Tweak GitHub actions

.github/workflows/basic-tests.yml

@@ -4,7 +4,7 @@ on: [push, pull_request]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: false
 
 jobs:
   build:
@@ -15,6 +15,7 @@ jobs:
         os: [ubuntu-20.04]
         python-version: [3.7, 3.8, 3.9, '3.10', '3.11']
         test-type: [help, unittest, search, inference, docs]
+      fail-fast: false
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
@@ -24,7 +25,7 @@ jobs:
     - name: installing system packages
       run: |
         sudo apt-get -o Acquire::Retries=3 update
-        sudo apt-get -o Acquire::Retries=3 install *fftw3* mpi intel-mkl* git-lfs graphviz
+        sudo apt-get -o Acquire::Retries=3 install git-lfs graphviz
         pip install "tox<4.0.0" pip setuptools --upgrade
     - name: installing auxiliary data files
       run: |

.github/workflows/build_venv.yml

@@ -4,7 +4,7 @@ on: [push, pull_request]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: false
 
 jobs:
   build:

.github/workflows/distribution.yml

@@ -4,7 +4,7 @@ on: [push, pull_request]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: false
 
 jobs:
   build_wheels:
@@ -13,7 +13,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-20.04, macos-latest]
-
+      fail-fast: false
     steps:
       - uses: actions/checkout@v3
         with:

.github/workflows/docker-build.yml

@@ -4,7 +4,7 @@ on: [push, pull_request]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: false
 
 jobs:
   build:

.github/workflows/inference-workflow.yml

@@ -26,7 +26,6 @@ jobs:
         echo "deb https://download.pegasus.isi.edu/pegasus/ubuntu bionic main" | sudo tee -a /etc/apt/sources.list
         sudo apt-get -o Acquire::Retries=3 update
         sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.3-1+ubuntu18
-    - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |
         python -m pip install --upgrade 'pip<22.0' setuptools

.github/workflows/search-workflow.yml

@@ -4,7 +4,7 @@ on: [push, pull_request]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: false
 
 jobs:
   build:
@@ -30,7 +30,6 @@ jobs:
         echo "deb https://download.pegasus.isi.edu/pegasus/ubuntu bionic main" | sudo tee -a /etc/apt/sources.list
         sudo apt-get -o Acquire::Retries=3 update
         sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.3-1+ubuntu18
-    - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |
         python -m pip install --upgrade 'pip<22.0' setuptools

.github/workflows/tmpltbank-workflow.yml

@@ -4,7 +4,7 @@ on: [push, pull_request]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: false
 
 jobs:
   build:
@@ -30,7 +30,6 @@ jobs:
         echo "deb https://download.pegasus.isi.edu/pegasus/ubuntu bionic main" | sudo tee -a /etc/apt/sources.list
         sudo apt-get -o Acquire::Retries=3 update
         sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.3-1+ubuntu18
-    - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |
         python -m pip install --upgrade 'pip<22.0' setuptools

.github/workflows/tut-test.yml

@@ -4,7 +4,7 @@ on: [push, pull_request]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: false
 
 jobs:
   build:
@@ -14,6 +14,7 @@ jobs:
       matrix:
         os: [ubuntu-20.04]
         python-version: [3.7, 3.8, 3.9, '3.10', '3.11']
+      fail-fast: false
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
@@ -23,7 +24,6 @@ jobs:
     - name: installing packages
       run: |
         sudo apt-get -o Acquire::Retries=3 update
-        sudo apt-get -o Acquire::Retries=3 install *fftw3* mpi intel-mkl*
         pip install tox pip setuptools notebook --upgrade
         pip install .
     - name: retrieving pycbc tutorials

.github/workflows/workflow-tests.yml

@@ -4,7 +4,7 @@ on: [push, pull_request]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
+  cancel-in-progress: false
 
 jobs:
   build:
@@ -14,6 +14,7 @@ jobs:
       matrix:
         os: [ubuntu-20.04]
         test-type: [simple_subworkflow_data, multilevel_subworkflow_data]
+      fail-fast: false    
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python
@@ -35,7 +36,6 @@ jobs:
         echo "deb https://download.pegasus.isi.edu/pegasus/ubuntu bionic main" | sudo tee -a /etc/apt/sources.list
         sudo apt-get -o Acquire::Retries=3 update
         sudo apt-get -o Acquire::Retries=3 install pegasus=5.0.3-1+ubuntu18
-    - run: sudo apt-get -o Acquire::Retries=3 install *fftw3* intel-mkl*
     - name: Install pycbc
       run: |
         python -m pip install --upgrade 'pip<22.0' setuptools

examples/inference/analytic-normal2d/run.sh

@@ -1,4 +1,17 @@
-#!/bin/sh
+#!/bin/bash
+
+# Debugging: see what our conda environment looks like
+
+echo "DEBUG: inspiral test"
+echo "CONDA_PREFIX= $CONDA_PREFIX"
+echo "Conda environment is:"
+conda list
+ls -lh $CONDA_PREFIX/lib/*gomp*
+echo "ldd of libgomp:"
+ldd $CONDA_PREFIX/lib/libgomp.so.1
+echo "ldd of matchedfilter_cpu.cpython"
+ldd $CONDA_PREFIX/lib/python3.11/site-packages/pycbc/filter/matchedfilter_cpu.cpython-311-x86_64-linux-gnu.so
+
 pycbc_inference --verbose \
         --config-files normal2d.ini \
         --output-file normal2d.hdf \

examples/inference/bbh-injection/run_test.sh

@@ -1,11 +1,24 @@
-#!/bin/sh
+#!/bin/bash
 
 # sampler parameters
 PRIOR_CONFIG=../priors/gw150914_like.ini
 DATA_CONFIG=data.ini
 SAMPLER_CONFIG=../samplers/emcee_pt-gw150914_like.ini
 OUTPUT_PATH=inference.hdf
 
+# Debugging: see what our conda environment looks like
+
+echo "DEBUG: inspiral test"
+echo "CONDA_PREFIX= $CONDA_PREFIX"
+echo "Conda environment is:"
+conda list
+ls -lh $CONDA_PREFIX/lib/*gomp*
+echo "ldd of libgomp:"
+ldd $CONDA_PREFIX/lib/libgomp.so.1
+echo "ldd of matchedfilter_cpu.cpython"
+ldd $CONDA_PREFIX/lib/python3.11/site-packages/pycbc/filter/matchedfilter_cpu.cpython-311-x86_64-linux-gnu.so
+
+
 # the following sets the number of cores to use; adjust as needed to
 # your computer's capabilities
 NPROCS=10

examples/inference/gw150914/run_test.sh

@@ -1,10 +1,22 @@
-#!/bin/sh
+#!/bin/bash
 
 # configuration files
 PRIOR_CONFIG=../priors/gw150914_like.ini
 DATA_CONFIG=data.ini
 SAMPLER_CONFIG=../samplers/emcee_pt-gw150914_like.ini
 
+# Debugging: see what our conda environment looks like
+
+echo "DEBUG: inspiral test"
+echo "CONDA_PREFIX= $CONDA_PREFIX"
+echo "Conda environment is:"
+conda list
+ls -lh $CONDA_PREFIX/lib/*gomp*
+echo "ldd of libgomp:"
+ldd $CONDA_PREFIX/lib/libgomp.so.1
+echo "ldd of matchedfilter_cpu.cpython"
+ldd $CONDA_PREFIX/lib/python3.11/site-packages/pycbc/filter/matchedfilter_cpu.cpython-311-x86_64-linux-gnu.so
+
 OUTPUT_PATH=inference.hdf
 
 # the following sets the number of cores to use; adjust as needed to

examples/inspiral/run.sh

@@ -74,6 +74,13 @@ pycbc_condition_strain \
 --gps-end-time 1126259946 \
 --output-strain-file DATA_FILE.gwf \
 
+# Debugging: see what our conda environment looks like
+
+echo "DEBUG: inspiral test"
+echo "CONDA_PREFIX= $CONDA_PREFIX"
+echo "Conda environment is:"
+conda list
+
 
 start=`date +%s`
 inspiral_run fftw 16 openmp

examples/live/run.sh

@@ -4,6 +4,13 @@
 
 set -e
 
+# Debugging: see what our conda environment looks like
+
+echo "DEBUG: "
+echo "CONDA_PREFIX= $CONDA_PREFIX"
+echo "Conda environment is:"
+conda list
+
 export OMP_NUM_THREADS=4
 export HDF5_USE_FILE_LOCKING="FALSE"
 

examples/multi_inspiral/run.sh

@@ -30,6 +30,13 @@ TRIG_START=$((GPS_START + START_PAD))
 TRIG_END=$((GPS_END - END_PAD))
 OUTPUT=GW170817_test_output.hdf
 
+# Debugging: see what our conda environment looks like
+
+echo "DEBUG: "
+echo "CONDA_PREFIX= $CONDA_PREFIX"
+echo "Conda environment is:"
+conda list
+
 echo -e "\\n\\n>> [`date`] Running pycbc_multi_inspiral on GW170817 data"
 pycbc_multi_inspiral \
     --verbose \

tox.ini

@@ -9,14 +9,25 @@ requires=tox-conda
 deps =
     :preinstall: -rrequirements.txt
     -rcompanion.txt
-    mkl;'arm' not in platform_machine
 
 [testenv]
 allowlist_externals = bash
 passenv=LAL_DATA_PATH
 conda_deps=
-    openssl=1.1
+    openssl
     m2crypto
+    mkl
+    fftw
+    blas=*=*mkl
+    blas-devel=*=*_mkl
+    libblas=*=*_mkl
+    libcblas=*=*_mkl
+    liblapack=*=*_mkl
+    liblal=*=mkl*
+    openmpi
+    mpi4py
+    llvm-openmp
+    _openmp_mutex=*=*_llvm
 conda_channels=conda-forge
 
 # This test should run on almost anybody's environment
@@ -32,14 +43,12 @@ commands = pytest
 [testenv:py-help]
 deps =
     {[base]deps}
-    mpi4py
 setenv = PYCBC_TEST_TYPE=help
 commands = bash tools/pycbc_test_suite.sh
 
 [testenv:py-search]
 deps =
     {[base]deps}
-    mpi4py
 setenv = PYCBC_TEST_TYPE=search
 commands = bash tools/pycbc_test_suite.sh
 
@@ -56,6 +65,7 @@ deps =
     git+https://github.com/mikekatz04/BBHx.git; sys_platform == 'linux'
     git+https://github.com/ConWea/BBHX-waveform-model.git; sys_platform == 'linux'
 conda_deps=
+    mkl	
     mysqlclient
     gcc_linux-64>=12.2.0
     gxx_linux-64>=12.2.0