[chimera-dev] Summit supercompuer

Fri Jan 18 17:33:17 PST 2019

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On Fri, Jan 18, 2019 at 8:27 PM Victor Padilla-Sanchez <70padillasan at cua.edu>
wrote:

> 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
>>> _______________________________________________
>>> Chimera-dev mailing list
>>> Chimera-dev at cgl.ucsf.edu
>>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev
>>>
>>>
>>> _______________________________________________
>> Chimera-dev mailing list
>> Chimera-dev at cgl.ucsf.edu
>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev
>>
>>
>>
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