Danger

This page is tailored to experienced users and collaborators developing ACCESS models.
This step is not required if you only want to run a model. If you are looking for information on how to run a model, refer to the Run a Model section.

Modify an ACCESS model's source code

About

The instructions below outline how to build an ACCESS model and its dependencies, using the build-from-source package manager Spack.
This build workflow is specifically designed to run on the National Computating Infrastructure (NCI) supercomputer Gadi.

As an example, in the following instructions we will show how to modify mom5 component for ACCESS-ESM1.5 and re-compile the relevant ACCESS-ESM1.5 dependencies. All the other components and packages (i.e., dependencies) will remain the same as the official ACCESS-ESM1.5 release.

Tip

The instructions below remain valid (with simple tweaks) for any model or package.

Prerequisites

NCI account
Before building a model, you need to Set Up your NCI Account.
Spack
To set up Spack on Gadi, refer to Set up Spack for building ACCESS models.

Navigate into your Spack directory

Navigate into the directory where you cloned the Spack repositories during the Spack setup.
The suggested directory is /g/data/$PROJECT/$USER/spack/0.22:

cd /g/data/$PROJECT/$USER/spack/0.22

Enable spack

Warning

This step needs to be carried out for any new login or new shell environment.

To add the spack command to your shell, as well as other settings, run:

module purge
. spack-config/spack-enable.bash

Warning

There is a space between the . and the path to the file, as we are sourcing the file.

Create a Spack development environment

Spack has environments that are, in some ways, similar to Conda environments or Python virtual environments: they create an isolated operating environment where Spack can only see and access specific packages. This allows the build and deployment of new packages in a coherent fashion.

Spack managed environments are located inside /g/data/$PROJECT/$USER/spack/0.22/environments, each in a separate directory. Each environment configuration is defined within its directory using the spack.yaml file.

Warning

Spack managed environments' location can be changed within Spack configuration files and the directory specified above represents the default location for a Spack instance that has been set up following the Spack setup instructions.

Create the environment

To ensure we keep all dependecies the same as the official release, we will create our Spack development environment as a copy of the released ACCESS-ESM1.5 Spack environment.
To create a Spack development environment called mom5_dev, run:

git clone https://github.com/ACCESS-NRI/ACCESS-ESM1.5.git
spack env create mom5_dev ACCESS-ESM1.5/spack.yaml

git clone https://github.com/ACCESS-NRI/ACCESS-ESM1.5.git Cloning into 'ACCESS-ESM1.5'... remote: Enumerating objects: 29, done. remote: Counting objects: 100% (19/19), done. remote: Compressing objects: 100% (17/17), done. remote: Total 29 (delta 6), reused 3 (delta 1), pack-reused 10 (from 1) Receiving objects: 100% (29/29), 16.40 KiB | 2.38 MiB/s, done. Resolving deltas: 100% (6/6), done. spack env create mom5_dev ACCESS-ESM1.5/spack.yaml ==> Created environment mom5_dev in: /g/data/$PROJECT/$USER/spack/0.22/environments/mom5_dev ==> Activate with: spack env activate mom5_dev

The newly-created mom5_dev Spack environment folder is /g/data/$PROJECT/$USER/spack/0.22/environments/mom5_dev.

Activate the environment

To activate the mom5_dev Spack environment, run:

spack env activate -p mom5_dev

spack env activate -p mom5_dev

Compile Spack environment packages (optional)

It is recommended to first compile all the packages in the newly created Spack environment as is, without making any changes.

Compiling all the packages present in a Spack environment is referred to as installing the environment.

Concretize the Spack environment

Concretizing the Spack environment is necessary anytime the environment's spack.yaml gets changed, to force Spack to update its knowledge of the environment configuration.

To concretize the mom5_dev environment, run:

spack concretize -f --fresh

Warning

This command might take a few minutes to complete

spack concretize -f --fresh ==> Concretized access-esm1p5@git.2024.05.1=2024.05.1 - nkvasig access-esm1p5@git.2024.05.1=2024.05.1%intel@19.0.3.199 build_system=bundle arch=linux-rocky8-x86_64_v4 - hhtnigw ^cice4@git.2024.05.21=access-esm1.5%intel@19.0.3.199 build_system=makefile arch=linux-rocky8-x86_64_v4 - j6yscmm ^gmake@4.4.1%intel@19.0.3.199~guile build_system=generic arch=linux-rocky8-x86_64_v4 - 5xcyy2h ^netcdf-fortran@4.5.2%intel@19.0.3.199~doc+pic+shared build_system=autotools patches=b050dbd arch=linux-rocky8-x86_64_v4 - py3awb7 ^oasis3-mct@git.access-esm1.5_2024.05.24=access-esm1.5%intel@19.0.3.199~deterministic~optimisation_report build_system=makefile arch=linux-rocky8-x86_64_v4 - yfo7fum ^hdf5@1.10.11%intel@19.0.3.199~cxx~fortran+hl~ipo~java+mpi+shared~szip~threadsafe+tools api=default build_system=cmake build_type=Release generator=make arch=linux-rocky8-x86_64_v4 [e] vc4y4c6 ^cmake@3.24.2%intel@19.0.3.199~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-rocky8-x86_64_v4 - ugenh6g ^pkgconf@2.2.0%intel@19.0.3.199 build_system=autotools arch=linux-rocky8-x86_64_v4 - h45fvyw ^zlib-ng@2.1.6%intel@19.0.3.199+compat+new_strategies+opt+pic+shared build_system=autotools arch=linux-rocky8-x86_64_v4 [e] ikhujrk ^openmpi@4.0.2%intel@19.0.3.199~atomics~cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~internal-libevent~internal-pmix~java~legacylaunchers~lustre~memchecker~openshmem~orterunprefix~romio+rsh~singularity~static+vt+wrapper-rpath build_system=autotools fabrics=none patches=073477a,60ce20b romio-filesystem=none schedulers=none arch=linux-rocky8-x86_64_v4 [e] mqjolvb ^glibc@2.28%intel@19.0.3.199 build_system=autotools arch=linux-rocky8-x86_64_v4 - oopqoqg ^mom5@git.access-esm1.5_2024.08.23=access-esm1.5%intel@19.0.3.199~deterministic~optimisation_report+restart_repro build_system=makefile type=ACCESS-CM arch=linux-rocky8-x86_64_v4 - 725rz7c ^netcdf-c@4.7.4%intel@19.0.3.199~blosc~byterange~dap~fsync~hdf4~jna+mpi~nczarr_zip+optimize~parallel-netcdf+pic+shared~szip~zstd build_system=autotools arch=linux-rocky8-x86_64_v4 - udr7pbn ^um7@git.2024.07.03=access-esm1.5%intel@19.0.3.199 build_system=generic optim=high arch=linux-rocky8-x86_64_v4 - qy5w2d7 ^dummygrib@1.0%intel@19.0.3.199 build_system=makefile arch=linux-rocky8-x86_64_v4 - ho2ie66 ^fcm@2021.05.0%intel@19.0.3.199 build_system=generic site=none arch=linux-rocky8-x86_64_v4 - xalavwv ^gcom4@git.2024.05.28=access-esm1.5%intel@19.0.3.199+mpi build_system=generic arch=linux-rocky8-x86_64_v4

Install the Spack environment

To compile the packages in the mom5_dev environment, run:

spack install

Tip

It takes 30-40 minutes to compile all the packages for the first time.
Subsequent installations, however, will compile quicker as the built dependencies are reused.

spack install ==> Installing glibc-2.28-mqjolvbeskcnhz5chvtdshk4x4sfnycs [1/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/glibc-2.28-mqjolvbeskcnhz5chvtdshk4x4sfnycs ==> Installing cmake-3.24.2-vc4y4c64s55j5u6kp37ciw2hcghuxhhc [2/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/cmake-3.24.2-vc4y4c64s55j5u6kp37ciw2hcghuxhhc ==> Installing openmpi-4.0.2-ikhujrkyukytbkxxyk3mub44v63vuzfz [3/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/openmpi-4.0.2-ikhujrkyukytbkxxyk3mub44v63vuzfz ==> Installing gmake-4.4.1-j6yscmmcn3qws7n35klote7rivw7foa6 [4/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/gmake-4.4.1-j6yscmmcn3qws7n35klote7rivw7foa6 ==> Installing fcm-2021.05.0-ho2ie66tizhxpjjiilnrjnlnbi6safwq [5/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/fcm-2021.05.0-ho2ie66tizhxpjjiilnrjnlnbi6safwq ==> Installing zlib-ng-2.1.6-h45fvywj47wc4uwa37mfzkdsqrgcqxux [6/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/zlib-ng-2.1.6-h45fvywj47wc4uwa37mfzkdsqrgcqxux ==> Installing dummygrib-1.0-qy5w2d7tmsbmvnqng2xlopdkd4m2grvb [7/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/dummygrib-1.0-qy5w2d7tmsbmvnqng2xlopdkd4m2grvb ==> Installing pkgconf-2.2.0-ugenh6g4dnhti4p6ktbkfku6pzlq5fkr [8/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/pkgconf-2.2.0-ugenh6g4dnhti4p6ktbkfku6pzlq5fkr ==> Installing gcom4-git.2024.05.28=access-esm1.5-xalavwvyp3jv6emsnj7yecrqprwp3kag [9/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/gcom4-git.2024.05.28_access-esm1.5-xalavwvyp3jv6emsnj7yecrqprwp3kag ==> Installing hdf5-1.10.11-yfo7fumh2agj6itfzqa6l2dpccrypp2l [10/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/hdf5-1.10.11-yfo7fumh2agj6itfzqa6l2dpccrypp2l ==> Installing netcdf-c-4.7.4-725rz7cn7qupsi4egyeaix2crssvtoxp [11/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/netcdf-c-4.7.4-725rz7cn7qupsi4egyeaix2crssvtoxp ==> Installing netcdf-fortran-4.5.2-5xcyy2h34vaq77ouwsgd6lfes5zycoii [12/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/netcdf-fortran-4.5.2-5xcyy2h34vaq77ouwsgd6lfes5zycoii ==> Installing oasis3-mct-git.access-esm1.5_2024.05.24=access-esm1.5-py3awb76nw3lwjw5ea3uktmh2nm254gi [13/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/oasis3-mct-git.access-esm1.5_2024.05.24_access-esm1.5-py3awb76nw3lwjw5ea3uktmh2nm254gi ==> Installing mom5-git.access-esm1.5_2024.08.23=access-esm1.5-oopqoqgqu65cybqht23l6m6coxbrpzqh [14/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/mom5-git.access-esm1.5_2024.08.23_access-esm1.5-oopqoqgqu65cybqht23l6m6coxbrpzqh ==> Installing um7-git.2024.07.03=access-esm1.5-udr7pbnflpwzuawejuuc4xpmfuwtpc4x [15/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/um7-git.2024.07.03_access-esm1.5-udr7pbnflpwzuawejuuc4xpmfuwtpc4x ==> Installing cice4-git.2024.05.21=access-esm1.5-hhtnigwxdyz7ta4dv3gvhwulze6hxqra [16/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/cice4-git.2024.05.21_access-esm1.5-hhtnigwxdyz7ta4dv3gvhwulze6hxqra ==> Installing access-esm1p5-git.2024.05.1=2024.05.1-nkvasig2zrq2ocz6evva6bmurdq7nh3h [17/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/access-esm1p5-git.2024.05.1_2024.05.1-nkvasig2zrq2ocz6evva6bmurdq7nh3h ==> Updating view at /g/data/$PROJECT/$USER/spack/0.22/environments/mom5_dev/.spack-env/view

Info

The full output has been truncated for brevity.

Create development package

When you develop a package within a Spack environment, Spack needs to know that the desired package is marked as "in development", and be able to access its source code.
This is done through the spack develop command.

Mark package as a development package

There are, in general, two cases that influence the command to run to mark a package as "in development", depending on the state of the package's source code:

The new source code does not exist
The new source code already exists

The new source does not exist

If the source code does not yet exist, Spack can create it as a copy of the current source code version, that can be later modified.

In this case we need to tell Spack which package tag (version) to copy as a starting base for the new source code.

For example, to retrieve the tag for the original mom5 package used in the mom5_dev Spack environment, we can run:

spack find mom5

spack find mom5

mom5@git.access-esm1.5_2024.08.23=access-esm1.5

To mark mom5 as a development package and copy the mom5@git.access-esm1.5_2024.08.23=access-esm1.5 version as a base copy, we can run:

spack develop mom5@git.access-esm1.5_2024.08.23=access-esm1.5

Tip

This command should not display any output

This adds the following lines at the end of the spack.yaml file inside the environment's folder:

develop:
    mom5:
      spec: mom5@git.access-esm1.5_2024.08.23=access-esm1.5

The source code is automatically copied inside the environment's folder.

Warning

As opposed to the case where the code already exists, there is no path specification inside the develop portion of the spack.yaml environment configuration file.
This means that Spack automatically expects to find the source code inside the environment's folder.

The new source code already exists

If the new source code for the development package already exists in the filesystem (this also includes cases when the new source code is in a git repo that can be cloned), to mark a package as "in development" we will need two things:

A name for the package's new tag
The path of the new source code

For example, to mark mom5 as a development package using the development_version tag and with the new source code in the /path/to/mom5/new/source/code folder, we can run:

spack develop --path /path/to/mom5/new/source/code mom5@development_version

Tip

This command should not display any output

This adds the following lines at the end of the spack.yaml file inside the environment's folder:

develop:
    mom5:
      spec: mom5@=development_version
      path: /path/to/mom5/new/source/code

Warning

Care needs to be taken when multiple Spack development environments point to the same source code location. If these environments require different independent changes of the source code, the user needs to make sure to sync the source code version (e.g., using different git branches for the different versions of the source code) with the desired one when switching between development environments.
This would still prevent building both environments simultaneously.

Compile modified Spack environment packages

After setting a development package the Spack environment needs to be re-concretized (because the spack.yaml file changed). The Spack environment can be concretized following the same steps listed in Concretize the Spack environment. Then, the new package can be built following the steps listed in Compile Spack environment packages:

spack concretize -f --fresh
spack install

Warning

Although this time the spack install command will only build the development package, it might still take a long time to complete, depending on the specific package.

spack concretize -f --fresh ==> Concretized access-esm1p5@git.2024.05.1=2024.05.1 - aysea5r access-esm1p5@git.2024.05.1=2024.05.1%intel@19.0.3.199 build_system=bundle arch=linux-rocky8-x86_64_v4 [+] hhtnigw ^cice4@git.2024.05.21=access-esm1.5%intel@19.0.3.199 build_system=makefile arch=linux-rocky8-x86_64_v4 [+] j6yscmm ^gmake@4.4.1%intel@19.0.3.199~guile build_system=generic arch=linux-rocky8-x86_64_v4 [+] 5xcyy2h ^netcdf-fortran@4.5.2%intel@19.0.3.199~doc+pic+shared build_system=autotools patches=b050dbd arch=linux-rocky8-x86_64_v4 [+] py3awb7 ^oasis3-mct@git.access-esm1.5_2024.05.24=access-esm1.5%intel@19.0.3.199~deterministic~optimisation_report build_system=makefile arch=linux-rocky8-x86_64_v4 [+] yfo7fum ^hdf5@1.10.11%intel@19.0.3.199~cxx~fortran+hl~ipo~java+mpi+shared~szip~threadsafe+tools api=default build_system=cmake build_type=Release generator=make arch=linux-rocky8-x86_64_v4 [e] vc4y4c6 ^cmake@3.24.2%intel@19.0.3.199~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-rocky8-x86_64_v4 [+] ugenh6g ^pkgconf@2.2.0%intel@19.0.3.199 build_system=autotools arch=linux-rocky8-x86_64_v4 [+] h45fvyw ^zlib-ng@2.1.6%intel@19.0.3.199+compat+new_strategies+opt+pic+shared build_system=autotools arch=linux-rocky8-x86_64_v4 [e] ikhujrk ^openmpi@4.0.2%intel@19.0.3.199~atomics~cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~internal-libevent~internal-pmix~java~legacylaunchers~lustre~memchecker~openshmem~orterunprefix~romio+rsh~singularity~static+vt+wrapper-rpath build_system=autotools fabrics=none patches=073477a,60ce20b romio-filesystem=none schedulers=none arch=linux-rocky8-x86_64_v4 [e] mqjolvb ^glibc@2.28%intel@19.0.3.199 build_system=autotools arch=linux-rocky8-x86_64_v4 - oopqoqg ^mom5@git.access-esm1.5_2024.08.23=access-esm1.5%intel@19.0.3.199~deterministic~optimisation_report+restart_repro build_system=makefile dev_path=/path/to/source/code/for/mom5 type=ACCESS-CM arch=linux-rocky8-x86_64_v4 [+] 725rz7c ^netcdf-c@4.7.4%intel@19.0.3.199~blosc~byterange~dap~fsync~hdf4~jna+mpi~nczarr_zip+optimize~parallel-netcdf+pic+shared~szip~zstd build_system=autotools arch=linux-rocky8-x86_64_v4 [+] udr7pbn ^um7@git.2024.07.03=access-esm1.5%intel@19.0.3.199 build_system=generic optim=high arch=linux-rocky8-x86_64_v4 [+] qy5w2d7 ^dummygrib@1.0%intel@19.0.3.199 build_system=makefile arch=linux-rocky8-x86_64_v4 [+] ho2ie66 ^fcm@2021.05.0%intel@19.0.3.199 build_system=generic site=none arch=linux-rocky8-x86_64_v4 [+] xalavwv ^gcom4@git.2024.05.28=access-esm1.5%intel@19.0.3.199+mpi build_system=generic arch=linux-rocky8-x86_64_v4 spack install [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/glibc-2.28-mqjolvbeskcnhz5chvtdshk4x4sfnycs [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/cmake-3.24.2-vc4y4c64s55j5u6kp37ciw2hcghuxhhc [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/openmpi-4.0.2-ikhujrkyukytbkxxyk3mub44v63vuzfz [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/gmake-4.4.1-j6yscmmcn3qws7n35klote7rivw7foa6 [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/fcm-2021.05.0-ho2ie66tizhxpjjiilnrjnlnbi6safwq [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/zlib-ng-2.1.6-h45fvywj47wc4uwa37mfzkdsqrgcqxux [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/dummygrib-1.0-qy5w2d7tmsbmvnqng2xlopdkd4m2grvb [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/pkgconf-2.2.0-ugenh6g4dnhti4p6ktbkfku6pzlq5fkr [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/gcom4-git.2024.05.28_access-esm1.5-xalavwvyp3jv6emsnj7yecrqprwp3kag [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/hdf5-1.10.11-yfo7fumh2agj6itfzqa6l2dpccrypp2l [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/netcdf-c-4.7.4-725rz7cn7qupsi4egyeaix2crssvtoxp [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/netcdf-fortran-4.5.2-5xcyy2h34vaq77ouwsgd6lfes5zycoii [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/oasis3-mct-git.access-esm1.5_2024.05.24_access-esm1.5-py3awb76nw3lwjw5ea3uktmh2nm254gi ==> Installing mom5-git.access-esm1.5_2024.08.23=access-esm1.5-l34w7is54xzer7s4ztvb5ymgjbtduknh [14/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/mom5-git.access-esm1.5_2024.08.23_access-esm1.5-l34w7is54xzer7s4ztvb5ymgjbtduknh [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/um7-git.2024.07.03_access-esm1.5-udr7pbnflpwzuawejuuc4xpmfuwtpc4x [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/cice4-git.2024.05.21_access-esm1.5-hhtnigwxdyz7ta4dv3gvhwulze6hxqra ==> Installing access-esm1p5-git.2024.05.1_2024.05.1-nkvasig2zrq2ocz6evva6bmurdq7nh3h [17/17] [+] /g/data/$PROJECT/$USER/spack/0.22/restricted/ukmo/release/linux-rocky8-x86_64_v4/intel-19.0.3.199/access-esm1p5-git.2024.05.1_2024.05.1-nkvasig2zrq2ocz6evva6bmurdq7nh3h ==> Updating view at /g/data/$PROJECT/$USER/spack/0.22/environments/mom5_dev/.spack-env/view

Info

The full output has been truncated for brevity.

Tip

From now on, the source code can be modified and the Spack environment installed without repeating the concretization step.
The Spack environment will need to be re-concretized only if further changes occur in the spack.yaml file.

Output directory for compiled packages

For the Spack instance obtained through the Spack setup instructions, all compiled packages will be placed in directories having the following format: <install_tree.root>/<architecture>/<compiler.name>-<compiler.version>/<name>-<version>-<hash>.

<install_tree.root> depends on the install_tree.root configuration field. Spack reads this configuration field from files in several directories, following Spack's configuration scopes.

Warning

For instances of Spack on Gadi you should ignore the system scope.

For the example above, mom5_dev Spack environment's configuration file (spack.yaml) contains the following lines that fall in the environment scope:

config:
    install_tree:
      root: $spack/../restricted/ukmo/release

Tip

For the Spack instance obtained through the Spack setup instructions, $spack (referred to as $(prefix) in Spack configuration scopes documentation above) corresponds to the /g/data/$PROJECT/$USER/spack/0.22/spack directory.

This means the packages built in this example can be found in /g/data/$PROJECT/$USER/spack/0.22/spack/../restricted/ukmo/release/<architecture>/<compiler.name>-<compiler.version>/<name>-<version>-<hash>.

Troubleshooting build errors

Sometimes you might encounter errors while compiling the packages.
Spack prints out the error message and generates a full build log that can be viewed by the user. The location of the build log is shown at the end of the error message.

For example, if we try to install the mom5_dev environment with an error in the new mom5 source code (in this example a use statement in the <new-mom5-source-code-folder>/src/accessom_coupler/ocean_solo.F90 file has been purposely commented out to force an error in compilation), we might get an output error similar to the following:

...
 >> 415    /g/data/$PROJECT/$USER/spack/0.22/environments/mom5_dev/mom5/src/access_coupler/ocean_solo.F90:224: undefined reference to `constant s_init_'
 >> 416    make: *** [Makefile:931: fms_ACCESS-CM.x] Error 1
...
See build log for details:
  /scratch/$PROJECT/$USER/tmp/path/to/the/spack-stage-mom5-git.access-esm1.5_2024.08.23_access-esm1.5-l34w7is54xzer7s4ztvb5ymgjbtduknh/spack-build-out.txt
...
==> Error: access-esm1p5-git.2024.05.1=2024.05.1-aysea5r7rbwy22lluvl64baperlokktv: Package was not installed
==> Error: Installation request failed.  Refer to reported errors for failing package(s).

If the error is not obvious from the error message, see the build log for more information.

- https://spack.readthedocs.io/en/latest/ - https://spack-tutorial.readthedocs.io/en/latest/tutorial_developer_workflows.html

Last update: December 13, 2024