Posts by FrancescoAsnicar [SSC11]
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21) Message boards : Development : Application version v0.04 (problems thread) (Message 313)
Posted 21 Jan 2014 by Profile FrancescoAsnicar [SSC11]
It doesn't make sense to me because we fix the problem of critical section since the 0.03 version. Moreover, before writing the checkpoint we don't have any critical section!
We will surely investigate this issues (already saved in the to-do list ;-)
22) Message boards : News : gene@home: System restarted with new application (Message 311)
Posted 20 Jan 2014 by Profile FrancescoAsnicar [SSC11]
Changelog of the new, and previous, version of the Gene Network Application can be fond here: http://gene.disi.unitn.it/test/forum_thread.php?id=65#310
23) Message boards : Development : [changelog] Gene Network Application (Message 310)
Posted 20 Jan 2014 by Profile FrancescoAsnicar [SSC11]
Changelog of the Gene Network Application

v0.09
    - Fixed writing score
    - Better time estimation


v0.08

    - Removed the input file "experiments"
    - One input file sticky (compressed)
    - One single input for the application (compressed)
    - Change the score computation


v0.07

    - Removed the score file


v0.06

    - Fixed the stderr output


v0.05

    - Windows executables statically compiled
    - Linux glibc problem solved
    - Re-introduced the "score.txt" output file (not used for validation, we will use it for statistics)
    - The application can handle a variable number of input files (this should reduce the network usage)
    - The application now compute part of the post-processing analysis


v0.04

    - Standard error more compact
    - Removed the "score.txt" output file and the related MD5 library


v0.03

    - Compact standard error
    - Results file problem with carriage return/new line solved


v0.02

    - BOINC suspend working. Critical sections problem solved


v0.01

    - First release

24) Message boards : Wish List : Future requests (Message 305)
Posted 20 Jan 2014 by Profile FrancescoAsnicar [SSC11]
Now the project is beta but, in the future, may be stable and public
So, these are usually requests from volunteers for all boinc projects:
1) A GPU client (better OpenCL, for all gpu cards)

We think about to this possibility when we started integrating the software with the BOINC API... Unfortunately our algorithm is not so much parallelizable, hence is not suitable for the GPU hardware. I don't think there will be a GPU version of our project.

2) Screensaver

We think about it, and it will eventually develop. So far we had and we are still having more important issues to resolve.

3) Android client (for smartphone)

I don't think that our project would be suitable for a mobile platform, also because we have very big input file.

4) Extension for better performance (like AVX)

We have this point in our TO-DO list but our implementation is already very fast w.r.t. other implementation, hence is not a priority for the moment.

You have been warned!! :-)

Thanks for your suggestion!
25) Message boards : Number crunching : Disk space (Message 304)
Posted 20 Jan 2014 by Profile FrancescoAsnicar [SSC11]
I reset the project in order to test the new application version, as soon as there will be new wus. It didn't happen to me that the client downloaded files without wus.
Did you try to reset the project instead of clean the directory? Could you try to remove the project and re-add.
26) Message boards : Web site : Peter-Sprites (Message 301)
Posted 17 Jan 2014 by Profile FrancescoAsnicar [SSC11]
In the scientific description of the PC algorithm is wrote: "In particular, the PC (Peter-Sprites) is an improving of the SGS algorithm [..]"
There are two errors:
    1) "Sprites" is a mistake it should be "Spirtes";
    2) PC means Peter-Clark, Spirtes is the second name of Peter.

27) Message boards : Development : Application group request (compact stderr) (Message 252)
Posted 5 Jan 2014 by Profile FrancescoAsnicar [SSC11]
I've computed some wus with the new application... There are still a thousand lines in the stderr with 500 tiles, but I think that the lines printed are necessary for future debug!
28) Message boards : News : New work available (intermittently) (Message 251)
Posted 5 Jan 2014 by Profile FrancescoAsnicar [SSC11]
Every wus need of two files, the one with the data and another that contains the portion of work to be done. If you remove one of this file the application cannot execute. Anyway the stderr that you posted, in particular this part:
<message>
Uno o pi� argomenti non validi. (0x80000003) - exit code -2147483645 (0x80000003)
</message>

and this part:
ERROR: Invalid parameter detected in function (null). File: (null) Line: 0
ERROR: Expression: (null)

I don't recognise as our output, so I guess that the two previous messages are coming from BOINC.
29) Message boards : Development : Application group request (compact stderr) (Message 243)
Posted 4 Jan 2014 by Profile FrancescoAsnicar [SSC11]
Please try to make the stderr output more compact. From
#132 Tue Dec 24 02:05:01 2013
Graph created File: complete_gene_net read Standard deviations computed Correlations computed l: 0 1 2 3 4 5 6 7 8 9 # of arcs: 2223
Writing checkpoint's file
to something like
132|13-12-24 02:05:01|G F S|C(9:2223)
CHK
I mean, all the needed info squeezed in few bytes.


I did not work on that, but I think that the new version we already sent has a more compact stderr.


Yes, the new application version have a more compact stderr with timestamp!

Also, do you need to read the complete_gene_net at every iteration? Shouldn't be more efficient to just read it at start or returning from checkpoint and keep it (or a copy of it) in memory?


When we developed the first versions of the application, we had no bounds on the complete_gene size, so the best strategy was to read on-the-fly the lines needed.
I think that we should discuss this with professor Blanzieri, reading it once should be faster, but I suspect that working with different species could lead to far bigger input files, compared to the Arabidopsis. Splitting those files may be a solution, though..


We cannot read and store all in ram. For arabidopsis, that is a small genome, we calculated that the ram needed will be around 8 GB!
30) Message boards : News : New work available (intermittently) (Message 242)
Posted 4 Jan 2014 by Profile FrancescoAsnicar [SSC11]
We developed and give the new version of the application, with the problem of "\n" resolved and a little bug fix, the 28th of December 2013 to the server group!
31) Message boards : News : New work available (intermittently) (Message 222)
Posted 2 Jan 2014 by Profile FrancescoAsnicar [SSC11]
Why the applications are not updated?
We give to the server group the latest version of the applications, with the requested changes, the last week, but I don't see them on the server.

Thanks
32) Message boards : Development : Meeting proposal - Dec 30, 15:00, at my office (Message 202)
Posted 27 Dec 2013 by Profile FrancescoAsnicar [SSC11]
I'm sorry, I'll not be in Trento until the 7th of January.
If you want I'm available for a Skype call.
33) Message boards : Development : Application error on Windows x64 (Message 166)
Posted 24 Dec 2013 by Profile FrancescoAsnicar [SSC11]
We looked at the stderr of the wus. All of hem reported the same error. Searching the web for that error we found that is related with some missing libraries of windows. The problem lay on the pc of DanT.
34) Message boards : Web site : Problems... a lot of them! (Message 162)
Posted 24 Dec 2013 by Profile FrancescoAsnicar [SSC11]
In the "about Us" page is still missing the space between the "!" and the "(".

Here I attached two screenshot to show what I stil see in the home page.






The red bar shows the alignment.

Am I the only one that see that difference?
35) Message boards : Web site : Problems... a lot of them! (Message 159)
Posted 24 Dec 2013 by Profile FrancescoAsnicar [SSC11]
I'm sorry... I checked but the point 1, 6, 7 doesn't look fixed on my pc!
36) Message boards : Web site : Problems... a lot of them! (Message 158)
Posted 24 Dec 2013 by Profile FrancescoAsnicar [SSC11]
Good!


Let's consider this page now: http://gene.disi.unitn.it/test/genehome/joinus/system-requirements.php

The section "How to participate" is completely wrong! Doesn't make sense. I suggest to remove it, also because in the menu the title of that page is "System requirements".

I suggeste to remove also the whole part called "Management of users". I don't get the point of that section.
37) Message boards : News : We are (almost) ready to start a test phase (stage 1) (Message 150)
Posted 23 Dec 2013 by Profile FrancescoAsnicar [SSC11]
I noticed that, when I attached a linux machine to the project, BOINC downloaded 4 files with size about 70 MB!
Is it possible to compress that files?
38) Message boards : News : Suspend/Resume Problem (Message 147)
Posted 22 Dec 2013 by Profile FrancescoAsnicar [SSC11]
It seems that we fix the problem. I will reply tomorrow after tested all the platform available (we just tested only linux 64, windows 64 and mac).
39) Message boards : Windows : Windows application (first impressions) (Message 105)
Posted 19 Dec 2013 by Profile FrancescoAsnicar [SSC11]
We used
int boinc_time_to_checkpoint();
when we write the checkpoint file.
So I guess that is not related to the suspend issue.
40) Message boards : Windows : Windows application (first impressions) (Message 89)
Posted 19 Dec 2013 by Profile FrancescoAsnicar [SSC11]
Also on Mac OSX the suspend does not suspend the task... In the BOINC API there is nothing about suspension code-side.


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