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Merge pull request #191 from jtwhite79/feat_partial
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Feat partial
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@jtwhite79
jtwhite79 committed Jun 6, 2022
2 parents f9f8a06 + 0cb1d75 commit 6592d2b
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108 changes: 72 additions & 36 deletions .github/workflows/ci.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ on:
jobs:
pestppCI:
name: benchmarks
runs-on: ubuntu-latest #${{ matrix.os }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
Expand All @@ -34,11 +34,14 @@ jobs:
- { test_dir: "pestpp-ies_benchmarks", test_repo: "https://github.com/pestpp/pestpp-ies_benchmarks", test_script: "ies_test_part4.py"}
- { test_dir: "pestpp-glm_benchmarks", test_repo: "https://github.com/pestpp/pestpp-glm_benchmarks", test_script: "glm_test_base.py"}
- { test_dir: "pestpp-mou_benchmarks", test_repo: "https://github.com/pestpp/pestpp-mou_benchmarks", test_script: "mou_tests.py"}
- { test_dir: "pestpp-mou_benchmarks", test_repo: "https://github.com/pestpp/pestpp-mou_benchmarks", test_script: "mou_tests_2.py"}
#- { test_dir: "pestpp-mou_benchmarks", test_repo: "https://github.com/pestpp/pestpp-mou_benchmarks", test_script: "mou_tests_2.py"}
- { test_dir: "pestpp-mou_benchmarks", test_repo: "https://github.com/pestpp/pestpp-mou_benchmarks", test_script: "henry_test.py"}
- { test_dir: "pestpp-da_benchmarks", test_repo: "https://github.com/pestpp/pestpp-da_benchmarks", test_script: "da_tests.py"}
- { test_dir: "pestpp-da_benchmarks", test_repo: "https://github.com/pestpp/pestpp-da_benchmarks", test_script: "lorenz96_tests.py"}
- { test_dir: "pestpp-sqp_benchmarks", test_repo: "https://github.com/pestpp/pestpp-sqp_benchmarks", test_script: "sqp_tests.py"}
include:
- os: ubuntu-latest
env: { test_dir: "pestpp-mou_benchmarks", test_repo: "https://github.com/pestpp/pestpp-mou_benchmarks", test_script: "mou_tests_2.py"}
env: ${{ matrix.env }}

steps:
Expand All @@ -61,49 +64,53 @@ jobs:
if: runner.os == 'Windows'
uses: ilammy/msvc-dev-cmd@v1

# - name: Get specific version CMake, v3.19
# if: ${{ runner.os == 'Windows' }}
# uses: lukka/get-cmake@latest

- name: clone test repo ${{ env.test_repo }}
shell: bash -l {0}
run: |
git clone ${{ env.test_repo }}
- name: PESTPP exe install
shell: bash -l {0}
run: |
mkdir build && cd build
if [[ "$RUNNER_OS" == "Windows" ]]; then
cmake -GNinja -DCMAKE_CXX_COMPILER=cl -DCMAKE_C_COMPILER=cl -DCMAKE_BUILD_TYPE=Release ..
ninja
else
cmake -DCMAKE_BUILD_TYPE=Release ..
make -j2
fi
cd ..


# Standard python fails on windows without GDAL installation
# Using custom bash shell ("shell: bash -l {0}") with Miniconda
- name: Setup Miniconda
uses: conda-incubator/setup-miniconda@v2.0.0
uses: conda-incubator/setup-miniconda@v2
with:
# python-version: ${{ matrix.python-version }}
# #mamba-version: "0.20.0"
# channels: conda-forge
# auto-update-conda: true
# activate-environment: pyemu
# use-only-tar-bz2: true
miniforge-version: latest
# miniconda-version: "latest"
python-version: ${{ matrix.python-version }}
mamba-version: "0.20.0"
channels: conda-forge
auto-update-conda: true
# mamba-version: "*"
# channels: conda-forge
miniforge-variant: Mambaforge
# auto-update-conda: true
activate-environment: pyemu
use-only-tar-bz2: true
use-mamba: true
# environment-file: etc/environment.yml
# use-only-tar-bz2: true

# - name: Add packages to pyemu environment using mamba or conda
# shell: bash -l {0}
# run: |
# if [ "$RUNNER_OS" == "Windows" ]; then
# conda env update --name pyemu --file etc/environment.yml
# else
# conda env update --name pyemu --file etc/environment.yml
# fi

- name: Add packages to pyemu environment using mamba or conda
- name: Add packages to pyemu environment using conda
if: ${{ matrix.python-version < 3.8 }}
# if: ${{ runner.os == 'Windows' || matrix.python-version < 3.8 }}
shell: bash -l {0}
run: |
if [ "$RUNNER_OS" == "Windows" ]; then
conda env update --name pyemu --file etc/environment.yml
else
conda env update --name pyemu --file etc/environment.yml
fi
- name: Add packages to pyemu environment using mamba
# if: ${{ runner.os != 'Windows' && matrix.python-version >= 3.8 }}
if: ${{ matrix.python-version >= 3.8 }}
shell: bash -l {0}
run: |
mamba env update --name pyemu --file etc/environment.yml
- name: Install Flopy & pyemu?
shell: bash -l {0}
Expand All @@ -117,24 +124,53 @@ jobs:
cd pyemu
python setup.py install
cd ..
# - name: Get specific version CMake, v3.19
# if: ${{ runner.os == 'Windows' }}
# uses: lukka/get-cmake@latest

- name: clone test repo ${{ env.test_repo }}
shell: bash -l {0}
run: |
git clone ${{ env.test_repo }}
- name: PESTPP exe install
shell: bash -l {0}
run: |
mkdir build && cd build
if [[ "$RUNNER_OS" == "Windows" ]]; then
cmake -GNinja -DCMAKE_CXX_COMPILER=cl -DCMAKE_C_COMPILER=cl -DCMAKE_BUILD_TYPE=Release ..
ninja
else
cmake -DCMAKE_BUILD_TYPE=Release ..
make -j2
fi
cd ..
- name: aux bin path hackery
shell: bash -l {0}
run: |
cp -r benchmarks/test_bin/win $HOME/bin
echo "../../test_bin/win" >> $GITHUB_PATH
if [[ "$RUNNER_OS" == "Windows" ]]; then
echo "..\..\test_bin\win" >> $GITHUB_PATH
cp -r benchmarks/test_bin/win $HOME/bin
echo "../../test_bin/win" >> $GITHUB_PATH
else
echo "../../test_bin/linux" >> $GITHUB_PATH
cp -r benchmarks/test_bin/win $HOME/bin
fi
echo "$HOME/.local/bin" >> $GITHUB_PATH
- name: run test script ${{ env.test_script }} in ${{ env.test_dir }}
shell: bash -l {0}
run: |
ls -l
cd ${{ env.test_dir }}
nosetests -v ${{ env.test_script }}
cd



49 changes: 38 additions & 11 deletions benchmarks/basic_tests.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -733,6 +733,10 @@ def tplins1_test():
jco = pyemu.Jco.from_binary(os.path.join(t_d,"pest.jcb")).to_dataframe().apply(np.abs)
assert jco.sum().sum() == 0, jco.sum()

pst.control_data.noptmax = 0
pst.write(os.path.join(t_d,"pest.pst"))
pyemu.os_utils.run("{0} pest.pst".format(exe_path.replace("-ies","-glm")),cwd=t_d)

# check the input file - the last two number should be the same
arr = np.loadtxt(os.path.join(t_d,"hk_Layer_1.ref"))
assert arr[-2] == arr[-1],arr[-2] - arr[-1]
Expand All @@ -742,6 +746,7 @@ def tplins1_test():
assert len(lines_tpl) - 1 == len(lines_in)

pst = pyemu.Pst(os.path.join(t_d,"pest.pst"))
pst.control_data.noptmax = -1
pst.pestpp_options["fill_tpl_zeros"] = True
pst.write(os.path.join(t_d,"pest_fill.pst"))
pyemu.os_utils.run("{0} pest_fill.pst".format(exe_path.replace("-ies","-glm")),cwd=t_d)
Expand All @@ -758,6 +763,10 @@ def tplins1_test():
jco = pyemu.Jco.from_binary(os.path.join(t_d,"pest_fill.jcb")).to_dataframe().apply(np.abs)
assert jco.sum().sum() == 0, jco.sum()

pst.control_data.noptmax = 0
pst.write(os.path.join(t_d,"pest.pst"))
pyemu.os_utils.run("{0} pest.pst".format(exe_path.replace("-ies","-glm")),cwd=t_d)

# check the input file - the last two number should be the same
arr = np.loadtxt(os.path.join(t_d,"hk_Layer_1.ref"))
assert arr[-2] == arr[-1]
Expand All @@ -773,6 +782,7 @@ def tplins1_test():
pst.model_output_data = pd.DataFrame({"pest_file":"out1dum.dat.ins",
"model_file":'out1.dat'},index=["out1dum.dat.ins"])
#pst.instruction_files = ['out1dum.dat.ins']
pst.control_data.noptmax = -1
pst.write(os.path.join(t_d, "pest_dum.pst"))
pyemu.os_utils.run("{0} pest_dum.pst".format(exe_path.replace("-ies", "-glm")), cwd=t_d)
obf_df = pd.read_csv(os.path.join(t_d, "out1.dat.obf"), delim_whitespace=True, header=None,
Expand Down Expand Up @@ -872,6 +882,20 @@ def mf6_v5_ies_test():
pyemu.os_utils.run("{0} freyberg6_run_ies.pst".format(exe_path),cwd=t_d)

pst.control_data.noptmax = 3

m_d = os.path.join(model_d, "master_ies_glm_noloc_standard")
if os.path.exists(m_d):
shutil.rmtree(m_d)
pst = pyemu.Pst(os.path.join(t_d, "freyberg6_run_ies.pst"))
pst.pestpp_options.pop("ies_localizer",None)
pst.pestpp_options.pop("ies_autoadaloc",None)
pst.pestpp_options["ies_bad_phi_sigma"] = 2.5
pst.control_data.noptmax = 3
pst.write(os.path.join(t_d, "freyberg6_run_ies_glm_noloc_standard.pst"))
pyemu.os_utils.start_workers(t_d, exe_path, "freyberg6_run_ies_glm_noloc_standard.pst", num_workers=15,
master_dir=m_d, worker_root=model_d, port=port)

return
pst.write(os.path.join(t_d,"freyberg6_run_ies_glm_loc.pst"))

m_d = os.path.join(model_d, "master_ies_glm_covloc")
Expand Down Expand Up @@ -1106,7 +1130,7 @@ def fr_fail_test():
assert not os.path.exists(oe_file)
m_d = os.path.join(model_d,"fr_fail_master")
try:
pyemu.os_utils.start_workers(new_d,exe_path,"pest.pst",num_workers=1,worker_root=model_d,master_dir=m_d)
pyemu.os_utils.start_workers(new_d,exe_path,"pest.pst",num_workers=5,worker_root=model_d,master_dir=m_d)
except:
pass
else:
Expand Down Expand Up @@ -1175,29 +1199,29 @@ def fr_timeout_test():
f.write("import os\nimport time\nimport pyemu\npyemu.os_utils.run('mfnwt 10par_xsec.nam')\n")
f.write("if not os.path.exists('run.info'):\n exit()\n")
f.write("lines = open('run.info','r').readlines()\nrnum = int(lines[-1].split()[-1].split('=')[-1])\n")
f.write("if rnum % 2 == 0:\n time.sleep(100000)\n")
f.write("if rnum % 2 == 0:\n time.sleep(10000000)\n")
pst.model_command = "python run.py"
oe_file = os.path.join(new_d, "pest.0.obs.csv")
if os.path.exists(oe_file):
os.remove(oe_file)
pst.control_data.noptmax = -1
pst.pestpp_options["overdue_giveup_fac"] = 1.0e+10
pst.pestpp_options["overdue_giveup_minutes"] = 0.1
pst.pestpp_options["overdue_giveup_minutes"] = 0.25
pst.pestpp_options["ies_num_reals"] = 10
pst.pestpp_options["ies_include_base"] = False
pst.pestpp_options["max_run_fail"] = 1

#pst.pestpp_options["panther_transfer_on_fail"] = "10par_xsec.list"
pst.pestpp_options["panther_agent_freeze_on_fail"] = True
pst.pestpp_options["panther_agent_freeze_on_fail"] = False
pst.write(os.path.join(new_d, "pest.pst"))
pyemu.os_utils.run("{0} pest.pst".format(exe_path),cwd=new_d)

assert os.path.exists(oe_file)
m_d = os.path.join(model_d,"fr_timeout_master")
pyemu.os_utils.start_workers(new_d,exe_path,"pest.pst",num_workers=1,worker_root=model_d,master_dir=m_d)
pyemu.os_utils.start_workers(new_d,exe_path,"pest.pst",num_workers=5,worker_root=model_d,master_dir=m_d)
oe_file = os.path.join(m_d, "pest.0.obs.csv")
assert os.path.exists(oe_file)
oe = pd.read_csv(oe_file,index_col=0)
print(oe.shape)
assert oe.shape[0] == 4
assert oe.shape[0] == 5,oe.shape

def ins_missing_e_test():
import os
Expand Down Expand Up @@ -1248,7 +1272,7 @@ def ins_missing_e_test():
#salib_verf()
#tplins1_test()
#secondary_marker_test()
ext_stdcol_test()
#ext_stdcol_test()

# parallel_consist_test()
# ext_stdcol_test()
Expand All @@ -1261,17 +1285,20 @@ def ins_missing_e_test():

#da_prep_4_mf6_freyberg_seq_tbl()
#da_mf6_freyberg_test_2()
#shutil.copy2(os.path.join("..","exe","windows","x64","Debug","pestpp-ies.exe"),os.path.join("..","bin","win","pestpp-ies.exe"))
shutil.copy2(os.path.join("..","exe","windows","x64","Debug","pestpp-ies.exe"),os.path.join("..","bin","win","pestpp-ies.exe"))
#tplins1_test()
#mf6_v5_ies_test()
#mf6_v5_sen_test()



#shutil.copy2(os.path.join("..","exe","windows","x64","Debug","pestpp-opt.exe"),os.path.join("..","bin","win","pestpp-opt.exe"))
#mf6_v5_opt_stack_test()
#mf6_v5_glm_test()
#mf6_v5_ies_test()
#cmdline_test()
#basic_sqp_test()
#mf6_v5_ies_test()
#fr_timeout_test()
fr_timeout_test()
#fr_fail_test()
#tplins1_test()
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