diffusion error

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kocogl...@gmail.com

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Apr 24, 2018, 12:17:24 PM4/24/18
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Hi,

I am trying to run diffusion on my network but, receive the error about connecting to the cloud. I ensured that there is nothing wrong with the internet connection, since I am actually running it on the server. Do you have any suggestions? Thanks.

Barry Demchak

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Apr 24, 2018, 12:23:51 PM4/24/18
to cytoscape...@googlegroups.com, Eric Sage
Hi,

Thanks for this report ... it's very valuable.

Would you be able to supply a picture of the error you're getting?

What happens if you ask for the diffusion again? Does it finish properly?

Is this session (and exact diffusion selection) something you can share with us to see if we can duplicate this?

Thanks!
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Cemile Koçoğlu

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May 8, 2018, 5:42:11 AM5/8/18
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Hi,

Thanks for the reply. I tried again it never comes to an end.

I don't know whether if I need a specific type or network to run the diffusion though. But, I guess this error is unrelated. 

This is the error I receive.



24 Nisan 2018 Salı 18:23:51 UTC+2 tarihinde Barry Demchak yazdı:
Hi,

Thanks for this report ... it's very valuable.

Would you be able to supply a picture of the error you're getting?

What happens if you ask for the diffusion again? Does it finish properly?

Is this session (and exact diffusion selection) something you can share with us to see if we can duplicate this?

Thanks!

-----Original Message-----
From: cytoscape...@googlegroups.com <cytoscape...@googlegroups.com> On Behalf Of kocogl...@gmail.com
Sent: Tuesday, April 24, 2018 9:05 AM
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Subject: [cytoscape-helpdesk] diffusion error

Hi,

I am trying to run diffusion on my network but, receive the error about connecting to the cloud. I ensured that there is nothing wrong with the internet connection, since I am actually running it on the server. Do you have any suggestions? Thanks.

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Cemile Koçoğlu

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May 8, 2018, 5:46:23 AM5/8/18
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By the way, I forgot to add the file. I tried in several subgroups of this session. 

8 Mayıs 2018 Salı 11:42:11 UTC+2 tarihinde Cemile Koçoğlu yazdı:
Merged_imex_intact_biogrid_mint_innate_6genes_240418.cys

Barry Demchak

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May 8, 2018, 12:30:06 PM5/8/18
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Hi, Cemile –

 

I just tried diffusion with one of the sample networks … Yeast Perturbation. It works fine here.

 

I also just tried it with the session you supplied. I used the nodes that were selected in your session. It also worked fine here.

 

To execute a Diffusion, your Cytoscape calls a web service located in the USA. If you’re calling from Turkey, there could be a lag, but I don’t think it would be significant enough to cause failure.

 

Does Diffusion *ever* work?? … How is the bandwidth on your network connection? … Could you be behind a proxy that doesn’t allow a call to this web service??

 

Digging a bit deeper here …

 

From: cytoscape...@googlegroups.com <cytoscape...@googlegroups.com> On Behalf Of Cemile Koçoglu
Sent: Tuesday, May 08, 2018 2:46 AM
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Subject: Re: [cytoscape-helpdesk] diffusion error

 

By the way, I forgot to add the file. I tried in several subgroups of this session. 

8 Mayıs 2018 Salı 11:42:11 UTC+2 tarihinde Cemile Koçoğlu yazdı:

Hi,

 

Thanks for the reply. I tried again it never comes to an end.

 

I don't know whether if I need a specific type or network to run the diffusion though. But, I guess this error is unrelated. 

 

This is the error I receive.

 

https://lh3.googleusercontent.com/-Hm5waTlQdL4/WvFwgy0sYgI/AAAAAAAAPQw/sqM4CdaDzG0GTbNLNUZ2ADBuxcQYCVh3wCLcBGAs/s320/diffusion%2Berror.PNG



24 Nisan 2018 Salı 18:23:51 UTC+2 tarihinde Barry Demchak yazdı:

Hi,

Thanks for this report ... it's very valuable.

Would you be able to supply a picture of the error you're getting?

What happens if you ask for the diffusion again? Does it finish properly?

Is this session (and exact diffusion selection) something you can share with us to see if we can duplicate this?

Thanks!

-----Original Message-----
From: cytoscape...@googlegroups.com <cytoscape...@googlegroups.com> On Behalf Of kocogl...@gmail.com
Sent: Tuesday, April 24, 2018 9:05 AM
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Subject: [cytoscape-helpdesk] diffusion error

Hi,

I am trying to run diffusion on my network but, receive the error about connecting to the cloud. I ensured that there is nothing wrong with the internet connection, since I am actually running it on the server. Do you have any suggestions? Thanks.

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Cemile Koçoğlu

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May 14, 2018, 5:20:11 AM5/14/18
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Hi Barry,

Indeed, I also tried on a different computer connected to a different internet it worked fine. However, it did not work when I used the same internet connection.

I don't know details about internet connection but.. Would this give an idea?



Thanks a lot!



8 Mayıs 2018 Salı 18:30:06 UTC+2 tarihinde Barry Demchak yazdı:

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Barry Demchak

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May 14, 2018, 12:17:08 PM5/14/18
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Hi, Cemile –

 

Thanks for the information. I haven’t used slurm before, so I loaded it onto one of our workstations and got the following:

 

 

As you can see, my numbers are much bigger. I suspect that your slurm was taken while your internet link was idle. A more representative measurement would be to run slurm at the same time as transferring a large file/directory to your PC .. like maybe during a Cytoscape download (http://www.cytoscape.org/download.php).

 

It’s interesting that you get a good answer from one computer as distinct from a different computer. I gather that both computers are located close to each other and share a common external internet feed?  If so, maybe the difference is in the computers themselves. Do they have similar memory and operating systems? Are both computers relatively unloaded? Can you tell me more?

 

Also, for the computer that’s not working, can you give me an idea of when you last tried and failed a Diffusion? We would be very happy to look into our logs to see what could have happened? Alternately, if you can choose a time tomorrow (early in the day?) and tell us what time the failure occurred, we’ll look in the logs tomorrow.

 

Thanks!

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