[chimera-dev] Summit supercompuer

Victor Padilla-Sanchez 70padillasan at cua.edu
Fri Jan 18 17:27:36 PST 2019


Hi Eric,

Thank you very much for your answer.
I need Chimera in Summit because I want to use their big ram memory to be
able to visualize huge protein assemblies like the entire bacteriophage t4
virus and beyond and only a supercomputer can achieve that kind of memory.
It wouldn't be important if molecular surfaces can't be processed.

What about higher order structures like multi scale models ?
Since I work a lot with them.

I can see that Chimera X does not have that option.

The Director Jack Wells at Oak Ridge National Laboratory wants to know if
you can be involved in being successfully porting Chimera in Summit.
Actually I asked him for permission to install Chimera but the engineer
Jack Morrison saw the disclaimer and said is not possible.
I am trying to scale up my work with Chimera to a higher level but I need a
supercomputer to do that.
I am using Rhea in Oak Ridge but it will be decommission therefore I want
to try Summit if possible.

Would you be able to help us installing Chimera in Summit ?

Please let me know if you need further explanations of this work.

I am sending an attachment figure which I am able to do in their big
supercomputer Rhea and which I want to continue in Summit.
They use power pc so the engineer said is not possible.
But apparently is possible. It is just that will take more effort if I
understand correctly.

Please help me install Chimera in Summit. I think I will be able to achieve
a lot in Summit.

Kind regards,

Victor Padilla-Sanchez, PhD


On Fri, Jan 18, 2019 at 7:51 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Victor,
> You haven’t said anything about your motivation for porting Chimera to
> Summit, so it’s hard to provide good guidance here.  That disclaimer about
> the code means that you can in fact compile Chimera from the provided
> source, but the result will not be able to compute/show molecular surfaces
> or any attributes based on such calculations (such as solvent-exposed
> surface area).  Depending on why you need Chimera on Summit, this may or
> may not be good enough.  The other disclaimer in the code about getting the
> compile to work being challenging is absolutely true, so that should be
> taken into account when deciding what course of action you want to take
> from here.
> Another option to consider is compiling ChimeraX on Summit instead.
> Again, since I don’t know your motivation I can’t say if ChimeraX’s current
> capabilities would meet your needs, but it seemed like something worth
> mentioning.
>
> —Eric
>
> On Jan 18, 2019, at 8:31 AM, Victor Padilla-Sanchez <70padillasan at cua.edu>
> wrote:
>
> Hi Eric,
>
> The engineer at Oak Ridge says Summit architecture is incompatible:
>
> SummitDev is based on the PowerPC (ppc64le) architecture, and is binary
>     incompatible with Chimera as it's distributed. The Chimera
>     documentation warns
>     that "it's not possible to re-compile a fully functional Chimera from
>     the
>     source code distributed here."
>
> Do you know anyway around about this problem so we are able to install
> Chimera in Summit at Oak Ridge ?
>
> Please let me know
>
> Regards,
>
> Victor
>
> On Thu, Jan 10, 2019 at 1:34 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
>> Hi Victor,
>> As far as we know, no one has specifically ported Chimera to Oak Ridge’s
>> Summit.  I’m not sure why you would need Chimera to run on a supercomputer,
>> but nonetheless Summit runs Red Had Enterprise 7.4, so I see no reason that
>> the “headless” version of Chimera wouldn't just work.
>>
>> —Eric
>>
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>>
>>
>> On Jan 10, 2019, at 3:53 AM, Victor Padilla-Sanchez <70padillasan at cua.edu>
>> wrote:
>>
>> Dear Chimera,
>>
>> Would you tell me if someone has developed/ported Chimera to Summit
>> supercomputer at Oak Ridge National Laboratory ?
>>
>> Please let me know,
>>
>> Thank you very much,
>>
>> Victor Padilla-Sanchez, PhD
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>>
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