files:

Ising3DL32mpiprocs4.out.xml Ising3DL32mpiprocs4.task1.out.run1.xml Ising3DL32mpiprocs4.task1.out.run2.xml Ising3DL32mpiprocs4.task1.out.run3.xml Ising3DL32mpiprocs4.task1.out.run4.xml

more other files. I am a bit surprised since in every file Ising3DL32mpiprocs4.task1.out.run*.xml It looks like I have a separate simulation of the same model and it doesn't seems like that the whole simulation (the one generated by the file Ising3DL32mpiprocs4.in.xml) is being partitioned in 4 parts.

In fact the simulation takes exactly the same time if I run it on 2, 4, 8, 12 .... processors. I don't have any gain in time with the parallelization of the program.

Why? Do I missing any flags in the command above or is the program really written for parallelization?

Thank you very much for the help.

Waiting for your answer, all the best

Rachele Nerattini

I have to run very long simulations of classical O(n) model in
three spatial dimensions. In particular  I study the  Ising model,
the XY model, the Heisenberg model and the O(4) model at the
critical value of the temperature.
To gain time I wanted to run the simulations in parallel.

An example of the input file I used is:

============================

LATTICE="simple cubic lattice"
LATTICE_LIBRARY="lattices.xml"
T=4.511441614
J=1
THERMALIZATION=200000
SWEEPS=1000000
UPDATE="cluster"
MODEL="Ising"
{L=32;}
============================

And the command I used to run the simulation on 4 processors is

mpirun -np 4 spinmc --mpi --Tmin 300 --time-limit 2400 --write-xml
Ising3DL32mpiprocs4.out.xml     (1)

-------------------------------------------------------------------------------------------
To run the same simulation in a serial manner I use the command

spinmc --Tmin 300 --time-limit 2400 --write-xml
Ising3DL32serial.out.xml (2)
--------------------------------------------------------------------------------------------
In both cases the simulation runs properly BUT I the gain, in
terms of time, of the parallel run with respect to the serial run
is almost zero. This is true  independentely on the number of
processors that I used (2,4,8,12).

Am I doing some mistakes in the command line  (1) ?  Am I missing
any flags or something like that?
Or the parallelization of the program is done only at a compliler
level (In the sense that the program spinmc can run on different
processors but as a matter of fact it is not really optimized in
this sense...)?

Thank you for your attention and for your answer.

With best regards,

Rachele





2012/7/1 Rachele Nerattini <r.nerattini@gmail.com
<mailto:r.nerattini@gmail.com>>

    Thank you again for the quick and precise help.


    2012/7/1 Rachele Nerattini <r.nerattini@gmail.com
    <mailto:r.nerattini@gmail.com>>

        ok, I'll try to run it on CINECA and I'll tell you if it
        works.


        2012/7/1 Matthias Troyer <troyer@phys.ethz.ch
        <mailto:troyer@phys.ethz.ch>>


            On 1 Jul 2012, at 15:25, Rachele Nerattini wrote:

...

            Thank you all very much!
            Yes, I think this could help. I'll send your mail to
            the CINECA-help-desk so that they will tell me if
            this is all we need and how to concatenate jobs.

            In any case, if I understand well, all I have to do is:

            Nearly

...

            0)use parameter2xml to generate the file .*.in.xml;

...

            1) to run the first block inserting the flag '
            --time-limit #sec ' in the command line wich tells
            the program to stop after #sec seconds;

...

            2) to run the second block using again the flag '
            --time-limit #sec ' in the command line and the file
            .out.xml as input file;

            3) to go on with this till the end of the simulations.

            Yes

...

            Is that ok?
            For what concerns the walltime limit I think it is 24
            hours (24:00:00)...

            24 ho0urs will be 86400 seconds, but the code will
            need time to write the checkpoints, thus specify about
            1000 seconds less to be on the safe side.

...

            Thnak you again I'll let you know if everything works.
            Bye for now
            Rachele

...

            2012/7/1 Fabien Alet <alet@irsamc.ups-tlse.fr
            <mailto:alet@irsamc.ups-tlse.fr>>

                Dear Rachele,

                if I understood correctly, what you need to do is
                to  :
                0) run for 10 seconds or so your job locally on
                the main server such that
                file Ising3DL10mpiprocs10.out.xml gets generated
                (e.g. something like spinmc --time-limit 10
                --write-xml Ising3DL10mpiprocs10.in.xml,
                alternatively just stop the job with CTRL-C)

                1) add the time limit of 2.4 hours in the command
                line where you execute your observable, such as e.g.
                mpirun -np 10 spinmc --mpi --Tmin 100
                --time-limit 9000 --write-xml
                Ising3DL10mpiprocs10.out.xml
                [actually you should give slightly less than 2.4
                hours such that files have the time to be written
                to disk, this is why I used 9000 seconds]

                Remark that I used .out.xml , and not .in.xml
                such that your script really continues your
                ongoing jobs, and does not restart from scratch
                every time.

                I hope this can help,
                Best
                Fabien

                Le 1 juil. 2012 à 14:40, Rachele Nerattini a écrit :

...

                Dear Mr. Troyer,

                I read the page you suggested me but I still
                don't understand. It says how to restart a
                simulation stopped because the computer shut
                down or how to make it stop before its natural
                end in case you achieved the required error but
                I don't understad how to stop it in a controlled
                way.

                For istance, let's suppose I have to run a
                simulation which is 24 hours long.
                I want to divide the long run in 10 runs of 2.4
                hours each. The output of the first run must be
                the input of the following and I want to do all
                the runs in cascade.

                What do I have to write in the input file to do
                that? Sorry but I didn't find it in the page

                http://alps.comp-phys.org/mediawiki/index.php/Documentation:Running

                certeinly because I'm not an expert in these
                kind of things.

                I copy and paste here in the following an
                example of input file I've wrote for the CINECA
                and an example of script I had to write to run a
                tet job....
                Can you tell me what I have to change to make it
                stop after a certain numeber of seconds? Then
                I'll ask to CINECA assistence how to make all
                the block run in cascade.

                Thank you and all the best,

                Rachele Nerattini

                input file = Ising3DL10mpiprocs10

                LATTICE="simple cubic lattice"
                LATTICE_LIBRARY="lattices.xml"
                T=4.511441614
                J=1
                THERMALIZATION=200000
                SWEEPS=1000000
                UPDATE="cluster"
                MODEL="Ising"
                {L=10;}

                script = Ising3DL10mpiprocs10.sh

                #!/bin/bash
                #PBS -A name_of_the_project
                #PBS -l walltime=1:00:00
                #PBS -l select=1:ncpus=10:mpiprocs=10:mem=40GB
                #PBS -q parallel
                #PBS -o Ising3DL10mpiprocs10.out
                #PBS -e Ising3DL10mpiprocs10.err
                # put the executable in the PATH
                module load autoload alps
                # cd in the directory where you have input e job.sh
                cd $PBS_O_WORKDIR
                # prep gli input
                parameter2xml Ising3DL10mpiprocs10

                # it mounts openmpi to have mpirun in the PATH

                module load profile/advanced
                openmpi/1.4.4--intel--co-2011.6.233--binary

                mpirun -np 10 spinmc --mpi --Tmin 100
                --write-xml Ising3DL10mpiprocs10.in.xml

                qsub Ising3DL10mpiprocs10.sh

                What do I have to add to have what I need?

                Thank you again for the help,

                I whish you all the best

                Rachele Nerattini


                2012/7/1 Rachele Nerattini
                <r.nerattini@gmail.com
                <mailto:r.nerattini@gmail.com>>

                    Thank you very much for the help! I'll do it
                    immediately.
                    All the best
                    Rachele Nerattini


                    2012/7/1 Matthias Troyer
                    <troyer@phys.ethz.ch
                    <mailto:troyer@phys.ethz.ch>>

                        It is explained here:

                        http://alps.comp-phys.org/mediawiki/index.php/Documentation:Running

                        Best regards

                        Matthias Troyer

                        On Jul 1, 2012, at 12:18 PM, Rachele
                        Nerattini wrote:

...

                        Dear Mr.Troyer,

                        I'm using Monte Carlo simulations for
                        classical O(n) spin models. To be more
                        precise I'm using the spinmc algorithm
                        for Ising, XY and Heisenberg models.

                        Thank you for the help,

                        all the best

                        Rachele Nerattini


                        2012/6/28 Matthias Troyer
                        <troyer@phys.ethz.ch
                        <mailto:troyer@phys.ethz.ch>>

                            Dear Rachele Nerattini,

                            Are you using Monte Carlo
                            simulations or one of the other codes?

                            With best regards

                            Matthias Troyer

                            On 28 Jun 2012, at 16:59, Rachele
                            Nerattini wrote:

                            > Dear Mr.Troyer,
                            >
                            > I'm running some simulations
                            using ALPS at the CINECA cluster in
                            Bologna. I will have to run really
                            long simulations which go well
                            beyond the walltime limit of the
                            machine.
                            >
                            > To do that I have to divide the
                            whole run in several subsections
                            and then run all the processes in
                            cascade.
                            >
                            > Can you tell me how can I do that
                            with ALPS? Which are the commands
                            of stop/restart that I have to use?
                            >
                            > Thank you for your help,
                            >
                            > Rachele Nerattini

Dear Rachele,

actually you should reason in terms of the statistical error you want to achieve for a given observable, not in terms of the running time.

Say you want an error of 1.0e-4 on the total energy, and that with 2 processors this will be achieved after 30 minutes. Now, with 8 processors, the same statistical error will be achieved after about 15 minutes (in the ideal case). So, this means that you can run your simulation for only 15 minutes instead of 30 minutes, and get the same statistical error. That's how parallelisation can greatly help in this case.

Ciao,

Giuseppe (not Carlo)

Dear Evgeni and Carlo,

thank you very much for your answers.

Naively I thought that if I run a Monte Carlo simulation on several processors (let's say 4 processors), the time needed to the simulation to finish should be much less (let's say around 4 times less) then the time nedeed by the same simulation on 1 processor.

This means that if I want to simulate the Ising model on a cubic lattice of edge 8, the simulation will take ~200 seconds to finish on 1 processor ~100 seconds to finish on 2 processors ~50 seconds to finish on 4 processors and so on...

I see instead, and you confirm my suspicious, that I can only improve the statistical error on the results but not the running time.

Thank you very much for your help. I whish you all the best, Rachele

2012/9/19 Giuseppe Carleo <giuscarl@gmail.com mailto:giuscarl@gmail.com>

Dear Rachele,

if I understand correctly your situation, the fact that each
simulation on 2,4,8,12.. processors takes exactly the same
computational time means that the total number of Monte Carlo
iterations on each processor is always the same. In other words,
on each processor you make a certain number of iterations which is
**independent** on the total number of processors.

The advantage of using more processors is that the statistical
error you will have with say 8 processors should be about a factor
2 smaller than the statistical error you have when running with 2
processor.

You might verify if this is the case.

Regards,

Giuseppe

...

Dear Mr Troyer,

sorry if I write again is only that I didn't hear anything from
you and I'm not sure you received my mail.
I have to run MC simulations for classical O(n) spin model in
parallel.

I used the command

mpirun -np 4 spinmc --mpi --Tmin 300 --time-limit 2400
--write-xml Ising3DL32mpiprocs4.out.xml

to mean that I want to run it on 4 processors. The simulation
goes fine and in the end I have these output files:

Ising3DL32mpiprocs4.out.xml
Ising3DL32mpiprocs4.task1.out.run1.xml
Ising3DL32mpiprocs4.task1.out.run2.xml
Ising3DL32mpiprocs4.task1.out.run3.xml
Ising3DL32mpiprocs4.task1.out.run4.xml

more other files. I am a bit surprised since in every file
Ising3DL32mpiprocs4.task1.out.run*.xml It looks like I have a
separate simulation of the same model and it doesn't seems like
that the whole simulation (the one generated by the file
Ising3DL32mpiprocs4.in.xml) is being partitioned  in 4 parts.

In fact the simulation takes exactly the same time if I run it on
2, 4, 8, 12 .... processors. I don't have any gain in time with
the parallelization of the program.

Why? Do I missing any flags in the command above or is the
program really written for parallelization?

Thank you very much for the help.

Waiting for your answer, all the best

Rachele Nerattini






    I have to run very long simulations of classical O(n) model
    in three spatial dimensions. In particular  I study the 
    Ising model, the XY model, the Heisenberg model and the O(4)
    model at the critical value of the temperature.
    To gain time I wanted to run the simulations in parallel.

    An example of the input file I used is:

    ============================

    LATTICE="simple cubic lattice"
    LATTICE_LIBRARY="lattices.xml"
    T=4.511441614
    J=1
    THERMALIZATION=200000
    SWEEPS=1000000
    UPDATE="cluster"
    MODEL="Ising"
    {L=32;}
    ============================

    And the command I used to run the simulation on 4 processors is

    mpirun -np 4 spinmc --mpi --Tmin 300 --time-limit 2400
    --write-xml Ising3DL32mpiprocs4.out.xml (1)

    -------------------------------------------------------------------------------------------
    To run the same simulation in a serial manner I use the command

    spinmc --Tmin 300 --time-limit 2400 --write-xml
    Ising3DL32serial.out.xml (2)
    --------------------------------------------------------------------------------------------
    In both cases the simulation runs properly BUT I the gain, in
    terms of time, of the parallel run with respect to the serial
    run is almost zero. This is true  independentely on the
    number of processors that I used (2,4,8,12).

    Am I doing some mistakes in the command line  (1) ?  Am I
    missing any flags or something like that?
    Or the parallelization of the program is done only at a
    compliler level (In the sense that the program spinmc can run
    on different processors but as a matter of fact it is not
    really optimized in this sense...)?

    Thank you for your attention and for your answer.

    With best regards,

    Rachele





    2012/7/1 Rachele Nerattini <r.nerattini@gmail.com
    <mailto:r.nerattini@gmail.com>>

        Thank you again for the quick and precise help.


        2012/7/1 Rachele Nerattini <r.nerattini@gmail.com
        <mailto:r.nerattini@gmail.com>>

            ok, I'll try to run it on CINECA and I'll tell you if
            it works.


            2012/7/1 Matthias Troyer <troyer@phys.ethz.ch
            <mailto:troyer@phys.ethz.ch>>


                On 1 Jul 2012, at 15:25, Rachele Nerattini wrote:

...

                Thank you all very much!
                Yes, I think this could help. I'll send your
                mail to the CINECA-help-desk so that they will
                tell me if this is all we need and how to
                concatenate jobs.

                In any case, if I understand well, all I have to
                do is:

                Nearly

...

                0)use parameter2xml to generate the file .*.in.xml;

...

                1) to run the first block inserting the flag '
                --time-limit #sec ' in the command line wich
                tells the program to stop after #sec seconds;

...

                2) to run the second block using again the flag
                ' --time-limit #sec ' in the command line and
                the file .out.xml as input file;

                3) to go on with this till the end of the
                simulations.

                Yes

...

                Is that ok?
                For what concerns the walltime limit I think it
                is 24 hours (24:00:00)...

                24 ho0urs will be 86400 seconds, but the code
                will need time to write the checkpoints, thus
                specify about 1000 seconds less to be on the safe
                side.

...

                Thnak you again I'll let you know if everything
                works.
                Bye for now
                Rachele

...

                2012/7/1 Fabien Alet <alet@irsamc.ups-tlse.fr
                <mailto:alet@irsamc.ups-tlse.fr>>

                    Dear Rachele,

                    if I understood correctly, what you need to
                    do is to  :
                    0) run for 10 seconds or so your job locally
                    on the main server such that
                    file Ising3DL10mpiprocs10.out.xml gets generated
                    (e.g. something like spinmc --time-limit 10
                    --write-xml Ising3DL10mpiprocs10.in.xml,
                    alternatively just stop the job with CTRL-C)

                    1) add the time limit of 2.4 hours in the
                    command line where you execute your
                    observable, such as e.g.
                    mpirun -np 10 spinmc --mpi --Tmin 100
                    --time-limit 9000 --write-xml
                    Ising3DL10mpiprocs10.out.xml
                    [actually you should give slightly less than
                    2.4 hours such that files have the time to
                    be written to disk, this is why I used 9000
                    seconds]

                    Remark that I used .out.xml , and not
                    .in.xml such that your script really
                    continues your ongoing jobs, and does not
                    restart from scratch every time.

                    I hope this can help,
                    Best
                    Fabien

                    Le 1 juil. 2012 à 14:40, Rachele Nerattini a
                    écrit :

...

                    Dear Mr. Troyer,

                    I read the page you suggested me but I
                    still don't understand. It says how to
                    restart a simulation stopped because the
                    computer shut down or how to make it stop
                    before its natural end in case you achieved
                    the required error but I don't understad
                    how to stop it in a controlled way.

                    For istance, let's suppose I have to run a
                    simulation which is 24 hours long.
                    I want to divide the long run in 10 runs of
                    2.4 hours each. The output of the first run
                    must be the input of the following and I
                    want to do all the runs in cascade.

                    What do I have to write in the input file
                    to do that? Sorry but I didn't find it in
                    the page

                    http://alps.comp-phys.org/mediawiki/index.php/Documentation:Running

                    certeinly because I'm not an expert in
                    these kind of things.

                    I copy and paste here in the following an
                    example of input file I've wrote for the
                    CINECA and an example of script I had to
                    write to run a tet job....
                    Can you tell me what I have to change to
                    make it stop after a certain numeber of
                    seconds? Then I'll ask to CINECA assistence
                    how to make all the block run in cascade.

                    Thank you and all the best,

                    Rachele Nerattini

                    input file = Ising3DL10mpiprocs10

                    LATTICE="simple cubic lattice"
                    LATTICE_LIBRARY="lattices.xml"
                    T=4.511441614
                    J=1
                    THERMALIZATION=200000
                    SWEEPS=1000000
                    UPDATE="cluster"
                    MODEL="Ising"
                    {L=10;}

                    script = Ising3DL10mpiprocs10.sh

                    #!/bin/bash
                    #PBS -A name_of_the_project
                    #PBS -l walltime=1:00:00
                    #PBS -l select=1:ncpus=10:mpiprocs=10:mem=40GB
                    #PBS -q parallel
                    #PBS -o Ising3DL10mpiprocs10.out
                    #PBS -e Ising3DL10mpiprocs10.err
                    # put the executable in the PATH
                    module load autoload alps
                    # cd in the directory where you have input
                    e job.sh
                    cd $PBS_O_WORKDIR
                    # prep gli input
                    parameter2xml Ising3DL10mpiprocs10

                    # it mounts openmpi to have mpirun in the PATH

                    module load profile/advanced
                    openmpi/1.4.4--intel--co-2011.6.233--binary

                    mpirun -np 10 spinmc --mpi --Tmin 100
                    --write-xml Ising3DL10mpiprocs10.in.xml

                    qsub Ising3DL10mpiprocs10.sh

                    What do I have to add to have what I need?

                    Thank you again for the help,

                    I whish you all the best

                    Rachele Nerattini


                    2012/7/1 Rachele Nerattini
                    <r.nerattini@gmail.com
                    <mailto:r.nerattini@gmail.com>>

                        Thank you very much for the help! I'll
                        do it immediately.
                        All the best
                        Rachele Nerattini


                        2012/7/1 Matthias Troyer
                        <troyer@phys.ethz.ch
                        <mailto:troyer@phys.ethz.ch>>

                            It is explained here:

                            http://alps.comp-phys.org/mediawiki/index.php/Documentation:Running

                            Best regards

                            Matthias Troyer

                            On Jul 1, 2012, at 12:18 PM,
                            Rachele Nerattini wrote:

...

                            Dear Mr.Troyer,

                            I'm using Monte Carlo simulations
                            for classical O(n) spin models. To
                            be more precise I'm using the
                            spinmc algorithm for Ising, XY and
                            Heisenberg models.

                            Thank you for the help,

                            all the best

                            Rachele Nerattini


                            2012/6/28 Matthias Troyer
                            <troyer@phys.ethz.ch
                            <mailto:troyer@phys.ethz.ch>>

                                Dear Rachele Nerattini,

                                Are you using Monte Carlo
                                simulations or one of the
                                other codes?

                                With best regards

                                Matthias Troyer

                                On 28 Jun 2012, at 16:59,
                                Rachele Nerattini wrote:

                                > Dear Mr.Troyer,
                                >
                                > I'm running some simulations
                                using ALPS at the CINECA
                                cluster in Bologna. I will
                                have to run really long
                                simulations which go well
                                beyond the walltime limit of
                                the machine.
                                >
                                > To do that I have to divide
                                the whole run in several
                                subsections and then run all
                                the processes in cascade.
                                >
                                > Can you tell me how can I do
                                that with ALPS? Which are the
                                commands of stop/restart that
                                I have to use?
                                >
                                > Thank you for your help,
                                >
                                > Rachele Nerattini

Hi Rachele Nerattini,

Is the time it takes 40 minutes? If so, probably the simulation is not finished yet and just stops after the time limit you have specified. Or is it 5 minutes? In that case the reason is that you told it to run for at least 5 minutes even if is already finished.

Matthias Troyer

On Sep 19, 2012, at 6:57 AM, Rachele Nerattini r.nerattini@gmail.com wrote:

Dear Mr Troyer,

sorry if I write again is only that I didn't hear anything from you and I'm not sure you received my mail. I have to run MC simulations for classical O(n) spin model in parallel.

I used the command

mpirun -np 4 spinmc --mpi --Tmin 300 --time-limit 2400 --write-xml Ising3DL32mpiprocs4.out.xml

to mean that I want to run it on 4 processors. The simulation goes fine and in the end I have these output files:

Ising3DL32mpiprocs4.out.xml Ising3DL32mpiprocs4.task1.out.run1.xml Ising3DL32mpiprocs4.task1.out.run2.xml Ising3DL32mpiprocs4.task1.out.run3.xml Ising3DL32mpiprocs4.task1.out.run4.xml

more other files. I am a bit surprised since in every file Ising3DL32mpiprocs4.task1.out.run*.xml It looks like I have a separate simulation of the same model and it doesn't seems like that the whole simulation (the one generated by the file Ising3DL32mpiprocs4.in.xml) is being partitioned in 4 parts.

In fact the simulation takes exactly the same time if I run it on 2, 4, 8, 12 .... processors. I don't have any gain in time with the parallelization of the program.

Why? Do I missing any flags in the command above or is the program really written for parallelization?

Thank you very much for the help.

Waiting for your answer, all the best

Rachele Nerattini

I have to run very long simulations of classical O(n) model in three spatial dimensions. In particular I study the Ising model, the XY model, the Heisenberg model and the O(4) model at the critical value of the temperature. To gain time I wanted to run the simulations in parallel.

An example of the input file I used is:

============================

LATTICE="simple cubic lattice" LATTICE_LIBRARY="lattices.xml" T=4.511441614 J=1 THERMALIZATION=200000 SWEEPS=1000000 UPDATE="cluster" MODEL="Ising" {L=32;} ============================

And the command I used to run the simulation on 4 processors is

mpirun -np 4 spinmc --mpi --Tmin 300 --time-limit 2400 --write-xml Ising3DL32mpiprocs4.out.xml (1)

---

To run the same simulation in a serial manner I use the command

spinmc --Tmin 300 --time-limit 2400 --write-xml Ising3DL32serial.out.xml (2)

In both cases the simulation runs properly BUT I the gain, in terms of time, of the parallel run with respect to the serial run is almost zero. This is true independentely on the number of processors that I used (2,4,8,12).

Am I doing some mistakes in the command line (1) ? Am I missing any flags or something like that? Or the parallelization of the program is done only at a compliler level (In the sense that the program spinmc can run on different processors but as a matter of fact it is not really optimized in this sense...)?

Thank you for your attention and for your answer.

With best regards,

Rachele

2012/7/1 Rachele Nerattini r.nerattini@gmail.com Thank you again for the quick and precise help.

2012/7/1 Rachele Nerattini r.nerattini@gmail.com ok, I'll try to run it on CINECA and I'll tell you if it works.

2012/7/1 Matthias Troyer troyer@phys.ethz.ch

On 1 Jul 2012, at 15:25, Rachele Nerattini wrote:

...

Thank you all very much! Yes, I think this could help. I'll send your mail to the CINECA-help-desk so that they will tell me if this is all we need and how to concatenate jobs.

In any case, if I understand well, all I have to do is:

Nearly

...

0)use parameter2xml to generate the file .*.in.xml;

...

1. to run the first block inserting the flag ' --time-limit #sec ' in the command line wich tells the program to stop after #sec seconds;

...

2. to run the second block using again the flag ' --time-limit #sec ' in the command line and the file .out.xml as input file;

3. to go on with this till the end of the simulations.

Yes

...

Is that ok? For what concerns the walltime limit I think it is 24 hours (24:00:00)...

24 ho0urs will be 86400 seconds, but the code will need time to write the checkpoints, thus specify about 1000 seconds less to be on the safe side.

...

Thnak you again I'll let you know if everything works. Bye for now Rachele

...

2012/7/1 Fabien Alet alet@irsamc.ups-tlse.fr Dear Rachele,

if I understood correctly, what you need to do is to : 0) run for 10 seconds or so your job locally on the main server such that file Ising3DL10mpiprocs10.out.xml gets generated (e.g. something like spinmc --time-limit 10 --write-xml Ising3DL10mpiprocs10.in.xml, alternatively just stop the job with CTRL-C)

1. add the time limit of 2.4 hours in the command line where you execute your observable, such as e.g.

mpirun -np 10 spinmc --mpi --Tmin 100 --time-limit 9000 --write-xml Ising3DL10mpiprocs10.out.xml [actually you should give slightly less than 2.4 hours such that files have the time to be written to disk, this is why I used 9000 seconds]

Remark that I used .out.xml , and not .in.xml such that your script really continues your ongoing jobs, and does not restart from scratch every time.

I hope this can help, Best Fabien

Le 1 juil. 2012 à 14:40, Rachele Nerattini a écrit :

...

Dear Mr. Troyer,

I read the page you suggested me but I still don't understand. It says how to restart a simulation stopped because the computer shut down or how to make it stop before its natural end in case you achieved the required error but I don't understad how to stop it in a controlled way.

For istance, let's suppose I have to run a simulation which is 24 hours long. I want to divide the long run in 10 runs of 2.4 hours each. The output of the first run must be the input of the following and I want to do all the runs in cascade.

What do I have to write in the input file to do that? Sorry but I didn't find it in the page

http://alps.comp-phys.org/mediawiki/index.php/Documentation:Running

certeinly because I'm not an expert in these kind of things.

I copy and paste here in the following an example of input file I've wrote for the CINECA and an example of script I had to write to run a tet job.... Can you tell me what I have to change to make it stop after a certain numeber of seconds? Then I'll ask to CINECA assistence how to make all the block run in cascade.

Thank you and all the best,

Rachele Nerattini

input file = Ising3DL10mpiprocs10

LATTICE="simple cubic lattice" LATTICE_LIBRARY="lattices.xml" T=4.511441614 J=1 THERMALIZATION=200000 SWEEPS=1000000 UPDATE="cluster" MODEL="Ising" {L=10;}

script = Ising3DL10mpiprocs10.sh

#!/bin/bash #PBS -A name_of_the_project #PBS -l walltime=1:00:00 #PBS -l select=1:ncpus=10:mpiprocs=10:mem=40GB #PBS -q parallel #PBS -o Ising3DL10mpiprocs10.out #PBS -e Ising3DL10mpiprocs10.err # put the executable in the PATH module load autoload alps # cd in the directory where you have input e job.sh cd $PBS_O_WORKDIR # prep gli input parameter2xml Ising3DL10mpiprocs10

# it mounts openmpi to have mpirun in the PATH

module load profile/advanced openmpi/1.4.4--intel--co-2011.6.233--binary

mpirun -np 10 spinmc --mpi --Tmin 100 --write-xml Ising3DL10mpiprocs10.in.xml

qsub Ising3DL10mpiprocs10.sh

What do I have to add to have what I need?

Thank you again for the help,

I whish you all the best

Rachele Nerattini

2012/7/1 Rachele Nerattini r.nerattini@gmail.com Thank you very much for the help! I'll do it immediately. All the best Rachele Nerattini

2012/7/1 Matthias Troyer troyer@phys.ethz.ch It is explained here:

http://alps.comp-phys.org/mediawiki/index.php/Documentation:Running

Best regards

Matthias Troyer

On Jul 1, 2012, at 12:18 PM, Rachele Nerattini wrote:

...

Dear Mr.Troyer,

I'm using Monte Carlo simulations for classical O(n) spin models. To be more precise I'm using the spinmc algorithm for Ising, XY and Heisenberg models.

Thank you for the help,

all the best

Rachele Nerattini

2012/6/28 Matthias Troyer troyer@phys.ethz.ch Dear Rachele Nerattini,

Are you using Monte Carlo simulations or one of the other codes?

With best regards

Matthias Troyer

On 28 Jun 2012, at 16:59, Rachele Nerattini wrote:

...

Dear Mr.Troyer,

I'm running some simulations using ALPS at the CINECA cluster in Bologna. I will have to run really long simulations which go well beyond the walltime limit of the machine.

To do that I have to divide the whole run in several subsections and then run all the processes in cascade.

Can you tell me how can I do that with ALPS? Which are the commands of stop/restart that I have to use?

Thank you for your help,

Rachele Nerattini