# How to build ACCESS-OM2 on Gadi **URL:** \ **Category:** spack\ **Tags:** spack, access-om2\ **Created:** [25 October 2023 03:11 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om2-on-gadi/1545 "2023-10-25T03:11:28Z")\ **Posts on this page:** 13\ **Page:** 1
**Author:** ![harshula](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/harshula/32/256_2.png) [@harshula](https://forum.access-hive.org.au/u/harshula)\ **Post date:** [25 October 2023 03:11 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om2-on-gadi/1545/1 "2023-10-25T03:11:28Z")
If you want to run an official ACCESS-NRI release of `ACCESS-OM2`, there is no need to build it. Simply follow the instructions on how to [Run ACCESS-OM2](https://access-hive.org.au/models/run-a-model/run-access-om/). # How to rebuild ACCESS-OM2 on Gadi v11 [15/06/2026: Use shared Spack instance] 1. Login to Gadi: > ```auto > ssh USERNAME@gadi.nci.org.au > > ``` 1. Follow these instructions to [How to use Spack on Gadi for building ACCESS models](https://access-hive.org.au/getting_started/spack/) . 1. Build ACCESS-OM2 (initialisation may take a long time without any output): > ```auto > cd /g/data/$PROJECT/$USER/ > git clone https://github.com/ACCESS-NRI/ACCESS-OM2.git > spack env activate -p ./ACCESS-OM2 > spack concretize -f > spack install > > ``` # How to modify and rebuild ACCESS-OM2 on Gadi v2 - [Modify and build an ACCESS model's source code - ACCESS-Hive Docs](https://docs.access-hive.org.au/models/build_a_model/build_source_code/) ---
**Author:** ![harshula](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/harshula/32/256_2.png) [@harshula](https://forum.access-hive.org.au/u/harshula)\ **Post date:** [26 October 2023 10:33 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om2-on-gadi/1545/2 "2023-10-26T10:33:01Z")
If the `spack install ...` command is failing with the following error: ```auto ==> Installing cmake-3.26.3-4hg4d2a6d72efysvvyfkepnvl6khes3o ==> No binary for cmake-3.26.3-4hg4d2a6d72efysvvyfkepnvl6khes3o found: installing from source ==> Fetching file:///g/data///spack-mirror-access-om2/_source-cache/archive/bb/bbd8d39217509d163cb544a40d6428ac666ddc83e22905d3e52c925781f0f659.tar.gz ==> No patches needed for cmake ==> cmake: Executing phase: 'bootstrap' Killed ``` you may be using v1 of the instructions where CMake was being built by Spack. To avoid this problem, please use v2 of the instructions where the system CMake is used ---
**Author:** ![aekiss](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/aekiss/32/46_2.png) [@aekiss](https://forum.access-hive.org.au/u/aekiss)\ **Post date:** [2 November 2023 03:09 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om2-on-gadi/1545/3 "2023-11-02T03:09:15Z")
> [@harshula](#): > > ```auto > - compiler: > spec: intel@=19.0.5.281 > ... > modules: [intel-compiler/2019.5.281] > > ``` @harshula what is meant by `...` here? Where do I find what should go there? ---
**Author:** ![harshula](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/harshula/32/256_2.png) [@harshula](https://forum.access-hive.org.au/u/harshula)\ **Post date:** [2 November 2023 04:38 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om2-on-gadi/1545/4 "2023-11-02T04:38:09Z")
1. [What’s an Ellipsis? Definition and Examples | Grammarly Blog](https://www.grammarly.com/blog/ellipsis/) 2. The previous step would have auto-populated the remainder of that section. ---
**Author:** ![paulleopardi](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/paulleopardi/32/92_2.png) [@paulleopardi](https://forum.access-hive.org.au/u/paulleopardi)\ **Post date:** [2 November 2023 05:45 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om2-on-gadi/1545/5 "2023-11-02T05:45:31Z")
I have just used the instructions to successfully build on Gadi login at `/g/data/tm70/pcl851/spack` ---
**Author:** ![aekiss](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/aekiss/32/46_2.png) [@aekiss](https://forum.access-hive.org.au/u/aekiss)\ **Post date:** [6 November 2023 21:43 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om2-on-gadi/1545/7 "2023-11-06T21:43:31Z")
I couldn’t get it to work - build logs here `/scratch/v45/aek156/tmp/spack-stage/` ---
**Author:** ![harshula](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/harshula/32/256_2.png) [@harshula](https://forum.access-hive.org.au/u/harshula)\ **Post date:** [6 November 2023 23:14 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om2-on-gadi/1545/8 "2023-11-06T23:14:04Z")
Hi @aekiss, I don’t have permission to access `v45`. Let’s go through the steps together when you’re in the office. ---
**Author:** ![harshula](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/harshula/32/256_2.png) [@harshula](https://forum.access-hive.org.au/u/harshula)\ **Post date:** [12 November 2023 22:36 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om2-on-gadi/1545/9 "2023-11-12T22:36:37Z")
Hi @aekiss , Your Spack instance was unable to compile the required build tools. e.g. `gmake`: ```auto ==> gmake: Executing phase: 'build' ==> [2023-11-06-21:27:41.679695] '/scratch/[...]/tmp/spack-stage/spack-stage-gmake-4.4.1-h5uwuoe6h3nknjnagjbskugtwch7q5c3/spack-src/build.sh' config.status: creating ./lib/alloca.h__ compiling lib/concat-filename.c... In file included from /usr/include/bits/floatn.h(119), from /usr/include/stdlib.h(55), from /scratch/v45/aek156/tmp/spack-stage/spack-stage-gmake-4.4.1-h5uwuoe6h3nknjnagjbskugtwch7q5c3/spack-src/lib/concat-filename.h(20), from /scratch/v45/aek156/tmp/spack-stage/spack-stage-gmake-4.4.1-h5uwuoe6h3nknjnagjbskugtwch7q5c3/spack-src/lib/concat-filename.c(22): /usr/include/bits/floatn-common.h(214): error: invalid combination of type specifiers typedef float _Float32; ``` Looks like a problem with your compiler config. Do you remember why you made the following changes to your `.spack/linux/compilers.yaml`? ```auto @@ -13,9 +13,22 @@ environment: {} extra_rpaths: [] - compiler: + spec: gcc@=13.2.0 + paths: + cc: /g/data/hh5/public/apps/miniconda3/envs/analysis3-23.07/bin/gcc + cxx: null + f77: null + fc: null + flags: {} + operating_system: rocky8 + target: x86_64 + modules: [] + environment: {} + extra_rpaths: [] +- compiler: spec: gcc@=8.5.0 paths: - cc: /opt/nci/bin/gcc + cc: /bin/gcc cxx: /opt/nci/bin/g++ f77: /opt/nci/bin/gfortran fc: /opt/nci/bin/gfortran ``` Perhaps move your `.spack` to another location and try the instructions with a new empty `.spack`. ---
**Author:** ![aekiss](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/aekiss/32/46_2.png) [@aekiss](https://forum.access-hive.org.au/u/aekiss)\ **Post date:** [14 November 2023 00:16 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om2-on-gadi/1545/10 "2023-11-14T00:16:11Z")
`spack find` picked up `gcc@13.2.0` because I had the `conda/analysis3-23.07` module loaded. It builds successfully if I do `module purge` before step 1. ---
**Author:** ![harshula](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/harshula/32/256_2.png) [@harshula](https://forum.access-hive.org.au/u/harshula)\ **Post date:** [14 November 2023 01:13 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om2-on-gadi/1545/11 "2023-11-14T01:13:24Z")
Thanks @aekiss for testing and providing feedback. As a result, I’m planning on disabling local config (i.e. `~/.spack`) to avoid similar issues. ---
**Author:** ![Aidan](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/aidan/32/42_2.png) [@Aidan](https://forum.access-hive.org.au/u/Aidan)\ **Post date:** [22 February 2024 06:54 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om2-on-gadi/1545/12 "2024-02-22T06:54:06Z")
5 posts were split to a new topic: [Modifying ACCESS-OM2 spack package](https://forum.access-hive.org.au/t/modifying-access-om2-spack-package/1847) ---
**Author:** ![Aidan](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/aidan/32/42_2.png) [@Aidan](https://forum.access-hive.org.au/u/Aidan)\ **Post date:** [23 February 2024 05:27 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om2-on-gadi/1545/13 "2024-02-23T05:27:36Z")
Slightly peripheral question, but the [`spack.yaml`](https://github.com/ACCESS-NRI/ACCESS-OM2/blob/main/spack.yaml) that defines the model uses `git` tags to identify the model component: ```yaml spack: # add package specs to the `specs` list specs: - access-om2@git.2023.11.23 packages: cice5: require: '@git.2023.10.19' mom5: require: '@git.2023.11.09' libaccessom2: require: '@git.2023.10.26' oasis3-mct: require: '@git.2023.11.09' netcdf-c: require: '@4.7.4' netcdf-fortran: require: '@4.5.2' parallelio: require: '@2.5.2' nci-openmpi: require: '@4.0.2' all: compiler: [intel@19.0.5.281] ``` That means having installed all the `access-om2` components with `spack` the versions of the model components are not displayed in the same way as components installed by version ```auto $ spack find -vl -- linux-rocky8-x86_64 / intel@19.0.5.281 ----------------------- ... nyxvikk json-fortran@8.3.0~ipo build_system=cmake build_type=Release generator=make ajlvl3k libaccessom2@master~deterministic~ipo~optimisation_report build_system=cmake build_type=Release generator=make uznvr36 mom5@master~deterministic~optimisation_report build_system=makefile i3inxza netcdf-c@4.7.4~blosc~byterange~dap~fsync~hdf4~jna+mpi~nczarr_zip+optimize~parallel-netcdf+pic+shared~szip~zstd build_system=autotools ``` e.g. `json-fortran@8.3.0` vs `mom5@master` I couldn’t find a way get the `git tag` value, for example for `mom5` it would be `2023.11.09`. ---
**Author:** ![harshula](https://sea2.discourse-cdn.com/flex020/user_avatar/forum.access-hive.org.au/harshula/32/256_2.png) [@harshula](https://forum.access-hive.org.au/u/harshula)\ **Post date:** [23 February 2024 06:28 UTC](https://forum.access-hive.org.au/t/how-to-build-access-om2-on-gadi/1545/14 "2024-02-23T06:28:45Z")
Please use a new topic. Did you use the `spack.yaml` to install the packages? This is how it should look: ```auto $ spack find -- linux-rocky8-x86_64 / intel@19.0.5.281 ----------------------- access-om2@git.2023.11.23=2023.11.23 mom5@git.2023.11.09=2023.11.09 cice5@git.2023.10.19=2023.10.19 nci-openmpi@4.0.2 cmake@3.24.2 netcdf-c@4.7.4 datetime-fortran@1.7.0 netcdf-fortran@4.5.2 gmake@4.4.1 oasis3-mct@git.2023.11.09=2023.11.09 hdf5@1.14.1-2 parallelio@2.5.10 json-fortran@8.3.0 pkgconf@1.9.5 libaccessom2@git.2023.10.26=2023.10.26 zlib@1.2.13 ==> 16 installed packages ```