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Linux Create and Debug Model
- Download: latest binary files and source code
- Documentation: Linux Quick Start for Developers
- check your g++ --version:
g++ (Debian 12.2.0-14) 12.2.0
g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
g++ (GCC) 11.5.0 20240719 (Red Hat 11.5.0-2)
Optional:
If you want to debug your model then you will need to rebuild openM++ runtime library first as described at Linux Quick Start for Developers
To build and run debug version of the model use desktop (non-MPI) version of openM++:
wget https://github.com/openmpp/main/releases/download/v1.8.3/openmpp_debian_20210304.tar.gz
tar xzf openmpp_debian_20210304.tar.gz
cd openmpp_debian_20210304/openm/
make libopenm
- create new directory for your model under models subfolder i.e.:
models/MyModel
- copy other test model makefile into your model folder, copy your model files and data files:
cd openmpp_debian_20210304/models/
mkdir MyModel
cd MyModel
cp ../NewCaseBased/makefile .
mkdir code
cp ~/my_model_sources/*mpp code
cp ~/my_model_sources/*.cpp code
cp ~/my_model_sources/*.h code
mkdir -p parameters/Default
cp ~/my_model_data/*dat parameters/Default
- build your model and "publish" it:
make all publish
- run the model:
cd ompp-linux/bin
./MyModelD
cd ..
Please note: It is recommended (not required) to have directory name exactly the same as model name. Linux file and directory names are case-sensitive and myModel
is not the same as MyModel
In example above we were creating only one "Default" scenario for our model from *.dat files in parameters/Default
directory. It is also possible to create multiple input sets of parameters (multiple scenarios) when you are building the model:
make SCENARIO_NAME=Default,Other OMC_SCENARIO_PARAM_DIR=parameters/Default,parameters/SomeOther all publish
Above command will create two input sets of parameters:
- scenario "Default" from *.dat, *.odat, *.csv and *.tsv files in parameters/Default directory
- scenario "Other" from *.csv and *.tsv files in parameters/SomeOther directory
Please notice: additional scenario directory can contain only CSV or TSV files and not .dat or .odat files.
To find out more about CSV and TSV parameter files please read: How to use CSV or TSV files for input parameters values
There is an excellent AddressSanitizer tool which allow to catch most of memory violation bugs. For example:
int x[10];
int main (int argc, char ** argv)
{
x[20] = 20; // error: global buffer overflow
........
}
It is not recommended to use AddressSanitizer in production, it slows down model code execution approximately by 70% and double memory usage. For that reason openM++ binary release does not enable AddressSanitizer by default and you will need to re-build openM++ run-time libraries to use it for your models testing.
To enable AddressSanitizer for your developement do:
- unpack openM++ release in separate folder, for example:
~/openmpp-asan
. It is not recommended to use it in your main development folder - re-build openM++ run-time library:
cd ~/openmpp-asan
rm -rf lib
rm -rf build
cd openm
make USE_ASAN=1 libopenm
make USE_ASAN=1 RELEASE=1 libopenm
- rebuild your model with AddressSanitizer, for example if your model name is
RiskPaths
you can build Debug and Release model versions by:
cd ~/ompp-main/models/RiskPaths
make clean-all
make USE_ASAN=1 all publish
make USE_ASAN=1 RELEASE=1 all publish
- and now you can run Debug or Release version of your model:
cd ompp-linux/bin
./RiskPathsD
./RiskPaths
Please notice, Debug version of the model executable is always significantly slower than Release. It is recommended to prepare smaller version of your test scenario to run it with Debug model. Or, maybe adjust some parameters from default scenario, for example:
cd ompp-linux/bin
./RiskPathsD -Parameter.SimulationCases 1234
Prerequisites:
- install Visual Studio Code
- follow steps described above to create new model
Note: In example below we are using RiskPaths demo model, please replace "RiskPaths" with your actual model name.
Make sure you have GDB, g++, make and other build tools installed on your system. For example on Ubuntu:
sudo apt install sqlite
sudo apt install g++
sudo apt install make
sudo apt install curl
sudo apt install git
For example on RedHat (CentOS):
dnf install gcc-c++
dnf install make
dnf install sqlite
dnf install gdb
dnf install git
Start Visual Studio Code and go to: File -> Open Folder... -> ~/openmpp_debian_20210304/models/RiskPaths
Create build task for your model using menu: Terminal -> Configure Tasks...
{
"version": "2.0.0",
"tasks": [
{
"label": "build-RiskPaths",
"type": "shell",
"command": "make all publish",
"problemMatcher": "$gcc",
"group": {
"kind": "build",
"isDefault": true
},
"dependsOrder": "sequence",
"dependsOn": [
"build-libopenm",
"stop-ui-RiskPaths"
]
},
{
"label": "build-RiskPaths-release",
"type": "shell",
"command": "make RELEASE=1 all publish",
"problemMatcher": "$gcc",
"group": "build",
"dependsOrder": "sequence",
"dependsOn": [
"build-libopenm-release",
"stop-ui-RiskPaths"
]
},
{
"label": "start-ui-RiskPaths",
"type": "shell",
"command": "../start-model-ui-linux.sh",
"problemMatcher": []
},
{
"label": "start-ui-RiskPaths-release",
"type": "shell",
"command": "RELEASE=1 ../start-model-ui-linux.sh",
"problemMatcher": []
},
{
"label": "stop-ui-RiskPaths",
"type": "shell",
"command": "../stop-model-ui-linux.sh",
"problemMatcher": []
},
{
"label": "clean-RiskPaths",
"type": "shell",
"command": "make clean-all && make RELEASE=1 clean-all",
"group": "build",
"problemMatcher": []
},
{
"label": "build-libopenm",
"type": "shell",
"command": "make libopenm",
"options": {
"cwd": "../../openm"
},
"problemMatcher": "$gcc",
"group": "build"
},
{
"label": "build-libopenm-release",
"type": "shell",
"command": "make RELEASE=1 libopenm",
"options": {
"cwd": "../../openm"
},
"problemMatcher": "$gcc",
"group": "build"
}
]
}
You also can find file above at ~/openmpp_debian_20210304/models/RiskPaths/.vscode-linux/tasks.json
Some models may require special settings in order to run, for example, you may need to increase ulimit
resources for OncSimX model:
{
"label": "start-ui-OncoSimX",
"type": "shell",
"command": "ulimit -S -s 65536 && ../start-ompp-ui-linux.sh",
"problemMatcher": []
},
{
"label": "start-ui-OncoSimX-release",
"type": "shell",
"command": "ulimit -S -s 65536 && RELEASE=1 ../start-ompp-ui-linux.sh",
"problemMatcher": []
},
Create model debug configuration using menu: Debug -> Add Configuration...:
{
"version": "0.2.0",
"configurations": [
{
"name": "debug RiskPaths",
"type": "cppdbg",
"request": "launch",
"program": "${workspaceFolder}/ompp-linux/bin/RiskPathsD",
"args": [],
"stopAtEntry": false,
"cwd": "${workspaceFolder}/ompp-linux/bin",
"environment": [
{ "name": "OM_RiskPaths", "value": "${workspaceFolder}" }
],
"externalConsole": false,
"MIMode": "gdb",
"setupCommands": [
{
"description": "Enable pretty-printing for gdb",
"text": "-enable-pretty-printing",
"ignoreFailures": true
}
]
}
]
}
You also can find file above at ~/openmpp_debian_20210304/models/RiskPaths/.vscode-linux/launch.json
In order to debug *.mpp and *.ompp files as c++ go to menu File -> Preferences -> Settings -> Text Editor -> Files -> Associations -> click on "Edit in settings.json" and add into settings.json
:
{
"files.associations": {
"*.mpp": "cpp",
"*.ompp": "cpp"
}
}
You also can find file above at `~/openmpp_debian_20210304/models/RiskPaths/.vscode-linux/settings.json
Build your model using Terminal -> Run Build Task...
Start model debugging by using Run -> Start Debugging
- open any model.ompp or *.mpp file and put breakpoint in it
- (optional) add breakpoint(s) at
RunSimulation
entry point using File -> Open File... ->use/case_based/case_based_common.ompp -> RunSimulation()
- (optional) you may also add breakpoint(s) at
main
entry point: File -> Open File... -> openm/libopenm/main.cpp - open model with UI by using Terminal -> Run Task... ->
start-ui-RiskPaths
. You can see UI screenshots at UI: openM++ user interface page.
To inspect model parameters add Watch variable:
It is a convenient to see Doxygen comments in your model code when you hover:
If such functionality does not work for you then it maybe a result of missing include path in your c++ model settings. To fix it find a missing (red underscored) include, in example below it is #include "omc/omSimulation.h"
and select Quick Fix
-> Edit includePath settings
:
It should open Microsoft C/C++ extension settings page. Add "${workspaceFolder}/../../include/**"
to your Include Path list. It is also a good idea to set C++ standard as c++20
:
That can be done by adding .vscode/c_cpp_properties.json
to your model folder, but such JSON maybe specific to the particular version of VSCode:
{
"configurations": [
{
"name": "Linux",
"includePath": [
"${workspaceFolder}/**",
"${workspaceFolder}/../../include/**"
],
"defines": [],
"compilerPath": "/usr/bin/gcc",
"cStandard": "c17",
"cppStandard": "c++20",
"intelliSenseMode": "linux-gcc-x64"
}
],
"version": 4
}
You also can find file above at ~/openmpp_debian_20210304/models/RiskPaths/.vscode-linux/c_cpp_properties.json
As described at Linux Quick Start for Model Users you can run the model with different options. For example, you can calculate 8 sub-values (a.k.a. sub-samples, members, replicas), use 4 threads and simulate 8000 cases:
./RiskPathsD -OpenM.SubValues 8 -OpenM.Threads 4 -Parameter.SimulationCases 8000
You can supply run options as model command line arguments or by using model.ini file:
[OpenM]
SubValues = 8
Threads = 4
[Parameter]
SimulationCases=8000
./RiskPathsD -ini RiskPathsD.ini
There are two possible ways to use model ini-file with Visual Studio Code:
- by adding
-ini RiskPaths.ini
command line argument to model executable. Go to menu -> Run -> Open Configurations and editlaunch.json
at"program"
line:
{
// .... .... ....
"program": "${workspaceFolder}/ompp-linux/bin/RiskPathsD -ini RiskPaths.ini",
// .... .... ....
}
- by adding
MODEL_INI=RiskPaths.ini
command line argument to model make. Go to menu -> Terminal -> Configure Task -> build-RiskPaths and edittasks.json
at"command": "make ....
line:
{
"tasks": [
{
"label": "build-RiskPaths",
"command": "make MODEL_INI=RiskPaths.ini all publish run",
// .... .... ....
}]
}
That MODEL_INI
argument will be passed to model executable when make
run the model as:
ompp-linux/bin/RiskPathsD -ini RiskPaths.ini
- Windows: Quick Start for Model Users
- Windows: Quick Start for Model Developers
- Linux: Quick Start for Model Users
- Linux: Quick Start for Model Developers
- MacOS: Quick Start for Model Users
- MacOS: Quick Start for Model Developers
- Model Run: How to Run the Model
- MIT License, Copyright and Contribution
- Model Code: Programming a model
- Windows: Create and Debug Models
- Linux: Create and Debug Models
- MacOS: Create and Debug Models
- MacOS: Create and Debug Models using Xcode
- Modgen: Convert case-based model to openM++
- Modgen: Convert time-based model to openM++
- Modgen: Convert Modgen models and usage of C++ in openM++ code
- Model Localization: Translation of model messages
- How To: Set Model Parameters and Get Results
- Model Run: How model finds input parameters
- Model Output Expressions
- Model Run Options and ini-file
- OpenM++ Compiler (omc) Run Options
- OpenM++ ini-file format
- UI: How to start user interface
- UI: openM++ user interface
- UI: Create new or edit scenario
- UI: Upload input scenario or parameters
- UI: Run the Model
- UI: Use ini-files or CSV parameter files
- UI: Compare model run results
- UI: Aggregate and Compare Microdata
- UI: Filter run results by value
- UI: Disk space usage and cleanup
- UI Localization: Translation of openM++
-
Highlight: hook to self-scheduling or trigger attribute
-
Highlight: The End of Start
-
Highlight: Enumeration index validity and the
index_errors
option -
Highlight: Simplified iteration of range, classification, partition
-
Highlight: Parameter, table, and attribute groups can be populated by module declarations
- Oms: openM++ web-service
- Oms: openM++ web-service API
- Oms: How to prepare model input parameters
- Oms: Cloud and model runs queue
- Use R to save output table into CSV file
- Use R to save output table into Excel
- Run model from R: simple loop in cloud
- Run RiskPaths model from R: advanced run in cloud
- Run RiskPaths model in cloud from local PC
- Run model from R and save results in CSV file
- Run model from R: simple loop over model parameter
- Run RiskPaths model from R: advanced parameters scaling
- Run model from Python: simple loop over model parameter
- Run RiskPaths model from Python: advanced parameters scaling
- Windows: Use Docker to get latest version of OpenM++
- Linux: Use Docker to get latest version of OpenM++
- RedHat 8: Use Docker to get latest version of OpenM++
- Quick Start for OpenM++ Developers
- Setup Development Environment
- 2018, June: OpenM++ HPC cluster: Test Lab
- Development Notes: Defines, UTF-8, Databases, etc.
- 2012, December: OpenM++ Design
- 2012, December: OpenM++ Model Architecture, December 2012
- 2012, December: Roadmap, Phase 1
- 2013, May: Prototype version
- 2013, September: Alpha version
- 2014, March: Project Status, Phase 1 completed
- 2016, December: Task List
- 2017, January: Design Notes. Subsample As Parameter problem. Completed
GET Model Metadata
- GET model list
- GET model list including text (description and notes)
- GET model definition metadata
- GET model metadata including text (description and notes)
- GET model metadata including text in all languages
GET Model Extras
GET Model Run results metadata
- GET list of model runs
- GET list of model runs including text (description and notes)
- GET status of model run
- GET status of model run list
- GET status of first model run
- GET status of last model run
- GET status of last completed model run
- GET model run metadata and status
- GET model run including text (description and notes)
- GET model run including text in all languages
GET Model Workset metadata: set of input parameters
- GET list of model worksets
- GET list of model worksets including text (description and notes)
- GET workset status
- GET model default workset status
- GET workset including text (description and notes)
- GET workset including text in all languages
Read Parameters, Output Tables or Microdata values
- Read parameter values from workset
- Read parameter values from workset (enum id's)
- Read parameter values from model run
- Read parameter values from model run (enum id's)
- Read output table values from model run
- Read output table values from model run (enum id's)
- Read output table calculated values from model run
- Read output table calculated values from model run (enum id's)
- Read output table values and compare model runs
- Read output table values and compare model runs (enun id's)
- Read microdata values from model run
- Read microdata values from model run (enum id's)
- Read aggregated microdata from model run
- Read aggregated microdata from model run (enum id's)
- Read microdata run comparison
- Read microdata run comparison (enum id's)
GET Parameters, Output Tables or Microdata values
- GET parameter values from workset
- GET parameter values from model run
- GET output table expression(s) from model run
- GET output table calculated expression(s) from model run
- GET output table values and compare model runs
- GET output table accumulator(s) from model run
- GET output table all accumulators from model run
- GET microdata values from model run
- GET aggregated microdata from model run
- GET microdata run comparison
GET Parameters, Output Tables or Microdata as CSV
- GET csv parameter values from workset
- GET csv parameter values from workset (enum id's)
- GET csv parameter values from model run
- GET csv parameter values from model run (enum id's)
- GET csv output table expressions from model run
- GET csv output table expressions from model run (enum id's)
- GET csv output table accumulators from model run
- GET csv output table accumulators from model run (enum id's)
- GET csv output table all accumulators from model run
- GET csv output table all accumulators from model run (enum id's)
- GET csv calculated table expressions from model run
- GET csv calculated table expressions from model run (enum id's)
- GET csv model runs comparison table expressions
- GET csv model runs comparison table expressions (enum id's)
- GET csv microdata values from model run
- GET csv microdata values from model run (enum id's)
- GET csv aggregated microdata from model run
- GET csv aggregated microdata from model run (enum id's)
- GET csv microdata run comparison
- GET csv microdata run comparison (enum id's)
GET Modeling Task metadata and task run history
- GET list of modeling tasks
- GET list of modeling tasks including text (description and notes)
- GET modeling task input worksets
- GET modeling task run history
- GET status of modeling task run
- GET status of modeling task run list
- GET status of modeling task first run
- GET status of modeling task last run
- GET status of modeling task last completed run
- GET modeling task including text (description and notes)
- GET modeling task text in all languages
Update Model Profile: set of key-value options
- PATCH create or replace profile
- DELETE profile
- POST create or replace profile option
- DELETE profile option
Update Model Workset: set of input parameters
- POST update workset read-only status
- PUT create new workset
- PUT create or replace workset
- PATCH create or merge workset
- DELETE workset
- POST delete multiple worksets
- DELETE parameter from workset
- PATCH update workset parameter values
- PATCH update workset parameter values (enum id's)
- PATCH update workset parameter(s) value notes
- PUT copy parameter from model run into workset
- PATCH merge parameter from model run into workset
- PUT copy parameter from workset to another
- PATCH merge parameter from workset to another
Update Model Runs
- PATCH update model run text (description and notes)
- DELETE model run
- POST delete model runs
- PATCH update run parameter(s) value notes
Update Modeling Tasks
Run Models: run models and monitor progress
Download model, model run results or input parameters
- GET download log file
- GET model download log files
- GET all download log files
- GET download files tree
- POST initiate entire model download
- POST initiate model run download
- POST initiate model workset download
- DELETE download files
- DELETE all download files
Upload model runs or worksets (input scenarios)
- GET upload log file
- GET all upload log files for the model
- GET all upload log files
- GET upload files tree
- POST initiate model run upload
- POST initiate workset upload
- DELETE upload files
- DELETE all upload files
Download and upload user files
- GET user files tree
- POST upload to user files
- PUT create user files folder
- DELETE file or folder from user files
- DELETE all user files
User: manage user settings
Model run jobs and service state
- GET service configuration
- GET job service state
- GET disk usage state
- POST refresh disk space usage info
- GET state of active model run job
- GET state of model run job from queue
- GET state of model run job from history
- PUT model run job into other queue position
- DELETE state of model run job from history
Administrative: manage web-service state
- POST a request to refresh models catalog
- POST a request to close models catalog
- POST a request to close model database
- POST a request to delete the model
- POST a request to open database file
- POST a request to cleanup database file
- GET the list of database cleanup log(s)
- GET database cleanup log file(s)
- POST a request to pause model run queue
- POST a request to pause all model runs queue
- PUT a request to shutdown web-service