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NOAA-EMC / hpc-stack

Create a software stack for HPC's
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[INSTALL] MAPL 2.34.0 #515

Closed junwang-noaa closed 1 year ago

junwang-noaa commented 1 year ago

Note: Please search to see if an issue already exists for the software you are requesting to be installed.

Which software in the stack would you like installed? Please install MAPL 2.34.0. We need to update GOCART with threading capability using this MAPL version.

What is the version/tag of the software? MAPL 2.34.0

What compilation options would you like set? The same as MAPL 2.22.0

Which machines would you like to have the software installed? All the UFS supported platforms, wcoss2, acorn, hera, orion, jet, gaea and cheyenne.

Any other relevant information that we should know to correctly install the software?? Please describe in as much detail as possible.

Additional context Add any other context or screenshots about the install request here.

Hang-Lei-NOAA commented 1 year ago

@junwang-noaa I can quickly add an installation together with ESMF/8.4.0, and waiting for UFS test to get together into the code delivery. what do you think?

junwang-noaa commented 1 year ago

Excellent! Also let me know if you have an installation on R&D platform, I can do some testing

Hang-Lei-NOAA commented 1 year ago

@Jun Wang - NOAA Federal @.***> We have a problem to install it on Hera and WCOSS2, since it requires the system lib FARGPARSE, which is different from v2.22.0. So, it won't be quick as expected.

On Wed, Feb 1, 2023 at 1:32 PM Jun Wang @.***> wrote:

Excellent! Also let me know if you have an installation on R&D platform, I can do some testing

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junwang-noaa commented 1 year ago

@Hang-Lei-NOAA I asked our NASA collaborators, they said the dependent libraries are specified in the release note. Please see the notes below to turn off all the extra libraries. We only need gFTL, gFTL_shared and ESMF 8.4.0. Thanks

https://github.com/GEOS-ESM/MAPL/releases/tag/v2.34.0

The libraries this version of MAPL is currently tested with are below.

Baselibs 7.7.0 netcdf-c 4.9.0 (Needed for quantize support, but not required for all of MAPL) netcdf-fortran 4.6.0 (Needed for quantize support, but not required for all of MAPL) ESMF 8.4.0 (Required) GFE 1.8.0 gFTL 1.8.1 gFTL-shared 1.5.0 pFUnit 4.6.1 (optional) fArgParse 1.4.1 (if -DBUILD_WITH_FARGPARSE=YES, default=YES) pFlogger 1.9.1 (if -DBUILD_WITH_PFLOGGER=YES, default=YES) yaFyaml 1.0.4 (if -DUSE_EXTDATA2G=YES, default=YES) FLAP geos/v1.10.0 (if -DBUILD_WITH_FLAP=YES, default=YES)

Hang-Lei-NOAA commented 1 year ago

@Jun Wang - NOAA Federal @.***> mapl/2.34.0 on Hera has been successfully built at /scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack-gfsv16 But , build on wcoss2 still have some problems on netcdf associated issues.

On Thu, Feb 2, 2023 at 9:44 AM Jun Wang @.***> wrote:

@Hang-Lei-NOAA https://github.com/Hang-Lei-NOAA I asked our NASA collaborators, they said the dependent libraries are specified in the release note. Please see the notes below to turn off all the extra libraries. We only need gFTL, gFTL_shared and ESMF 8.4.0. Thanks

https://github.com/GEOS-ESM/MAPL/releases/tag/v2.34.0

The libraries this version of MAPL is currently tested with are below.

Baselibs 7.7.0 netcdf-c 4.9.0 (Needed for quantize support, but not required for all of MAPL) netcdf-fortran 4.6.0 (Needed for quantize support, but not required for all of MAPL) ESMF 8.4.0 (Required) GFE 1.8.0 gFTL 1.8.1 gFTL-shared 1.5.0 pFUnit 4.6.1 (optional) fArgParse 1.4.1 (if -DBUILD_WITH_FARGPARSE=YES, default=YES) pFlogger 1.9.1 (if -DBUILD_WITH_PFLOGGER=YES, default=YES) yaFyaml 1.0.4 (if -DUSE_EXTDATA2G=YES, default=YES) FLAP geos/v1.10.0 (if -DBUILD_WITH_FLAP=YES, default=YES)

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jkbk2004 commented 1 year ago

@natalie-perlin follow up of mapl-2.34.0 is on our to-do list. I will check on gaea.

natalie-perlin commented 1 year ago

@junwang-noaa , @jkbk2004 - I could start installing. We have the following dependencies for MAPL that are currently specified explicitly during building of hpc-stacks, as shown below. The versions that are currently available are given in a regular font, or bolditalic if they need to be installed

MAPL/2.34.0 esmf/8.3.0b09 esmf/8.5.0 esmf/8.4.0 sqlite/3.36.0 esmacmake/v3.4.3 cmakemodules/v1.2.0 ecbuild/ecmwf-3.6.1 gftl-shared/v1.5.0 yafyaml/v0.5.1 yafyaml/v1.0.4 hdf5/1.10.6 netcdf/4.7.4 netcdf-c/4.9.0 netcdf-fortran/4.6.0 pFlogger 1.9.1 gFTL 1.8.1 GFE 1.8.0 fArgParse 1.4.1 pFUnit 4.6.1_

We also have geos/3.8.1 (from https://download.osgeo.org/geos/), but it might be different geos from the list (FLAP geos?)

Please let me know of any specifics with these packages.

junwang-noaa commented 1 year ago

@natalie-perlin We need to update following libraries along with MAPL 2.34.0.

ESMF: 8.4.1b07 HDF5: 1.14.0 netcdf: 4.9.1

would you please let us know when you have those libraries available on NOAA R&D platform (e.g. hera) for us to test?

Hang-Lei-NOAA commented 1 year ago

Jun means that mapl/2.34.0 installation should have the dependency on HDF/1.14.0; netcdf/4.9.1 and ESMF/8.4.1b07.

On Sat, Feb 25, 2023 at 10:33 PM Jun Wang @.***> wrote:

@natalie-perlin https://github.com/natalie-perlin We need to update following libraries along with MAPL 2.34.0.

ESMF: 8.4.1b07 HDF5: 1.14.0 netcdf: 4.9.1

would you please let us know when you have those libraries available on NOAA R&D platform (e.g. hera) for us to test?

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natalie-perlin commented 1 year ago

@Hang-Lei-NOAA @junwang-noaa @jkbk2004 - Some updates so far:

These builds (hdf5/1.14.0, netcdf-c/4.9.0, netcdf-fortran/4.6.0, esmf/8.4.1b07) are done for the following platforms and compilers:

Hera: /scratch1/NCEPDEV/nems/role.epic/hpc-stack/libs/intel-2022.1.2 /scratch1/NCEPDEV/nems/role.epic/hpc-stack/libs/gnu-9.2/ /scratch1/NCEPDEV/nems/role.epic/hpc-stack/libs/gnu-10.2/

Orion: (currently building) /work/noaa/epic-ps/role-epic-ps/hpc-stack/libs/intel-2022.1.2

junwang-noaa commented 1 year ago

@natalie-perlin @Hang-Lei-NOAA FYI. GOCART developers are working on MAPL 2.35 release, we need to go to that version in order to get GOCART to work in UFS WM.

Hang-Lei-NOAA commented 1 year ago

@Jun Wang - NOAA Federal @.> Thanks for this update! @Natalie Perlin - NOAA Affiliate @.> For netcdf/4.9.1 installation, you have to add options: --disable-libxml2 --disable-byterange You can refer to my Hera installations on /scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack-gfsv16

On Tue, Feb 28, 2023 at 1:26 PM Jun Wang @.***> wrote:

@natalie-perlin https://github.com/natalie-perlin @Hang-Lei-NOAA https://github.com/Hang-Lei-NOAA FYI. GOCART developers are working on MAPL 2.35 release, we need to go to that version in order to get GOCART working in UFS WM.

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natalie-perlin commented 1 year ago

@junwang-noaa @Hang-Lei-NOAA - thank you for updated Re: netcdf/4.9.1 and MAPL/2.35 needed! I will continue with installation of netcdf/4.9.1 and use Hang's hpc-stack installation on Hera as an example.

natalie-perlin commented 1 year ago

@Hang-Lei-NOAA - I was able to locate only 4.7.4 and 4.9.0 versions of netcdf modules, but not 4.9.1, in /scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack-gfsv16 that you mentioned. Please let me know if you have netcdf/4.9.1 elsewhere by any chance. I'll attempt to compile with "--disable-libxml2 --disable-byterange" for the meanwhile. Thank you!

junwang-noaa commented 1 year ago

@natalie-perlin Is it possible that we can have a MAPL 2.23.1. installed with ESMF: 8.4.1b07 HDF5: 1.14.0 netcdf: 4.9.1 on hera so that we can test those version before MAPL 2.35 comes out? It helps us verify ESMF 8.4.1b07 for the ESMF 8.4.1 release.

Hang-Lei-NOAA commented 1 year ago

@Jun Wang - NOAA Federal @.***> Report to you, after you pointed out the mapl/2.35.0, I checked the mapl repo and found that 2.34.3 is the latest bug fixed one. I installed it on Acorn and tested it. All tests still fail.

On Wed, Mar 1, 2023 at 11:38 AM Jun Wang @.***> wrote:

@natalie-perlin https://github.com/natalie-perlin Is it possible that we can have a MAPL 2.23.1. installed with ESMF: 8.4.1b07 HDF5: 1.14.0 netcdf: 4.9.1 on hera so that we can test those version before MAPL 2.35 comes out? It helps us verify ESMF 8.4.1b07 for the ESMF 8.4.1 release.

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junwang-noaa commented 1 year ago

@Hang-Lei-NOAA Thanks for testing, the 2.34.3 is an old version that does not have the changes yet.

natalie-perlin commented 1 year ago

So far, the following combination is currently available on Hera: hdf1.14.0-netcdf-c-4.9.1-netcdf-fortran-4.6.0-esmf-8.4.1b07-mapl-2.23.1 for Intel-2022.1.2 and gnu-9.2 compilers (so far): /scratch1/NCEPDEV/nems/role.epic/hpc-stack/libs/intel-2022.1.2 /scratch1/NCEPDEV/nems/role.epic/hpc-stack/libs/gnu-9.2

UPDATE: Also on Hera: /scratch1/NCEPDEV/nems/role.epic/hpc-stack/libs/gnu-10.2 Orion: /work/noaa/epic-ps/role-epic-ps/hpc-stack/libs/intel-2022.1.2

Please note that these modules are within the default hpc-stack locations, so you when loading, explicit versions of each package needs to be provided, in order to fulfill the dependencies, as in the chain shown above.

natalie-perlin commented 1 year ago

@junwang-noaa @Hang-Lei-NOAA Updates for Hera installation with intel/2022.1.2 compiler.

Installed the target configuration: hdf/1.14.0, netcdf-c/4.9.1, netcdf-fortran/4.6.0, fms/2022.04, pio/2.5.10, esmf-8.4.1, mapl/2.35.2

Additional updates and modules that [mostly] help to resolve mapl dependencies: yafyaml/1.0.4, fargparse/1.4.1, pflogger/1.9.1, pfunit/4.6.1, gftl/1.8.1, gftl-shared/v1.5.1 esma_cmake/v3.24.0

cmake options used for configuring MAPL (if relevant): _-DCMAKE_BUILD_TYPE=Release -DBUILD_WITH_FLAP=OFF -DBUILD_WITH_PFLOGGER=ON -DESMA_USE_GFE_NAMESPACE=ON -DBUILD_SHARED_MAPL=OFF -DUSEEXTDATA2G=ON

New stack location is used because of conflicting dependencies with the currently used versions (e.g., fms/2022.04 is built off hdf/1.10.6 and netcdf/4.7.4), in

/scratch1/NCEPDEV/nems/role.epic/hpc-stack/libs/intel-2022.1.2_ncdf49

module use /scratch1/NCEPDEV/nems/role.epic/hpc-stack/libs/intel-2022.1.2_ncdf49/modulefiles/stack/ module load intel/2022.1.2 module load impi/2022.1.2 module load hpc/1.2.0 module load hpc-intel module load hpc-impi module load hdf5/1.14.0 module load netcdf/4.9.1 module load fms/2022.04 module load esmf/8.4.1 module load pio/2.5.10 module load gftl/1.8.1 module load gftl-shared/v1.5.1 module load yafyaml/1.0.4 module load fargparse/1.4.1 module load pflogger/1.9.1 module load pfunit/4.6.1 module load mapl/2.35.2-esmf-8.4.1

Please let me know if this configuration works successfully, especially mapl/2.35.2 and dependencies built. It is possible MAPL could be installed with fewer additional modules, but it requires knowledge what features are needed.

aerorahul commented 1 year ago

Has this been resolved? If so, please close?

Hang-Lei-NOAA commented 1 year ago

This task has been changed due to new mapl bugfix version release. The replacement task have been included in UFS ticket https://github.com/ufs-community/ufs-weather-model/issues/1621 This ticket can be closed.