Posts by Jesús Carro

21) Message boards : Number crunching : HTTPS and more WU's (Message 2158) Posted 25 Jul 2023 by Jesús Carro Post: I allow it. Best, Jesús.
22) Questions and Answers : Getting started : Project URL (Message 2157) Posted 25 Jul 2023 by Jesús Carro Post: Yes, it is. The project should appear in the boinc client list. Best, Jesús.
23) Message boards : Number crunching : Invalid tasks (Message 2143) Posted 29 Jun 2023 by 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.
24) Message boards : Number crunching : Stats not uploading (Message 2133) Posted 23 Jun 2023 by 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.
25) Message boards : Number crunching : ARM/ARM64 (Raspberry Pi) support (Message 2132) Posted 23 Jun 2023 by 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
26) Message boards : News : Results and new simulations // Resultados y nuevas simulaciones (Message 2127) Posted 21 Jun 2023 by 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.
27) Message boards : Number crunching : Server Out of Space (Message 2123) Posted 20 Jun 2023 by Jesús Carro Post: Thank you. We know about it, and we are working to try to avoid it in the future. Best, Jesús.
28) Message boards : News : Results and new simulations // Resultados y nuevas simulaciones (Message 2122) Posted 20 Jun 2023 by 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.
29) Message boards : News : Status of the project // Estado del proyecto (Message 2119) Posted 19 Jun 2023 by Jesús Carro Post: I noticed we now have Beta work (Myocyte). Is there a new piece of the project getting ready to start? Yes... This is a first test, I hope to start sending new work this week to the application HuVeMOp. Best, Jesús.
30) Message boards : News : Status of the project // Estado del proyecto (Message 2106) Posted 16 Jun 2023 by Jesús Carro Post: Why does this project block Russian IPs? We are not or not in general. We have a firewall to protect the web page: we received several atacks years ago. This is managed by the IT deparment. If you indicate me the IPs you are having problems with, I can ask them. Best, Jesús.
31) Message boards : News : Status of the project // Estado del proyecto (Message 2098) Posted 12 Jun 2023 by Jesús Carro Post: Hello, It is not only a question of efficiency (although also). To generate a new iteration, we need all the results from the previous iteration, the 45 markers in the 1000 points. We have to wait for all the results. That's why there is a time limit (it varies depending on the simulation but it is between 2 and 3 days). If we give you time, why not wait for the time we have given you? If a user does not send the result in the established time, it is sent to another volunteer. Are there ways to not expect all the results? Yes, but they imply that part of the simulations that you would do would never be used. That, for us, is a misuse of your resources (efficiency in another sense). Can some tasks take forever if multiple users don't submit them? Yes, but in those cases we launch the last ones on a server (a few) to finish the iteration. When there are more than 200 left, it is better to wait than to execute them locally. Below that number, we earn time. It's a good balance between how long you/us have to wait and how many simulations are duplicated. Also remember that between iterations, there is a process that still involves manual actions, so part of the pause is caused by this. We hope to be able to automate as much as possible, but it is again a balance between the technical part and the scientific part of the project. We need to grow in both. We could stop everything and work on the technical part for a long time until it was perfect (without producing scientific results and practically without sending you work beyond betas), or gradually improve the technical part while we use it to already be able to do research. As already mentioned, luckily there are other projects to which you can give your time. That's why we want to be efficient: If we waste your resources, we don't just take it only from you, we take also from other scientists. This project has had its ups and downs, but we are achieving sustained growth. I think this is the way, although I understand that many of you would like another situation. I also want there to be a more constant flow (and less manual part...) To all of you, with the bit of your time that you give us, thank you very much. Best, Jesús.
32) Message boards : News : Status of the project // Estado del proyecto (Message 2094) Posted 31 May 2023 by Jesús Carro Post: Hi Jean-David, This is exactly our idea. Little by little, we want to add more optimizations to mantain an stable load of work. Currently, we are running 3 versions of the model optimization (each one with an small variation on the options of the algorithm). One of the limitations is that the postprocessing of your results is done out of the server, and it requieres a manual step, so the three tend to be synchronized because even if one finishes earlier, if that happens at night or during the weekend, the post-processing is done at the same time. Yesterday we sent a lot of work (from the three of them), but I guess they won't last long :-). I will publish an update of the results the next week (we are finishing the validation process of the first version of the optimization), and I will explain there the new versions we have started (the validation of the first one does not look good, so we will still need your help). Best, Jesús.
33) Message boards : Number crunching : What is this? (Message 2088) Posted 28 Apr 2023 by Jesús Carro Post: Hi, We discussed this in another thread: https://denis.usj.es/denisathome/forum_thread.php?id=259 Best, Jesús
34) Message boards : News : Status of the project // Estado del proyecto (Message 2087) Posted 28 Apr 2023 by Jesús Carro Post: Yesterday... but you are too fast getting the tasks... Probably, we will send more tasks tomorrow Best, Jesús.
35) Message boards : Number crunching : Invalid task (Message 2081) Posted 21 Apr 2023 by Jesús Carro Post: Only in this project? It is too much.
36) Message boards : Number crunching : What does 1 credit equal? (Message 2079) Posted 19 Apr 2023 by Jesús Carro Post: Hi GreekScorpion, The credits you get from a valid results is related to the mean time used to compute it. It depends on the time you spend and in the time the other user spents. It is a mechanism designed to encourage volunteers with low computing capacity not to fall out of the projects. You can read more about the systems in https://boinc.berkeley.edu/trac/wiki/CreditOptions (we use the default one), and a longer explanation in https://boinc.berkeley.edu/trac/wiki/CreditNew Best, Jesús.
37) Message boards : Number crunching : Checksum error (Message 2073) Posted 17 Apr 2023 by Jesús Carro Post: Hi Crystal, I needed to remove the project and the files of the project in the BOINC folder (C:\ProgramData\BOINC in my case) to get them without errors. I think that the client is not updating the MD5 value (or no so fast). But the files you downloaded are right (the checksum you get is the right one) Best, Jesús.
38) Message boards : News : Status of the project // Estado del proyecto (Message 2070) Posted 14 Apr 2023 by Jesús Carro Post: Hi Marcin, Yes, the algorithm now explores more space, but based on an polinomical aproximation of the behavior of the model. The polinomical aproximation within the trust region is fixed with all the simulations you send to us. I am also looking forward to the results of the third iteration. Best, Jesús.
39) Message boards : Number crunching : New tasks? (Message 2069) Posted 14 Apr 2023 by Jesús Carro Post: Hi vaugahn, I'm sorry but no, we cannot ensure a continuous flow of tasks. In the optimization algorithm, one iteration starts when the previous one ended. We usually send around 180.000 task per iteration, and when then end we are able to analyze and to start the next one. Little by little we are going to add new optimizations of other models, so that while we wait for an iteration of a model to finish, we are sending you others. We are currently with 2, but we need to grow little by little to control that it does not break. Each optimization requires quite a bit of disk space until the results are post-processed. Indeed, in this project we have no other way of thanking you for your effort than in the statistics, since the final result does not depend on a single simulation (which in my opinion is also nice because no matter how little you do, you also contribute to the final result). I appreciate the effort you make, however, please, seeing how the current volume of work is and the number of volunteers you are, it is not necessary that you rent machines for it. This thread has been quite tense, please, let's be understanding of the situations and motivations of others. For my part, I have no objection to explain more and better why we cannot send more, I hope you can understand it. Best, Jesús.
40) Message boards : Number crunching : Invalid task (Message 2068) Posted 14 Apr 2023 by Jesús Carro Post: Hi Dayle, We have observed an small increment in the non valid results. We are analazying what is happening. Neverless, the percentage of non valid is still very small. More than checkpointing problems, it is related usually with problems opening or saving the file (which depends on the operative system). I will keep you updated. Best, Jesús.

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