Operation suffered fatal failure! Exit code: -9 Exit message: ('', '')

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JIAQI ZHANG

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Sep 7, 2021, 11:25:32 AMSep 7
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Hi!I'm new to TVB and I‘ve run my simulation (BOLD Region ROI only with surface)for some hours and have the error:'Operation suffered fatal failure! Exit code: -9 Exit message: ('', '')'. I don't know why and want some help, please!

My project has 51000 vertex and I wonder if that matters.


Julie Courtiol

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Sep 7, 2021, 1:44:15 PMSep 7
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Hi,

Surface-based simulations are heavy processes that require a lot of memory. Probably, your OS killed your process because it was out of memory. Did you check it? 
---
Best regards,

Julie Courtiol





Le mar. 7 sept. 2021 à 17:25, JIAQI ZHANG <smile.z...@gmail.com> a écrit :


Hi!I'm new to TVB and I‘ve run my simulation (BOLD Region ROI only with surface)for some hours and have the error:'Operation suffered fatal failure! Exit code: -9 Exit message: ('', '')'. I don't know why and want some help, please!

My project has 51000 vertex and I wonder if that matters.


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JIAQI ZHANG

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Sep 7, 2021, 8:11:06 PMSep 7
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Thanks for your advice and I‘ll try it again! And I have three questions :
1、I don't know the difference between 'BOLD' and ' BOLD Region ROI only with surface ' in 'monitors', can both of them be used to calculate FC ?
2、How to calculate ‘Local connectivity’ in 'Cortical Surface', can I use python or some other tools, such as freesurfer?
3、If the number of vertex is too large, our result will be better or worse?
I know these questions may be easy but I'm really puzzled, sorry to bother you!

Julie Courtiol

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Sep 8, 2021, 6:35:25 AMSep 8
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Please, see below my reply.

Best, Julie

---
Best regards,

Julie Courtiol




Le mer. 8 sept. 2021 à 02:11, JIAQI ZHANG <smile.z...@gmail.com> a écrit :
Thanks for your advice and I‘ll try it again! And I have three questions :
 
1、I don't know the difference between 'BOLD' and ' BOLD Region ROI only with surface ' in 'monitors', can both of them be used to calculate FC ?

TVB computes two types of simulation: region-based and surface-based. For a region-based simulation, each node of the brain network represents a region; while for surface-based simulation, each node represents a vertex on the surface.

The monitor 'BOLDRegionROI' is specifically designed to generate BOLD activity at the surface level, using the region mapping.

More generally, we use region-based simulations as it is simpler and with lesser computational cost.
Surface-based are used for answering specific question that demands a more complex brain models. For example, it was used in Jirsa et al., 2017 for studying the connectivity influence of a local lesion in an epileptic patient; or in Spiegler et al. 2016, for investigating the networks activation after a stimulation, etc.
So, the use of region- versus surface- depends on which process you want to simulate, your scientific question.

If you are starting with TVB, I would suggest to use first region-based simulations to understand the principles.

I would also suggest to have a look at the paper of Sanz-Leon et al. 2015
 

2、How to calculate ‘Local connectivity’ in 'Cortical Surface', can I use python or some other tools, such as freesurfer?

The local connectivity is computing using a kernel function, that you can choose within TVB.
I would suggest to read this specific part in the paper mentioned above.

 
3、If the number of vertex is too large, our result will be better or worse?

Finer parcellation brings more information but once again, it depends of what you want to simulate.

I hope that helps and give you some working directions.
 
I know these questions may be easy but I'm really puzzled, sorry to bother you!
在2021年9月8日星期三 UTC+8 上午1:44:15<courtio...@gmail.com> 写道:
Hi,

Surface-based simulations are heavy processes that require a lot of memory. Probably, your OS killed your process because it was out of memory. Did you check it? 
---
Best regards,

Julie Courtiol





Le mar. 7 sept. 2021 à 17:25, JIAQI ZHANG <smile.z...@gmail.com> a écrit :


Hi!I'm new to TVB and I‘ve run my simulation (BOLD Region ROI only with surface)for some hours and have the error:'Operation suffered fatal failure! Exit code: -9 Exit message: ('', '')'. I don't know why and want some help, please!

My project has 51000 vertex and I wonder if that matters.


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JIAQI ZHANG

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Sep 9, 2021, 6:13:49 AMSep 9
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Sorry to bother you again. I try to expand ' Max hard disk space per user ' to 3T but I get the same error after simulate for 7h.

在2021年9月8日星期三 UTC+8 上午1:44:15<courtio...@gmail.com> 写道:

JIAQI ZHANG

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Sep 9, 2021, 6:14:55 AMSep 9
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Thanks for your explanation!

JIAQI ZHANG

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Sep 9, 2021, 6:52:02 AMSep 9
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The settings is in picture.QQ图片20210909184427.png1.png2.png3.png4.png

在2021年9月8日星期三 UTC+8 上午1:44:15<courtio...@gmail.com> 写道:

WOODMAN Michael

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Sep 9, 2021, 11:13:16 AMSep 9
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hi

Can you use the Activity Monitor on macOS, with the Memory pane, to watch memory use during the simulation?

Cheers,
Marmaduke

On 9 Sep 2021, at 12:52, JIAQI ZHANG <smile.z...@gmail.com> wrote:

The settings is in picture.<QQ图片20210909184427.png><1.png><2.png><3.png><4.png>

JIAQI ZHANG

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Sep 9, 2021, 11:25:36 AMSep 9
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Thanks for your letter. I deployed TVB on linux server and use pmap -d to watch memory use as you can seepamp.png in the picture.

WOODMAN Michael

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Sep 10, 2021, 3:14:36 AMSep 10
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hi

That seems fine. Can you share the content of TVB log files in ~/TVB/logs ? By private message is fine, if you prefer not to put on the mailing list

Cheers,
Marmaduke

On 9 Sep 2021, at 17:25, JIAQI ZHANG <smile.z...@gmail.com> wrote:

Thanks for your letter. I deployed TVB on linux server and use pmap -d to watch memory use as you can see<pamp.png> in the picture.


在2021年9月9日星期四 UTC+8 下午11:13:16<marmaduke.woodman> 写道:
hi

Can you use the Activity Monitor on macOS, with the Memory pane, to watch memory use during the simulation?

Cheers,
Marmaduke

On 9 Sep 2021, at 12:52, JIAQI ZHANG <smile.z...@gmail.com> wrote:

The settings is in picture.<QQ图片20210909184427.png><1.png><2.png><3.png><4.png>


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JIAQI ZHANG

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Sep 10, 2021, 4:31:07 AMSep 10
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Thanks for your letter and my web_application.logs are in picture.web_application_log.png

WOODMAN Michael

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Sep 10, 2021, 7:41:37 AMSep 10
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hi

Sorry, so far it is insufficient for identifying the cause. You can watch top and dmesg -w to see for memory issues and if the process is killed. If it's hard disk space, check df -h, etc.

Cheers,
Marmaduke

> On 10 Sep 2021, at 10:31, JIAQI ZHANG <smile.z...@gmail.com> wrote:
>
> <web_application_log.png>

Lia Domide

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Sep 10, 2021, 7:48:13 AMSep 10
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Hi. Do you have anything in an operation...logs file ?

JIAQI ZHANG

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Sep 10, 2021, 8:16:39 AMSep 10
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Thanks for your advice and I'll try it later.
Actually I wonder if the 'Local Connectivity'  is necessary for surface-based model?
Besides, I simulate another region-based model and I get the simulated FC as sfc_sub1.png shows, however the empirical FC is very different from it as esfc_sub1.pngefc_sub1.pngfc_sub1.png shows that the pearson correlation between them is about 0.07....
I wonder if the most effective improvement is to optimize large-range connections or parameter?

JIAQI ZHANG

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Sep 10, 2021, 8:18:44 AMSep 10
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Hi. Actually I see the operations tab and find the error operation is local-connectivity calculation. I don't if it's necessary to have it to simulate a surface-based model.

WOODMAN Michael

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Sep 10, 2021, 8:32:58 AMSep 10
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Hi

Local connectivity is required for surface simulations, but in your case, you may wish to start with the region simulations to tune your FC, and then add the surface in.  It should shorten the overall process. 

For the error, probably the surface is too large for the local connectivity calculation, which can require a lot of memory for large surfaces. A 500k vertex with default parameters surface results in a ~30 GB local connectivity, and intermediate calculations can require more memory than that. 

Cheers,
Marmaduke

JIAQI ZHANG

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Sep 10, 2021, 9:20:32 AMSep 10
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Thanks for your letter!!! Actually I apply 3T space which is enough for my simulation. And I wonder how can I calculate local connectivity,  I do not see the tab that I can upload local connectivity as red lines in pic1.png. And I cannot load local connectivity as red linespic1.pngpic2.png in pic2.png. I know it's a basic question but I wonder which tools I can use to calculate local connectivity?

WOODMAN Michael

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Sep 10, 2021, 9:41:16 AMSep 10
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hi

The button is there on the right, "Create new Local Connectivity" with a grey plus sign. It's not the most obvious place to look, but I can see it on your screenshot.

Cheers,
Marmaduke


> On 10 Sep 2021, at 15:20, JIAQI ZHANG <smile.z...@gmail.com> wrote:
>
> Thanks for your letter!!! Actually I apply 3T space which is enough for my simulation. And I wonder how can I calculate local connectivity, I do not see the tab that I can upload local connectivity as red lines in pic1.png. And I cannot load local connectivity as red lines<pic1.png><pic2.png> in pic2.png. I know it's a basic question but I wonder which tools I can use to calculate local connectivity?

JIAQI ZHANG

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Sep 11, 2021, 3:39:01 AMSep 11
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Thanks for you reminder!  I create a new local-connectivity and get the error 'Operation suffered fatal failure! Exit code: -9 Exit message: ('', '')' again.
My space is 3T, which is enough for it.
And my settings are in picture. Some logs are in attachment. Sorry to bothor you again!!settings.pngerror.png
operations_executions.log.2021-09-10

Lia Domide

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Sep 11, 2021, 6:18:52 AMSep 11
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Hi. Could you try reducing the cutoff distance? Maybe progressively (from 40, 10, even down to 1) to see the impact on the used RAM ?

JIAQI ZHANG

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Sep 11, 2021, 8:48:31 PMSep 11
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Thanks a lot! It's ok
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