Several Issues

[JohnLevander]

1. link to FRED version that LSDTM works with (USE THE DOI) We mention FRED but don't explain what it is.
2. It says that LSDTM is a collection of scripts. But lsdtm.sh is a single script
3. "Synthia-formatted" is mentioned, but no explanation of what Synthia is
4. LSDTM is Olympus specific right, but the Home says it's for "a computing cluster" which implies "any computing cluster"
5. Home has a "How to Run LSDTM" section, and there is a "Running LSDTM" page. Confusing.
6. "Running LSTDM" page is basically just "usage" or "lsdtm" paramters
7. "how to run" step 2 has this (module avail) with with explanation. This should probably be a section that explains how to check for dependencies
8. step 3 on "how to run" should go into much greater detail on how to find/determine population ID (file system location, etc)
9. step 3 mentions SPEW but there is no explanation on what that is
10. Need some examples: using LSTDM to Run FRED on USA, using running FRED on Florida

General comment: I think what we want is a "User Guide." Something that explains everything that someone needs to know that wants to run FRED with LSTDM. We don't want to assume too much prior knowledge.

[TerenceSperringerJr]

1. link to FRED version that LSDTM works with (USE THE DOI) We mention FRED but don't explain what it is.

I need to go back to double check which changes are absolutely necessary to get PHDL FRED working on a non-Mac environment before I can create a proper DOI, so for now there is a link to the porting-fixes repository.

2. It says that LSDTM is a collection of scripts. But lsdtm.sh is a single script

It now says "The LSDTM project is a collection of scripts (named after the primary script, lsdtm.sh) for running..."

3. "Synthia-formatted" is mentioned, but no explanation of what Synthia is

This one is a bit tough because there is no definition page for Synthia other than the data formats documentation we are working on. U.S. Synthetic Population 2010 Version 1.0 is what PHDL FRED references, so I can only assume that this is what Synthia is. I've linked 'Synthia-formatted' to our file formats documentation for the time being (still under construction, though).

4. LSDTM is Olympus specific right, but the Home says it's for "a computing cluster" which implies "any computing cluster"

It now says "The LSDTM project is a collection of scripts (named after the primary script, lsdtm.sh) for running the MIDAS-ISG version of the Public Health Dynamics Laboratory branch of FRED on the Olympus cluster of the Pittsburgh Supercomputing Center through Portable Batch System (PBS)."

5. Home has a "How to Run LSDTM" section, and there is a "Running LSDTM" page. Confusing.

Renamed the section to "How to Install and Run LSDTM" and renamed the page to "Using LSDTM"

6. "Running LSTDM" page is basically just "usage" or "lsdtm" paramters

I will update this more, but I did try to re-arrange things a little to be more specific about required versus optional or other flags. The usage quote has been moved to under the -h flag explanation.

7. "how to run" step 2 has this (module avail) with with explanation. This should probably be a section that explains how to check for dependencies

I have created the LSDTM Dependencies section and relocated this step into it.

8. step 3 on "how to run" should go into much greater detail on how to find/determine population ID (file system location, etc)

The method I use is a bit convoluted (requires sensitive environment paths) so I am just going to link to Adam's nice workflow page.

9. step 3 mentions SPEW but there is no explanation on what that is

I refer to the data format repository again.

10. Need some examples: using LSTDM to Run FRED on USA, using running FRED on Florida

I'll work on making step-by-step examples.