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Posts by Jesús Carro

1) Message boards : News : Project status update // Actualización del estado del proyecto (Message 2253)
Posted 17 days ago by Profile Jesús Carro
Post:
Hi Jay,
While we are preparing the new simulations, we are testing some modifications in the optimization algorithm. In particular, the ones related to ORdInc, are working quite well. The differences are related on how we modify the region in which we look for new combinations of parameters. In the original one, we reduce the zone if the approximation was bad, and we increase if a parameter was in the limit of the region. In the ORdInc, we are also increasing if the approximation is really good. The smallest error has been found with this new approximation, but this result needs to be validated out of the optimization... we need to be cautious

By now, not, WU will not be highly produced yet.

Best,
Jesús.
2) Message boards : Number crunching : DENIS@home app for Raspberry Pi 32-bit? (Message 2250)
Posted 27 days ago by Profile Jesús Carro
Post:
Hi denismac,
At the moment we do not plan to expand to 32 bits. Maybe in the future, but not in the short term.

best,
Jesús.
3) Message boards : News : Project status update // Actualización del estado del proyecto (Message 2243)
Posted 17 Jan 2024 by Profile Jesús Carro
Post:
No, it is the same app, but we are trying a parameters in the simulation far away from the usuall ones. I don't know if it could generate any problem and I prefer to send in the Beta. We are testing some modifications in the optimization algorithm, not in the model. It will requiere a lot of time.

Best,
Jesús.
4) Message boards : News : Project status update // Actualización del estado del proyecto (Message 2241)
Posted 12 Jan 2024 by Profile Jesús Carro
Post:
Dear volunteers,
I am writing to update you on how the different experiments we had launched have been going and the next steps we will take.

On the one hand, we have finished (at least temporarily) the optimization of our model. As we had already told you, with the results that you have sent us, we managed to greatly improve how our model represented different physiological markers, but a problem that we thought we had solved had reappeared. We have tried different options but it reappeared in all of them. That forces us to stop and take steps back in the definition of the model, so, for the moment, we will not be launching new simulations in NHuVe.

On the other hand, as we had told you, we are trying to use our optimization algorithm in another existing model. The results seem to be very good, but we have to work in parallel on their validation.

In the coming weeks we will be working on requesting funding from the Government of Aragon for a new research project that will use DENIS as a computing platform, so you may have noticed that our activity has decreased a little. If this goes well (hopefully!) we will keep you informed, but keep in mind that these things are slow so the answer will take months to arrive.

Thank you all very much for staying there and for your support.

Sincerely,
Jesus.

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

Estimados voluntarios:
Os escribo para actualizar cómo han ido yendo los diferentes experimentos que teníamos lanzados y los próximos pasos que seguiremos.

Por un lado, hemos terminado (al menos temporalmente) la optimización de nuestro modelo. Como ya os habíamos comentado, con los resultados que nos habéis ido mandando conseguíamos mejorar mucho cómo nuestro modelo representaba diferentes marcadores fisiológicos pero había reaparecido un problema que creíamos haber solucionado. Hemos probado diversas opciones pero en todas ellas reaparecía. Eso nos obliga a parar y dar pasos atrás en la definición del modelo, por lo que, por el momento, no estaremos lanzando nuevas simulaciones en NHuVe.

Por otro lado, como os habíamos adelantado, estamos probando a utilizar nuestro algoritmo de optimización en otro modelo ya existente. Los resultados parecen ser muy buenos, pero tenemos que ir trabajando en paralelo en la validación de los mismos.

En las próximas semanas estaremos trabajando en pedir financiación al Gobierno de Aragón para un nuevo proyecto de investigación que utilizará DENIS como plataforma de cómputo por lo que habréis notado que ha bajado un poco nuestra actividad. Si esto saliera bien (¡ojalá!) os mantendremos informados, pero contad que estas cosas son lentas así que la respuesta tardará meses en llegar.

Muchas gracias a todos por seguir ahí y por vuestro apoyo.

Atentamente,
Jesús.
5) Message boards : Number crunching : Invalid tasks (Message 2219)
Posted 15 Nov 2023 by Profile Jesús Carro
Post:
No, most of the invalid causes are problems due to differences in the OS we have no considered. We need to still improve the program to avoid them.

Best,
Jesús
6) Questions and Answers : Getting started : Project URL (Message 2207)
Posted 17 Oct 2023 by Profile Jesús Carro
Post:
I don't know. As far I know, the client takes the projects from https://boinc.berkeley.edu/projects.php. The client updates it with a low frequency, but this mechanism is present since years
7) Message boards : Number crunching : Upload errors: server is out of disk space (Message 2203)
Posted 9 Oct 2023 by Profile Jesús Carro
Post:
Dear all,
Thank you very much for understanding.
Indeed there have been space problems this weekend. They have not been as serious as on previous occasions, but the cause is the same: not having eliminated all the previous results before launching the new simulations (this time only a part was left).
The system has not completely failed because with the results that arrived it was able to validate and thus save only 1 of the 2 versions that we received. That's why there have been times when it seemed to work.
We have already freed up space and got everything working, there may be a small transition until it is right.

Best,
Jesús.

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

Estimados voluntarios:
Muchas gracias por la comprensión.
Efectivamente ha habido problemas de espacio este fin de semana. No han sido tan graves como en ocasiones anteriores, pero la causa es la misma: no haber eliminado todos los resultados previos antes de lanzar las nuevas simulaciones (esta vez solo había quedado una parte).
No ha caido del todo el sistema porque con resultados que llegaban era capaz de validar y así guardar solo 1 de las 2 versiones que recibimos. Por eso ha habido momentos que parecía que funcionaba.
Ya hemos liberado espacio y puesto todo a funcionar, puede haber un pequeño transitorio hasta que esté bien.

Un saludo,
Jesús.
8) Message boards : Science : What exactly is this project about? (Message 2179)
Posted 4 Sep 2023 by Profile Jesús Carro
Post:
Of course. I've added it to the todo list. It shows some information when you are not logged in. I will review it.

Thanks for remember this after de modification of the web page.
9) Message boards : News : University network maintenance // Mantenimiento en la red de la universidad (Message 2174)
Posted 30 Aug 2023 by Profile Jesús Carro
Post:
Dear volunteers,
The IT department has notified us that tomorrow, starting at 3:00 p.m. (CEST), maintenance work will be carried out on the university network. It is possible that from that moment on there will be problems accessing DENIS.

Sorry for any inconvenience this may cause.

Best,
Jesús.

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

Estimados voluntarios:
El departamento de Sistemas de Información nos ha avisado de que mañana, a partir de las 15:00 (CEST), se realizarán trabajos de mantenimiento en la red de la universidad. Es posible que a partir de ese momento haya problemas de acceso a denis.

Disculpad las molestias que pueda genera.

Un saludo,
Jesús.
10) Message boards : News : Reduction in the number of tasks during the month of August // Reducción en el número de tareas durante el mes de agosto (Message 2173)
Posted 30 Aug 2023 by Profile Jesús Carro
Post:
The break has been fantastic!

Thank you!
11) Message boards : News : Reduction in the number of tasks during the month of August // Reducción en el número de tareas durante el mes de agosto (Message 2170)
Posted 11 Aug 2023 by Profile Jesús Carro
Post:
Spam deleted and user banished. Thank you for the reports.

Best, Jesús.
12) Message boards : News : Reduction in the number of tasks during the month of August // Reducción en el número de tareas durante el mes de agosto (Message 2161)
Posted 28 Jul 2023 by Profile Jesús Carro
Post:
Dear volunteers,
We are approaching the month of August in which the university rests for vacations. While we may not stop completely, the number of tasks available this month will be fewer. Our attention to the state of the server will be reduced, so we do not want to take the risk of saturating it.

Between the 20th to 28th the stop of new tasks will be total, resuming normal activity from the 29th or 30th.

I take this opportunity to tell you that the different variations of the optimization are continuing, in some cases it seems that we could obtain better results, but we are going to be cautious, when they are finished we will inform you of the final result.

Good summer everyone.

All the best,
Jesus.

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


Estimados voluntarios,
Nos acercamos al mes de agosto en el que en la universidad descansamos por vacaciones. Si bien es posible que no nos detengamos del todo, el número de tareas disponibles en este mes será menor. Nuestra atención al estado del servidor se verá reducida por lo que no queremos asumir el riesgo de saturarlo.

Entre los días 20 a al 28 la parada de nuevas tareas será total, retomandose a partir del día 29 o 30 la actividad normal.

Aprovecho para indicaros que las diferentes variaciones de la optimización siguen su curso, en algunos de los casos parece que podemos obtener mejores resultados, pero vamos a ser cautos, cuando hayan concluido os informaremos del resultado final.

Buen verano a todos.

Un saludo,
Jesús.
13) Message boards : Number crunching : HTTPS and more WU's (Message 2158)
Posted 25 Jul 2023 by Profile Jesús Carro
Post:
I allow it.

Best,
Jesús.
14) Questions and Answers : Getting started : Project URL (Message 2157)
Posted 25 Jul 2023 by Profile Jesús Carro
Post:
Yes, it is. The project should appear in the boinc client list.

Best,
Jesús.
15) Message boards : Number crunching : Invalid tasks (Message 2143)
Posted 29 Jun 2023 by Profile Jesús Carro
Post:
Hi all,
The percentage of invalid task is very small. The validation is not done with the output result, is done with the results files (out and markers). It compares both files of the results with other user. Small differences could appear due to different implementations of the opperations in different processors. The validation uses an error margin, but if the differences are bigger, a new simulation is requested.

Some differences could be solved or reduced with the implementation and we work on analyze that. At begining of this restart of the project, we had some problems with the checkpoints, but that is now solved.

We will continue working to try to reduce it further.

Best,
Jesús.
16) Message boards : Number crunching : Stats not uploading (Message 2133)
Posted 23 Jun 2023 by Profile Jesús Carro
Post:
Hi dskagcommunity,
The stats are working well but we need your authorization to export them to other websites. You can consent on https://denis.usj.es/denisathome/prefs.php?subset=project.

Best,
Jesús.
17) Message boards : Number crunching : ARM/ARM64 (Raspberry Pi) support (Message 2132)
Posted 23 Jun 2023 by Profile Jesús Carro
Post:
I have 16 Raspberry Pi's version 5.10.103-v7l+ which are 32 bit and would like to try them on Dennis@Home. I currently get the message:"

5994 DENIS@home 23/06/2023 2:34:42 AM Message from server: This project doesn't support computers of type arm-unknown-linux-gnueabihf

Thanks


It is in the to-do list
18) Message boards : News : Results and new simulations // Resultados y nuevas simulaciones (Message 2127)
Posted 21 Jun 2023 by Profile Jesús Carro
Post:
Other than the occasional server issue (growing pains) it sounds like your theories are progressing well.

Are you monitoring your system on the weekend for troubles?
I run my system 8 or so hours at night and 24hrs a day saturday and sunday. So if I get a server error I will know you saw it and will fix it. I hate having a backlog of tasks sitting on my system.

Is there some place we can go to look up what you are referring to?
Any way to provide a screen shot of what a "model" looks like?
What is the O'Hara and Rudy model?


Yes, we monitoring on the weekend, but with less frequency than other days. I understood you want to upload your tasks as soon as possible, and for that reason we are working on prevent the issues.

On the other hand, it is very complicated to explain how a model looks like. They are a lot of equations trying to represent how the different variables of a cell interact. The O'Hara and Rudy model is described in https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002061. At some point I want to start writing some more informative articles on the basis of our research so that I can explain more complex things later. Classes have finished and a quieter period is approaching... Let's see if I can start with this idea.

Best,
Jesús.
19) Message boards : Number crunching : Server Out of Space (Message 2123)
Posted 20 Jun 2023 by Profile Jesús Carro
Post:
Thank you. We know about it, and we are working to try to avoid it in the future.

Best,
Jesús.
20) Message boards : News : Results and new simulations // Resultados y nuevas simulaciones (Message 2122)
Posted 20 Jun 2023 by Profile Jesús Carro
Post:
Dear volunteers,
I am writing to update you on how the project is going and the results we are obtaining.

First of all, the optimization of the new model we are developing has already finished (the first one we released). Unfortunately the results have not been as expected. The optimization has worked very well and many markers have been improved, but one of the model issues that we are trying to fix has reappeared after the optimization. We think we understand where the problem is coming from and why it seemed like we fixed it, but really didn't. If we are right, this will require rethinking the model and starting over. Before starting again, we are testing various optimization settings to try to optimize the model without getting to the point where the problem reappears. We're not sure if it will work (this is science), but before we have to start over, we want to test this option.

On the other hand, some of you have already noticed that we are launching work in the Beta version. One of our pending projects was to use DENIS not only to improve the model we were developing, but also to try to improve other existing models. Let's start with this part of the project. For now, we will use the O'Hara and Rudy model, one of the most used in research. We have released the simulations in Beta version because we have never tested this model in DENIS before, but they will soon be released in HuVeMOp.

Finally, you may have noticed that we have run out of space a couple of times lately: the increase in the number of simulations requires more speed to get the results out and post-process them. We are working on further automating these processes in order to continue growing.

Thank you all very much for your support of the project and we will keep you informed of new developments.

Sincerely,
Jesus.

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

Estimados voluntarios:
Os escribo para actualizaros cómo va el proyecto y los resultados que estamos obteniendo.

En primer lugar, la optimización del nuevo modelo que estamos desarrollando ya ha terminado (la primera que lanzamos). Lamentablemente los resultados no han sido como esperábamos. La optimización ha funcionado muy bien y se han mejorado muchos marcadores, pero uno de los problemas del modelo que estabamos intentando solucionar, ha reaparecido tras la optimización. Creemos entender de dónde viene el problema y por qué parecía que lo habíamos solucionado, pero realmente no lo habíamos hecho. Si estamos en lo cierto, esto requerirá replantear el modelo y comenzar de nuevo. Antes de recomenzar de nuevo, estamos probando varias configuraciones de la optimización para intentar optimizar el modelo sin llegar al punto en el que reaparece el problema. No estamos seguros de si funcionará (esto es ciencia), pero antes de tener que volver a empezar, queremos probar esta opción.

Por otro lado, algunos ya habéis notado que estamos lanzando trabajo en la versión Beta. Uno de nuestros proyectos pendientes, era utilizar DENIS no solo para mejorar el modelo que estabamos desarrollando, sino para intentar mejorar otros modelos ya existentes. Vamos a arrancar con esta parte del proyecto. De momento lo haremos con el modelo de O'Hara y Rudy, uno de los más utilizados en investigación. Hemos lanzado las simulaciones en la versión Beta porque nunca habíamos probado este modelo en DENIS, pero en breve pasarán a lanzarse en HuVeMOp.

Finalmente, habréis notado que nos hemos quedado un par de veces sin espacio últimamente: el aumento en el número de simulaciones requiere mayor rapidez a la hora de sacar los resultados y post procesarlos. Estamos trabajando en automatizar más estos procesos para poder seguir creciendo.

Muchas gracias a todos por vuestro apoyo al proyecto y os mantenemos informados de los nuevos avances.

Atentamente,
Jesús.


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