Merge pull request #31 from simonsobs/omp_debug

Fix OpenMP dynamic linking across the environment
simonsobs · Apr 4, 2024 · 59264ce · 59264ce
2 parents da11241 + c345236
commit 59264ce
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Showing 14 changed files with 78 additions and 85 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -70,6 +70,9 @@ jobs:
           export OMP_NUM_THREADS=2 &&
           export MPI_DISABLE=1 &&
           export CI=1 &&
+          python3 -c 'import scipy; import toast' &&
+          python3 -c 'import so3g; from spt3g import core' &&
+          python3 -c 'from sotodlib import core' &&
           python3 -c 'import toast.tests; toast.tests.run()' &&
           git clone --depth=1 --single-branch --branch=master https://github.com/simonsobs/sotodlib.git &&
           pushd sotodlib &&

diff --git a/config/common.txt b/config/common.txt
@@ -13,12 +13,8 @@ packaging
 #
 # Require the OpenBLAS + OpenMP flavor of linear algebra packages
 #
-openblas=*=openmp_*
 libopenblas=*=openmp_*
 libblas=*=*openblas
-libcblas=*=*openblas
-liblapack=*=*openblas
-liblapacke=*=*openblas
 #
 # Install requirements of our local and pip packages
 #

diff --git a/pkgs/libactpol/build.sh b/pkgs/libactpol/build.sh
@@ -11,3 +11,5 @@ CFLAGS="-O3 -g -fPIC" \
 
 make
 make install
+rm -f "${PREFIX}/lib/libactpol_deps*.la"
+rm -f "${PREFIX}/lib/libarcher.so"
diff --git a/pkgs/libactpol/meta.yaml b/pkgs/libactpol/meta.yaml
@@ -14,8 +14,6 @@ source:
 build:
   number: {{ build }}
   skip: true  # [win]
-  run_exports:
-    - libactpol
 
 requirements:
   build:
@@ -27,23 +25,23 @@ requirements:
     - m4
     - libtool
   host:
-    - llvm-openmp
-    - _openmp_mutex * *_llvm
-    - libopenblas * openmp_*
-    - openblas * openmp_*
-    # This constraint is to force compatibility with the healpy package.
-    # remove once healpy is building with cfitsio-4.4.x.
-    - cfitsio <4.4.0
+    - llvm-openmp # [osx]
+    - libgomp # [linux]
+    - libopenblas * *openmp*
+    - libblas * *openblas
+    - cfitsio
     - wcslib
     - libactpol_deps
     # Remove until this perl bug is fixed
     # https://github.com/conda-forge/perl-feedstock/issues/56
     - libxcrypt1   # [linux]
   run:
     - llvm-openmp # [osx]
-    - openblas * openmp_*
-    - libopenblas * openmp_*
+    - libopenblas * *openmp*
+    - libblas * *openblas
     - {{ pin_compatible("cfitsio") }}
+    - {{ pin_compatible("libopenblas") }}
+    - {{ pin_compatible("libblas") }}
     - {{ pin_compatible("libactpol_deps") }}
     - {{ pin_compatible("wcslib") }}
 

diff --git a/pkgs/libactpol_deps/build.sh b/pkgs/libactpol_deps/build.sh
@@ -18,4 +18,5 @@ CXXFLAGS="-O3 -g -fPIC" \
 ./configure --prefix="${PREFIX}" --with-zzip
 make
 make install
+rm -f "${PREFIX}/lib/libactpol_deps*.la"
 popd
diff --git a/pkgs/libactpol_deps/meta.yaml b/pkgs/libactpol_deps/meta.yaml
@@ -14,8 +14,6 @@ source:
 build:
   number: {{ build }}
   skip: true  # [win]
-  run_exports:
-    - libactpol_deps
 
 requirements:
   build:
@@ -30,9 +28,8 @@ requirements:
   host:
     - llvm-openmp # [osx]
     - libgomp # [linux]
-    - openblas * openmp_*
-    - libopenblas * openmp_*
-    - liblapack
+    - libopenblas * *openmp*
+    - libblas * *openblas
     - zziplib
   run:
 

diff --git a/pkgs/moby2/dep_names.patch b/pkgs/moby2/dep_names.patch
diff --git a/pkgs/moby2/meta.yaml b/pkgs/moby2/meta.yaml
@@ -11,7 +11,6 @@ source:
   url: https://github.com/ACTCollaboration/moby2/archive/{{ version }}.tar.gz
   sha256: {{ sha256 }}
   patches:
-    - dep_names.patch
     - np_bool.patch
 
 build:
@@ -25,9 +24,8 @@ requirements:
   host:
     - llvm-openmp # [osx]
     - libgomp # [linux]
-    - openblas * openmp_*
-    - libopenblas * openmp_*
-    - liblapack
+    - libopenblas * *openmp*
+    - libblas * *openblas
     - python
     - fftw
     - gsl
@@ -40,16 +38,16 @@ requirements:
     - numba
   run:
     - llvm-openmp # [osx]
-    - openblas * openmp_*
-    - libopenblas * openmp_*
+    - libopenblas * *openmp*
+    - libblas * *openblas
     - {{ pin_compatible("numpy") }}
+    - {{ pin_compatible("scipy") }}
     - {{ pin_compatible("fftw") }}
-    - {{ pin_compatible("liblapack") }}
+    - {{ pin_compatible("libopenblas") }}
+    - {{ pin_compatible("libblas") }}
     - {{ pin_compatible("gsl") }}
     - {{ pin_compatible("libactpol") }}
     - python
-    - numpy
-    - scipy
     - future
     - matplotlib
     - astropy

diff --git a/pkgs/pixell/meta.yaml b/pkgs/pixell/meta.yaml
@@ -1,5 +1,5 @@
 {% set version = "0.23.8" %}
-{% set sha256 = "1f9f89193550892e8e90b95d7fccfaf57d47ff5e99b45854e95231eb5a919a4f" %}
+{% set sha256 = "b50dbc38b26543a36e8ab0f62876fcd25d573c2b78ea58e9e16b51f61ae50107" %}
 
 {% set build = 0 %}
 
@@ -29,9 +29,8 @@ requirements:
   host:
     - llvm-openmp # [osx]
     - libgomp # [linux]
-    - openblas * openmp_*
-    - libopenblas * openmp_*
-    - liblapack
+    - libopenblas * *openmp*
+    - libblas * *openblas
     - python
     - cython
     - numpy >=1.26
@@ -48,13 +47,13 @@ requirements:
     - libxcrypt1   # [linux]
   run:
     - llvm-openmp # [osx]
-    - openblas * openmp_*
-    - libopenblas * openmp_*
+    - libopenblas * *openmp*
+    - libblas * *openblas
     - {{ pin_compatible("numpy") }}
-    - {{ pin_compatible("liblapack") }}
+    - {{ pin_compatible("scipy") }}
+    - {{ pin_compatible("libopenblas") }}
+    - {{ pin_compatible("libblas") }}
     - python
-    - numpy
-    - scipy
     - astropy
     - healpy
     - matplotlib

diff --git a/pkgs/qpoint/meta.yaml b/pkgs/qpoint/meta.yaml
@@ -24,9 +24,8 @@ requirements:
   host:
     - llvm-openmp # [osx]
     - libgomp # [linux]
-    - openblas * openmp_*
-    - libopenblas * openmp_*
-    - liblapack
+    - libopenblas * *openmp*
+    - libblas * *openblas
     - python
     - setuptools
     - numpy >=1.26
@@ -39,13 +38,13 @@ requirements:
     - astropy
   run:
     - llvm-openmp # [osx]
-    - openblas * openmp_*
-    - libopenblas * openmp_*
+    - libopenblas * *openmp*
+    - libblas * *openblas
     - {{ pin_compatible("numpy") }}
-    - {{ pin_compatible("liblapack") }}
+    - {{ pin_compatible("scipy") }}
+    - {{ pin_compatible("libopenblas") }}
+    - {{ pin_compatible("libblas") }}
     - python
-    - numpy
-    - scipy
     - astropy
 
 test:

diff --git a/pkgs/so3g/build.sh b/pkgs/so3g/build.sh
@@ -2,8 +2,8 @@
 set -e
 set -x
 
-CFLAGS="-O3 -g -fPIC" \
-CXXFLAGS='-O3 -g -fPIC -std=c++14' \
+CFLAGS="-Wno-error -O3 -g -fPIC -I${PREFIX}/include" \
+CXXFLAGS="-Wno-error -O3 -g -fPIC -std=c++14 -I${PREFIX}/include" \
 BOOST_ROOT="${PREFIX}" \
 FLAC_ROOT="${PREFIX}" \
 python -m pip install -vvv --ignore-installed --no-deps --prefix "${PREFIX}" .
diff --git a/pkgs/so3g/meta.yaml b/pkgs/so3g/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "0.1.12" %}
-{% set sha256 = "7028a87fc6b4b85b1c18bc7cfbb24da90506e84c7a13186fa4d32b93855d6b41" %}
+{% set version = "0.1.13" %}
+{% set sha256 = "468b1a813fa1baf1134f7041898380b0552fe3a02f0fdbe450ac1e452bbae349" %}
 
 {% set build = 0 %}
 
@@ -13,13 +13,11 @@ source:
   patches:
     - setup_requires.patch
     - cxx_werror.patch
+    - parallel.patch
 
 build:
   number: {{ build }}
   skip: true  # [win]
-  script_env:
-    - CFLAGS=-Wno-error -O3 -g -fPIC
-    - CXXFLAGS=-Wno-error -O3 -g -fPIC -std=c++14
 
 requirements:
   build:
@@ -31,9 +29,9 @@ requirements:
   host:
     - llvm-openmp # [osx]
     - libgomp # [linux]
-    - openblas * openmp_*
-    - libopenblas * openmp_*
-    - liblapack
+    - libopenblas * *openmp*
+    - libblas * *openblas
+    - openblas * *openmp*
     - python
     - numpy >=1.26
     - scipy
@@ -47,16 +45,16 @@ requirements:
     - numba
   run:
     - llvm-openmp # [osx]
-    - openblas * openmp_*
-    - libopenblas * openmp_*
+    - libopenblas * *openmp*
+    - libblas * *openblas
     - {{ pin_compatible("numpy") }}
-    - {{ pin_compatible("liblapack") }}
+    - {{ pin_compatible("scipy") }}
+    - {{ pin_compatible("libopenblas") }}
+    - {{ pin_compatible("libblas") }}
     - {{ pin_compatible("libboost-python") }}
     - {{ pin_compatible("libboost") }}
     - {{ pin_compatible("libflac") }}
     - python
-    - numpy
-    - scipy
     - astropy
     - qpoint
     - matplotlib

diff --git a/pkgs/so3g/parallel.patch b/pkgs/so3g/parallel.patch
@@ -0,0 +1,17 @@
+diff -urN so3g-0.1.13_orig/setup.py so3g-0.1.13/setup.py
+--- so3g-0.1.13_orig/setup.py	2024-03-29 08:40:04.000000000 -0700
++++ so3g-0.1.13/setup.py	2024-04-02 22:41:13.998376523 -0700
+@@ -152,7 +152,12 @@
+     sp.check_call(["cmake", cmake_list_dir] + cmake_args, cwd=build_dir, env=env)
+
+     print("-" * 10, "Building {}".format(pkg), "-" * 40)
+-    cmake_cmd = ["cmake", "--build", "."] + build_args + ["--", "-j2"]
++    if "CPU_COUNT" in os.environ:
++        # Running in conda-build
++        parallel_args = ["--parallel", os.environ["CPU_COUNT"]]
++    else:
++        parallel_args = ["--parallel", "2"]
++    cmake_cmd = ["cmake", "--build", "."] + build_args + parallel_args
+     sp.check_call(cmake_cmd, cwd=build_dir)
+     cmake_cmd = ["cmake", "--install", "."] + build_args
+     sp.check_call(cmake_cmd, cwd=build_dir)
diff --git a/pkgs/toast/meta.yaml b/pkgs/toast/meta.yaml
@@ -11,8 +11,8 @@ package:
 source:
   url: https://github.com/hpc4cmb/toast/archive/refs/tags/{{ version }}.tar.gz
   sha256: {{ sha256 }}
-  patches:
-    - openmp_linking.patch
+  #patches:
+  #  - openmp_linking.patch
   #  - debug_lapack.patch
 
 build:
@@ -31,10 +31,8 @@ requirements:
   host:
     - llvm-openmp # [osx]
     - libgomp # [linux]
-    - openblas * openmp_*
-    - libopenblas * openmp_*
-    - libblas
-    - liblapack
+    - libopenblas * *openmp*
+    - libblas * *openblas
     - python
     - numpy >=1.26
     - scipy
@@ -44,18 +42,17 @@ requirements:
     - libflac
   run:
     - llvm-openmp # [osx]
-    - openblas * openmp_*
-    - libopenblas * openmp_*
+    - libopenblas * *openmp*
+    - libblas * *openblas
     - {{ pin_compatible("numpy") }}
+    - {{ pin_compatible("scipy") }}
     - {{ pin_compatible("fftw") }}
+    - {{ pin_compatible("libopenblas") }}
     - {{ pin_compatible("libblas") }}
-    - {{ pin_compatible("liblapack") }}
     - {{ pin_compatible("suitesparse") }}
     - {{ pin_compatible("libaatm") }}
     - {{ pin_compatible("libflac") }}
     - python
-    - numpy
-    - scipy
     - ruamel.yaml
     - matplotlib
     - astropy
@@ -65,7 +62,7 @@ requirements:
     - tomlkit
     - traitlets>=5.0
     - psutil
-    - pshmem>=1.0.4
+    - pshmem>=1.1.0
 
 test:
   imports: