[StarCluster] StarGenetics issues
Jacob Barhak
jacob.barhak at gmail.com
Thu Jul 15 15:55:56 EDT 2021
Thanks Ramon,
This is wonderful - you will get a private email from me now.
And I am happy that the StartCluster email list still helps to connect
people - I agree not only it was a decade before its time, The community it
built still helps a decade later.
Jacob
On Thu, Jul 15, 2021 at 2:53 PM Ramon Ramirez-Linan <rlinan at navteca.com>
wrote:
> Hi Jacob,
>
> That is pretty cool, what you are doing. I am helping NASA with JupyterHub
> and Dask Gateway, feel free to contact me directly if you want to see a
> demo or even get access to our Daskhub cluster for testing.
>
> We have actually set up a system where you can deploy an HPC cluster on
> AWS straight from a Notebook though an integration of JupyterHub with AWS
> Parallel Cluster (https://aws.amazon.com/hpc/parallelcluster/).
> In other words, from JupyterHub you can sbatch a job straigh to Slurm or
> similar and it will execute the job for you on a cluster of spot
> instances or on demand instances
>
> If anyone is interested in seeing a demo let me know, I am using open
> source technology
>
> Ramon
>
>
>
> On Thu, Jul 15, 2021 at 3:30 PM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
>
>> Greetings,
>>
>> StartCluster was great - it allowed me to launch my disease modeling on
>> the Amazon cloud in those days. Some of you mentioned some newer solutions,
>> can you please elaborate?
>>
>> I am curious to what are the newer tools that can create a cluster of
>> nodes with a shared NFS directory,
>>
>> I moved away from StarCluster towards using services like Rescale or
>> other specialized solutions, on multiple clouds, Here are some recent
>> results from COVID modeling:
>>
>> -
>>
>> Jacob Barhak, The Reference Model is a Multi-Scale Ensemble Model of
>> COVID-19. Self Published Interactive Manuscript. Publication Date:
>> 27-May-2021
>> http://doi.org/10.34235/b7eaa32b-1a6b-444f-9848-76f83f5a733c
>> -
>>
>> Jacob Barhak: The Reference Model for COVID-19 - The First
>> Multi-Scale Ensemble Disease Model, MIDAS Webinar - 28 May 2021,
>> https://jacob-barhak.github.io/COVID19_Ensemble_MIDAS_Webinar.html
>> Video: https://youtu.be/-z8N40TdKDk?t=1860
>>
>>
>> -
>>
>> Jacob Barhak. How Dask Helped Model Diseases and Specifically
>> COVID-19. Blog at Coiled. June 23, 2021 *https://coiled.io/how-dask-helped-model-diseases-and-specifically-covid-19/
>> <https://coiled.io/how-dask-helped-model-diseases-and-specifically-covid-19/>*
>>
>>
>> I will be happy to learn more about new techniques to do the same thing -
>> and will be happy to learn people are still using StarCluster - I was great.
>>
>> Jacob
>>
>>
>>
>> On Wed, Jul 14, 2021 at 10:27 AM Arman Eshaghi <arman.eshaghi at gmail.com>
>> wrote:
>>
>>> StarCluster was a decade ahead of its time in 2010. But is it still
>>> relevant with AWS batch?
>>>
>>> Arman
>>>
>>> On Wed, Jul 14, 2021 at 4:00 PM Ramon Ramirez-Linan <rlinan at navteca.com>
>>> wrote:
>>>
>>>> That is a great use Ed.
>>>> We use Pcluster at everage Spot Instances too, from earth science to
>>>> space science
>>>>
>>>> Ramon
>>>>
>>>> On Wed, Jul 14, 2021 at 10:15 AM Ed Gray <gray_ed at hotmail.com> wrote:
>>>>
>>>>> We used StarCluster to leverage spot instance pricing for
>>>>> bioinformatics. Many compute years over a weekend to chug through 40000
>>>>> genes over 10 species.
>>>>>
>>>>>
>>>>> -------- Original message --------
>>>>> From: Ramon Ramirez-Linan <rlinan at navteca.com>
>>>>> Date: 7/14/21 8:01 AM (GMT-06:00)
>>>>> To: Ed Gray <gray_ed at hotmail.com>
>>>>> Cc: Ryan G <ngsbioinformatics at gmail.com>, "Marcey, David" <
>>>>> marcey at callutheran.edu>, starcluster at mit.edu
>>>>> Subject: Re: [StarCluster] StarGenetics issues
>>>>>
>>>>> I was an active user of StarCluster for HPC on the agency I work for,
>>>>> but since AWS launched Pcluster I dont see the point and have switched to
>>>>> this other tool.
>>>>>
>>>>> Ramon
>>>>>
>>>>> On Tue, Jul 13, 2021 at 6:47 PM Ed Gray <gray_ed at hotmail.com> wrote:
>>>>>
>>>>>> oh man, finally a StarCluster group email and its unrelated.
>>>>>>
>>>>>> wow.
>>>>>>
>>>>>> oh how the mighty have fallen.
>>>>>>
>>>>>>
>>>>>> -------- Original message --------
>>>>>> From: Ryan G <ngsbioinformatics at gmail.com>
>>>>>> Date: 7/13/21 5:40 PM (GMT-06:00)
>>>>>> To: "Marcey, David" <marcey at callutheran.edu>
>>>>>> Cc: starcluster at mit.edu
>>>>>> Subject: Re: [StarCluster] StarGenetics issues
>>>>>>
>>>>>> To my knowledge, that tool is not related to starcluster.
>>>>>>
>>>>>> Please excuse any typos -- Sent from my iPad
>>>>>>
>>>>>> On Jul 13, 2021, at 3:24 PM, Marcey, David <marcey at callutheran.edu>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> I’m using the Star Genetics Instructor page to create new SG problems
>>>>>> (http://star-genetics-instructor.surge.sh/).
>>>>>>
>>>>>>
>>>>>>
>>>>>> The encrypt and save does not work for me if I use genes on different
>>>>>> chromosomes. Firefox or Chrome browser.
>>>>>>
>>>>>>
>>>>>>
>>>>>> I can encrypt and save if multiple genes are on different chromosomes.
>>>>>>
>>>>>>
>>>>>>
>>>>>> However, I am getting anomalous results in simple dihybrid crosses
>>>>>> with unlinked genes.
>>>>>>
>>>>>>
>>>>>>
>>>>>> Any advice would be most appreciated!
>>>>>>
>>>>>>
>>>>>>
>>>>>> David Marcey
>>>>>>
>>>>>>
>>>>>>
>>>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>>>>
>>>>>> David J. Marcey
>>>>>>
>>>>>> Fletcher Jones Professor of Developmental Biology
>>>>>>
>>>>>> The Center for Active Learning
>>>>>>
>>>>>> California Lutheran University
>>>>>>
>>>>>> 60 West Olsen Road., MC#3700
>>>>>>
>>>>>> Thousand Oaks, CA 91360
>>>>>>
>>>>>> marcey at callutheran.edu
>>>>>>
>>>>>>
>>>>>>
>>>>>> *he/him/his*
>>>>>>
>>>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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>>>>>> _______________________________________________
>>>>>> StarCluster mailing list
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>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>> Ramon Ramirez-Linan |
>>>>> * Navteca | C: 301.789.9139 | * @ramonlinan
>>>>> <https://twitter.com/RamonLinan>
>>>>> Emerging Technology, Innovation Solutions
>>>>> (NAICS Codes - 518210, 541511, 541512, 541519, 541990)
>>>>> *Co-founder*
>>>>>
>>>>> www.navteca.com | @Navteca <https://twitter.com/Navteca>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> www.navteca.com | @Navteca <https://twitter.com/Navteca>
>>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> Ramon Ramirez-Linan |
>>>> *Navteca | C: 301.789.9139 | * @ramonlinan
>>>> <https://twitter.com/RamonLinan>
>>>> Emerging Technology, Innovation Solutions
>>>> (NAICS Codes - 518210, 541511, 541512, 541519, 541990)
>>>> *Co-founder*
>>>>
>>>> www.navteca.com | @Navteca <https://twitter.com/Navteca>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> www.navteca.com | @Navteca <https://twitter.com/Navteca>
>>>> _______________________________________________
>>>> StarCluster mailing list
>>>> StarCluster at mit.edu
>>>> http://mailman.mit.edu/mailman/listinfo/starcluster
>>>>
>>>
>>>
>>> --
>>> *---------------------------------------------*
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>>> _______________________________________________
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>>>
>>
>
> --
>
> Ramon Ramirez-Linan |
> *Navteca | C: 301.789.9139 | * @ramonlinan
> <https://twitter.com/RamonLinan>
> Emerging Technology, Innovation Solutions
> (NAICS Codes - 518210, 541511, 541512, 541519, 541990)
> *Co-founder*
>
> www.navteca.com | @Navteca <https://twitter.com/Navteca>
>
>
>
>
>
>
> www.navteca.com | @Navteca <https://twitter.com/Navteca>
>
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