attachments On Fri, Jan 18, 2019 at 8:27 PM Victor Padilla-Sanchez <70padillasan@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@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@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@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@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@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
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