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Posted to dev@airavata.apache.org by Deepika <de...@gmail.com> on 2015/01/12 17:39:09 UTC
Re: [marpierc@iu.edu: Re: [SciGaP-Dev] CIPRES-Airavata integration proposal]
Hi,
I want to be out of this. How do I not get further updates? whom should I
contact?
-
Regards
Deepika T
On Thu, Jul 3, 2014 at 1:48 PM, K Yoshimoto <ke...@sdsc.edu> wrote:
>
> Posting this also to dev@airavata, at Marlon's request.
>
> On 7/3/14, 1:39 PM, K Yoshimoto wrote:
> > Another question. I was able to create a project and experiment,
> > then launch the experiment. It was EXECUTING, but is now SUSPENDED.
> > How should the gateway developer investigate the cause of suspension?
> > I think that job state would not normally happen on the Trestles
> resource,
> > at least.
> >
> > php createExperiment.php
> > php createExperiment.php <username> <experiment_name> <project_ID>
> > john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
> php createExperiment.php kenneth kennethexp1
> kennethtest_a26036de-d58c-4f6c-b38d-e60d30c13704
> > object(Airavata\Model\Workspace\Experiment\Experiment)#9 (18) {
> > ["experimentID"]=>
> > string(21) "DO_NOT_SET_AT_CLIENTS"
> > ["projectID"]=>
> > string(48) "kennethtest_a26036de-d58c-4f6c-b38d-e60d30c13704"
> > ["creationTime"]=>
> > NULL
> > ["userName"]=>
> > string(7) "kenneth"
> > ["name"]=>
> > string(11) "kennethexp1"
> > ["description"]=>
> > NULL
> > ["applicationId"]=>
> > string(11) "SimpleEcho2"
> > ["applicationVersion"]=>
> > NULL
> > ["workflowTemplateId"]=>
> > NULL
> > ["workflowTemplateVersion"]=>
> > NULL
> > ["userConfigurationData"]=>
> > object(Airavata\Model\Workspace\Experiment\UserConfigurationData)#6
> (7) {
> > ["airavataAutoSchedule"]=>
> > int(0)
> > ["overrideManualScheduledParams"]=>
> > int(0)
> > ["shareExperimentPublicly"]=>
> > bool(false)
> > ["computationalResourceScheduling"]=>
> >
> object(Airavata\Model\Workspace\Experiment\ComputationalResourceScheduling)#4
> (10) {
> > ["resourceHostId"]=>
> > string(17) "trestles.sdsc.edu"
> > ["totalCPUCount"]=>
> > int(1)
> > ["nodeCount"]=>
> > int(1)
> > ["numberOfThreads"]=>
> > int(0)
> > ["queueName"]=>
> > string(6) "normal"
> > ["wallTimeLimit"]=>
> > int(15)
> > ["jobStartTime"]=>
> > int(0)
> > ["totalPhysicalMemory"]=>
> > int(0)
> > ["computationalProjectAccount"]=>
> > NULL
> > ["ComputationalProjectAccount"]=>
> > string(6) "sds128"
> > }
> > ["advanceInputDataHandling"]=>
> > NULL
> > ["advanceOutputDataHandling"]=>
> > NULL
> > ["qosParams"]=>
> > NULL
> > }
> > ["workflowExecutionInstanceId"]=>
> > NULL
> > ["experimentInputs"]=>
> > array(1) {
> > [0]=>
> > object(Airavata\Model\Workspace\Experiment\DataObjectType)#7 (4) {
> > ["key"]=>
> > string(10) "echo_input"
> > ["value"]=>
> > string(23) "echo_output=Hello World"
> > ["type"]=>
> > int(0)
> > ["metaData"]=>
> > NULL
> > }
> > }
> > ["experimentOutputs"]=>
> > array(1) {
> > [0]=>
> > object(Airavata\Model\Workspace\Experiment\DataObjectType)#8 (4) {
> > ["key"]=>
> > string(11) "echo_output"
> > ["value"]=>
> > string(0) ""
> > ["type"]=>
> > int(0)
> > ["metaData"]=>
> > NULL
> > }
> > }
> > ["experimentStatus"]=>
> > NULL
> > ["stateChangeList"]=>
> > NULL
> > ["workflowNodeDetailsList"]=>
> > NULL
> > ["errors"]=>
> > NULL
> > }
> > Experiment kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92 created!
> >
> > john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
> php launchExperiment.php
> > Please provide an experimentID.
> > john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
> php launchExperiment.php kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92
> > Experiment kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92 is launched.
> > john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
> php getExperimentStatus.php kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92
> > experiment status = EXECUTING
> > <br>
> > john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
> php getExperimentStatus.php kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92
> > experiment status = SUSPENDED
> > <br>
> > john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
> php getExperimentStatus.php kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92
> > experiment status = SUSPENDED
> > <br>
> > john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
> php getExperimentStatus.php kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92
> > experiment status = SUSPENDED
> > <br>
> > john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
> php getExperimentStatus.php kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92
> > experiment status = SUSPENDED
> > <br>
> > john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
> php getExperimentStatus.php kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92
> > experiment status = SUSPENDED
> > <br>
> > john@buffy
> :/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
> >
> > On Thu, Jul 03, 2014 at 10:23:14AM -0700, K Yoshimoto wrote:
> >> That works now. Thanks!
> >>
> >> On Thu, Jul 03, 2014 at 05:00:21PM +0000, Singh, Raminder jeet wrote:
> >>> Hi Kenneth,
> >>>
> >>> With help from a Student in Sri Lanka we are able to identify and fix
> the issue. Issue was related to the socket send timeout. I updated the
> clients to add following property. Please take a git pull and test.
> >>>
> >>> $transport->setSendTimeout($airavataconfig['AIRAVATA_TIMEOUT']);
> >>>
> >>> Thanks
> >>> Raminder
> >>>
> >>> On Jul 3, 2014, at 12:17 AM, K Yoshimoto <ke...@sdsc.edu> wrote:
> >>>
> >>>> Still timed out.
> >>>>
> >>>> On Thu, Jul 03, 2014 at 04:06:42AM +0000, Singh, Raminder jeet wrote:
> >>>>> Hi Kenneth
> >>>>>
> >>>>> Try to increase the AIRAVATA_TIMEOUT = 5000 to 20000 (in ms) in
> airavata-client-properties.ini. Its the connection timeout connecting to
> the server.
> >>>>>
> >>>>> Thanks
> >>>>> Raminder
> >>>>>
> >>>>> On Jul 2, 2014, at 11:57 PM, K Yoshimoto <ke...@sdsc.edu> wrote:
> >>>>>
> >>>>>> I tried the new clients (had to set servername from localhost to
> >>>>>> the iu server). I'm still seeing a timeout:
> >>>>>>
> >>>>>>
> airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
> php getAPIVersion.php
> >>>>>> PHP Fatal error: Uncaught exception 'Thrift\Exception\TException'
> with message 'TSocket: Could not connect to gw111.iu.xsede.org:8930
> (Connection timed out [110])' in
> /media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Thrift/Transport/TSocket.php:235
> >>>>>> Stack trace:
> >>>>>> #0
> /media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getAPIVersion.php(39):
> Thrift\Transport\TSocket->open()
> >>>>>> #1 {main}
> >>>>>> thrown in
> /media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Thrift/Transport/TSocket.php
> on line 235
> >>>>>>
> >>>>>>
> >>>>>> On Wed, Jul 02, 2014 at 09:40:39PM -0400, Marlon Pierce wrote:
> >>>>>>> Hi Kenneth--
> >>>>>>>
> >>>>>>> I did a quick successful check with the Airavata php clients (in
> airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples)
> >>>>>>> (see other email for details).
> >>>>>>>
> >>>>>>> Please use these instead of the obsolete PHP client samples.
> >>>>>>>
> >>>>>>> Thanks--
> >>>>>>>
> >>>>>>> Marlon
> >>>>>>>
> >>>>>>> On 7/2/14, 7:04 PM, K Yoshimoto wrote:
> >>>>>>>> I've started playing with the php client samples.
> >>>>>>>> I'm trying to create project, but running into some kind
> >>>>>>>> of connection timeout. I can telnet to the port, so
> >>>>>>>> maybe the timeout is too short? Or I'm missing some config
> >>>>>>>> I should have done for the client samples? I'm going by the
> >>>>>>>> README at:
> >>>>>>>>
> https://github.com/SciGaP/Airavata-PHP-Client-Samples/blob/master/client-samples/README-PHP-CLI-Examples.txt
> >>>>>>>>
> >>>>>>>> and getting this kind of error:
> >>>>>>>>
> >>>>>>>> john@buffy:/media/mdhpss/scigap/phpclientsamples/Airavata-PHP-Client-Samples/client-samples$
> telnet gw111.iu.xsede.org 8930
> >>>>>>>> Trying 149.165.228.109...
> >>>>>>>> Connected to gw111.iu.xsede.org.
> >>>>>>>> Escape character is '^]'.
> >>>>>>>> ^]
> >>>>>>>>
> >>>>>>>> telnet> quit
> >>>>>>>> Connection closed.
> >>>>>>>> john@buffy:/media/mdhpss/scigap/phpclientsamples/Airavata-PHP-Client-Samples/client-samples$
> php createProject.php kenneth
> >>>>>>>> PHP Fatal error: Uncaught exception
> 'Thrift\Exception\TException' with message 'TSocket: Could not connect to
> gw111.iu.xsede.org:8930 (Connection timed out [110])' in
> /media/mdhpss/scigap/phpclientsamples/Airavata-PHP-Client-Samples/lib/Thrift/Transport/TSocket.php:235
> >>>>>>>> Stack trace:
> >>>>>>>> #0
> /media/mdhpss/scigap/phpclientsamples/Airavata-PHP-Client-Samples/client-samples/createProject.php(45):
> Thrift\Transport\TSocket->open()
> >>>>>>>> #1 {main}
> >>>>>>>> thrown in
> /media/mdhpss/scigap/phpclientsamples/Airavata-PHP-Client-Samples/lib/Thrift/Transport/TSocket.php
> on line 235
> >>>>>>>> john@buffy
> :/media/mdhpss/scigap/phpclientsamples/Airavata-PHP-Client-Samples/client-samples$
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On Wed, Jun 25, 2014 at 02:56:22PM -0400, Marlon Pierce wrote:
> >>>>>>>>> The CCGrid demo server is running on gw111.iu.xsede.org. This
> where
> >>>>>>>>> the PHP client samples from GitHub are pointing.
> >>>>>>>>>
> >>>>>>>>> Marlon
> >>>>>>>>>
> >>>>>>>>> On 6/25/14, 2:28 PM, K Yoshimoto wrote:
> >>>>>>>>>> Is there an instance of SciGap services available for testing
> >>>>>>>>>> and development now?
> >>>>>>>>>>
> >>>>>>>>>> On Wed, Jun 25, 2014 at 01:09:58PM -0400, Suresh Marru wrote:
> >>>>>>>>>>> Hi Kenneth,
> >>>>>>>>>>>
> >>>>>>>>>>> I see that Marlon already listed the PHP samples below -
> https://github.com/SciGaP/PHP-Reference-Gateway
> >>>>>>>>>>>
> >>>>>>>>>>> The functionality which is not so easy is the registration of
> the applications.
> >>>>>>>>>>>
> >>>>>>>>>>> Suresh
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>> On Jun 23, 2014, at 12:58 PM, Marlon Pierce <ma...@iu.edu>
> wrote:
> >>>>>>>>>>>
> >>>>>>>>>>>> Hi Kenneth--
> >>>>>>>>>>>>
> >>>>>>>>>>>> The Airavata repo information is here:
> http://airavata.apache.org/development/source.html. This includes a link
> to the GitHub mirror, which is probably best.
> >>>>>>>>>>>>
> >>>>>>>>>>>> The Thrift definitions are at
> https://github.com/apache/airavata/tree/master/airavata-api/thrift-interface-descriptions.
> Our apachecon slides may be useful supplements:
> http://www.slideshare.net/smarru/restless-design-with-apache-thrift-experiances
> >>>>>>>>>>>>
> >>>>>>>>>>>> The PHP command line samples (
> https://github.com/SciGaP/Airavata-PHP-Client-Samples/), not currently in
> Apache, illustrate how the API works.
> >>>>>>>>>>>>
> >>>>>>>>>>>> Marlon
> >>>>>>>>>>>>
> >>>>>>>>>>>> On 6/23/14, 12:34 PM, K Yoshimoto wrote:
> >>>>>>>>>>>>> Suresh,
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Could you please send out a URL to the current Airavata repo?
> >>>>>>>>>>>>> And the API documentation? I want to look through the
> current
> >>>>>>>>>>>>> interface code.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Kenneth
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> On Mon, Jun 23, 2014 at 08:13:14AM -0400, Suresh Marru wrote:
> >>>>>>>>>>>>>> Hi Borries,
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Can we take up on your demo offer and make an additional
> request to you and Gary? Please bare my long email, I am sorry I do not
> have much time to make this shorter.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> XSEDE 14 tutorial is our opportunity to mint more and more
> Demeler's, Miller's, Majumdhar's and Pampidighantam's. I say this
> seriously, all of you have sacrificed your own science and enabled lot of
> more science by 100's of fellow researchers. There are not many more who
> can dedicate their careers to do this. So we need to show building and
> operating gateways will not necessarily suck up their own science. SciGaP
> will absorb the banal tasks and help them focus on their gateway mission -
> "server a community of users enabling better science".
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> One way we can demonstrate SciGaP is by hands-on tutorial
> of building a bare-bone gateway within half a day. But in addition, we need
> to assure its beyond a tutorial and is indeed the same software used by
> partnering gateways. We need a beta version of LIMS instance which uses
> same thrift API's and served by the same set of Airavata services.
> Preciously put, it will be nice to say current ultrascan production using
> Airavata 0.8, but there is also development in progress to roll out
> Ultrascan with latest Airavata (0.12).
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Can Raminder and Gary work together to make this happen
> within the next 3 weeks?
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Hi All,
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> As for the distracting banter, if you all prefer to know
> the details, there is nothing secretive about it. We got a highest panel
> rating standing ahead of 176 other proposals. Its natural the community
> wants us to succeed. Some say this by clapping hands, some challenge us by
> saying we will fail. Both are equal motivators. I am personally not so
> worried about iPlant. But I am a bit concerned the negativity is spreading
> and we directly took punches from Jay Boisseau, Dan Stanzione, Shantenu Jha
> and unfortunately from Nancy Wilkins-Diehr (on SciGaP and S2I2 gateway
> institute context, which we will resolve very soon). There are other folks
> too, but there is nothing we can or should (in my opinion) do about this
> directly. Its simply not worth and is a unnecessary drain of pre-XSEDE 14
> energy.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> We certainly need to disprove "every one in this team will
> do their own thing". But I do not see SciGaP as
> Airavata+CIPRES+NSG+Ultrascan nor IU+SDSC+UTHSA. To me, SciGaP means
> SciGaP, the mission is to provides software and centralized operations and
> the team believes and practices full openness - both software and
> operations. We wrote a proposal on these beliefs and we need to play our
> part in changing the gateway eco system working alongside friends and some
> more dear friends.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Suresh
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> On Jun 21, 2014, at 10:34 PM, Marlon Pierce <
> marpierc@iu.edu> wrote:
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Hi Borries--
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> I was a little too frustrated on Friday in dealing with
> the iPlant Agave lead developer. Mark and Terri have had previous bad
> experiences. It isn't worth any time or effort, I believe. Working to
> succeed in our SSI is the best path.
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> Marlon
> >>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>> On 6/21/14, 9:10 PM, Miller, Mark wrote:
> >>>>>>>>>>>>>>>> I am not at all surprised, we tried to interact with
> those people and were told in no uncertain terms we should just discard our
> software and wait for further instructions. This was not a suggestion we
> were comfortable with. There are plenty of ways we can interact
> productively with any given infrastructure.
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> In my experience there are always groups who say negative
> things as a tool for positioning their project with a competitive
> advantage, and to sew panic among collaborators.
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> I tend to be driven by what makes sense for users, and
> ignore the political winds from people who are not stakeholders.
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> However, it certainly would be useful to learn more about
> what this conversation was about, as this is a pretty strong statement.
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>> Mark
> >>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> On Jun 21, 2014, at 3:51 AM, "Borries Demeler" <
> demeler@biochem.uthscsa.edu> wrote:
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> Hi Marlon,
> >>>>>>>>>>>>>>>>> I am a bit alarmed by your statement that apparently
> there are
> >>>>>>>>>>>>>>>>> folks, esp. at Austin, who expect and want us to fail. I
> would
> >>>>>>>>>>>>>>>>> appreciate if you could elaborate on what exactly is
> bugging
> >>>>>>>>>>>>>>>>> these people so maybe we could resolve this? We cannot
> afford
> >>>>>>>>>>>>>>>>> to have this antipathy against our project, and I want
> to prove
> >>>>>>>>>>>>>>>>> them wrong. It is absolutely clear that at least the
> UltraScan
> >>>>>>>>>>>>>>>>> integration has been a big success and can serve as a
> model
> >>>>>>>>>>>>>>>>> for other integrations. I am sure with CIPRES similar
> success
> >>>>>>>>>>>>>>>>> can be achieved, but I may need some more background
> info to
> >>>>>>>>>>>>>>>>> understand exactly what issues are raising concern.
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> A certain amount of re-write is always necessary, and we
> fully
> >>>>>>>>>>>>>>>>> expected and welcomed the opportunities to improve our
> software,
> >>>>>>>>>>>>>>>>> and there is a lot of code we ultimately abandoned,
> re-wrote
> >>>>>>>>>>>>>>>>> from scratch or refactored/adapted to new and better
> methods.
> >>>>>>>>>>>>>>>>> I must honestly say that I feel very fortunate that we
> have
> >>>>>>>>>>>>>>>>> your group and the AIravata concept to make our software
> more
> >>>>>>>>>>>>>>>>> portable and robust. These are the two major benefits
> for us,
> >>>>>>>>>>>>>>>>> but there are others, too.
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> Any chance we can give these people a demo of UltraScan
> to
> >>>>>>>>>>>>>>>>> show them how well it worked?
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>> -b.
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>> On Fri, Jun 20, 2014 at 09:32:18PM -0400, Marlon Pierce
> wrote:
> >>>>>>>>>>>>>>>>>> Thanks for your thoughts on the matter, Gary. I intend
> to give a
> >>>>>>>>>>>>>>>>>> follow up in more detail on Monday. In any event, we
> will need a
> >>>>>>>>>>>>>>>>>> path forward to deliver on the project goals. I was
> reminded
> >>>>>>>>>>>>>>>>>> unpleasantly and unambiguously today that at least one
> of our
> >>>>>>>>>>>>>>>>>> colleagues in Austin wants and expects us to fail.
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>> Marlon
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>> On 6/20/14, 9:25 PM, Gary E. Gorbet wrote:
> >>>>>>>>>>>>>>>>>>> I was interested in the presentation by Saminda on
> CIPRES-Airvata integration. I would like to comment on one issue that arose.
> >>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>> The presentation spoke of a "new CIPRES Portal". The
> CIPRES developers expressed dismay at the prospect of a "total rewrite" of
> CIPRES to make it compatible with Airavata. But I did not get the
> impression that a complete rewrite was being proposed. Rather, I interpret
> "CIPRES Portal" as that portion of the Gateway that is directly concerned
> with interface with the middleware. Terri expressed a desire to limit
> changes to the CIPRES SDK. I see no conflict to that idea in what Saminda
> proposed.
> >>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>> I have only a cursory understanding of CIPRES.
> However, I believe that its functions broadly mirror those of the UltraScan
> gateway that I work on. The UltraScan gateway consists primarily of a set
> of PHP scripts. There are also CSS and JS (JavaScript) components. I would
> not anticipate making any changes to CSS or JS as the gateway transitions
> to SciGaP, since they are concerned with web page presentation and
> parameter specification. Nor would I think that many of the PHP scripts
> would change.
> >>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>> Where I do see a necessity for a rewrite is in
> specific scripts that directly interface to the middleware. Two examples
> come to mind.
> >>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>> First, there is the basic action at submit time.
> Presently, task parameters are incapsulated into an XML job file. Analysis
> parameters are incapsulated into another XML file that is combined with
> data files in a single archive (TAR) file. The task XML and archive files
> are passed to GFAC in the course of posting to the GFAC service via URI. In
> SciGaP, this procedure will be changed considerably. The post to a service
> will be replaced with Thrift API calls. The task will be defined by
> building a structure that is passed via Thrift. The changes are substantial
> enough that it makes sense to me to rewrite the specific PHP script charged
> with submitting a job.
> >>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>> Similarly, the job monitoring procedure will change
> considerably with SciGaP. Where currently UltraScan and GFAC communicate
> task status via a shared database, SciGaP will put all responsibility for
> determining task status on Airavata/SciGaP and the gateway will be advised
> of changes by a callback mechanism. The gateway will advise that status may
> need re-evaluation with Thrift calls. So, here again, the specific parts of
> the code related to task state monitoring should probably be rewritten.
> >>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>> Perhaps CIPRES has similar functions and modules. As I
> said, I don't know the specifics of CIPRES, but I imagine that user web
> interface code need not be changed, while parts of the code dealing with
> middleware interface might need substantial enough changes that a rewrite
> of selected modules would be indicated. Perhaps all that code is within
> CIPRES's SDK.
> >>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>> Saminda or Marlon: please correct me if I got this
> wrong. My impression was the "total rewrite" might better be characterized
> as "selective modular rewrite".
> >>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>> - Gary
> >>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>> To unsubscribe from this group and stop receiving
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>
Re: [marpierc@iu.edu: Re: [SciGaP-Dev] CIPRES-Airavata integration
proposal]
Posted by Marlon Pierce <ma...@iu.edu>.
You unsubscribe in the usual way. See
https://airavata.apache.org/community/mailing-lists.html
Marlon
On 1/12/15 11:39 AM, Deepika wrote:
> Hi,
>
> I want to be out of this. How do I not get further updates? whom should I
> contact?
>
> -
> Regards
> Deepika T
>
> On Thu, Jul 3, 2014 at 1:48 PM, K Yoshimoto <ke...@sdsc.edu> wrote:
>
>> Posting this also to dev@airavata, at Marlon's request.
>>
>> On 7/3/14, 1:39 PM, K Yoshimoto wrote:
>>> Another question. I was able to create a project and experiment,
>>> then launch the experiment. It was EXECUTING, but is now SUSPENDED.
>>> How should the gateway developer investigate the cause of suspension?
>>> I think that job state would not normally happen on the Trestles
>> resource,
>>> at least.
>>>
>>> php createExperiment.php
>>> php createExperiment.php <username> <experiment_name> <project_ID>
>>> john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>> php createExperiment.php kenneth kennethexp1
>> kennethtest_a26036de-d58c-4f6c-b38d-e60d30c13704
>>> object(Airavata\Model\Workspace\Experiment\Experiment)#9 (18) {
>>> ["experimentID"]=>
>>> string(21) "DO_NOT_SET_AT_CLIENTS"
>>> ["projectID"]=>
>>> string(48) "kennethtest_a26036de-d58c-4f6c-b38d-e60d30c13704"
>>> ["creationTime"]=>
>>> NULL
>>> ["userName"]=>
>>> string(7) "kenneth"
>>> ["name"]=>
>>> string(11) "kennethexp1"
>>> ["description"]=>
>>> NULL
>>> ["applicationId"]=>
>>> string(11) "SimpleEcho2"
>>> ["applicationVersion"]=>
>>> NULL
>>> ["workflowTemplateId"]=>
>>> NULL
>>> ["workflowTemplateVersion"]=>
>>> NULL
>>> ["userConfigurationData"]=>
>>> object(Airavata\Model\Workspace\Experiment\UserConfigurationData)#6
>> (7) {
>>> ["airavataAutoSchedule"]=>
>>> int(0)
>>> ["overrideManualScheduledParams"]=>
>>> int(0)
>>> ["shareExperimentPublicly"]=>
>>> bool(false)
>>> ["computationalResourceScheduling"]=>
>>>
>> object(Airavata\Model\Workspace\Experiment\ComputationalResourceScheduling)#4
>> (10) {
>>> ["resourceHostId"]=>
>>> string(17) "trestles.sdsc.edu"
>>> ["totalCPUCount"]=>
>>> int(1)
>>> ["nodeCount"]=>
>>> int(1)
>>> ["numberOfThreads"]=>
>>> int(0)
>>> ["queueName"]=>
>>> string(6) "normal"
>>> ["wallTimeLimit"]=>
>>> int(15)
>>> ["jobStartTime"]=>
>>> int(0)
>>> ["totalPhysicalMemory"]=>
>>> int(0)
>>> ["computationalProjectAccount"]=>
>>> NULL
>>> ["ComputationalProjectAccount"]=>
>>> string(6) "sds128"
>>> }
>>> ["advanceInputDataHandling"]=>
>>> NULL
>>> ["advanceOutputDataHandling"]=>
>>> NULL
>>> ["qosParams"]=>
>>> NULL
>>> }
>>> ["workflowExecutionInstanceId"]=>
>>> NULL
>>> ["experimentInputs"]=>
>>> array(1) {
>>> [0]=>
>>> object(Airavata\Model\Workspace\Experiment\DataObjectType)#7 (4) {
>>> ["key"]=>
>>> string(10) "echo_input"
>>> ["value"]=>
>>> string(23) "echo_output=Hello World"
>>> ["type"]=>
>>> int(0)
>>> ["metaData"]=>
>>> NULL
>>> }
>>> }
>>> ["experimentOutputs"]=>
>>> array(1) {
>>> [0]=>
>>> object(Airavata\Model\Workspace\Experiment\DataObjectType)#8 (4) {
>>> ["key"]=>
>>> string(11) "echo_output"
>>> ["value"]=>
>>> string(0) ""
>>> ["type"]=>
>>> int(0)
>>> ["metaData"]=>
>>> NULL
>>> }
>>> }
>>> ["experimentStatus"]=>
>>> NULL
>>> ["stateChangeList"]=>
>>> NULL
>>> ["workflowNodeDetailsList"]=>
>>> NULL
>>> ["errors"]=>
>>> NULL
>>> }
>>> Experiment kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92 created!
>>>
>>> john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>> php launchExperiment.php
>>> Please provide an experimentID.
>>> john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>> php launchExperiment.php kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92
>>> Experiment kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92 is launched.
>>> john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>> php getExperimentStatus.php kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92
>>> experiment status = EXECUTING
>>> <br>
>>> john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>> php getExperimentStatus.php kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92
>>> experiment status = SUSPENDED
>>> <br>
>>> john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>> php getExperimentStatus.php kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92
>>> experiment status = SUSPENDED
>>> <br>
>>> john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>> php getExperimentStatus.php kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92
>>> experiment status = SUSPENDED
>>> <br>
>>> john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>> php getExperimentStatus.php kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92
>>> experiment status = SUSPENDED
>>> <br>
>>> john@buffy:/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>> php getExperimentStatus.php kennethexp1_7364a59d-4bd0-4cd8-9f59-82a39863df92
>>> experiment status = SUSPENDED
>>> <br>
>>> john@buffy
>> :/media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>>> On Thu, Jul 03, 2014 at 10:23:14AM -0700, K Yoshimoto wrote:
>>>> That works now. Thanks!
>>>>
>>>> On Thu, Jul 03, 2014 at 05:00:21PM +0000, Singh, Raminder jeet wrote:
>>>>> Hi Kenneth,
>>>>>
>>>>> With help from a Student in Sri Lanka we are able to identify and fix
>> the issue. Issue was related to the socket send timeout. I updated the
>> clients to add following property. Please take a git pull and test.
>>>>> $transport->setSendTimeout($airavataconfig['AIRAVATA_TIMEOUT']);
>>>>>
>>>>> Thanks
>>>>> Raminder
>>>>>
>>>>> On Jul 3, 2014, at 12:17 AM, K Yoshimoto <ke...@sdsc.edu> wrote:
>>>>>
>>>>>> Still timed out.
>>>>>>
>>>>>> On Thu, Jul 03, 2014 at 04:06:42AM +0000, Singh, Raminder jeet wrote:
>>>>>>> Hi Kenneth
>>>>>>>
>>>>>>> Try to increase the AIRAVATA_TIMEOUT = 5000 to 20000 (in ms) in
>> airavata-client-properties.ini. Its the connection timeout connecting to
>> the server.
>>>>>>> Thanks
>>>>>>> Raminder
>>>>>>>
>>>>>>> On Jul 2, 2014, at 11:57 PM, K Yoshimoto <ke...@sdsc.edu> wrote:
>>>>>>>
>>>>>>>> I tried the new clients (had to set servername from localhost to
>>>>>>>> the iu server). I'm still seeing a timeout:
>>>>>>>>
>>>>>>>>
>> airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples$
>> php getAPIVersion.php
>>>>>>>> PHP Fatal error: Uncaught exception 'Thrift\Exception\TException'
>> with message 'TSocket: Could not connect to gw111.iu.xsede.org:8930
>> (Connection timed out [110])' in
>> /media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Thrift/Transport/TSocket.php:235
>>>>>>>> Stack trace:
>>>>>>>> #0
>> /media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getAPIVersion.php(39):
>> Thrift\Transport\TSocket->open()
>>>>>>>> #1 {main}
>>>>>>>> thrown in
>> /media/mdhpss/scigap/phpclientsamples/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/lib/Thrift/Transport/TSocket.php
>> on line 235
>>>>>>>>
>>>>>>>> On Wed, Jul 02, 2014 at 09:40:39PM -0400, Marlon Pierce wrote:
>>>>>>>>> Hi Kenneth--
>>>>>>>>>
>>>>>>>>> I did a quick successful check with the Airavata php clients (in
>> airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples)
>>>>>>>>> (see other email for details).
>>>>>>>>>
>>>>>>>>> Please use these instead of the obsolete PHP client samples.
>>>>>>>>>
>>>>>>>>> Thanks--
>>>>>>>>>
>>>>>>>>> Marlon
>>>>>>>>>
>>>>>>>>> On 7/2/14, 7:04 PM, K Yoshimoto wrote:
>>>>>>>>>> I've started playing with the php client samples.
>>>>>>>>>> I'm trying to create project, but running into some kind
>>>>>>>>>> of connection timeout. I can telnet to the port, so
>>>>>>>>>> maybe the timeout is too short? Or I'm missing some config
>>>>>>>>>> I should have done for the client samples? I'm going by the
>>>>>>>>>> README at:
>>>>>>>>>>
>> https://github.com/SciGaP/Airavata-PHP-Client-Samples/blob/master/client-samples/README-PHP-CLI-Examples.txt
>>>>>>>>>> and getting this kind of error:
>>>>>>>>>>
>>>>>>>>>> john@buffy:/media/mdhpss/scigap/phpclientsamples/Airavata-PHP-Client-Samples/client-samples$
>> telnet gw111.iu.xsede.org 8930
>>>>>>>>>> Trying 149.165.228.109...
>>>>>>>>>> Connected to gw111.iu.xsede.org.
>>>>>>>>>> Escape character is '^]'.
>>>>>>>>>> ^]
>>>>>>>>>>
>>>>>>>>>> telnet> quit
>>>>>>>>>> Connection closed.
>>>>>>>>>> john@buffy:/media/mdhpss/scigap/phpclientsamples/Airavata-PHP-Client-Samples/client-samples$
>> php createProject.php kenneth
>>>>>>>>>> PHP Fatal error: Uncaught exception
>> 'Thrift\Exception\TException' with message 'TSocket: Could not connect to
>> gw111.iu.xsede.org:8930 (Connection timed out [110])' in
>> /media/mdhpss/scigap/phpclientsamples/Airavata-PHP-Client-Samples/lib/Thrift/Transport/TSocket.php:235
>>>>>>>>>> Stack trace:
>>>>>>>>>> #0
>> /media/mdhpss/scigap/phpclientsamples/Airavata-PHP-Client-Samples/client-samples/createProject.php(45):
>> Thrift\Transport\TSocket->open()
>>>>>>>>>> #1 {main}
>>>>>>>>>> thrown in
>> /media/mdhpss/scigap/phpclientsamples/Airavata-PHP-Client-Samples/lib/Thrift/Transport/TSocket.php
>> on line 235
>>>>>>>>>> john@buffy
>> :/media/mdhpss/scigap/phpclientsamples/Airavata-PHP-Client-Samples/client-samples$
>>>>>>>>>>
>>>>>>>>>> On Wed, Jun 25, 2014 at 02:56:22PM -0400, Marlon Pierce wrote:
>>>>>>>>>>> The CCGrid demo server is running on gw111.iu.xsede.org. This
>> where
>>>>>>>>>>> the PHP client samples from GitHub are pointing.
>>>>>>>>>>>
>>>>>>>>>>> Marlon
>>>>>>>>>>>
>>>>>>>>>>> On 6/25/14, 2:28 PM, K Yoshimoto wrote:
>>>>>>>>>>>> Is there an instance of SciGap services available for testing
>>>>>>>>>>>> and development now?
>>>>>>>>>>>>
>>>>>>>>>>>> On Wed, Jun 25, 2014 at 01:09:58PM -0400, Suresh Marru wrote:
>>>>>>>>>>>>> Hi Kenneth,
>>>>>>>>>>>>>
>>>>>>>>>>>>> I see that Marlon already listed the PHP samples below -
>> https://github.com/SciGaP/PHP-Reference-Gateway
>>>>>>>>>>>>> The functionality which is not so easy is the registration of
>> the applications.
>>>>>>>>>>>>> Suresh
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Jun 23, 2014, at 12:58 PM, Marlon Pierce <ma...@iu.edu>
>> wrote:
>>>>>>>>>>>>>> Hi Kenneth--
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> The Airavata repo information is here:
>> http://airavata.apache.org/development/source.html. This includes a link
>> to the GitHub mirror, which is probably best.
>>>>>>>>>>>>>> The Thrift definitions are at
>> https://github.com/apache/airavata/tree/master/airavata-api/thrift-interface-descriptions.
>> Our apachecon slides may be useful supplements:
>> http://www.slideshare.net/smarru/restless-design-with-apache-thrift-experiances
>>>>>>>>>>>>>> The PHP command line samples (
>> https://github.com/SciGaP/Airavata-PHP-Client-Samples/), not currently in
>> Apache, illustrate how the API works.
>>>>>>>>>>>>>> Marlon
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On 6/23/14, 12:34 PM, K Yoshimoto wrote:
>>>>>>>>>>>>>>> Suresh,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Could you please send out a URL to the current Airavata repo?
>>>>>>>>>>>>>>> And the API documentation? I want to look through the
>> current
>>>>>>>>>>>>>>> interface code.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Kenneth
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Mon, Jun 23, 2014 at 08:13:14AM -0400, Suresh Marru wrote:
>>>>>>>>>>>>>>>> Hi Borries,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Can we take up on your demo offer and make an additional
>> request to you and Gary? Please bare my long email, I am sorry I do not
>> have much time to make this shorter.
>>>>>>>>>>>>>>>> XSEDE 14 tutorial is our opportunity to mint more and more
>> Demeler's, Miller's, Majumdhar's and Pampidighantam's. I say this
>> seriously, all of you have sacrificed your own science and enabled lot of
>> more science by 100's of fellow researchers. There are not many more who
>> can dedicate their careers to do this. So we need to show building and
>> operating gateways will not necessarily suck up their own science. SciGaP
>> will absorb the banal tasks and help them focus on their gateway mission -
>> "server a community of users enabling better science".
>>>>>>>>>>>>>>>> One way we can demonstrate SciGaP is by hands-on tutorial
>> of building a bare-bone gateway within half a day. But in addition, we need
>> to assure its beyond a tutorial and is indeed the same software used by
>> partnering gateways. We need a beta version of LIMS instance which uses
>> same thrift API's and served by the same set of Airavata services.
>> Preciously put, it will be nice to say current ultrascan production using
>> Airavata 0.8, but there is also development in progress to roll out
>> Ultrascan with latest Airavata (0.12).
>>>>>>>>>>>>>>>> Can Raminder and Gary work together to make this happen
>> within the next 3 weeks?
>>>>>>>>>>>>>>>> Hi All,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> As for the distracting banter, if you all prefer to know
>> the details, there is nothing secretive about it. We got a highest panel
>> rating standing ahead of 176 other proposals. Its natural the community
>> wants us to succeed. Some say this by clapping hands, some challenge us by
>> saying we will fail. Both are equal motivators. I am personally not so
>> worried about iPlant. But I am a bit concerned the negativity is spreading
>> and we directly took punches from Jay Boisseau, Dan Stanzione, Shantenu Jha
>> and unfortunately from Nancy Wilkins-Diehr (on SciGaP and S2I2 gateway
>> institute context, which we will resolve very soon). There are other folks
>> too, but there is nothing we can or should (in my opinion) do about this
>> directly. Its simply not worth and is a unnecessary drain of pre-XSEDE 14
>> energy.
>>>>>>>>>>>>>>>> We certainly need to disprove "every one in this team will
>> do their own thing". But I do not see SciGaP as
>> Airavata+CIPRES+NSG+Ultrascan nor IU+SDSC+UTHSA. To me, SciGaP means
>> SciGaP, the mission is to provides software and centralized operations and
>> the team believes and practices full openness - both software and
>> operations. We wrote a proposal on these beliefs and we need to play our
>> part in changing the gateway eco system working alongside friends and some
>> more dear friends.
>>>>>>>>>>>>>>>> Suresh
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Jun 21, 2014, at 10:34 PM, Marlon Pierce <
>> marpierc@iu.edu> wrote:
>>>>>>>>>>>>>>>>> Hi Borries--
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I was a little too frustrated on Friday in dealing with
>> the iPlant Agave lead developer. Mark and Terri have had previous bad
>> experiences. It isn't worth any time or effort, I believe. Working to
>> succeed in our SSI is the best path.
>>>>>>>>>>>>>>>>> Marlon
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On 6/21/14, 9:10 PM, Miller, Mark wrote:
>>>>>>>>>>>>>>>>>> I am not at all surprised, we tried to interact with
>> those people and were told in no uncertain terms we should just discard our
>> software and wait for further instructions. This was not a suggestion we
>> were comfortable with. There are plenty of ways we can interact
>> productively with any given infrastructure.
>>>>>>>>>>>>>>>>>> In my experience there are always groups who say negative
>> things as a tool for positioning their project with a competitive
>> advantage, and to sew panic among collaborators.
>>>>>>>>>>>>>>>>>> I tend to be driven by what makes sense for users, and
>> ignore the political winds from people who are not stakeholders.
>>>>>>>>>>>>>>>>>> However, it certainly would be useful to learn more about
>> what this conversation was about, as this is a pretty strong statement.
>>>>>>>>>>>>>>>>>> Mark
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Jun 21, 2014, at 3:51 AM, "Borries Demeler" <
>> demeler@biochem.uthscsa.edu> wrote:
>>>>>>>>>>>>>>>>>>> Hi Marlon,
>>>>>>>>>>>>>>>>>>> I am a bit alarmed by your statement that apparently
>> there are
>>>>>>>>>>>>>>>>>>> folks, esp. at Austin, who expect and want us to fail. I
>> would
>>>>>>>>>>>>>>>>>>> appreciate if you could elaborate on what exactly is
>> bugging
>>>>>>>>>>>>>>>>>>> these people so maybe we could resolve this? We cannot
>> afford
>>>>>>>>>>>>>>>>>>> to have this antipathy against our project, and I want
>> to prove
>>>>>>>>>>>>>>>>>>> them wrong. It is absolutely clear that at least the
>> UltraScan
>>>>>>>>>>>>>>>>>>> integration has been a big success and can serve as a
>> model
>>>>>>>>>>>>>>>>>>> for other integrations. I am sure with CIPRES similar
>> success
>>>>>>>>>>>>>>>>>>> can be achieved, but I may need some more background
>> info to
>>>>>>>>>>>>>>>>>>> understand exactly what issues are raising concern.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> A certain amount of re-write is always necessary, and we
>> fully
>>>>>>>>>>>>>>>>>>> expected and welcomed the opportunities to improve our
>> software,
>>>>>>>>>>>>>>>>>>> and there is a lot of code we ultimately abandoned,
>> re-wrote
>>>>>>>>>>>>>>>>>>> from scratch or refactored/adapted to new and better
>> methods.
>>>>>>>>>>>>>>>>>>> I must honestly say that I feel very fortunate that we
>> have
>>>>>>>>>>>>>>>>>>> your group and the AIravata concept to make our software
>> more
>>>>>>>>>>>>>>>>>>> portable and robust. These are the two major benefits
>> for us,
>>>>>>>>>>>>>>>>>>> but there are others, too.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Any chance we can give these people a demo of UltraScan
>> to
>>>>>>>>>>>>>>>>>>> show them how well it worked?
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> -b.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Fri, Jun 20, 2014 at 09:32:18PM -0400, Marlon Pierce
>> wrote:
>>>>>>>>>>>>>>>>>>>> Thanks for your thoughts on the matter, Gary. I intend
>> to give a
>>>>>>>>>>>>>>>>>>>> follow up in more detail on Monday. In any event, we
>> will need a
>>>>>>>>>>>>>>>>>>>> path forward to deliver on the project goals. I was
>> reminded
>>>>>>>>>>>>>>>>>>>> unpleasantly and unambiguously today that at least one
>> of our
>>>>>>>>>>>>>>>>>>>> colleagues in Austin wants and expects us to fail.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Marlon
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> On 6/20/14, 9:25 PM, Gary E. Gorbet wrote:
>>>>>>>>>>>>>>>>>>>>> I was interested in the presentation by Saminda on
>> CIPRES-Airvata integration. I would like to comment on one issue that arose.
>>>>>>>>>>>>>>>>>>>>> The presentation spoke of a "new CIPRES Portal". The
>> CIPRES developers expressed dismay at the prospect of a "total rewrite" of
>> CIPRES to make it compatible with Airavata. But I did not get the
>> impression that a complete rewrite was being proposed. Rather, I interpret
>> "CIPRES Portal" as that portion of the Gateway that is directly concerned
>> with interface with the middleware. Terri expressed a desire to limit
>> changes to the CIPRES SDK. I see no conflict to that idea in what Saminda
>> proposed.
>>>>>>>>>>>>>>>>>>>>> I have only a cursory understanding of CIPRES.
>> However, I believe that its functions broadly mirror those of the UltraScan
>> gateway that I work on. The UltraScan gateway consists primarily of a set
>> of PHP scripts. There are also CSS and JS (JavaScript) components. I would
>> not anticipate making any changes to CSS or JS as the gateway transitions
>> to SciGaP, since they are concerned with web page presentation and
>> parameter specification. Nor would I think that many of the PHP scripts
>> would change.
>>>>>>>>>>>>>>>>>>>>> Where I do see a necessity for a rewrite is in
>> specific scripts that directly interface to the middleware. Two examples
>> come to mind.
>>>>>>>>>>>>>>>>>>>>> First, there is the basic action at submit time.
>> Presently, task parameters are incapsulated into an XML job file. Analysis
>> parameters are incapsulated into another XML file that is combined with
>> data files in a single archive (TAR) file. The task XML and archive files
>> are passed to GFAC in the course of posting to the GFAC service via URI. In
>> SciGaP, this procedure will be changed considerably. The post to a service
>> will be replaced with Thrift API calls. The task will be defined by
>> building a structure that is passed via Thrift. The changes are substantial
>> enough that it makes sense to me to rewrite the specific PHP script charged
>> with submitting a job.
>>>>>>>>>>>>>>>>>>>>> Similarly, the job monitoring procedure will change
>> considerably with SciGaP. Where currently UltraScan and GFAC communicate
>> task status via a shared database, SciGaP will put all responsibility for
>> determining task status on Airavata/SciGaP and the gateway will be advised
>> of changes by a callback mechanism. The gateway will advise that status may
>> need re-evaluation with Thrift calls. So, here again, the specific parts of
>> the code related to task state monitoring should probably be rewritten.
>>>>>>>>>>>>>>>>>>>>> Perhaps CIPRES has similar functions and modules. As I
>> said, I don't know the specifics of CIPRES, but I imagine that user web
>> interface code need not be changed, while parts of the code dealing with
>> middleware interface might need substantial enough changes that a rewrite
>> of selected modules would be indicated. Perhaps all that code is within
>> CIPRES's SDK.
>>>>>>>>>>>>>>>>>>>>> Saminda or Marlon: please correct me if I got this
>> wrong. My impression was the "total rewrite" might better be characterized
>> as "selective modular rewrite".
>>>>>>>>>>>>>>>>>>>>> - Gary
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> To unsubscribe from this group and stop receiving
>> emails from it, send an email to dev+unsubscribe@scigap.org.
>>>>>>>>>>>>>>>>>>>> To unsubscribe from this group and stop receiving
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>>>>>>>>>>>>>>>>>>> To unsubscribe from this group and stop receiving emails
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>>>>>>>>>>>>>>>>> To unsubscribe from this group and stop receiving emails
>> from it, send an email to dev+unsubscribe@scigap.org.
>>>>>>>>>>>>>>>> To unsubscribe from this group and stop receiving emails
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>>>>>>>>>>>>>>> To unsubscribe from this group and stop receiving emails
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>>>>>>>>>>>>>> To unsubscribe from this group and stop receiving emails from
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>>>>>>>>>>>>> To unsubscribe from this group and stop receiving emails from
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>>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
>> send an email to dev+unsubscribe@scigap.org.
>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
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>>>>>>> To unsubscribe from this group and stop receiving emails from it,
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>>
>> ----- End forwarded message -----
>>
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