feat: Adding error YAML file in GEOS #3828

MelReyCG · 2025-09-23T15:27:21Z

This PR aims to provide a file that stores warnings and errors regarding input data that occur during the current execution.

To do this, I created a class called ErrorLogger that retrieves, formats, and sends the desired information to a YAML file.
I also have (in the Logger.hpp file) two macros for each of the following cases:

Warning
Error
Throw

For each of these cases, one of these macro allows to attach contextual information about the error/warning.
Each of the macros is based on the ErrorLogger class.

- type: Exception
    rank: 0
    message: >-
      compositionalMultiphaseWell (simpleCo2Inj_inc_erreurTable.xml, l.34): wrong surface pressure / temperature.
      Table input error for water phase (in table from "/path/to/randomExemple/pvtliquid_erreur.txt").
      /Functions(simpleCo2Inj_inc_erreurTable.xml,l.203)/fluid_phaseModel1_PhillipsBrineDensity_table:
      Requested pressure of 101325 [Pa] is out of the table bounds
      ( lower bound: pressure of 10000000 [Pa] -> upper bound: pressure of 75000000 [Pa] ).
    contexts:
      - dataPath: /Functions(simpleCo2Inj_inc_erreurTable.xml,l.203)/fluid_phaseModel1_PhillipsBrineDensity_table
        priority: 0
      - dataPath: /domain/MeshBodies/cartesianMesh/meshLevels/Level0/ElementRegions/elementRegionsGroup/
                  wellRegion(simpleCo2Inj_inc_erreurTable.xml,l.64)/elementSubRegions/wellRegionUniqueSubRegion/
                  ConstitutiveModels/fluid
        priority: 2
      - inputFile: /path/to/randomExemple/simpleCo2Inj_inc_erreurTable.xml
        inputLine: 34
        priority: 1
    sourceLocation:
      file: /path/to/GEOS/src/coreComponents/functions/TableFunction.cpp
      line: 191
    sourceCallStack:
      - frame0:  geos::constitutive::PVTProps::PhillipsBrineDensity::checkTablesParameters(double, double) const 
      - frame1:  geos::constitutive::CO2BrineFluid::checkTablesParameters(double, double) const 
      - frame2:  geos::CompositionalMultiphaseWell::validateWellControlsForFluid() const 
      - frame3:  geos::CompositionalMultiphaseWell::validateConstitutiveModels(geos::DomainPartition const&) const 
      - frame4:  geos::CompositionalMultiphaseWell::initializePostSubGroups() 
      - frame5:  geos::dataRepository::Group::initialize()
      []

This PR is a duplicate ( #3690 ) and has been created because it was not possible to run the CI on external branches for security reasons.
Code review has been started on the old PR.

Note that future PRs are planned for:

Signals & external errors ( feat: Adding signal and external error detection & output #3856 )
DataContext referencing redundancy
Improving error log text formatting & unifying it with YAML output
Re-throwing exceptions with macros

…file

…necessary

… link between GEOS_THROW_CTX_IF and LVARRAY_THROW_IF_TEST( EXP, MSG, TYPE )

… in try/catch statements Problem: Retrieves everything that was thrown, so not just the message.

…/catch in main)": remove useless try/catch

…y spaces. The previous condition checked whether an argument was present and whether the option was immediately followed by a value like -test"value", which excluded valid cases like -test "value" et -test "value".

…t is expected.

…e CI does not like explicit 'common' dependency for 'physicsSolver' package)

MelReyCG · 2025-10-15T11:35:07Z

This PR seems to be blocked because of lack of space for the Ubuntu debug CI target

-- Set non-toolchain portion of runtime path of "/opt/GEOS/GEOS-b124508/lib/libwavePropagationSolvers.so" to "/opt/GEOS/GEOS-b124508/lib:/opt/GEOS/GEOS_TPL-320-766-c9a8986/gcc-10/vtk-9.4.2-vqvxywyhmuq3l47o5o4a6rlolhvvlbtg/lib:/opt/GEOS/GEOS_TPL-320-766-c9a8986/gcc-10/caliper-git.287b7f3ad2d12f520aad04268d44f353cd05403c_2.12.0-vpteto4r76bzi6i4i4qdsucx667ehjau/lib:/usr/lib/x86_64-linux-gnu/openmpi/lib:/opt/GEOS/GEOS_TPL-320-766-c9a8986/gcc-10/suite-sparse-5.10.1-pjcexvgnnyljjis4mt7gzpjjxnshhwst/lib:/opt/GEOS/GEOS_TPL-320-766-c9a8986/gcc-10/superlu-dist-git.0f6efc377df2440c235452d13d28d2c717f832a1_6.3.0-git.8-kkfnl3zx64cudbkbcyyjgm2jp5rfcsdn/lib:/usr/lib/x86_64-linux-gnu/blas:/usr/lib/x86_64-linux-gnu/lapack:/opt/GEOS/GEOS_TPL-320-766-c9a8986/gcc-10/trilinos-16.1.0-fec6c7ojutdmnaukulm3nokmqripbhv4/lib"
-- Installing: /opt/GEOS/GEOS-b124508/lib/libmultiPhysicsSolvers.so
CMake Error at coreComponents/physicsSolvers/multiphysics/cmake_install.cmake:60 (file):
  file INSTALL cannot copy file
  "/tmp/geos-build/lib/libmultiPhysicsSolvers.so" to
  "/opt/GEOS/GEOS-b124508/lib/libmultiPhysicsSolvers.so": No space left on
  device.
Call Stack (most recent call first):
  coreComponents/physicsSolvers/cmake_install.cmake:108 (include)
  coreComponents/cmake_install.cmake:137 (include)
  cmake_install.cmake:62 (include)

Can someone help?

wrtobin · 2025-10-16T14:17:28Z

@rrsettgast the ubuntu-debug build in the CI for this PR is running out of space for the install into /opt in the container.
does streak need cleanup, or do we need to increase the disk quota available to the containers to use? I would assume the latter offhand, but I'm not seeing any specification of disk quota in the TPL repo dockerfiles, is it a parameter on streak itself?

…y/create-yaml-file-and-structure-2

rrsettgast · 2025-10-21T17:48:46Z

@rrsettgast the ubuntu-debug build in the CI for this PR is running out of space for the install into /opt in the container. does streak need cleanup, or do we need to increase the disk quota available to the containers to use? I would assume the latter offhand, but I'm not seeing any specification of disk quota in the TPL repo dockerfiles, is it a parameter on streak itself?

This appears to be a GitHub runner??

wrtobin · 2025-10-21T17:54:38Z

@rrsettgast the ubuntu-debug build in the CI for this PR is running out of space for the install into /opt in the container. does streak need cleanup, or do we need to increase the disk quota available to the containers to use? I would assume the latter offhand, but I'm not seeing any specification of disk quota in the TPL repo dockerfiles, is it a parameter on streak itself?

This appears to be a GitHub runner??

I managed to totally miss that, yeah. You have any idea where/whether the limitations on the github-hosted runners are specified/set?

rrsettgast · 2025-10-21T17:55:35Z

@rrsettgast the ubuntu-debug build in the CI for this PR is running out of space for the install into /opt in the container. does streak need cleanup, or do we need to increase the disk quota available to the containers to use? I would assume the latter offhand, but I'm not seeing any specification of disk quota in the TPL repo dockerfiles, is it a parameter on streak itself?

This appears to be a GitHub runner??

I managed to totally miss that, yeah. You have any idea where/whether the limitations on the github-hosted runners are specified/set?

14 GB

wrtobin · 2025-10-21T17:57:15Z

It is also seemingly only failing on the install, where we copy the libs/headers on the system, so the build isn't breaking the quota, just the copy. If we were fine without the make install invocation (say on just the debug builds which are necessarily much larger) we could bypass it that way?

rrsettgast · 2025-10-21T19:15:44Z

@MelReyCG
perhaps don't run the install for debug builds.

wrtobin · 2025-10-21T19:19:04Z

@MelReyCG

https://github.com/GEOS-DEV/GEOS/blob/develop/scripts/ci_build_and_test_in_container.sh#L285

…y/create-yaml-file-and-structure-2

…structure-2

herve-gross · 2025-10-29T15:59:17Z

@jhuang2601 can you review the solid portion of this PR (6 files)? @MelReyCG is stuck on this and would like to merge this PR soon.

…y/create-yaml-file-and-structure-2

paveltomin · 2025-11-04T20:48:48Z

src/coreComponents/dataRepository/Group.cpp

  GEOS_ERROR_IF( !hasWrapper( name ),
-                 "Wrapper " << name << " doesn't exist in Group" << getDataContext() << '.' );
+                 "Wrapper " << name << " doesn't exist in Group" << getDataContext() << '.',
+                 getDataContext() );


@MelReyCG getDataContext() appears twice?

Don't worry you already made this feedback and we will address it, we will remove all these redondancies in a future PR soon :)

amandinehry added 30 commits April 25, 2025 17:05

creation of an object header that logs errors and warnings in a yaml …

c846586

…file

Set up ErrorHandling

f1713fa

traits errors commented (to treat)

4e5250f

Set up test

94b775c

Modification to properly format the yaml so that it can be parsed if …

1cb8aa3

…necessary

Test to add variadic arguments

9d5e16a

draft: retrieve data contexts info

2f7660c

Added additional information in the yaml - not functional missing the…

6036551

… link between GEOS_THROW_CTX_IF and LVARRAY_THROW_IF_TEST( EXP, MSG, TYPE )

First attempt at outputting exceptions

46b4904

Complete: code for outputting errors into yaml

e1aed93

Manage the text contained in the potential exception

bc953be

First attempt: Handling the text contained in the potential exception…

1a434bc

… in try/catch statements Problem: Retrieves everything that was thrown, so not just the message.

Complete: yaml output for PVT tables error

acf4d99

YAML error message well formatted

ee58884

Fix duplication error

32a0237

Add variadic parameters to GEOS_THROW_CTX_IF

589270f

Reorganization after operational tests

9b65581

Apply the output error functionality in yaml to all geos errors

b13f0a6

Latest update for exception handling (try/catch in main)

6de2c6a

Add priority to the error message into the yaml file

5830aee

Update of the commit named "latest update for exception handling (try…

2b27c41

…/catch in main)": remove useless try/catch

set priority

86f793e

errors cli modification: add --errors-output

8a8117e

errors cli modification: add --errors-output

2c0f5aa

Replace original macros

eb2f691

Correction: replace original macros

7b5f293

Reacting with the command line option -e / --errors-output

670ddfa

Add the rank on which the error is catch for error and warning outputs

d08a30f

Unit test to check if the contents of the yaml file match exactly wha…

5a6c1a0

…t is expected.

⏪ revert geos::logger::internal variables->functions refactor (becaus…

b124508

…e CI does not like explicit 'common' dependency for 'physicsSolver' package)

Merge remote-tracking branch 'origin/develop' into feature/amandinehr…

b1fdcf9

…y/create-yaml-file-and-structure-2

💚 removing "make install" in ci jobs

8cd54ab

jhuang2601 unassigned MelReyCG and amandinehry Oct 22, 2025

MelReyCG assigned MelReyCG and amandinehry and unassigned amandinehry Oct 23, 2025

MelReyCG mentioned this pull request Oct 23, 2025

feat: Missed std::map #3877

Merged

MelReyCG and others added 4 commits October 23, 2025 10:27

Merge remote-tracking branch 'origin/develop' into feature/amandinehr…

fa283db

…y/create-yaml-file-and-structure-2

📦 schema

5579881

💡 TODO reenable cmake install

7f11fbb

Merge branch 'develop' into feature/amandinehry/create-yaml-file-and-…

316214c

…structure-2

acitrain approved these changes Oct 29, 2025

View reviewed changes

jhuang2601 approved these changes Oct 29, 2025

View reviewed changes

MelReyCG added 3 commits October 31, 2025 09:47

Merge remote-tracking branch 'origin/develop' into feature/amandinehr…

4652188

…y/create-yaml-file-and-structure-2

Merge remote-tracking branch 'origin/develop' into feature/amandinehr…

cee4cad

…y/create-yaml-file-and-structure-2

⏪ revert file

57696b2

MelReyCG merged commit 889ea4e into develop Nov 4, 2025
23 of 24 checks passed

MelReyCG deleted the feature/amandinehry/create-yaml-file-and-structure-2 branch November 4, 2025 16:23

paveltomin reviewed Nov 4, 2025

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