Subject: Marine Geospatial Ecology Tools (MGET) help
Text archives
- From: Jason Roberts <>
- To: "Bakker, Anna Cassandra" <>
- Cc: "" <>
- Subject: RE: [mget-help] MGET tool
- Date: Sun, 18 Aug 2019 13:44:38 +0000
- Accept-language: en-US
- Arc-authentication-results: i=1; mx.microsoft.com 1; spf=pass smtp.mailfrom=duke.edu; dmarc=pass action=none header.from=duke.edu; dkim=pass header.d=duke.edu; arc=none
- Arc-message-signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=microsoft.com; s=arcselector9901; h=From:Date:Subject:Message-ID:Content-Type:MIME-Version:X-MS-Exchange-SenderADCheck; bh=dplPfh5d1E6I/ganL7sU3QsbrqT2m6dwxbz4OUxRv1o=; b=PQTbWpV6icuN7JPqewSR3WEq3fEmMBXia/SrUH34IbAKmlMfcBqfBiKTRhvuJoQ/xUvx4VwsvLpSLCweqVAmIWPSWUrqh0XHBEmIZgdf+PlFhXUbe0voQkRKL1FQgjAu2wXibyfN7tSCQT3yIgYqkobQmJIMDMw3KMIOrgahAPupBevLGbYnRtHxr2Tih43yTGNdHyHqZknkZ+is0TDx1CpufhUVfF0A/ApNtup5CrCDiVKogFkCj3dTyH32cHrJn2Gl+E3POruRzWtAH5KpHc0z/sxeiaZ9ftQJgl1C8dvkVwCsD+nMwIH7KieGZzjJaHZV2EEeNPGgQxihOKCW1w==
- Arc-seal: i=1; a=rsa-sha256; s=arcselector9901; d=microsoft.com; cv=none; b=W+sHmG9LjEsQcn2thSS6Lhcopx48RvFxp+ZGJAS/RJxZSA3S1qtGbwJh9t4g23vFIsR0Z8uMNG3AXjr+4bD3nvJxIUS56zmxu2kThY8d266mWDeKRv7ud3ICYjudS0CWUo1TfbduC1Dy7B8U7HVTUiY4YT6Sz6AjQZKJAqEGEym/VI5JPeP3AbPJxnugxEjIiP4EO6RhKFVLsk53jEP4IMdBJs6jPc5/TCOqrlsQ9cH3eA+v9iAPTkNflloChb0TVhic40i+7XIn8HJosezOse0CSjEmf0iPhRdxoL+fI5asYuhEtVw5OxKY8dMWreCmiBM/feIzYNai4MU5fkYn3Q==
|
Dear Anna,
Thanks for your interest in MGET and sorry for my slow reply. I am on vacation until 26 August. I can offer more help starting that week.
That is a very unusual error. It comes from the MATLAB Component Runtime (MCR). I cannot look into it in detail right now but a simple thing you could try would be to stop all ArcGIS programs, uninstall the MCR, install it again, and try the MGET tool from ArcGIS again. However, if the tool works when loading currents data from 2011 but not later years, it would be odd to receive that error. There is nothing that I can recall that would prompt that kind of failure simply from loading additional data, or data from an additional year. But I can’t look at the code at the moment so I’m not sure.
It is possible for you to run this from a Python script outside of ArcGIS. Also, if you are comfortable with MATLAB, I can give you the MATLAB code for the core algorithm and you can work with your university folks to run it on your cluster. This approach would also get around the memory limitation of running it within 32-bit Python (MGET currently does not support 64-bit Python), which would allow simulations that covered larger areas, longer time periods, and higher spatial resolutions. However I urge caution in expanding those things, as it is easy to parameterize up a simulation that requires weeks of computation for questionable benefit. (We can talk about that more, later, if you decide to go there.)
Finally, it might be possible to leverage connectivity results from previous projects I’ve collaborated on. This would depend on your exact needs, particularly study areas and time periods.
Feel free to contact me again after 26 August if you’d like to discuss any of this more.
Best, Jason
From: <>
On Behalf Of Bakker, Anna Cassandra
Hello,
I hope this email finds you well. My name is Anna and I’m a PhD student at the University of Miami’s Rosenstiel School of Marine and Atmospheric Science. I’m working on a thesis project to understand the biophysical and anthropogenic variables which mediate coral reef health in the South Pacific. One of the variables I’d like to include is reef connectivity.
I came across your Arc MGET toolbox and am interested in using it for my connectivity variable. I’ve already created a simulation for September - October 2011 as a test run, but would now like to expand that to create simulations for the entirety of 2015, 2016, and 2017 (El Nino, La Niña, and neither regimes) - though I’m doing 3 months at a time because of computational limitations. However, when "Loading HYCOM GLBa0.08 Currents Into Larval Dispersal Simulation," I receive the following error:
python.exe: Timed out while waiting to acquire an exclusive lock on the CTF directory. If you are running multiple simutaneous instances of this application, initialization errors may occur. Would you happen to know what is causing this? All other instances of ArcMap are closed. I’ve also tried adjusting the dates and other parameters when initializing the loading of the currents.
I realize you must get many requests to get this tool to work, so I’m also willing to try a different approach. I’m hoping to write up a script in Python (or MATLAB) so that I can send the instance to our university supercomputer cluster, because running all of 2015-2017 on ArcMap would take months on our regular lab computers. If possible, do you know of any open source scripts already written to do this? I read through some of the links on this page but was wondering if there were already others who’ve tried to run models for the same areas/time frames that I’m interested in (so as not to repeat work that was already done!). I’d greatly appreciate any guidance and am excited to get a running connectivity model for the South Pacific as soon as I can.
And, of course, I would be happy to cite you where appropriate, and share data as we develop them. We’re happy to collaborate and contribute to your larval connectivity tool however you see fit.
Let me know your thoughts, and thank you very much in advance for your time.
All the best,
Anna Bakker
|
- [mget-help] MGET tool, Bakker, Anna Cassandra, 08/12/2019
- RE: [mget-help] MGET tool, Jason Roberts, 08/18/2019
Archive powered by MHonArc 2.6.19.