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Profile valterc
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Message 1290 - Posted: 11 May 2018, 16:50:17 UTC

The experiments on Vitis vinifera are almost finished, thank you all. We will soon switch to a new organism. We made some tests some time ago but we found that the outputs of the Windows and Linux applications didn't match each other. The new forthcoming Windows applications should behave correctly.
The next Monday we will distribute them and (slowly) start creating new work.

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Message 1291 - Posted: 12 May 2018, 13:20:58 UTC - in response to Message 1290.

Great news!!

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Message 1294 - Posted: 15 May 2018, 13:05:25 UTC - in response to Message 1291.

I just made available the new Windows x64 sse2 application (other Windows applications will follow if everything works well)

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Message 1295 - Posted: 16 May 2018, 1:10:40 UTC

It looks like Windows app versions 1.10 and 1.11 might be giving conflicting results on Hs tasks, similar to the Linux/Windows issue before

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Message 1296 - Posted: 16 May 2018, 9:18:53 UTC - in response to Message 1295.

It looks like Windows app versions 1.10 and 1.11 might be giving conflicting results on Hs tasks, similar to the Linux/Windows issue before

Well, it should, that's why I have "deprecated" all the 1.10 Windows apps, I don't know why they are still around....

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Message 1297 - Posted: 16 May 2018, 19:01:01 UTC - in response to Message 1296.

From the checks I just made it seems that the new applications work correctly. There might be some issues while cross-validating against ARM applications, please tell me if you noticed this.
Also remember please to REMOVE the anonymous platform if you use it on Windows.

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Message 1298 - Posted: 17 May 2018, 14:50:53 UTC

I could not get one :-(

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Message 1299 - Posted: 17 May 2018, 15:20:00 UTC - in response to Message 1298.

I could not get one :-(

Be patient, at the moment we want to go forward slowly...

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Message 1300 - Posted: 18 May 2018, 15:05:48 UTC - in response to Message 1299.

I could not get one :-(

Be patient, at the moment we want to go forward slowly...


Wooww. Some wus!!

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Message 1301 - Posted: 18 May 2018, 17:03:24 UTC

These new, longer WUs are glorious. No more obsessively updating my machines to keep them from running dry =)

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Message 1316 - Posted: 24 May 2018, 16:29:52 UTC - in response to Message 1301.
Last modified: 24 May 2018, 16:30:16 UTC

Ok, after a lot of problems we are almost ready to start again (even not at full speed, by now). The new workunits (starting with id 141380_) are 10% longer, with a much smaller output file.

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Message 1317 - Posted: 24 May 2018, 17:34:46 UTC

i know this is low prio right now, but when do you update the science status page?

http://gene.disi.unitn.it/test/gene_science.php

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Message 1318 - Posted: 25 May 2018, 9:09:37 UTC - in response to Message 1317.

i know this is low prio right now, but when do you update the science status page?

http://gene.disi.unitn.it/test/gene_science.php

Right now we are doing the experiments on selected genes (chosen by the biologists), varying the parameters and also trying to figure out which modifications (filtering) we need to do on the input dataset. This is a preliminary phase, when we'll switch to the extensive analysis of all the genes of the selected dataset (the OneGenE experiment) I'll update the science page.

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Message 1319 - Posted: 26 May 2018, 18:01:03 UTC

The uploads seem smaller...

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Message 1320 - Posted: 26 May 2018, 18:51:09 UTC - in response to Message 1316.

Ok, after a lot of problems we are almost ready to start again (even not at full speed, by now). The new workunits (starting with id 141380_) are 10% longer, with a much smaller output file.


Good to hear. Double win for project server space. All good so far.

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Message 1397 - Posted: 3 Dec 2018, 3:10:36 UTC - in response to Message 1290.

It has been about 7 months since the start of plans to start working on a new Organism were first announced.

Can you give us an update on where we are on the change. Maybe what type of organism are we now working on and how big of a project this will in years of crunching.

Thank you
Bill F
Dallas TX
____________

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Message 1398 - Posted: 3 Dec 2018, 8:10:18 UTC - in response to Message 1397.

Can you give us an update on where we are on the change. Maybe what type of organism are we now working on and how big of a project this will in years of crunching.


A.Thaliana

Prostate Cancer

Coronary artery diseases

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Message 1399 - Posted: 3 Dec 2018, 10:04:34 UTC - in response to Message 1397.
Last modified: 3 Dec 2018, 10:05:11 UTC

The main 'new' organism is 'us', Homo sapiens. See here http://gene.disi.unitn.it/test/forum_thread.php?id=217. Being 'us' so complicated and obviously important, this project will keep us busy for a long time, at least one year from now.

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Message 1400 - Posted: 3 Dec 2018, 10:51:51 UTC - in response to Message 1399.

You have used GPUs in the past. But as I understand it, you didn't have enough work for them, and the output files were too big anyway.

Might this now change? Could you consider GPUs again?

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Message 1402 - Posted: 3 Dec 2018, 14:24:33 UTC - in response to Message 1400.

You have used GPUs in the past. But as I understand it, you didn't have enough work for them, and the output files were too big anyway.

Might this now change? Could you consider GPUs again?

We never had a GPU application available. Our algorithm is intrinsically not suited for the kind of parallelization needed by a a GPU. We were thinking, in the past, about a slightly modified version of the algorithm that may be good but we never get into it, mainly because we don't have anyone available here with the proper cuda/opencl skills.

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