What is the relationship between GridRepublic, Charity Engine and FiND?
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skgiven
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Message 2780 - Posted: 27 Nov 2016, 12:17:54 UTC
Last modified: 27 Nov 2016, 12:18:07 UTC

As far as I can tell there is no mechanism to choose apps (what we run) and no advice regarding what the tasks do.

I've already asked in the forums what the tasks are, as have others, without reply!

I noticed this comment,
"Matt Blumberg in Boston - a company called GridRepublic which uses BOINC-like computation for charitable work (Charity Engine)."
- https://www.charityengine.com/about/us

Can you please explain what the relationship is between GridRepublic, Charity Enging and FiND and if the apps we have been running are Charity Enging apps (rather than FiND apps); does the ce in ce12 1.05 stand for charity engine?

Dayle Diamond
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Message 2781 - Posted: 27 Nov 2016, 15:43:40 UTC - in response to Message 2780.

More to the point, are you running for-profit computations on my computers?

I managed to become the 10th biggest donor in the USA for this project, all while dealing with poverty and some pretty alarming life circumstances, including being so poor that I'm still living with my employer.

And when this project ended I took my crunching power to WorldCommunityGrid where we know it's doing something good. So if you've turned my scarifies into your personal profit, and then you're pretending like MY gift is your charity, we have a right to know.

https://www.charityengine.com/charities/research

Dayle Diamond
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Message 2782 - Posted: 27 Nov 2016, 15:46:48 UTC - in response to Message 2781.

It looks like you're privatizing the profits and socializing the costs.

skgiven
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Message 2783 - Posted: 27 Nov 2016, 17:06:43 UTC - in response to Message 2782.
Last modified: 27 Nov 2016, 17:24:25 UTC

Seems that Charity Engine is not a charity! It's a trading name of a Limited Company registered in the UK called The Worldwide Computer Company Limited.

https://en.wikipedia.org/wiki/Charity_Engine

https://beta.companieshouse.gov.uk/company/06723910/filing-history

So, again, what is the relationship between GridRepublic, Charity Engine and FiND?
Is the GridRepublic piping Charity Engine work to Boinc users registered with FiND?

Col323
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Message 2785 - Posted: 28 Nov 2016, 11:01:31 UTC

I'd like to know this as well, along with the answer to "What are we crunching?" I was able to receive a pretty steady diet of work after switching the project URL to compute.gridrepublic.org. However, the lack of information and synchronization seems a little "bait and switch" to me. I've set "no new work" on the two computers I pointed to the new URL, and have not bothered to point any of my others to the new URL. I'll keep an eye out for more information, but I'm perfectly happy with my FiND contribution where it is and crunching more World Community Grid and TN-Grid.

Profile Steve Hawker*
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Message 2791 - Posted: 29 Nov 2016, 17:04:52 UTC

It's really confusing.

On one side we have Dr Chubb and Rytis, whose prior works are unimpeachable I'd suggest. It seems that they are trying to do something unusual on the server side. It's clearly early days so we should expect alpha-like behavior and we're sure seeing that.

On the other hand, we aren't seeing any response whatsoever to reasonable requests for clarity about the whole Charity Engine situation. This coupled with the inability to see our tasks does not create confidence in this project. Worse still, for me, is that WUProp isn't logging the hours, just as they didn't log hours for Charity Engine.

So good guys keeping quiet means NNW, I'm afraid.

Is it too much to ask for some statement on this topic?

Richard Haselgrove
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Message 2792 - Posted: 29 Nov 2016, 17:28:17 UTC

Although we can't see the output of our tasks on the webserver at the moment, we can see the work being done by, and on, our machines, before it's uploaded and reported.

I've stuck with the old URL, not changed to Grid republic, and all the tasks I've run since the restart have looked and behaved the same - and very like the old Dublin tasks.

More particularly, the stderr.txt of tasks in progress on my machine starts

################################################################# # If you used AutoDock Vina in your work, please cite: # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, Journal of Computational Chemistry 31 (2010) # # 455-461 # # # # DOI 10.1002/jcc.21334 # # # # Please see http://vina.scripps.edu for more information. # #################################################################

AutoDock Vina was the application Ben was running in Dublin before the break, so that's some evidence of continuity.

But I agree an authoritative clarification from the scientists and administrators involved is vital.

skgiven
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Message 2793 - Posted: 30 Nov 2016, 13:47:25 UTC - in response to Message 2792.
Last modified: 30 Nov 2016, 13:47:32 UTC

When connected to FiND@home the name automatically changed to Fight Neglected Diseases.
The Boinc Manager log files left the message “This project is using an old URL” and the instruction was to remove the project and add https://compute.gridrepublic.org/.
Boinc Manager displayed that it was running the app ce12 10.5.
In Jan 2016 Charity Engine had an app called ce11.
Despite repeated requests for information there have been no comments from the admins regarding any of this. They have answered other unrelated questions though...

Richard Haselgrove
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Message 2794 - Posted: 30 Nov 2016, 14:01:44 UTC - in response to Message 2793.

All of which is transparent, and can be tracked by reading BOINC's XML files - most notably sched_request, sched_reply, and client_state.

I have

<app> <name>vina</name> <user_friendly_name>Autodock Vina</user_friendly_name> <non_cpu_intensive>0</non_cpu_intensive> </app> <app> <name>ce12</name> <user_friendly_name>ce12</user_friendly_name> <non_cpu_intensive>0</non_cpu_intensive> </app> ... <app_version> <app_name>vina</app_name> <version_num>102</version_num> ... <file_ref> <file_name>vina_1.2_windows_intelx86.exe</file_name> <main_program/> </file_ref> </app_version> <app_version> <app_name>ce12</app_name> <version_num>105</version_num> <platform>windows_intelx86</platform> <avg_ncpus>1.000000</avg_ncpus> <max_ncpus>1.000000</max_ncpus> <flops>15899371657.141815</flops> <api_version>7.7.0</api_version> <file_ref> <file_name>wrapper_26016_windows_intelx86.exe</file_name> <main_program/> </file_ref> <file_ref> <file_name>ce12-1.04-job.xml</file_name> <open_name>job.xml</open_name> </file_ref> <file_ref> <file_name>ce12-1_1_2_windows_intelx86.exe</file_name> <open_name>vina.exe</open_name> </file_ref> <is_wrapper/> </app_version>

It's curious, and it deserves explanation, but I don't immediately class it as fraudulent.

skgiven
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Message 2795 - Posted: 30 Nov 2016, 15:16:16 UTC - in response to Message 2794.

sched_request_compute.gridrepublic.org:

    <app_versions>
    <app_version>
    <app_name>ce12</app_name>
    <version_num>105</version_num>
    <platform>windows_intelx86</platform>
    <avg_ncpus>1.000000</avg_ncpus>
    <max_ncpus>1.000000</max_ncpus>
    <flops>19444655700.768513</flops>
    <api_version>7.7.0</api_version>
    <is_wrapper/>
    </app_version>
    </app_versions>


sched_reply_compute.gridrepublic.org:

    <scheduler_reply>
    <scheduler_version>707</scheduler_version>
    <dont_use_dcf/>
    <master_url>https://compute.gridrepublic.org/</master_url>
    <request_delay>7.000000</request_delay>
    <project_name>Fight Neglected Diseases</project_name>


client_state:
<project>
<master_url>https://compute.gridrepublic.org/</master_url>
<project_name>Fight Neglected Diseases</project_name>

<scheduler_url>https://compute.gridrepublic.org/cgi/cgi</scheduler_url>

</project>
<app>
<name>ce12</name>
<user_friendly_name>ce12</user_friendly_name>
<non_cpu_intensive>0</non_cpu_intensive>
</app>
<file>
<name>wrapper_26016_windows_intelx86.exe</name>
<nbytes>994088.000000</nbytes>
<max_nbytes>0.000000</max_nbytes>
<status>1</status>
<executable/>
<signature_required/>
<file_signature>
d67b145a35fe859d5d69d2c325c7fffd2adac42f07fc8425cf65397d9903b224
141741baf2bf715c0d7a1ec5aac18ea764d1ee8312d29ce93aed96a59a5f9065
f092e9d064735a30ea49f83fd6a9f4949bd601c07495c236f56eaabcf32388b6
eb6713ed578dd24360ace1ee5e92a09b945b0fcb94512960c3c2bbc399a5eee9
.
</file_signature>
<download_url>https://compute.gridrepublic.org/download/wrapper_26016_windows_intelx86.exe</download_url>
</file>
<file>
<name>ce12-1.04-job.xml</name>
<nbytes>241.000000</nbytes>
<max_nbytes>0.000000</max_nbytes>
<status>1</status>
<executable/>
<signature_required/>
<file_signature>
a34fa9401a19dcd8cbc6226af78dfc9d10759a39f6c31bd10455a331b644f947
ebd6f69ea13e3fcd56385d2499196d9630994e43b68b4e2f0b9852078b4973fa
1e36b0abf0ff942427145fea41bd2bd401681ec5d66a2be2d229046d0296b60d
d88ec2b9008c0a7b22551038652da9490e5ebb2b51b33a567686fcdfa1337b26
.
</file_signature>
<download_url>https://compute.gridrepublic.org/download/ce12-1.04-job.xml</download_url>
</file>
<file>
<name>ce12-1_1_2_windows_intelx86.exe</name>
<nbytes>781824.000000</nbytes>
<max_nbytes>0.000000</max_nbytes>
<status>1</status>
<executable/>
<download_gzipped/>
<gzipped_nbytes>345914</gzipped_nbytes>
<signature_required/>
<file_signature>
6bbd3303d79800ae155e56524c36e0aa4b13a67d986d7d19c8aa271772d1d136
2294749e9b4024c03233beb2260e75185b90f1edeaf4694f4ab0201b5782c41e
a4a0d2e7a6da6a654b33ef23dd3e4bbda126a36fdec1ea04afe74f367735d64f
ac581f587954f8df4c7439694ea8d47fdb05a296391a40d3cb898e2cf98f9247
.
</file_signature>
<download_url>https://compute.gridrepublic.org/download/ce12-1_1_2_windows_intelx86.exe.gz</download_url>
</file>
<app_version>
<app_name>ce12</app_name>
<version_num>105</version_num>
<platform>windows_intelx86</platform>
<avg_ncpus>1.000000</avg_ncpus>
<max_ncpus>1.000000</max_ncpus>
<flops>19444655700.768513</flops>
<api_version>7.7.0</api_version>
<file_ref>
<file_name>wrapper_26016_windows_intelx86.exe</file_name>
<main_program/>
</file_ref>
<file_ref>
<file_name>ce12-1.04-job.xml</file_name>
<open_name>job.xml</open_name>
</file_ref>
<file_ref>
<file_name>ce12-1_1_2_windows_intelx86.exe</file_name>
<open_name>vina.exe</open_name>
</file_ref>
<is_wrapper/>
</app_version>

Col323
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Message 2804 - Posted: 2 Dec 2016, 19:30:51 UTC - in response to Message 2794.

It's curious, and it deserves explanation, but I don't immediately class it as fraudulent.

Right, I'd agree. I'd also add frustrating. Instead of seeing an announcement pushed to my Boinc client reading something like, "Big news! FiND has partnered with Grid Republic and Charity Engine to perform further research. Expect to see some work trickling in and some changes to the website. Stay tuned for more details!", which might actually drive excitement and participation, my experience has been:

1) Notice my computer downloaded 40 FiND units. Sweet!
2) Oh, not so fast. They all errored out. What's going on?
3) Check the homepage to see if any news is posted. Nope.
4) Check the event logs. Repeatedly see the message "Unit XYZ is no longer needed by project."
5) Check the forums, see others talking about other oddities, but no official explanation.
6) Let the client sit to see if it sorts itself and grabs new work since others seem to be getting work sporadically.
7) No luck grabbing work after over 24 hours, check the event log to see a message to the effect "You are using the old project URL, please update to the Grid Republic URL."
8) Follow the instructions in the event log, and immediately snag 50+ units. Excellent!
9) Update one more machine which has also failed to get work and get another 50+ units.
10) As others noted, find no way to track work, credit, or validation status.
11) Read every new thread on the forum (previously skimmed in line 5) and note my similar experiences to what's been posted. Click around Grid Republic and see there's not much to see.
12) Set no new work for FiND.
13) Check Free-DC to see just what I was credited for these ~100 units. Huh, just about 300 points.

I know there's a lot to configure, etc. But a little up front (or even parallel) communication can go a long way here.

Anthony Chubb
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Message 2819 - Posted: 5 Dec 2016, 1:01:30 UTC - in response to Message 2791.

Dear all,
I mentioned many months ago - some time in early 2015 - that GridRepublic in Boston offered to take over the server management of FiND@H.
It was - and still is - my intention to make results from the FiND@H project publically available. I've built a website that displays the first results - http://chemware.ucd.ie/FiNDaH/.
The idea is that anyone, anywhere, has access to this data and can validate the results in the lab.

That's where things get tricky. If an academic lab - or for that matter a biotech company - puts their own time and money into validating these data, then they get the patents and profit. Ideally government money should pay for these validation studies - socialising the profits - but as I am in Ireland and computational drug discovery is off the bottom of the priority list, I repeatedly failed to get funding for the validation studies from the HRB, SFI and EI research funding agencies.

I am now no longer employed to be a research scientist and have been forced to take an admin role at a college to break out of the annual contract life of postdocs. Hence the project went dormant until GR picked it up again.

But I still want the results validated in the lab. I repeatedly tried to get funding from the Gates foundation, but ironically they refused to fund projects that where computational. I tried croudfunding, and the generous donations we received covered the cost of new hard drives - a far cry from the 100,000s needed to support lab validation studies.

So I'm still hopeful that some angel investor will swoop in and offer to validate the work. Will the profits be shared? - no. My contract with the FiND@H volunteers ends with porting the data onto the web. Now anyone in the world with deep pockets can take advantage of the data. The risk is still high and there is no final guarantee. Of course I hope I'm right, and that this project works. But the person who puts hard cash down to validate the data is the one who walks away with the spoils. At the moment this could be a lab/company in India or South Africa or wherever... for all I know.

I'm just delighted that GridRepublic have offered to keep the project alive... I think we could use this method for all sorts of infectious diseases, given the chance. In the end I hope someone, somewhere, puts in the effort to validate the data in vitro.

Ciao,
Ant

Ps: I have not heard of any BOINC project socialising the profits from the computation work. For instance, the WCG project similar to ours - Go Fight Malaria At Home - also put all their data online. I have no idea if this has been validated in house by them - then they could hold patents on good results and license to large pharma and (potentially) make profits from it. I have no idea... just saying. The nett result of this work are possible hypothetical interactions, which will take a lot of time and money to validate.

Message 2823 - Posted: 6 Dec 2016, 4:20:09 UTC - in response to Message 2819.
Last modified: 6 Dec 2016, 4:20:44 UTC

Dr Chubb,
Thank you so much for this post!
Please, please PLEASE put this content on the home page!!
Contributors ("crunchers") ought not to have to dig and dig to find these key points.

LLP, PhD PE

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My thinking neither is the source of my being,
not proves it to you
God Is Love, Jesus proves it ∴ we are!

Anthony Chubb
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Message 2833 - Posted: 7 Dec 2016, 4:46:22 UTC - in response to Message 2823.
Last modified: 7 Dec 2016, 4:58:00 UTC

Will do! Sorry for the confusion. I have not been looking at these message boards for months, and they started lighting up again after Rytis and Matt re-energised the project.

In this case some news is good news! It means the FiND@H project lives to see another day.

Thanks again to all the old faithful who have stuck with it all these years.

Until we get funding to validate in the lab, we won't be able to publish new confirmed targets. But I'm still optimistic and will keep trying to get some funding. I'll also keep adding docking data to the results website when it becomes available (after cleanup/analysis - Rytis is helping me there also).

Probably won't happen soon as it's no longer part of my day job.

Ciao,
Ant

Ps: Matt posted re CE and GR and FiND@H here:
https://boinc.berkeley.edu/dev/forum_thread.php?id=11309

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Message 2836 - Posted: 7 Dec 2016, 8:41:51 UTC - in response to Message 2833.

Thanks for the update Ant. After reading Matt's post I'm now happy to allow work requests again despite the (current) lack of visibility of our results.
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Anthony Chubb
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Message 2839 - Posted: 8 Dec 2016, 6:36:58 UTC - in response to Message 2836.

http://chemware.ucd.ie/FiNDaH/Malaria.php

Message boards : Science : What is the relationship between GridRepublic, Charity Engine and FiND?


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