Hardware requirements

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Hardware requirements

Alex Donath
Hi,

Sorry if this has been discussed previously.

I was wondering if you have any recommendations concerning the hardware requirements for (Web)Apollo.

Our aim is to set up a server that hosts dozens of genome browsers - similar to i5k but mostly for usage within our institute.

I am happy to share additional details if necessary.

Thanks,
Alex

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Re: Hardware requirements

nathandunn

Just did some experiments on Docker.  

I think you can get by on 0.5 GB of memory for tomcat and a single processor, but for an optimal lab environment running the newest Apollo I would recommend 2-4 CPU (on your host machine), 2GB’s of memory allocated for tomcat (max 4 GBs) on a machine with at least 4 GB’s of memory, but probably closer to 8.  On AWS I usually do a t2.medium for production.  

I think the hardest part is setting the tomcat memory. Hopefully this section will be helpful:  https://genomearchitect.readthedocs.io/en/latest/Troubleshooting.html#tomcat-memory

Nathan


On Nov 5, 2019, at 1:27 AM, Alex Donath <[hidden email]> wrote:

Hi,

Sorry if this has been discussed previously.

I was wondering if you have any recommendations concerning the hardware requirements for (Web)Apollo.

Our aim is to set up a server that hosts dozens of genome browsers - similar to i5k but mostly for usage within our institute.

I am happy to share additional details if necessary.

Thanks,
Alex

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Re: Hardware requirements

Alex Donath
Thanks a lot, Nathan!

And these recommendations multiply with the number of workspaces/genomes?

My idea would be to set up multiple workspaces because not all users should be able to annotate all genomes. Similar to what i5k does.
Or is there another possibility to achieve this?

Thanks,
Alex

On Tuesday, November 5, 2019 at 4:28:20 PM UTC+1, Nathan Dunn wrote:

Just did some experiments on Docker.  

I think you can get by on 0.5 GB of memory for tomcat and a single processor, but for an optimal lab environment running the newest Apollo I would recommend 2-4 CPU (on your host machine), 2GB’s of memory allocated for tomcat (max 4 GBs) on a machine with at least 4 GB’s of memory, but probably closer to 8.  On AWS I usually do a t2.medium for production.  

I think the hardest part is setting the tomcat memory. Hopefully this section will be helpful:  <a href="https://genomearchitect.readthedocs.io/en/latest/Troubleshooting.html#tomcat-memory" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FTroubleshooting.html%23tomcat-memory\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGjQOgrmhsxftVFH8FFo3DpD9aZNw&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FTroubleshooting.html%23tomcat-memory\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGjQOgrmhsxftVFH8FFo3DpD9aZNw&#39;;return true;">https://genomearchitect.readthedocs.io/en/latest/Troubleshooting.html#tomcat-memory

Nathan


On Nov 5, 2019, at 1:27 AM, Alex Donath <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="R7NQ-Mo7AgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">alexand...@...> wrote:

Hi,

Sorry if this has been discussed previously.

I was wondering if you have any recommendations concerning the hardware requirements for (Web)Apollo.

Our aim is to set up a server that hosts dozens of genome browsers - similar to i5k but mostly for usage within our institute.

I am happy to share additional details if necessary.

Thanks,
Alex

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Re: Hardware requirements

nathandunn


On Nov 6, 2019, at 1:40 PM, Alex Donath <[hidden email]> wrote:

Thanks a lot, Nathan!

And these recommendations multiply with the number of workspaces/genomes?

For multiple genomes you’ll mostly need more disk space.  

They other specs only increase with the number of users, but they should max out at around 4/8 GB’s of memory, more won’t really get you anywhere.

My idea would be to set up multiple workspaces because not all users should be able to annotate all genomes. Similar to what i5k does.
Or is there another possibility to achieve this?

You should use the permissions system to limit who has access to what genome.  They should all go on the same server. 

Mostly you edit organism permissions via the user and group tabs: https://genomearchitect.readthedocs.io/en/latest/UsersGuide.html#users-tab

Nathan


Thanks,
Alex

On Tuesday, November 5, 2019 at 4:28:20 PM UTC+1, Nathan Dunn wrote:

Just did some experiments on Docker.  

I think you can get by on 0.5 GB of memory for tomcat and a single processor, but for an optimal lab environment running the newest Apollo I would recommend 2-4 CPU (on your host machine), 2GB’s of memory allocated for tomcat (max 4 GBs) on a machine with at least 4 GB’s of memory, but probably closer to 8.  On AWS I usually do a t2.medium for production.  

I think the hardest part is setting the tomcat memory. Hopefully this section will be helpful:  <a href="https://genomearchitect.readthedocs.io/en/latest/Troubleshooting.html#tomcat-memory" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FTroubleshooting.html%23tomcat-memory\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGjQOgrmhsxftVFH8FFo3DpD9aZNw';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FTroubleshooting.html%23tomcat-memory\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGjQOgrmhsxftVFH8FFo3DpD9aZNw';return true;" class="">https://genomearchitect.readthedocs.io/en/latest/Troubleshooting.html#tomcat-memory

Nathan


On Nov 5, 2019, at 1:27 AM, Alex Donath <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="R7NQ-Mo7AgAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;" class="">alexand...@...> wrote:

Hi,

Sorry if this has been discussed previously.

I was wondering if you have any recommendations concerning the hardware requirements for (Web)Apollo.

Our aim is to set up a server that hosts dozens of genome browsers - similar to i5k but mostly for usage within our institute.

I am happy to share additional details if necessary.

Thanks,
Alex


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Re: Hardware requirements

Alex Donath
Thanks a lot, Nathan!

Alex

On Wednesday, November 6, 2019 at 11:00:09 PM UTC+1, Nathan Dunn wrote:


On Nov 6, 2019, at 1:40 PM, Alex Donath <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="WapoiHJcBgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">alexand...@...> wrote:

Thanks a lot, Nathan!

And these recommendations multiply with the number of workspaces/genomes?

For multiple genomes you’ll mostly need more disk space.  

They other specs only increase with the number of users, but they should max out at around 4/8 GB’s of memory, more won’t really get you anywhere.

My idea would be to set up multiple workspaces because not all users should be able to annotate all genomes. Similar to what i5k does.
Or is there another possibility to achieve this?

You should use the permissions system to limit who has access to what genome.  They should all go on the same server. 

Mostly you edit organism permissions via the user and group tabs: <a href="https://genomearchitect.readthedocs.io/en/latest/UsersGuide.html#users-tab" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FUsersGuide.html%23users-tab\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG9UWug1ahB9P3gfEVjk9Y8tiX8qw&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FUsersGuide.html%23users-tab\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNG9UWug1ahB9P3gfEVjk9Y8tiX8qw&#39;;return true;">https://genomearchitect.readthedocs.io/en/latest/UsersGuide.html#users-tab

Nathan


Thanks,
Alex

On Tuesday, November 5, 2019 at 4:28:20 PM UTC+1, Nathan Dunn wrote:

Just did some experiments on Docker.  

I think you can get by on 0.5 GB of memory for tomcat and a single processor, but for an optimal lab environment running the newest Apollo I would recommend 2-4 CPU (on your host machine), 2GB’s of memory allocated for tomcat (max 4 GBs) on a machine with at least 4 GB’s of memory, but probably closer to 8.  On AWS I usually do a t2.medium for production.  

I think the hardest part is setting the tomcat memory. Hopefully this section will be helpful:  <a href="https://genomearchitect.readthedocs.io/en/latest/Troubleshooting.html#tomcat-memory" rel="nofollow" target="_blank" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FTroubleshooting.html%23tomcat-memory\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGjQOgrmhsxftVFH8FFo3DpD9aZNw&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgenomearchitect.readthedocs.io%2Fen%2Flatest%2FTroubleshooting.html%23tomcat-memory\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGjQOgrmhsxftVFH8FFo3DpD9aZNw&#39;;return true;">https://genomearchitect.readthedocs.io/en/latest/Troubleshooting.html#tomcat-memory

Nathan


On Nov 5, 2019, at 1:27 AM, Alex Donath <[hidden email]> wrote:

Hi,

Sorry if this has been discussed previously.

I was wondering if you have any recommendations concerning the hardware requirements for (Web)Apollo.

Our aim is to set up a server that hosts dozens of genome browsers - similar to i5k but mostly for usage within our institute.

I am happy to share additional details if necessary.

Thanks,
Alex


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