From 0d11fc3208f82d8e25626947b27ccdf0681be51d Mon Sep 17 00:00:00 2001 From: souheil-yazji Date: Tue, 19 Dec 2023 14:01:58 +0000 Subject: [PATCH 1/3] fix(microsim): add file extension --- docs/en/8-MicroSim/Additions.md | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 docs/en/8-MicroSim/Additions.md diff --git a/docs/en/8-MicroSim/Additions.md b/docs/en/8-MicroSim/Additions.md new file mode 100644 index 000000000..05070bf8e --- /dev/null +++ b/docs/en/8-MicroSim/Additions.md @@ -0,0 +1,27 @@ +## Adding a New Model + +**Note**: use a notebook with at least 4Gb of memory for this full guide. + +First clone the model's repository or download and extract the archived model on your AAW notebook. In our example, we clone oncosim from gitlab: + +![Oncosim dir is now available](image.png) + +### Compiling the model + +In this case, we are compiling for mpi, so we retrieved the appropriate OMPP release from the [openmpp releases page](https://github.com/openmpp/main/releases). Make sure to use the archived releases provided by openM and not auto-generated by Github. + +We can follow the readme of the model. In this case, we set our `OM_ROOT` environment variable to the same directory as our OMPP release using `export OM_ROOT=~/buckets/aaw-unclassified/microsim/openmpp_ubuntu_mpi_20231115`. + +We can now compile. We make sure that we're in the oncosim directory then run `make OM_MSG_USE=MPI RELEASE=1 all publish`. + +Once compilation is complete, our compiled model files appear under `/ompp-linux/bin/`. Using the terminal, `cp` the files in the `bin` directory to `~/buckets/aaw-unclassified/microsim/models/bin`. + +![oncosim model files under bin](image-2.png) + +Using the terminal, `cp -r ` the entire model directory to `~/buckets/aaw-unclassified/microsim/models` + +![oncosim under microsim](image-1.png) + +Once complete, run `restart-oms.sh` in the terminal. This will restart the OpenM web service and allow it to pick up the new model. + +![model in UI](image-3.png) \ No newline at end of file From 0eb809a7499f78aa2245c826685d16f104a23a20 Mon Sep 17 00:00:00 2001 From: souheil-yazji Date: Fri, 26 Jan 2024 16:24:52 +0000 Subject: [PATCH 2/3] docs(ompp): update model location --- docs/en/8-MicroSim/Additions.md | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/docs/en/8-MicroSim/Additions.md b/docs/en/8-MicroSim/Additions.md index 05070bf8e..eebeea158 100644 --- a/docs/en/8-MicroSim/Additions.md +++ b/docs/en/8-MicroSim/Additions.md @@ -1,6 +1,6 @@ ## Adding a New Model -**Note**: use a notebook with at least 4Gb of memory for this full guide. +**Note**: use a notebook with at least 6Gb of memory for this full guide. First clone the model's repository or download and extract the archived model on your AAW notebook. In our example, we clone oncosim from gitlab: @@ -14,14 +14,10 @@ We can follow the readme of the model. In this case, we set our `OM_ROOT` enviro We can now compile. We make sure that we're in the oncosim directory then run `make OM_MSG_USE=MPI RELEASE=1 all publish`. -Once compilation is complete, our compiled model files appear under `/ompp-linux/bin/`. Using the terminal, `cp` the files in the `bin` directory to `~/buckets/aaw-unclassified/microsim/models/bin`. +Once compilation is complete, our compiled model files appear under `/ompp-linux/bin/`. Using the terminal, `cp` the files in the `bin` directory to `~/buckets/aaw-unclassified/microsim/models/bin`. ![oncosim model files under bin](image-2.png) -Using the terminal, `cp -r ` the entire model directory to `~/buckets/aaw-unclassified/microsim/models` - -![oncosim under microsim](image-1.png) - Once complete, run `restart-oms.sh` in the terminal. This will restart the OpenM web service and allow it to pick up the new model. ![model in UI](image-3.png) \ No newline at end of file From 0e5e03f356148d00d0d4da166cee01cf5a92b01f Mon Sep 17 00:00:00 2001 From: souheil-yazji Date: Mon, 29 Jan 2024 14:36:09 +0000 Subject: [PATCH 3/3] docs(microsim): direct link to Gitlab --- docs/en/8-MicroSim/Additions.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/en/8-MicroSim/Additions.md b/docs/en/8-MicroSim/Additions.md index eebeea158..65226329c 100644 --- a/docs/en/8-MicroSim/Additions.md +++ b/docs/en/8-MicroSim/Additions.md @@ -2,7 +2,7 @@ **Note**: use a notebook with at least 6Gb of memory for this full guide. -First clone the model's repository or download and extract the archived model on your AAW notebook. In our example, we clone oncosim from gitlab: +First clone the model's repository or download and extract the archived model on your AAW notebook. In our example, we clone oncosim from [gitlab](../6-Gitlab/Gitlab.md): ![Oncosim dir is now available](image.png)