Re: [External] Re: DockerSpawnner for Jupyterhub

[Hansaria, Himanshu]

Thanks Dimuthu.

Yeah, i'll follow that.




From: DImuthu Upeksha 
Sent: Saturday, July 2, 2022 12:14 AM
To: Airavata Dev 
Subject: [External] Re: DockerSpawnner for Jupyterhub

This message was sent from a non-IU address. Please exercise caution when 
clicking links or opening attachments from external sources.

Hi Himanshu,

Use the standard batch spawner provided by jupyterehub. Once you have it 
running in a SLURM cluster, you need to change the slurm script that spins up 
notebook processes to spinup notebook containers instead. The container image 
should be configurable.

[1] 
https://github.com/jupyterhub/batchspawner

Thanks
Dimuthu

On Fri, Jul 1, 2022 at 11:43 PM Hansaria, Himanshu 
mailto:hhan...@iu.edu>> wrote:
I plan to setup slurm spawner following this.

Please let me know if i should be following this for the same.

https://github.com/mkgilbert/slurmspawner
[https://opengraph.githubassets.com/3a058a2fadd040fea783725bf9b5a69f861b5f49942ac86b7584c9b57264cac2/mkgilbert/slurmspawner]
GitHub - mkgilbert/slurmspawner: Custom Spawner for Jupyterhub to start slurm 
jobs when users log 
in
slurmspawner for Jupyterhub. This is a custom spawner for Jupyterhub that is 
designed for installations on clusters using Slurm scheduling software.
github.com



For others, the idea is to instantiate single user notebook servers inside a 
container on the local machine with the Docker Spawner. The eventual goal is to 
write a custom spawner which is a merge of the Docker and the slurm Spawner.


Thanks and regards,
Himanshu

From: Hansaria, Himanshu mailto:hhan...@iu.edu>>
Sent: Friday, July 1, 2022 10:54 PM
To: dev@airavata.apache.org 
mailto:dev@airavata.apache.org>>
Subject: [External] Re: DockerSpawnner for Jupyterhub

This message was sent from a non-IU address. Please exercise caution when 
clicking links or opening attachments from external sources.

PS :- I'm able to run a notebook inside it as well.

Thanks,
Himanshu

From: Hansaria, Himanshu mailto:hhan...@iu.edu>>
Sent: Friday, July 1, 2022 10:48 PM
To: dev@airavata.apache.org 
mailto:dev@airavata.apache.org>>
Subject: [External] DockerSpawnner for Jupyterhub

This message was sent from a non-IU address. Please exercise caution when 
clicking links or opening attachments from external sources.

Hi Dimuthu,

I was able to get the DockerSpawner for jupyterhub working.

Can you confirm if this is the needed functionality?
Please see the screenshot attached for reference.

My container spawned using DockerSpawner is running on http://localhost:53320/.

Thanks and regards,
Himanshu

Re: DockerSpawnner for Jupyterhub

[DImuthu Upeksha]

Hi Himanshu,

Use the standard batch spawner provided by jupyterehub. Once you have it
running in a SLURM cluster, you need to change the slurm script that spins
up notebook processes to spinup notebook containers instead. The container
image should be configurable.

[1] https://github.com/jupyterhub/batchspawner

Thanks
Dimuthu

On Fri, Jul 1, 2022 at 11:43 PM Hansaria, Himanshu  wrote:

> I plan to setup slurm spawner following this.
>
> Please let me know if i should be following this for the same.
>
> https://github.com/mkgilbert/slurmspawner
> 
> GitHub - mkgilbert/slurmspawner: Custom Spawner for Jupyterhub to start
> slurm jobs when users log in 
> slurmspawner for Jupyterhub. This is a custom spawner for Jupyterhub that
> is designed for installations on clusters using Slurm scheduling software.
> github.com
> **
> **
> **
> For others, the idea is to instantiate single user notebook servers inside
> a container on the local machine with the Docker Spawner. The eventual
> goal is to write a custom spawner which is a merge of the Docker and the
> slurm Spawner.
>
>
> Thanks and regards,
> Himanshu
> --
> *From:* Hansaria, Himanshu 
> *Sent:* Friday, July 1, 2022 10:54 PM
> *To:* dev@airavata.apache.org 
> *Subject:* [External] Re: DockerSpawnner for Jupyterhub
>
> This message was sent from a non-IU address. Please exercise caution when
> clicking links or opening attachments from external sources.
>
> PS :- I'm able to run a notebook inside it as well.
>
> Thanks,
> Himanshu
> --
> *From:* Hansaria, Himanshu 
> *Sent:* Friday, July 1, 2022 10:48 PM
> *To:* dev@airavata.apache.org 
> *Subject:* [External] DockerSpawnner for Jupyterhub
>
> This message was sent from a non-IU address. Please exercise caution when
> clicking links or opening attachments from external sources.
>
> Hi Dimuthu,
>
> I was able to get the DockerSpawner for jupyterhub working.
>
> Can you confirm if this is the needed functionality?
> Please see the screenshot attached for reference.
>
> My container spawned using DockerSpawner is running on
> http://localhost:53320/.
>
> Thanks and regards,
> Himanshu
>
>
>
>

Re: DockerSpawnner for Jupyterhub

[Hansaria, Himanshu]

I plan to setup slurm spawner following this.

Please let me know if i should be following this for the same.

https://github.com/mkgilbert/slurmspawner
[https://opengraph.githubassets.com/3a058a2fadd040fea783725bf9b5a69f861b5f49942ac86b7584c9b57264cac2/mkgilbert/slurmspawner]
GitHub - mkgilbert/slurmspawner: Custom Spawner for Jupyterhub to start slurm 
jobs when users log in
slurmspawner for Jupyterhub. This is a custom spawner for Jupyterhub that is 
designed for installations on clusters using Slurm scheduling software.
github.com



For others, the idea is to instantiate single user notebook servers inside a 
container on the local machine with the Docker Spawner. The eventual goal is to 
write a custom spawner which is a merge of the Docker and the slurm Spawner.


Thanks and regards,
Himanshu

From: Hansaria, Himanshu 
Sent: Friday, July 1, 2022 10:54 PM
To: dev@airavata.apache.org 
Subject: [External] Re: DockerSpawnner for Jupyterhub

This message was sent from a non-IU address. Please exercise caution when 
clicking links or opening attachments from external sources.

PS :- I'm able to run a notebook inside it as well.

Thanks,
Himanshu

From: Hansaria, Himanshu 
Sent: Friday, July 1, 2022 10:48 PM
To: dev@airavata.apache.org 
Subject: [External] DockerSpawnner for Jupyterhub

This message was sent from a non-IU address. Please exercise caution when 
clicking links or opening attachments from external sources.

Hi Dimuthu,

I was able to get the DockerSpawner for jupyterhub working.

Can you confirm if this is the needed functionality?
Please see the screenshot attached for reference.

My container spawned using DockerSpawner is running on http://localhost:53320/.

Thanks and regards,
Himanshu

Re: DockerSpawnner for Jupyterhub

[Hansaria, Himanshu]

PS :- I'm able to run a notebook inside it as well.

Thanks,
Himanshu

From: Hansaria, Himanshu 
Sent: Friday, July 1, 2022 10:48 PM
To: dev@airavata.apache.org 
Subject: [External] DockerSpawnner for Jupyterhub

This message was sent from a non-IU address. Please exercise caution when 
clicking links or opening attachments from external sources.

Hi Dimuthu,

I was able to get the DockerSpawner for jupyterhub working.

Can you confirm if this is the needed functionality?
Please see the screenshot attached for reference.

My container spawned using DockerSpawner is running on http://localhost:53320/.

Thanks and regards,
Himanshu

[GitHub] [airavata-sandbox] dependabot[bot] opened a new pull request, #72: Bump kafka-clients from 0.10.1.1 to 0.10.2.2 in /airavata-kubernetes

[GitBox]

dependabot[bot] opened a new pull request, #72:
URL: https://github.com/apache/airavata-sandbox/pull/72

   Bumps kafka-clients from 0.10.1.1 to 0.10.2.2.
   
   
   [![Dependabot compatibility 
score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=org.apache.kafka:kafka-clients=maven=0.10.1.1=0.10.2.2)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
   
   Dependabot will resolve any conflicts with this PR as long as you don't 
alter it yourself. You can also trigger a rebase manually by commenting 
`@dependabot rebase`.
   
   [//]: # (dependabot-automerge-start)
   [//]: # (dependabot-automerge-end)
   
   ---
   
   
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   You can trigger Dependabot actions by commenting on this PR:
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Re: Regarding seagrid desktop client molecule viewer inetgration

[Aishwarya Sinhasane]

Hello Suresh

I will share it as soon as possible. Also I will take care from next week.
I apologize for the same.

Thanks and Regards
Aishwarya Sinhasane

On Fri, Jul 1, 2022, 2:25 PM Suresh Marru  wrote:

> Hi Aishwarya,
>
> I echo it as well. Please do not wait for the code to be perfect, try to
> make it a habit to commit early and often to a PR. A big commit will delay
> reviews or demotivate reviews (due to lack of time), smaller and focused
> chucks make it faster.
>
> Suresh
>
> On Jul 1, 2022, at 1:56 PM, Aishwarya Sinhasane <
> aishwaryasinhas...@gmail.com> wrote:
>
> Hii Dimuthu
>
> I will share document and code next week need some changes to do.
>
> Thanks and regards
> Aishwarya Sinhasane
>
> On Fri, Jul 1, 2022, 1:27 PM DImuthu Upeksha 
> wrote:
>
>> Hi Aishwarya,
>>
>> This is a very solid improvement. Is there a way we can try these out? Do
>> you have a working fork?
>>
>> Thanks
>> Dimuthu
>>
>> On Fri, Jul 1, 2022 at 12:59 PM Pamidighantam, Sudhakar 
>> wrote:
>>
>>> Aishwarya:
>>>
>>>
>>>
>>> Looks good. Keep this and then look at JS molecular Editors or third
>>> party editors such as Avagadro, or Ovito. Let us plan to meet next week to
>>> look at these and discuss further.
>>>
>>>
>>>
>>> Thanks,
>>>
>>> Sudhakar.
>>>
>>>
>>>
>>> *From: *Aishwarya Sinhasane 
>>> *Reply-To: *"dev@airavata.apache.org" 
>>> *Date: *Friday, July 1, 2022 at 12:02 PM
>>> *To: *"dev@airavata.apache.org" 
>>> *Subject: *Regarding seagrid desktop client molecule viewer inetgration
>>>
>>>
>>>
>>> Hello Sudhakar
>>>
>>>
>>>
>>> I was working on integrating a molecule viewer in seagrid desktop
>>> client. I used the NGL Viewer. I tried various other molecule viewers
>>> developed in javascript but some of them are not working properly so I
>>> choose NGLViewer. This molecule viewer supports mmCIF, PDB, mol2, SDF, MMTF
>>> structures.
>>>
>>>
>>>
>>> I am trying to implement a JSMol molecule viewer. Please refer to the
>>> attached screenshots.
>>>
>>
>

Re: Regarding seagrid desktop client molecule viewer inetgration

[Suresh Marru]

Hi Aishwarya,

I echo it as well. Please do not wait for the code to be perfect, try to make 
it a habit to commit early and often to a PR. A big commit will delay reviews 
or demotivate reviews (due to lack of time), smaller and focused chucks make it 
faster. 

Suresh

> On Jul 1, 2022, at 1:56 PM, Aishwarya Sinhasane 
>  wrote:
> 
> Hii Dimuthu 
> 
> I will share document and code next week need some changes to do. 
> 
> Thanks and regards
> Aishwarya Sinhasane 
> 
> On Fri, Jul 1, 2022, 1:27 PM DImuthu Upeksha  > wrote:
> Hi Aishwarya, 
> 
> This is a very solid improvement. Is there a way we can try these out? Do you 
> have a working fork?
> 
> Thanks
> Dimuthu
> 
> On Fri, Jul 1, 2022 at 12:59 PM Pamidighantam, Sudhakar  > wrote:
> Aishwarya:
> 
>  
> 
> Looks good. Keep this and then look at JS molecular Editors or third party 
> editors such as Avagadro, or Ovito. Let us plan to meet next week to look at 
> these and discuss further.
> 
>  
> 
> Thanks,
> 
> Sudhakar.
> 
>  
> 
> From: Aishwarya Sinhasane  >
> Reply-To: "dev@airavata.apache.org " 
> mailto:dev@airavata.apache.org>>
> Date: Friday, July 1, 2022 at 12:02 PM
> To: "dev@airavata.apache.org " 
> mailto:dev@airavata.apache.org>>
> Subject: Regarding seagrid desktop client molecule viewer inetgration
> 
>  
> 
> Hello Sudhakar
> 
>  
> 
> I was working on integrating a molecule viewer in seagrid desktop client. I 
> used the NGL Viewer. I tried various other molecule viewers developed in 
> javascript but some of them are not working properly so I choose NGLViewer. 
> This molecule viewer supports mmCIF, PDB, mol2, SDF, MMTF structures. 
> 
>  
> 
> I am trying to implement a JSMol molecule viewer. Please refer to the 
> attached screenshots. 
> 

Re: Regarding seagrid desktop client molecule viewer inetgration

[Aishwarya Sinhasane]

Hello Sudhakar

I  will try to implement editors and will update you.

Thanks and Regards
Aishwarya Sinhasane


On Fri, Jul 1, 2022, 12:59 PM Pamidighantam, Sudhakar 
wrote:

> Aishwarya:
>
>
>
> Looks good. Keep this and then look at JS molecular Editors or third party
> editors such as Avagadro, or Ovito. Let us plan to meet next week to look
> at these and discuss further.
>
>
>
> Thanks,
>
> Sudhakar.
>
>
>
> *From: *Aishwarya Sinhasane 
> *Reply-To: *"dev@airavata.apache.org" 
> *Date: *Friday, July 1, 2022 at 12:02 PM
> *To: *"dev@airavata.apache.org" 
> *Subject: *Regarding seagrid desktop client molecule viewer inetgration
>
>
>
> Hello Sudhakar
>
>
>
> I was working on integrating a molecule viewer in seagrid desktop client.
> I used the NGL Viewer. I tried various other molecule viewers developed in
> javascript but some of them are not working properly so I choose NGLViewer.
> This molecule viewer supports mmCIF, PDB, mol2, SDF, MMTF structures.
>
>
>
> I am trying to implement a JSMol molecule viewer. Please refer to the
> attached screenshots.
>

Re: Regarding seagrid desktop client molecule viewer inetgration

[Aishwarya Sinhasane]

Hii Dimuthu

I will share document and code next week need some changes to do.

Thanks and regards
Aishwarya Sinhasane

On Fri, Jul 1, 2022, 1:27 PM DImuthu Upeksha 
wrote:

> Hi Aishwarya,
>
> This is a very solid improvement. Is there a way we can try these out? Do
> you have a working fork?
>
> Thanks
> Dimuthu
>
> On Fri, Jul 1, 2022 at 12:59 PM Pamidighantam, Sudhakar 
> wrote:
>
>> Aishwarya:
>>
>>
>>
>> Looks good. Keep this and then look at JS molecular Editors or third
>> party editors such as Avagadro, or Ovito. Let us plan to meet next week to
>> look at these and discuss further.
>>
>>
>>
>> Thanks,
>>
>> Sudhakar.
>>
>>
>>
>> *From: *Aishwarya Sinhasane 
>> *Reply-To: *"dev@airavata.apache.org" 
>> *Date: *Friday, July 1, 2022 at 12:02 PM
>> *To: *"dev@airavata.apache.org" 
>> *Subject: *Regarding seagrid desktop client molecule viewer inetgration
>>
>>
>>
>> Hello Sudhakar
>>
>>
>>
>> I was working on integrating a molecule viewer in seagrid desktop client.
>> I used the NGL Viewer. I tried various other molecule viewers developed in
>> javascript but some of them are not working properly so I choose NGLViewer.
>> This molecule viewer supports mmCIF, PDB, mol2, SDF, MMTF structures.
>>
>>
>>
>> I am trying to implement a JSMol molecule viewer. Please refer to the
>> attached screenshots.
>>
>

[GitHub] [airavata] dependabot[bot] opened a new pull request, #314: Bump hadoop-client from 1.0.3 to 2.7.0 in /modules/distribution

[GitBox]

dependabot[bot] opened a new pull request, #314:
URL: https://github.com/apache/airavata/pull/314

   Bumps hadoop-client from 1.0.3 to 2.7.0.
   
   
   [![Dependabot compatibility 
score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=org.apache.hadoop:hadoop-client=maven=1.0.3=2.7.0)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
   
   Dependabot will resolve any conflicts with this PR as long as you don't 
alter it yourself. You can also trigger a rebase manually by commenting 
`@dependabot rebase`.
   
   [//]: # (dependabot-automerge-start)
   [//]: # (dependabot-automerge-end)
   
   ---
   
   
   Dependabot commands and options
   
   
   You can trigger Dependabot actions by commenting on this PR:
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   You can disable automated security fix PRs for this repo from the [Security 
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Re: Regarding seagrid desktop client molecule viewer inetgration

[DImuthu Upeksha]

Hi Aishwarya,

This is a very solid improvement. Is there a way we can try these out? Do
you have a working fork?

Thanks
Dimuthu

On Fri, Jul 1, 2022 at 12:59 PM Pamidighantam, Sudhakar 
wrote:

> Aishwarya:
>
>
>
> Looks good. Keep this and then look at JS molecular Editors or third party
> editors such as Avagadro, or Ovito. Let us plan to meet next week to look
> at these and discuss further.
>
>
>
> Thanks,
>
> Sudhakar.
>
>
>
> *From: *Aishwarya Sinhasane 
> *Reply-To: *"dev@airavata.apache.org" 
> *Date: *Friday, July 1, 2022 at 12:02 PM
> *To: *"dev@airavata.apache.org" 
> *Subject: *Regarding seagrid desktop client molecule viewer inetgration
>
>
>
> Hello Sudhakar
>
>
>
> I was working on integrating a molecule viewer in seagrid desktop client.
> I used the NGL Viewer. I tried various other molecule viewers developed in
> javascript but some of them are not working properly so I choose NGLViewer.
> This molecule viewer supports mmCIF, PDB, mol2, SDF, MMTF structures.
>
>
>
> I am trying to implement a JSMol molecule viewer. Please refer to the
> attached screenshots.
>

Re: Regarding seagrid desktop client molecule viewer inetgration

[Pamidighantam, Sudhakar]

Aishwarya:

Looks good. Keep this and then look at JS molecular Editors or third party 
editors such as Avagadro, or Ovito. Let us plan to meet next week to look at 
these and discuss further.

Thanks,
Sudhakar.

From: Aishwarya Sinhasane 
Reply-To: "dev@airavata.apache.org" 
Date: Friday, July 1, 2022 at 12:02 PM
To: "dev@airavata.apache.org" 
Subject: Regarding seagrid desktop client molecule viewer inetgration

Hello Sudhakar

I was working on integrating a molecule viewer in seagrid desktop client. I 
used the NGL Viewer. I tried various other molecule viewers developed in 
javascript but some of them are not working properly so I choose NGLViewer. 
This molecule viewer supports mmCIF, PDB, mol2, SDF, MMTF structures.

I am trying to implement a JSMol molecule viewer. Please refer to the attached 
screenshots.