From 7f87c93a403f46c44405fd320a75748b6eb7e201 Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Mon, 15 Feb 2021 21:40:27 +0100
Subject: [PATCH] [T] Removed Parsl example test.
We currently stick to Snakemake.
---
Applications/Utils/ExtractBoundary.py | 95 ---------------------------
Applications/Utils/Tests.cmake | 13 +---
scripts/cmake/Find.cmake | 1 -
scripts/cmake/PythonSetup.cmake | 7 --
web/data/versions.json | 1 -
5 files changed, 1 insertion(+), 116 deletions(-)
delete mode 100644 Applications/Utils/ExtractBoundary.py
diff --git a/Applications/Utils/ExtractBoundary.py b/Applications/Utils/ExtractBoundary.py
deleted file mode 100644
index 1ca93ddb0a9..00000000000
--- a/Applications/Utils/ExtractBoundary.py
+++ /dev/null
@@ -1,95 +0,0 @@
-# Usage, e.g.:
-# python3 ExtractBoundary.py ./buildinfo.yaml
-#
-# buildinfo.yaml contains variables such as Data_BINARY_DIR
-
-import os, parsl, sys, yaml
-from parsl import python_app, bash_app
-from parsl.data_provider.files import File
-
-output_path = "FileIO"
-elem_types = ["tri", "quad"]
-
-parsl.load()
-
-config = dict()
-with open(sys.argv[1]) as f:
- config = yaml.safe_load(f)
-
-os.environ["PATH"] += os.pathsep + os.pathsep.join([config["BIN_DIR"]])
-os.chdir(f"{config['Data_BINARY_DIR']}/{output_path}")
-
-print(f"{config['Data_BINARY_DIR']}/{output_path}")
-
-
-# Apps
-@bash_app
-def generate_meshes(
- elem_type, outputs=[], stderr=parsl.AUTO_LOGNAME, stdout=parsl.AUTO_LOGNAME
-):
- return f"""generateStructuredMesh -e {elem_type} \
- --lx 1 --ly 1 \
- --nx 10 --ny 10 \
- -o input_square_1x1_{elem_type}.vtu"""
-
-
-@bash_app
-def extract_boundary(
- elem_type,
- inputs=[],
- outputs=[],
- stderr=parsl.AUTO_LOGNAME,
- stdout=parsl.AUTO_LOGNAME,
-):
- return f"""ExtractBoundary -i {inputs[0].filepath} \
- -o square_1x1_{elem_type}_boundary.vtu"""
-
-
-# compares the files in inputs[0] and inputs[1]
-@bash_app
-def vtk_diff(
- fields, inputs=[], outputs=[], stderr=parsl.AUTO_LOGNAME, stdout=parsl.AUTO_LOGNAME
-):
- import os
-
- script = ""
- if os.path.exists(outputs[0]):
- os.remove(outputs[0])
- for field in fields:
- field_a = field[0]
- offset = 0
- if len(field) == 4:
- offset = 1
- field_b = field[0 + offset]
- abs_tol = field[1 + offset]
- rel_tol = field[2 + offset]
-
- script += f"""vtkdiff {inputs[0]} {inputs[1]} \
- -a {field_a} -b {field_b} \
- --abs {abs_tol} --rel {rel_tol} >> {outputs[0]}
- """
- return script
-
-
-# Workflow
-for elem_type in elem_types:
- gm = generate_meshes(elem_type, outputs=[File(f"input_square_1x1_{elem_type}.vtu")])
- eb = extract_boundary(
- elem_type,
- inputs=[gm.outputs[0]],
- outputs=[File(f"square_1x1_{elem_type}_boundary.vtu")],
- )
- diff = vtk_diff(
- fields=[
- # second field name can be omitted if identical
- ["bulk_node_ids", 0, 0],
- ["bulk_element_ids", 0, 0],
- ["bulk_face_ids", 0, 0],
- ],
- inputs=[
- eb.outputs[0],
- f"{config['Data_SOURCE_DIR']}/{output_path}/{eb.outputs[0].filename}",
- ],
- outputs=[File(f"square_1x1_{elem_type}_boundary_diff.out")],
- )
- print(diff.result())
diff --git a/Applications/Utils/Tests.cmake b/Applications/Utils/Tests.cmake
index 7f7fe8e6795..6c5ab390489 100644
--- a/Applications/Utils/Tests.cmake
+++ b/Applications/Utils/Tests.cmake
@@ -307,18 +307,7 @@ if(SNAKEMAKE AND NOT OGS_USE_MPI)
-s ${CMAKE_CURRENT_SOURCE_DIR}/ExtractBoundary.smk
)
endif()
-if(PARSL AND NOT OGS_USE_MPI)
- add_test(NAME parsl_ExtractBoundary
- COMMAND ${Python3_EXECUTABLE}
- ${CMAKE_CURRENT_SOURCE_DIR}/ExtractBoundary.py
- ${PROJECT_BINARY_DIR}/buildinfo.yaml
- )
- if(SNAKEMAKE)
- # Prevent race-condition with snakemake test
- set_tests_properties(parsl_ExtractBoundary PROPERTIES DEPENDS snakemake_ExtractBoundary)
- endif()
-endif()
-if(SNAKEMAKE OR PARSL)
+if(SNAKEMAKE)
add_dependencies(ctest ExtractBoundary)
endif()
diff --git a/scripts/cmake/Find.cmake b/scripts/cmake/Find.cmake
index f49ae383344..3dcb6f4f3dc 100644
--- a/scripts/cmake/Find.cmake
+++ b/scripts/cmake/Find.cmake
@@ -54,7 +54,6 @@ find_program(PANDOC_CITEPROC pandoc-citeproc)
find_program(MODULE_CMD lmod PATHS /software/lmod/lmod/libexec)
find_program(SNAKEMAKE snakemake HINTS ${LOCAL_VIRTUALENV_BIN_DIRS})
-find_program(PARSL parsl-visualize HINTS ${LOCAL_VIRTUALENV_BIN_DIRS})
find_program(GMSH gmsh)
diff --git a/scripts/cmake/PythonSetup.cmake b/scripts/cmake/PythonSetup.cmake
index 7e2dbe63a86..9c681984790 100644
--- a/scripts/cmake/PythonSetup.cmake
+++ b/scripts/cmake/PythonSetup.cmake
@@ -45,13 +45,6 @@ set(LOCAL_VIRTUALENV_BIN_DIRS
if(POETRY)
if(BUILD_TESTING)
list(APPEND PYTHON_PACKAGES snakemake=${ogs.minimum_version.snakemake})
- if(NOT WIN32)
- # Parsl is not supported on Windows yet
- # https://github.com/Parsl/parsl/issues/1878
- list(APPEND PYTHON_PACKAGES parsl=${ogs.minimum_version.parsl}
- asn1crypto # module dep of crypthography is missing on CI Linux
- )
- endif()
endif()
execute_process(COMMAND ${CMD_COMMAND} poetry add ${PYTHON_PACKAGES}
WORKING_DIRECTORY ${PROJECT_BINARY_DIR})
diff --git a/web/data/versions.json b/web/data/versions.json
index 1e8d67359e9..51e4de5824d 100644
--- a/web/data/versions.json
+++ b/web/data/versions.json
@@ -20,7 +20,6 @@
"qt": "5.14.2",
"python": "3.6",
"snakemake": "5.27.4",
- "parsl": "1.0.0",
"hdf5": "1.10.5"
},
"tested_version": {
--
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