[gvr-support:0015] Re: NERSC Support for XStack
Hajime Fujita
hfujita at uchicago.edu
Sun May 3 22:07:42 CDT 2015
Hi Richard,
Thank you for your reply.
I would choose libraries/programming if I were to choose from this list, as
Global Arrays, which is somehow similar to GVR in terms of globally
distributed array, is already in this category.
If you have any near-term plan to add other libraries for
checkpoint/restart or similar kind (e.g. Scalable Checkpoint Restart, as I
mentioned), I would propose libraries/resilience and add GVR under it.
And how can I actually place the files into the final location?
a) are you going to give me a write permission to some directory, or
b) do you need me to provide a source tarball and an installation procedure?
Thanks,
Hajime
On Mon, May 4, 2015 at 10:01 AM, Richard Gerber <ragerber at lbl.gov> wrote:
> Hi Hajime,
>
> Thanks for your questions. These are issues we will need address to
> support user-contributed software, so I'm glad you asked. You can put
> anything in there that you want. The string is used to populate a table on
> the web site with similar items. Look at the list of existing items below
> and see if any of them work for you. We can talk about what other software
> is most closely related, or you can define a new category.
>
> Richard
>
> +----------+--------------+
>
> | count(*) | category |
>
> +----------+--------------+
>
> | 3 | |
>
> | 2533 | applications |
>
> | 199 | compilers |
>
> | 1063 | deleted |
>
> | 968 | libraries |
>
> | 45 | os |
>
> | 166 | other |
>
> | 78 | pe_libraries |
>
> +----------+--------------+
>
>
> +----------+-------------------+
>
> | count(*) | sub_category |
>
> +----------+-------------------+
>
> | 3 | |
>
> | 13 | astronomy |
>
> | 689 | bioinformatics |
>
> | 124 | chemistry |
>
> | 4 | climate |
>
> | 141 | debugging |
>
> | 941 | deleted |
>
> | 444 | general |
>
> | 4 | genreal |
>
> | 318 | I/O |
>
> | 283 | material sciences |
>
> | 423 | math |
>
> | 11 | network |
>
> | 6 | network services |
>
> | 112 | performance |
>
> | 17 | physics |
>
> | 1181 | programming |
>
> | 30 | services |
>
> | 311 | visualization |
>
> +----------+-------------------+
>
> Richard Gerber, Ph.D.
> Senior Science Advisor | User Services Group Lead
> National Energy Research Scientific Computing Center
> <http://www.nersc.gov/> | Berkeley Lab <http://www.lbl.gov/>
> ragerber at lbl.gov | phone: (510) 486-6820 fax: 510-486-4316
>
> On Thu, Apr 30, 2015 at 11:30 AM, Hajime Fujita <hfujita at uchicago.edu>
> wrote:
>
>> Hi Richard,
>>
>> Thank you for your response.
>>
>> I got a few questions on the module description.
>>
>> > set nerscurl http://vis.lbl.gov/NERSC/Software/gnuplot/
>> > set maincategory applications
>> > set subcategory visualization
>>
>>
>> What should these values be?
>> I think the main category is programming, and the subcategory is
>> something like "resilience", which does not exist now though.
>>
>> If there is already something like user-level checkpoint library (e.g.
>> SCR), GVR should fall in to the same category.
>> However I could not find such software so far.
>>
>> Also, can you give me further instruction on file location etc.?
>>
>>
>> Thank you,
>> Hajime
>>
>> > On Apr 24, 2015, at 4:00 PM, Richard Gerber <ragerber at lbl.gov> wrote:
>> >
>> > Hi Hajime,
>> >
>> > I hope to have something in place very soon. The plan is to give you a
>> directory into which you can install your software and modulefiles. Access
>> to software on our machines is provided by loading and unloading modules.
>> If you are not familiar with modules, please take a look at
>> http://modules.sourceforge.net/
>> >
>> > The creation of a module file is not difficult, but we have a format
>> that you should follow. Here is a sample module file, this one for gnuplot
>> on edison. (The scripting language is TCL).
>> >
>> > #%Module1.0
>> >
>> > ##
>> >
>> >
>> >
>> > ## Required internal variables
>> >
>> >
>> >
>> > set name gnuplot
>> >
>> > set version 4.6.3
>> >
>> > set root /global/common/edison/contrib/$name/$version
>> >
>> >
>> >
>> > ## List conflicting modules here
>> >
>> >
>> >
>> > conflict $name
>> >
>> >
>> >
>> > ## List prerequisite modules here
>> >
>> >
>> >
>> > # prereq
>> >
>> >
>> >
>> > ## Required for SVN hook to generate SWDB entry
>> >
>> >
>> >
>> > set fullname gnuplot
>> >
>> > set externalurl http://www.gnuplot.info
>> >
>> > set nerscurl http://vis.lbl.gov/NERSC/Software/gnuplot/
>> >
>> > set maincategory applications
>> >
>> > set subcategory visualization
>> >
>> > set description "gnuplot is free and open-source software 2D/3D
>> plotting program."
>> >
>> >
>> >
>> > ## Required for "module help ..."
>> >
>> >
>> >
>> > proc ModulesHelp { } {
>> >
>> > global description nerscurl externalurl
>> >
>> > puts stderr "Description - $description"
>> >
>> > puts stderr "NERSC Docs - $nerscurl"
>> >
>> > puts stderr "Other Docs - $externalurl"
>> >
>> > }
>> >
>> >
>> >
>> > ## Required for "module display ..." and SWDB
>> >
>> >
>> >
>> > module-whatis "$description"
>> >
>> >
>> >
>> > ## Software-specific settings exported to user environment
>> >
>> >
>> >
>> > prepend-path PATH $root/bin
>> >
>> > prepend-path MANPATH $root/share/man
>> >
>> > setenv GNUPLOT_DIR $root
>> >
>> > prepend-path LD_LIBRARY_PATH $root/lib
>> >
>> >
>> >
>> > ## Log "module load ..." commands
>> >
>> >
>> >
>> > if [ module-info mode load ] {
>> >
>> > set usgsbin /global/common/shared/usg/sbin
>> >
>> > if [ expr [ file exists $usgsbin/logmod ] ] {
>> >
>> > exec $usgsbin/logmod ${name} ${version}
>> >
>> > }
>> >
>> > }
>> >
>> >
>> > Richard Gerber, Ph.D.
>> > Senior Science Advisor | User Services Group Lead
>> > National Energy Research Scientific Computing Center | Berkeley Lab
>> > ragerber at lbl.gov | phone: (510) 486-6820 fax: 510-486-4316
>> >
>> > On Thu, Apr 23, 2015 at 12:24 PM, Hajime Fujita <hfujita at uchicago.edu>
>> wrote:
>> > Hello Richard,
>> >
>> > My name is Hajime Fujita, a postdoc in the GVR project. I'll be taking
>> care of this GVR deployment to NERSC machines.
>> >
>> > First let me understand the latest situation. Have you completed the
>> transition to the new process for user-installed software?
>> > Please let me know where we can start.
>> >
>> >
>> > Thank you,
>> > Hajime
>> >
>> > > On Mar 12, 2015, at 6:33 PM, Richard Gerber <ragerber at lbl.gov> wrote:
>> > >
>> > > Hi Andrew,
>> > >
>> > > We're in a bit of a transition phase with our software management.
>> Part of our new scheme will involve a well-defined process for
>> user-installed and maintained software. We're not there yet, but I think I
>> will know more in a about a week. So I'd like to revisit this in about a
>> week and see what makes the most sense in the short run.
>> > >
>> > > Regards,
>> > > Richard
>> > >
>> > > Richard Gerber, Ph.D.
>> > > Senior Science Advisor | User Services Group Lead
>> > > National Energy Research Scientific Computing Center | Berkeley Lab
>> > > ragerber at lbl.gov | phone: (510) 486-6820 fax: 510-486-4316
>> > >
>> > > On Wed, Mar 11, 2015 at 1:58 PM, Andrew A. Chien <
>> achien at cs.uchicago.edu> wrote:
>> > > Richard,
>> > >
>> > > thanks for the effort, and message. I think they took it down to
>> make a minor patch.... amusingly this was triggered by my "heads up" that
>> you were asking about putting this up and NERSC.
>> > >
>> > > Let me make sure this is fixed (in general), and then we can pursue
>> the path that John (next message) is pointing out.
>> > >
>> > > cheers,
>> > > -Andrew
>> > >
>> > > On Wed, Mar 11, 2015 at 3:42 PM, Richard Gerber <ragerber at lbl.gov>
>> wrote:
>> > > I tried to download the software from the web site. It had me
>> register and wait for an email, which I never received (maybe I typed my
>> email incorrectly?)
>> > >
>> > > Richard
>> > >
>> > > Richard Gerber, Ph.D.
>> > > Senior Science Advisor | User Services Group Lead
>> > > National Energy Research Scientific Computing Center | Berkeley Lab
>> > > ragerber at lbl.gov | phone: (510) 486-6820 fax: 510-486-4316
>> > >
>> > > On Tue, Mar 10, 2015 at 11:09 PM, Richard Gerber <ragerber at lbl.gov>
>> wrote:
>> > > Andrew,
>> > >
>> > > We can give that a try. As long as it builds cleanly we should be OK.
>> Otherwise we'll ask you to find someone who can log in and build the
>> software.
>> > >
>> > > Regards,
>> > > Richard
>> > >
>> > > Richard Gerber, Ph.D.
>> > > Senior Science Advisor | User Services Group Lead
>> > > National Energy Research Scientific Computing Center | Berkeley Lab
>> > > ragerber at lbl.gov | phone: (510) 486-6820 fax: 510-486-4316
>> > >
>> > > On Tue, Mar 10, 2015 at 1:05 PM, Andrew A. Chien <
>> achien at cs.uchicago.edu> wrote:
>> > > Thanks Richard. Did you get a quick look at our website? I think we
>> may be a little further along than many of the xstacks. We have a public
>> release and extensive documentation. Thats all on the web page I mentioned.
>> > >
>> > > So, John's email suggested you could build and make available, and
>> put up our documentation. Is that right? If so what more do you need from
>> us?
>> > >
>> > > I will confirm the release bits are the right one to build for
>> Edison... Where we have been running for more than half a year with full
>> apps.
>> > >
>> > > Cheers, -Andrew
>> > >
>> > > On Mar 10, 2015 2:33 PM, "Richard Gerber" <ragerber at lbl.gov> wrote:
>> > > Hi Andrew,
>> > >
>> > > John's email gave a good description of the services we can offer. We
>> can arrange to have your software installed on our Cray systems, along with
>> a web describing how to use it at NERSC with pointers to more generic
>> documentation. I'd be happy to have a call to discuss this. Are you
>> available this Friday at 11:00 Pacific time?
>> > >
>> > > Regards,
>> > > Richard
>> > >
>> > > Richard Gerber, Ph.D.
>> > > Senior Science Advisor | User Services Group Lead
>> > > National Energy Research Scientific Computing Center | Berkeley Lab
>> > > ragerber at lbl.gov | phone: (510) 486-6820 fax: 510-486-4316
>> > >
>> > > On Tue, Mar 10, 2015 at 8:34 AM, Andrew A. Chien <
>> achien at cs.uchicago.edu> wrote:
>> > > John,
>> > >
>> > > Nice to hear from you. This support would be terrific! We're a
>> small project, so we only have one package, GVR, and have been running
>> edison and have been doing experiments for at least 9 months.
>> > >
>> > > Rebecca and Richard, there is release info on gvr.cs.uchicago.edu,
>> and user manual documentation. We also have numerous code examples
>> (including real applications), and publications describing how it can be
>> used.
>> > >
>> > > If you can take a quick look at what we have, and then we can have a
>> call do discuss what more we'd need to do?
>> > >
>> > > cheers,
>> > > -Andrew
>> > >
>> > >
>> > >
>> > > On Tue, Mar 10, 2015 at 10:27 AM, John Shalf <jshalf at lbl.gov> wrote:
>> > > Andrew,
>> > > I understand that for the XStack renewals, there is a requirement to
>> deploy some of your prototype GVR software on the DOE systems. I’m am
>> writing to offer NERSC’s active support for this requirement. I would like
>> to introduce you to Rebecca Hartman-Baker and Richard Gerber from user
>> services, who will also be assisting. For planning purposes, we would like
>> for you to identify, which prototypes of the software you are developing
>> for XStack that we could deploy on the NERSC systems to facilitate your
>> collaborations with members of the user community.
>> > > * Software Deployment: NERSC will provide the space to
>> install the software and make it 'module loadable' to simplify access to
>> the user community.
>> > > * Host Documentation: NERSC would also provide space on our
>> documentation system for your documentation (or point to your own web pages)
>> > > * Training: we would like to increase your visibility among
>> our users and facilitate your interactions by advertising/telecasting your
>> trainings or seminars on how to use your tools.
>> > >
>> > > Please let us know if this would be of interest to you. If so, can
>> you identify some prototype software that is sufficiently mature that you
>> would be willing to have it deployed on systems like Hopper and Edison (the
>> two primary HPC systems at NERSC). We'd want to know
>> > > 1) what is the name of the software
>> > > 2) a brief description of what it does and what
>> exascale-related problems it solves (e.g. why should an applications team
>> care?)
>> > > 3) how mature it is as a research prototype (is it ready for
>> public release, or would you prefer to have it installed with access
>> restricted to "friendly users")
>> > >
>> > > There will need to be a triage process to prioritize which research
>> prototypes should get deployed first, but we want to gather information
>> about what is currently available and its potential value to the community.
>> > >
>> > > Thanks!
>> > >
>> > > Sincerely,
>> > > John Shalf: NERSC CTO
>> > > Richard Gerber: Group Leader: NERSC User Services
>> > > Rebecca Hartman Baker: NERSC User Services
>> > >
>> > >
>> > >
>> > > --
>> > > Andrew A. Chien
>> > > William Eckhardt Professor in Computer Science
>> Senior Computer Scientist
>> > > Director, CERES Ctr for Unstoppable Computing Mathematics and
>> Computer Science
>> > > Senior Fellow, Computation Institute
>> Argonne National Laboratory
>> > > The University of Chicago
>> > > achien at cs.uchicago.edu
>> > > http://cs.uchicago.edu/people/aachien/
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > --
>> > > Andrew A. Chien
>> > > William Eckhardt Professor in Computer Science
>> Senior Computer Scientist
>> > > Director, CERES Ctr for Unstoppable Computing Mathematics and
>> Computer Science
>> > > Senior Fellow, Computation Institute
>> Argonne National Laboratory
>> > > The University of Chicago
>> > > achien at cs.uchicago.edu
>> > > http://cs.uchicago.edu/people/aachien/
>> > >
>> > >
>> > > _______________________________________________
>> > > Gvr-support mailing list
>> > > Gvr-support at mailman.cs.uchicago.edu
>> > > https://mailman.cs.uchicago.edu/mailman/listinfo/gvr-support
>> >
>> >
>> >
>> > --
>> > Hajime Fujita
>> > Postdoctoral Scholar, Large-Scale Systems Group
>> > Department of Computer Science, The University of Chicago
>> > http://www.cs.uchicago.edu/people/hfujita
>> >
>> >
>>
>>
>
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