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
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:
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 already exists
- The new source code does not yet exist
Case 1. 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.
Case 2. 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
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 Case 1, 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.
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:
October 28, 2024