WIP: Update MAPL and other GEOS-ESM packages #174

mathomp4 · 2022-09-19T13:03:13Z

This is an update to the MAPL and other GEOS-ESM packages in NOAA-EMC/spack.

The biggest changes would be in MAPL. I removed the ESMA_GFE_NAMESPACE option as it is nigh-ancient and I'm not sure any version here needs it (might be wrong, though.) I also added dependencies for yafyaml when building with ExtData2G support. There was an interface change at MAPL 2.23 so you need a newer yafyaml. (This also triggers a split in pflogger.)

cc: @climbfuji @tclune

Changed:

mapl
esmf (slight bug fix)
FMS (need a new variant)

Additions:

flap (A weird one. flap is also in canonical spack, but we use a fork of it. This can probably never go back to mainline spack. I've hesitated pushing our changes to the upstream flap repo as MAPL eventually will move to fargparse or, most likely, move away from command line arguments altogether and go to YAML.)
geosgcm (testing at the moment)
mepo (for geosgcm, though maybe it should go away in favor of tarfiles?)

Testing:

Building:
- Does it build in spack-stack?
UFS
- Do the libraries it builds, build with MAPL-in-UFS?
- Does the MAPL in this PR work with UFS?
- Can it run?
GEOSgcm
- Internal MAPL and Internal FMS
  - Does it build GEOSgcm?
  - Does GEOSgcm run?
- Internal MAPL and Spack FMS
  - Does it build GEOSgcm?
  - Does GEOSgcm run?
- Spack MAPL and Internal FMS
  - Does it build GEOSgcm?
  - Does GEOSgcm run?
- Spack MAPL and Spack FMS
  - Does it build GEOSgcm?
  - Does GEOSgcm run?

mathomp4 · 2022-09-19T20:10:54Z

A few updates to remind myself. I have gotten, I think, a good set of libraries. I did have to do a few things.

In the common/packages.yaml file for my empty environment I added:

     pflogger:
       variants: +mpi
     pfunit:
       variants: +mpi+fhamcrest

to lock in some variants we want.

I also really only want ESMF 8.3.0 but I just could not get spack to build it. The only way was to comment out the 8.3.0b09 line here:

https://github.com/NOAA-EMC/spack/blob/1248dfd679e9ee8095222b34b0a71217c52c272c/var/spack/repos/builtin/packages/esmf/package.py#L24-L34

because spack seemed to think 8.3.0b09 was newer than 8.3.0. Maybe @climbfuji knows a better way, but I'm at the "throw things at the wall" stage 😄

But I was able to build:

spack install mapl@2.26.0+extdata2g+flap+pflogger

I'm currently trying to build GEOSgcm...but not with spack MAPL, but instead an internal MAPL. I'm also going to try both a internal-FMS as well as an FMS-from-spack. But to do that, I'll need to slightly fix up the FMS here in this repo, I think. I'll report back!

tclune · 2022-09-21T13:03:22Z

A few updates to remind myself. I have gotten, I think, a good set of libraries. I did have to do a few things.

In the common/packages.yaml file for my empty environment I added:
     pflogger:
       variants: +mpi
     pfunit:
       variants: +mpi+fhamcrest

I wonder if pfunit should have an openmp variant as well?

mathomp4 · 2022-09-21T14:04:40Z

A few updates to remind myself. I have gotten, I think, a good set of libraries. I did have to do a few things.
In the common/packages.yaml file for my empty environment I added:
     pflogger:
       variants: +mpi
     pfunit:
       variants: +mpi+fhamcrest
I wonder if pfunit should have an openmp variant as well?

It does have one:

    variant("openmp", default=False, description="Enable OpenMP")

I just didn't turn it on by default. We might want to? I just figure I usually build it with --DSKIP_OPENMP=ON and...well crap. Now I think the package doesn't handle that correctly. Let me take a look...

ETA: Ah it does:

        if spec.satisfies("@4.0.0:"):
            args.append("-DSKIP_MPI=%s" % ("YES" if "~mpi" in spec else "NO"))
            args.append("-DSKIP_OPENMP=%s" % ("YES" if "~openmp" in spec else "NO"))
            args.append("-DSKIP_FHAMCREST=%s" % ("YES" if "~fhamcrest" in spec else "NO"))
            args.append("-DSKIP_ESMF=%s" % ("YES" if "~esmf" in spec else "NO"))
        else:
            args.append(self.define_from_variant("MPI", "mpi"))
            args.append(self.define_from_variant("OPENMP", "openmp"))

I was just looking in the wrong place.

tclune · 2022-09-21T14:27:31Z

@mathomp4 OK - glad you are on it. Agree that we want it off for now; I was just keying off the absence. So ignore what I wrote.

…-gfe-mapl

mathomp4 · 2023-02-27T17:45:09Z

@climbfuji So, I updated the files here and I was able to install MAPL. So, yay. I then wanted to test building geosgcm but I saw I needed a newer ESMF. Fine:

$ spack install esmf@8.4.0
==> Error: Package 'mapl' not found.
You may need to run 'spack clean -m'.

Huh. I'm new at all this stack/environment stuff. Any idea what I might have done wrong for spack to say this?

ETA: Oh. wait:

$ spack find esmf
==> In environment /gpfsm/dnb44/mathomp4/spack-stack/envs/geosgcm.discover
==> Root specs
geosgcm  mapl@spacktest  mapl@2.31.0 +extdata2g+fargparse+flap+pflogger+pfunit  mapl@2.34.3  mapl@develop  mepo  py-pyyaml

==> Installed packages
-- linux-sles12-skylake_avx512 / intel@2022.0.1 -----------------
esmf@8.4.0
==> 1 installed package

Already installed. Maybe I need to do some weird concretize things?

climbfuji · 2023-02-27T17:48:05Z

spack clean -a doesn’t help?

…

On Feb 27, 2023, at 10:45 AM, Matthew Thompson ***@***.***> wrote: @climbfuji <https://github.com/climbfuji> So, I updated the files here and I was able to install MAPL. So, yay. I then wanted to test building geosgcm but I saw I needed a newer ESMF. Fine: $ spack install ***@***.*** ==> Error: Package 'mapl' not found. You may need to run 'spack clean -m'. Huh. I'm new at all this stack/environment stuff. Any idea what I might have done wrong for spack to say this? — Reply to this email directly, view it on GitHub <#174 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB5C2RPYIF55NGZLTMG5BULWZTR3BANCNFSM6AAAAAAQQCZDLE>. You are receiving this because you were mentioned.

mathomp4 · 2023-02-27T18:54:43Z

spack clean -a doesn’t help?

Nope. But I'm going to try a few things. Worse comes to worst, I just reclone!

climbfuji · 2023-02-27T18:58:50Z

spack clean -a doesn’t help?

Nope. But I'm going to try a few things. Worse comes to worst, I just reclone!

If the spack version is too different, you may have to re-bootstrap from a fresh clone

mathomp4 · 2023-02-27T19:00:20Z

Well, I think my environment was just not good. I did a:

spack concretize -Uf

as that often fixes things and things changed. A lot. I think I just need to start afresh.

…-gfe-mapl

mathomp4 · 2023-03-07T18:50:37Z

@climbfuji I am still working on this and found a bug in my (every?) MAPL version if you try and build +pfunit. I think I have a fix, but the fun part is testing the fix. I added a new branch for MAPL, and the weird thing is, spack keeps wanting to patch it. But in my MAPL package.py I've commented out every patch command I see...and it's still trying to patch!

==> Installing mapl-spack-eprnncn4hdrgc6bllawpudthctbt7qhe
==> mapl exists in binary cache but with different hash
==> No binary for mapl-spack-eprnncn4hdrgc6bllawpudthctbt7qhe found: installing from source
==> Error: NoSuchPatchError: Couldn't find patch for package builtin.mapl with sha256: 7b9c28b9343403b0d1d8e58478982e575b839a811db3c95f0b3987dcfd841287

/gpfsm/dnb44/mathomp4/spack-stack/spack/lib/spack/spack/package_base.py:1456, in do_fetch:
       1453            self.stage.check()
       1454
       1455        self.stage.cache_local()
  >>   1456
       1457        for patch in self.spec.patches:
       1458            patch.fetch()
       1459            if patch.stage:

Any idea where this might be coming from?

climbfuji · 2023-03-07T19:00:23Z

You need to re-concretize for spack to see changes regarding patches

…

On Mar 7, 2023, at 11:50 AM, Matthew Thompson ***@***.***> wrote: @climbfuji <https://github.com/climbfuji> I am still working on this and found a bug in my (every?) MAPL version if you try and build +pfunit. I think I have a fix, but the fun part is testing the fix. I added a new branch for MAPL, and the weird thing is, spack keeps wanting to patch it. But in my MAPL package.py I've commented out every patch command I see...and it's still trying to patch! ==> Installing mapl-spack-eprnncn4hdrgc6bllawpudthctbt7qhe ==> mapl exists in binary cache but with different hash ==> No binary for mapl-spack-eprnncn4hdrgc6bllawpudthctbt7qhe found: installing from source ==> Error: NoSuchPatchError: Couldn't find patch for package builtin.mapl with sha256: 7b9c28b9343403b0d1d8e58478982e575b839a811db3c95f0b3987dcfd841287 /gpfsm/dnb44/mathomp4/spack-stack/spack/lib/spack/spack/package_base.py:1456, in do_fetch: 1453 self.stage.check() 1454 1455 self.stage.cache_local() >> 1456 1457 for patch in self.spec.patches: 1458 patch.fetch() 1459 if patch.stage: Any idea where this might be coming from? — Reply to this email directly, view it on GitHub <#174 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB5C2RK3IYYDZWALIXJJULLW257QRANCNFSM6AAAAAAQQCZDLE>. You are receiving this because you were mentioned.

mathomp4 · 2023-03-07T19:53:56Z

You need to re-concretize for spack to see changes regarding patches

Ahhh. Okay. I keep forgetting about that! On to other fun not using a version number!

mathomp4 · 2023-03-09T17:58:48Z

@AlexanderRichert-NOAA I think I finally have the MAPL package here in good shape. If you have a chance, can you try it out with your code? If it works, I can undraft this PR and even add it to spack mainline for you.

AlexanderRichert-NOAA · 2023-03-09T18:01:38Z

Awesome, I'll test it out ASAP.

mathomp4 · 2023-03-09T18:23:28Z

A note to @climbfuji. The pfunit here will of course be superseded by the newer better one in current develop spack. Same for fms. I've only added FMS here because this doesn't have the new "precision" one.

I'm debating if mepo, geosgcm and flap need to be here or not. I'm keeping them here just in case. Eventually FLAP use in GEOS is going away, and I'm pretty sure my GEOSgcm package doesn't need mepo anymore.

climbfuji · 2023-03-09T20:18:28Z

var/spack/repos/builtin/packages/fms/package.py

@@ -59,6 +59,11 @@ class Fms(CMakePackage):
        git = "https://github.com/JCSDA/fms.git"
    # *DH 20220602

+    variant(


Instead of this we should pull in the updates from https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/fms/package.py (can be a separate PR so you don't have to deal with it)

I can do this if you like

@climbfuji If you can, please. I have a PR in to spack mainline to update some other GFE packages.

It's also possible we might want to wait for the ESMF PR from @theurich before pulling in spack? Not sure.

Also, I will say I tried using the newer spack maintainers() function in this PR but spack wasn't happy. It's possible my spack was old?

We haven't yet pulled that functionality from main spack, so with NOAA-EMC spack it will yell at you about the function being undefined :)

climbfuji · 2023-03-09T20:24:04Z

var/spack/repos/jcsda-emc/packages/geosgcm/package.py

+    # but we don't want to do this in general due to the speed of MAPL development
+
+    # When we move to FMS as library, we'll need to add this:
+    #depends_on("fms@2022.04:~gfs_phys+fpic~quad_precision+32bit+64bit+yaml constants=GEOS")


When the time comes, we'll need a way to describe the different variants in the module names (not now!), e.g. fms/2022.04-geos based on the constants value).

AlexanderRichert-NOAA · 2023-03-09T20:29:43Z

This worked for me on hera with UFS (ea0b6e4) using ufs-weather-model-static. The only change needed was setting fms +32bit.

mathomp4 · 2023-03-09T23:34:08Z

This worked for me on hera with UFS (ea0b6e4) using ufs-weather-model-static. The only change needed was setting fms +32bit.

Ooh. Nice!

…-gfe-mapl

mathomp4 · 2023-05-12T14:29:40Z

Closing. Will make a new PR with geosgcm (and maybe mepo and flap) when #241 is pulled in and tested.

mathomp4 added 3 commits September 19, 2022 08:44

Update GFE and MAPL packages

1434223

Add FLAP

dd12538

Bring back old yafyaml

5e969bc

mathomp4 mentioned this pull request Sep 19, 2022

Upcoming library updates for ufs-weather-model changes JCSDA/spack-stack#344

Closed

mathomp4 added 7 commits September 19, 2022 09:21

Try and fix up CI issues

5fdccf7

Fix more formatting issues

7a88dd0

Fix more formatting issues. Again.

a1a5dbc

Hopefully final style issue

bff5c07

Split msg in hopes of passing CI

7c3c89c

Make msg small

d157dc1

Fix up depends_on

45f3e4a

mathomp4 added 2 commits September 21, 2022 09:45

Add mepo

2b0073c

Add 32bit option to FMS

4374475

mathomp4 added 7 commits September 28, 2022 07:20

Add python and perl as prereqs of MAPL

75f5978

Add geosgcm package

024e0e6

Merge branch 'jcsda_emc_spack_stack' into feature/mathomp4/update-add…

1802f57

…-gfe-mapl

Update for beta

37ad170

Update fargparse

e76cffb

Update pfunit

1d2b1e5

Add esmf 8.4.0

bb74cdb

mathomp4 added 2 commits February 27, 2023 12:15

Move to spack mainline pfunit

83bd44d

Revert back to older pfunit package

909df35

Merge branch 'jcsda_emc_spack_stack' into feature/mathomp4/update-add…

e37cfee

…-gfe-mapl

mathomp4 added 2 commits March 9, 2023 12:47

Fixes to allow pfunit variant to build

d61ce82

Add latest geosgcm version

9cea6e3

climbfuji requested changes Mar 9, 2023

View reviewed changes

Add list_url for mapl

3febd00

climbfuji mentioned this pull request Mar 14, 2023

Add esmf@8.4.1 and mapl@2.35.2 (replace existing versions in unified env) JCSDA/spack-stack#333

Closed

Merge branch 'jcsda_emc_spack_stack' into feature/mathomp4/update-add…

8662c6b

…-gfe-mapl

mathomp4 mentioned this pull request Mar 14, 2023

Updates for MAPL, GFE packages #241

Merged

climbfuji mentioned this pull request Mar 14, 2023

Add crtm@v3.0.0-rc.1 and mapl@2.35.2 #240

Merged

climbfuji assigned climbfuji and mathomp4 Apr 26, 2023

Merge branch 'jcsda_emc_spack_stack' into feature/mathomp4/update-add…

84e6e16

…-gfe-mapl

mathomp4 closed this May 12, 2023

mathomp4 deleted the feature/mathomp4/update-add-gfe-mapl branch May 12, 2023 14:31

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WIP: Update MAPL and other GEOS-ESM packages #174

WIP: Update MAPL and other GEOS-ESM packages #174

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WIP: Update MAPL and other GEOS-ESM packages #174

WIP: Update MAPL and other GEOS-ESM packages #174

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