From dfb2cdc6a52f474a5b4c258c414dc2c49e7d15ca Mon Sep 17 00:00:00 2001 From: Sevy Harris Date: Wed, 26 Feb 2025 10:12:30 -0500 Subject: [PATCH 1/4] require a more recent version of mkl for Cantera --- environment.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/environment.yml b/environment.yml index 2b9c4bd551..44ce193aaf 100644 --- a/environment.yml +++ b/environment.yml @@ -105,6 +105,11 @@ dependencies: # configure packages to use OpenBLAS instead of Intel MKL - blas=*=openblas +# except that Cantera is configured to use Intel MKL, so we have to make sure its version is recent +# but if we can switch over to the conda-forge version, we should be able to remove this line because it +# depends on OpenBLAS instead + - conda-forge::mkl >=2023.1.0 + # additional packages that are required, but not specified here (and why) # pydqed, pydas, mopac, and likely others require a fortran compiler (specifically gfortran) # in the environment. Normally we would add this to the environment file with From d45e26bfcf22ab2ed4e2ba64ce0f8d90b5cb5722 Mon Sep 17 00:00:00 2001 From: Sevy Harris Date: Wed, 26 Feb 2025 14:02:55 -0500 Subject: [PATCH 2/4] add libcurl version to avoid Julia bug --- environment.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/environment.yml b/environment.yml index 44ce193aaf..cd9817f059 100644 --- a/environment.yml +++ b/environment.yml @@ -109,6 +109,7 @@ dependencies: # but if we can switch over to the conda-forge version, we should be able to remove this line because it # depends on OpenBLAS instead - conda-forge::mkl >=2023.1.0 + - conda-forge::libcurl <= 8.9 # this is because of a Julia bug associated with libcurl 8.10+ # additional packages that are required, but not specified here (and why) # pydqed, pydas, mopac, and likely others require a fortran compiler (specifically gfortran) From 1c8443e655307a8cf5c8739b69511d0be1be995f Mon Sep 17 00:00:00 2001 From: Sevy Harris Date: Wed, 26 Feb 2025 15:41:45 -0500 Subject: [PATCH 3/4] add pyopenssl version constraint --- environment.yml | 1 + test/rmgpy/rmg/inputTest.py | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index cd9817f059..9965541b29 100644 --- a/environment.yml +++ b/environment.yml @@ -110,6 +110,7 @@ dependencies: # depends on OpenBLAS instead - conda-forge::mkl >=2023.1.0 - conda-forge::libcurl <= 8.9 # this is because of a Julia bug associated with libcurl 8.10+ + - conda-forge::pyopenssl >20 # additional packages that are required, but not specified here (and why) # pydqed, pydas, mopac, and likely others require a fortran compiler (specifically gfortran) diff --git a/test/rmgpy/rmg/inputTest.py b/test/rmgpy/rmg/inputTest.py index 95f53addea..01a5fa21b1 100644 --- a/test/rmgpy/rmg/inputTest.py +++ b/test/rmgpy/rmg/inputTest.py @@ -117,7 +117,7 @@ def test_ml_estimator(self): assert isinstance(rmg.ml_settings, dict) -class TestInputThemoCentralDatabase: +class TestInputThermoCentralDatabase: """ Contains unit tests rmgpy.rmg.input.thermo_central_database """ @@ -127,7 +127,7 @@ def teardown_class(self): global rmg rmg.thermo_central_database = None - def test_themo_central_database(self): + def test_thermo_central_database(self): """ Test that we can input. """ From fc5f4ab772ab38946c8cf852b74e5bfa741a4810 Mon Sep 17 00:00:00 2001 From: Sevy Harris Date: Thu, 27 Feb 2025 07:59:44 -0500 Subject: [PATCH 4/4] improve comments on mkl version requirements --- environment.yml | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/environment.yml b/environment.yml index 9965541b29..39ca25e1d9 100644 --- a/environment.yml +++ b/environment.yml @@ -105,12 +105,17 @@ dependencies: # configure packages to use OpenBLAS instead of Intel MKL - blas=*=openblas -# except that Cantera is configured to use Intel MKL, so we have to make sure its version is recent -# but if we can switch over to the conda-forge version, we should be able to remove this line because it -# depends on OpenBLAS instead +# Cantera 2.6 on the Cantera channel is configured to use Intel MKL. It doesn't specify a version minimum +# but crashes if MKL is too old, so we have to enforce a minimum version here. But, if we can switch over +# to the conda-forge version, we should be able to remove this line (and maybe the two after it) +# because it use OpenBLAS instead. - conda-forge::mkl >=2023.1.0 - - conda-forge::libcurl <= 8.9 # this is because of a Julia bug associated with libcurl 8.10+ + # 2023.1.0 is just a guess at the minimum version. Older versions might work too. + - conda-forge::libcurl <= 8.9 + # There's a Julia/PyCall installation bug associated with libcurl 8.10+: + # https://discourse.julialang.org/t/curl-multi-assign-and-segmentation-fault-when-installing-package/120901/3 - conda-forge::pyopenssl >20 + # ThermoCentralDatabaseInterface fails if pyopenssl is too old. 20 is just a guess at the version number. # additional packages that are required, but not specified here (and why) # pydqed, pydas, mopac, and likely others require a fortran compiler (specifically gfortran)