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ufs-community / ufs-mrweather-app

UFS Medium-Range Weather Application
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Complete WM and NCEPLIBS wiki instructions and ftp materials for the weather model GST #34

Closed ceceliadid closed 4 years ago

ceceliadid commented 4 years ago

@arunchawla-NOAA This can be simple. It may be useful to exercise the umbrella build for the prerequisites.

ceceliadid commented 4 years ago

@mark-a-potts @climbfuji @arunchawla-NOAA @rsdunlapiv @jedwards4b @ligiabernardet @mvertens To start graduate student testing at the end of this month, we would like to have Cheyenne, Stampede2, and Hera preconfigured with library dependencies built. Is anyone planning to build the dependencies on Stampede2? Could someone do that if not?

uturuncoglu commented 4 years ago

@ceceliadid I already did it on Stampede2 and we tested with @jedwards4b but I'll check it again tomorrow.

ceceliadid commented 4 years ago

@uturuncoglu Thanks Ufuk, that's fantastic. I will add Stampede2 to the list of pre-configured platforms on the weather model "Getting Started" wiki.

ceceliadid commented 4 years ago

@mark-a-potts @climbfuji @arunchawla-NOAA @rsdunlapiv @jedwards4b @ligiabernardet @danrosen25 @uturuncoglu @pjpegion This is mainly to Mark, but also for documentation & testing folks. To start graduate student testing at the end of the month, it will be important to have up-to-date documentation on how to build the dependencies if you are not on a pre-configured platform. Does the Getting Started documentation here: https://github.com/ufs-community/ufs-weather-model/wiki/Getting-Started under the header "Download and build libraries required by the model" have the best available description of how to do that? It's based on an email Mark had sent a month or so ago. For the documentation it could be helpful to know where the NCEPLIBS script has been tested successfully and very generally how long it is expected to take to complete all the builds. Also, it seems like the link that Mark had provided git@github.com:NOAA-EMC/NCEPLIBS.git does not work? Is there a better link to get to the right script in NCEPLIBS?

ligiabernardet commented 4 years ago

Some documentation is here: https://github.com/NOAA-EMC/NCEPLIBS/wiki/Cloning-and-Compiling-NCEPLIBS A chapter is also planned for the MR Weather App User's Guide. Pls help identify what else needs to be explained beyond this existing document.

On Tue, Jan 21, 2020 at 4:58 PM ceceliadid notifications@github.com wrote:

@mark-a-potts https://github.com/mark-a-potts @climbfuji https://github.com/climbfuji @arunchawla-NOAA https://github.com/arunchawla-NOAA @rsdunlapiv https://github.com/rsdunlapiv @jedwards4b https://github.com/jedwards4b @ligiabernardet https://github.com/ligiabernardet @danrosen25 https://github.com/danrosen25 @uturuncoglu https://github.com/uturuncoglu @pjpegion https://github.com/pjpegion This is mainly to Mark, but also for documentation & testing folks. To start graduate student testing at the end of the month, it will be important to have up-to-date documentation on how to build the dependencies if you are not on a pre-configured platform. Does the Getting Started documentation here: https://github.com/ufs-community/ufs-weather-model/wiki/Getting-Started under the header "Download and build libraries required by the model" have the best available description of how to do that? It's based on an email Mark had sent a month or so ago. For the documentation it could be helpful to know where the NCEPLIBS script has been tested successfully and very generally how long it is expected to take to complete all the builds. Also, it seems like the link that Mark had provided git@github.com:NOAA-EMC/NCEPLIBS.git does not work? Is there a better link to get to the right script in NCEPLIBS?

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mark-a-potts commented 4 years ago

Kyle and I are going to make a push to have a refactored version of both NCEPLIBS and the build for the model by this Friday. I'll make sure to get the documentation up to date as well.

-Mark

On 1/21/20 7:14 PM, ligiabernardet wrote:

Some documentation is here: https://github.com/NOAA-EMC/NCEPLIBS/wiki/Cloning-and-Compiling-NCEPLIBS A chapter is also planned for the MR Weather App User's Guide. Pls help identify what else needs to be explained beyond this existing document.

On Tue, Jan 21, 2020 at 4:58 PM ceceliadid notifications@github.com wrote:

@mark-a-potts https://github.com/mark-a-potts @climbfuji https://github.com/climbfuji @arunchawla-NOAA https://github.com/arunchawla-NOAA @rsdunlapiv https://github.com/rsdunlapiv @jedwards4b https://github.com/jedwards4b @ligiabernardet https://github.com/ligiabernardet @danrosen25 https://github.com/danrosen25 @uturuncoglu https://github.com/uturuncoglu @pjpegion https://github.com/pjpegion This is mainly to Mark, but also for documentation & testing folks. To start graduate student testing at the end of the month, it will be important to have up-to-date documentation on how to build the dependencies if you are not on a pre-configured platform. Does the Getting Started documentation here: https://github.com/ufs-community/ufs-weather-model/wiki/Getting-Started under the header "Download and build libraries required by the model" have the best available description of how to do that? It's based on an email Mark had sent a month or so ago. For the documentation it could be helpful to know where the NCEPLIBS script has been tested successfully and very generally how long it is expected to take to complete all the builds. Also, it seems like the link that Mark had provided git@github.com:NOAA-EMC/NCEPLIBS.git does not work? Is there a better link to get to the right script in NCEPLIBS?

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ceceliadid commented 4 years ago

@ligiabernardet @climbfuji Some thoughts about documentation organization and gaps:

arunchawla-NOAA commented 4 years ago

I agree that we let the NCEPLIBS be the place where libraries build are documented and let the other guides point to this. We can clean this up in early February as soon as the finalized builds are done.

Arun Chawla Chief Engineering & Implementation Branch Room 2083 National Center for Weather & Climate Prediction 5830 University Research Court College Park, MD 20740 Phone : 301-683-3740 Mobile : 240-564-5675 Fax : 301-683-3703

On Tue, Jan 21, 2020 at 8:16 PM ceceliadid notifications@github.com wrote:

@ligiabernardet https://github.com/ligiabernardet @climbfuji https://github.com/climbfuji Some thoughts about documentation organization and gaps:

  • It would be good to have this dependency build documentation in as few places as possible. Currently it is in at least three:

    1. the WM UG, 2) the NCEPLIBS github wiki, and 3) the WM github wiki. It seems fine to me to have the WM wiki just point to the NCEPLIBs wiki and reduce the number of places by one!

  • I think the NCEPLIBS wiki documentation should specify whether Intel and GNU are both expected to work at this point - it currently doesn't say anything about platforms. When we got the last documentation from Mark, it was only Intel that worked.

  • It would be great if the documentation on the NCEPLIBS wiki did indicate roughly how long users could expect it to take, especially if it's more than an hour or so.

  • A question is whether it is important or useful for either the NCEPLIBS wiki or WM UG documentation to indicate what versions of required libraries are needed. It seems like this information should be in the WM UG, which is versioned, while the wikis on GitHub maybe do not need to specify the version information for lib dependencies. That means the documentation would stay in two different places (the NCEPLIBS wiki and the WM UG), with that version info being the main difference. Do you think that make sense? Or will there be a versioned release of NCEPLIBS with its own versioned documentation, in which case the WM UG could just point to the build information in the NCEPLIBS UG?

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ceceliadid commented 4 years ago

@arunchawla-NOAA @ligiabernardet @climbfuji Could we please agree to have one place (say the NCEPLIBS github wiki) that will have the requested additions to the documentation on this dependency build by the end of this month? That seems doable, almost all of it is already there. It would also be helpful before the end of the month to get the question answered about whether there will be a versioned NCEPLIBS UG (I'm guessing not) and where we expect any version information about library dependencies to be located (I'm guessing the versioned WM UG, since it is already there).

ligiabernardet commented 4 years ago

It is okay with me to have the NCEPLIbs wiki be the place where users can find an overview and instructions for build. The other documents can point to that wiki. Regarding the timeline to have this documentation ready, I defer to the build team.

On Tue, Jan 21, 2020 at 8:08 PM ceceliadid notifications@github.com wrote:

@arunchawla-NOAA https://github.com/arunchawla-NOAA @ligiabernardet https://github.com/ligiabernardet @climbfuji https://github.com/climbfuji Could we please agree to have one place (say the NCEPLIBS github wiki) that will have the requested additions to the documentation on this dependency build by the end of this month? That seems doable, almost all of it is already there. It would also be helpful before the end of the month to get the question answered about whether there will be a versioned NCEPLIBS UG (I'm guessing not) and where we expect any version information about library dependencies to be located (I'm guessing the versioned WM UG, since it is already there).

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ceceliadid commented 4 years ago

@ligiabernardet I'm really not explaining the question that I have very well, or maybe its a dumb question. This is the issue: Dusan put a lot of effort into identifying and documenting the versions of dependent libraries that are needed for the upcoming release version of the code on the WM wiki. This is presumably going to change for each release. This kind of information seems like it belongs in the versioned WM UG. The wiki Getting Started information on the WM wiki probably should be somewhat "versionless," maybe more for people interested in working with the head, and that's what the current NCEPLIBS wiki information looks like as well. That's why I thought the NCEPLIBS wiki might stay "versionless", and the WM UG would include all the version information for the library dependencies. So the documentation would be in two places, but it would somewhat different information. Does that make sense?

ceceliadid commented 4 years ago

Kate uploaded the updated ftp materials with the default physics package change.

Dan with help from Linlin finished updating the WM Getting Started page: https://github.com/ufs-community/ufs-weather-model/wiki/Getting-Started

and the WM GST page: https://github.com/ufs-community/ufs-weather-model/wiki/Graduate-Student-Test%3A-Increasing-the-Number-of-Cloud-Condensation-Nuclei

There are still some TODOs marked on those wiki pages in the places WM beta tags are needed but they are otherwise ready for review.

ceceliadid commented 4 years ago

Hi @climbfuji and @jedwards4b, I've started putting a link to the NCEPLIBS wiki on the standard nav bar we've been using for the ufs-community wikis, see for example https://github.com/ufs-community/ufs-weather-model/wiki on the right nav bar at the bottom.

I'm going to go ahead and put a similar custom nav bar on the NCEPLIBS wiki, so that it's better integrated into the family of ufs wikis. Everything that I do will be reversible, so you can take a look and if you hate it I can remove it tomorrow. Let me know if you have any issues with this.

ceceliadid commented 4 years ago

Well, it looks like I cannot do this because I don't have permissions to edit the NCEPLIBS wiki. Could that be provided? I will not be changing any content.

climbfuji commented 4 years ago

Do you also need nceplibs-external permissions? Would be good if someone with an eye on consistency in instructions and layout had the option to work on this.

On Feb 10, 2020, at 4:05 PM, ceceliadid notifications@github.com wrote:

Well, it looks like I cannot do this because I don't have permissions to edit the NCEPLIBS wiki. Could that be provided? I will not be changing any content.

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ceceliadid commented 4 years ago

Maybe. Do you want that NCEPLIBS-external wiki to be the main place that models and apps would point to for building library dependencies, or the NCEPLIBS wiki?

arunchawla-NOAA commented 4 years ago

It will have to be both, the NCEPLIBS super project is building the libraries and the codes that NCEP has repos for, pre proc, upp etc

The NCEPLIBS-external is building external libraries that have been released and we are using. Here, NETCDF, HDF5, ESMF8 etc.

Developers may need to build both.

Arun Chawla Chief Engineering & Implementation Branch Room 2083 National Center for Weather & Climate Prediction 5830 University Research Court College Park, MD 20740 Phone : 301-683-3740 Mobile : 240-564-5675 Fax : 301-683-3703

On Mon, Feb 10, 2020 at 6:36 PM ceceliadid notifications@github.com wrote:

Maybe. Do you want that NCEPLIBS-external wiki to be the main place that models and apps would point to for building library dependencies, or the NCEPLIBS wiki?

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climbfuji commented 4 years ago

I am trying to get my head around how to organize it best. But probably like this

Does this sound reasonable? Take a look at https://github.com/NOAA-EMC/NCEPLIBS-external/ https://github.com/NOAA-EMC/NCEPLIBS-external/ (note: the references to the NCEPLIBS detailed instructions in there do not yet exist)

Dom

On Feb 10, 2020, at 5:10 PM, arun chawla notifications@github.com wrote:

It will have to be both, the NCEPLIBS super project is building the libraries and the codes that NCEP has repos for, pre proc, upp etc

The NCEPLIBS-external is building external libraries that have been released and we are using. Here, NETCDF, HDF5, ESMF8 etc.

Developers may need to build both.

Arun Chawla Chief Engineering & Implementation Branch Room 2083 National Center for Weather & Climate Prediction 5830 University Research Court College Park, MD 20740 Phone : 301-683-3740 Mobile : 240-564-5675 Fax : 301-683-3703

On Mon, Feb 10, 2020 at 6:36 PM ceceliadid notifications@github.com wrote:

Maybe. Do you want that NCEPLIBS-external wiki to be the main place that models and apps would point to for building library dependencies, or the NCEPLIBS wiki?

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arunchawla-NOAA commented 4 years ago

Dom if you can give Cecelia access to the wikis then she can help you (if that is ok with you Cecelia) organize this in a clear and succinct way that would be very clear to the external community.

Arun Chawla Chief Engineering & Implementation Branch Room 2083 National Center for Weather & Climate Prediction 5830 University Research Court College Park, MD 20740 Phone : 301-683-3740 Mobile : 240-564-5675 Fax : 301-683-3703

On Mon, Feb 10, 2020 at 7:21 PM Dom Heinzeller notifications@github.com wrote:

I am trying to get my head around how to organize it best. But probably like this

  • setup instructions for systems (how to install compilers etc before even trying to build NCEPLIBS-external) will be on the NCEPLIBS-external wiki
  • these setup instructions contain basic examples of how to build NCEPLIBS-external and NCEPLIBS, but refer to the corresponding pages on the NCEPLIBS-external / NCEPLIBS wiki for detailed installation instructions, troubleshooting etc
  • detailed instructions on building & installing NCEPLIBS-external will be on the NCEPLIBS-external wiki
  • detailed instructions on building & installing NCEPLIBS will be on the NCEPLIBS wiki

Does this sound reasonable? Take a look at https://github.com/NOAA-EMC/NCEPLIBS-external/ < https://github.com/NOAA-EMC/NCEPLIBS-external/> (note: the references to the NCEPLIBS detailed instructions in there do not yet exist)

Dom

On Feb 10, 2020, at 5:10 PM, arun chawla notifications@github.com wrote:

It will have to be both, the NCEPLIBS super project is building the libraries and the codes that NCEP has repos for, pre proc, upp etc

The NCEPLIBS-external is building external libraries that have been released and we are using. Here, NETCDF, HDF5, ESMF8 etc.

Developers may need to build both.

Arun Chawla Chief Engineering & Implementation Branch Room 2083 National Center for Weather & Climate Prediction 5830 University Research Court College Park, MD 20740 Phone : 301-683-3740 Mobile : 240-564-5675 Fax : 301-683-3703

On Mon, Feb 10, 2020 at 6:36 PM ceceliadid notifications@github.com wrote:

Maybe. Do you want that NCEPLIBS-external wiki to be the main place that models and apps would point to for building library dependencies, or the NCEPLIBS wiki?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/ufs-community/ufs-mrweather-app/issues/34?email_source=notifications&email_token=AL5NYI5LNWJLO3CKA64D47LRCHQGVA5CNFSM4J43BH2KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELKWT2A#issuecomment-584411624 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AL5NYIY3QFLTAWUVK5QCO7TRCHQGVANCNFSM4J43BH2A

.

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ceceliadid commented 4 years ago

I can give it a shot.

ceceliadid commented 4 years ago

fwiw I did go through and modify the wiki nav on models and apps to point to to both NCEPLIBS and NCEPLIBS-external. Happy to draft some intro material esp. for NCEPLIBS, add click buttons to get to the build user forum, add nav, generally try to organize as Dom outlined, etc.

climbfuji commented 4 years ago

Done. Thanks for helping!

ceceliadid commented 4 years ago

Thanks! I finished a first pass through and probably will not get back to it until tomorrow, please feel free to change anything. Thinking about three main things - 1) Getting information that applies to both nceplibs and nceplibs-external and an overview in one place. Currently that's nceplibs but I can move it to nceplibs-external if that makes more sense for some reason. Is there a preference or natural order for building nceplibs or nceplibs-external first? If so I'd put the common material on that wiki. 2) Maybe moving the required software and setup sections that have very version-dependent information into READMEs. If the info applies to both nceplibs and nceplibs-external would put in just one of the READMEs and point to it. 3) Getting a current list of supported/pre-configured platforms in one place and have all wikis point to it, it's in too many different places currently. That might make sense on the top ufs-level wiki.

ceceliadid commented 4 years ago

@arunchawla-NOAA @climbfuji @rsdunlapiv Think I am pretty much done with the nceplibs & nceplibs-external wikis and the supported platforms page. The gaps that are left someone with actual knowledge needs to fill in. Would still recommend moving the few sections that are very version-dependent to the READMEs. Not really sure I should try to do that.

The supported platforms page is now here. https://github.com/ufs-community/ufs/wiki/Supported-Platforms-and-Compilers Went with calling them support levels with 1-pre-configured, 2-configurable, 3-limited-test, 4-build-only.

arunchawla-NOAA commented 4 years ago

@ceceliadid can we close this ticket since the instructions should be good for the GST? I like your labels for testing much better than the tier labels we had

ceceliadid commented 4 years ago

@arunchawla-NOAA Sorry but I don't think this ticket should be closed until the nceplibs and nceplibs-external documentation is in decent shape, it needs quite a bit of help still. I wouldn't point anybody to it yet. The platform support page also needs info from the testing spreadsheet added to it, and I don't understand yet what the setup for Stampede2 is going to be - if we can have nceplibs and nceplibs-external on Stampede2 in somebody's user directory for the GST. So for me that isn't squared away yet either.

mvertens commented 4 years ago

@ceceliadid @jedwards4b - Jim as a directory on stampede that multiple projects are using and that can be used for the GST. Apart from the fact that it is under Jim's name - all other aspects on stampede correspond to a pre-configured system. We did not want to label it as preconfigured since its under a given persons directory name (although has all the permissions set up as if this was not the case). @jedwards4b can fill in more details.

On Wed, Feb 12, 2020 at 7:53 PM ceceliadid notifications@github.com wrote:

@arunchawla-NOAA https://github.com/arunchawla-NOAA Sorry but I don't think this ticket should be closed until the nceplibs and nceplibs-external documentation is in decent shape, it needs quite a bit of help still. I wouldn't point anybody to it yet. The platform support page also needs info from the testing spreadsheet added to it, and I don't understand yet what the setup for Stampede2 is going to be - if we can have nceplibs and nceplibs-external on Stampede2 in somebody's user directory for the GST. So for me that isn't squared away yet either.

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ceceliadid commented 4 years ago

@mvertens @jedwards4b That's excellent, would appreciate the details!

arunchawla-NOAA commented 4 years ago

The origin of this ticket was for the WM GST. Since the WM GST is not installing the libraries I suggest we close this ticket and open another one to finalize NCEPLIBS and NCEPLIBS-EXternal documentation in time for the public release. The build team is still tweaking the external build based on issues they are finding with Gaea.

Arun Chawla Chief Engineering & Implementation Branch Room 2083 National Center for Weather & Climate Prediction 5830 University Research Court College Park, MD 20740 Phone : 301-683-3740 Mobile : 240-564-5675 Fax : 301-683-3703

On Wed, Feb 12, 2020 at 9:53 PM ceceliadid notifications@github.com wrote:

@arunchawla-NOAA https://github.com/arunchawla-NOAA Sorry but I don't think this ticket should be closed until the nceplibs and nceplibs-external documentation is in decent shape, it needs quite a bit of help still. I wouldn't point anybody to it yet. The platform support page also needs info from the testing spreadsheet added to it, and I don't understand yet what the setup for Stampede2 is going to be - if we can have nceplibs and nceplibs-external on Stampede2 in somebody's user directory for the GST. So for me that isn't squared away yet either.

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ceceliadid commented 4 years ago

@arunchawla-NOAA I am planning on having someone try installing the libraries for the WM GST, and have a person from AOML waiting who wants to try that. I was just not waiting for that to get started, since we also have people who can use the pre-configured platforms. I think it would be a good idea to do a short round through the documentation now and get that basically usable, and include this in the GST. There's always going to be specific platform issues to work out.

arunchawla-NOAA commented 4 years ago

OK, do you know which platform they want to build the libs? I will put aside this afternoon to review some of the documentation. I am hoping the NCEPLIBS-EXternal documentation will be in god form when Dom gets the Gaea wrinkles figured out.

Arun Chawla Chief Engineering & Implementation Branch Room 2083 National Center for Weather & Climate Prediction 5830 University Research Court College Park, MD 20740 Phone : 301-683-3740 Mobile : 240-564-5675 Fax : 301-683-3703

On Thu, Feb 13, 2020 at 9:57 AM ceceliadid notifications@github.com wrote:

@arunchawla-NOAA https://github.com/arunchawla-NOAA I am planning on having someone try installing the libraries for the WM GST, and have a person from AOML waiting who wants to try that. I was just not waiting for that to get started, since we also have people who can use the pre-configured platforms. I think it would be a good idea to do a short round through the documentation now and get that basically usable, and include this in the GST. There's always going to be specific platform issues to work out.

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climbfuji commented 4 years ago

nceplibs-external documentation is ok in my opinion; what is missing is the nceplibs documentation itself.

Cecelia did a great job on the NCEPLIBS-external wiki, there is only one problem I think: it is difficult to find the actual installation instructions down on the first page. Users are distracted by all the general UFS "supported platform" stuff on the right panel. I think the installation steps need to be more present right at the top of the wiki entry page.

I will do the NCEPLIBS documentation part tomorrow (all-day meeting today) in the same format as NCEPLIBS-external.

Dom

On Feb 13, 2020, at 8:00 AM, arun chawla notifications@github.com wrote:

OK, do you know which platform they want to build the libs? I will put aside this afternoon to review some of the documentation. I am hoping the NCEPLIBS-EXternal documentation will be in god form when Dom gets the Gaea wrinkles figured out.

Arun Chawla Chief Engineering & Implementation Branch Room 2083 National Center for Weather & Climate Prediction 5830 University Research Court College Park, MD 20740 Phone : 301-683-3740 Mobile : 240-564-5675 Fax : 301-683-3703

On Thu, Feb 13, 2020 at 9:57 AM ceceliadid notifications@github.com wrote:

@arunchawla-NOAA https://github.com/arunchawla-NOAA I am planning on having someone try installing the libraries for the WM GST, and have a person from AOML waiting who wants to try that. I was just not waiting for that to get started, since we also have people who can use the pre-configured platforms. I think it would be a good idea to do a short round through the documentation now and get that basically usable, and include this in the GST. There's always going to be specific platform issues to work out.

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ceceliadid commented 4 years ago

@climbfuji thank you!

arunchawla-NOAA commented 4 years ago

@ceceliadid are the issues brought up here addressed? Can this ticket be closed now?

ceceliadid commented 4 years ago

@arunchawla-NOAA These probably shouldn't be closed until we have final tags that we can point to. There are inconsistent instructions now on the wikis because the tags are various betas. Do you know when we will get v1.0.0 final and latest_release tags?

ceceliadid commented 4 years ago

@arunchawla-NOAA These probably shouldn't be closed until we have final tags that we can point to. There are inconsistent instructions now on the wikis because the tags are various betas. Do you know when we will get v1.0.0 final and latest_release tags?

ligiabernardet commented 4 years ago

I believe this is complete and this issue can be closed.

ceceliadid commented 4 years ago

The tags are not updated yet on the wiki documentation.

arunchawla-NOAA commented 4 years ago

@ceceliadid I updated one tag there. Can you check please. Also I think instructions for checking out a specific tag is different in git (I need someone to confirm though)

ceceliadid commented 4 years ago

@arunchawla-NOAA This is done and I checked the build with the tag. The instructions for getting the specific tag work okay. Let me know if you see anything weird.