Ubuntu 24.04 update changes

rozsatib · Jan 10, 2025 · 18c4828 · 18c4828
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commit 18c4828
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Showing 8 changed files with 14 additions and 14 deletions.
diff --git a/.github/workflows/fast-model-mpi-explosion.yml b/.github/workflows/fast-model-mpi-explosion.yml
@@ -12,11 +12,11 @@ jobs:
     - name: Pytest Unit Tests
       uses: actions/setup-python@v2
       with:
-        python-version: '3.9'
+        python-version: '3.12'
     - name: Install prerequisites
       run: |
         sudo apt-get update
-        sudo apt-get install python3-setuptools subversion git libopenmpi-dev g++ libjpeg8 libjpeg8-dev libfreetype6 libfreetype6-dev zlib1g-dev libpng++-dev libncurses5 libncurses5-dev libreadline-dev liblapack-dev libblas-dev gfortran libgsl0-dev openmpi-bin python-tk cmake
+        sudo apt-get install python3 python3-dev python3-pip python3-setuptools subversion git libopenmpi-dev g++ libjpeg8 libjpeg8-dev libfreetype6 libfreetype6-dev zlib1g-dev libpng++-dev libncurses5-dev libreadline-dev liblapack-dev libblas-dev gfortran libgsl0-dev openmpi-bin python-tk cmake libboost-all-dev
         pip3 install pytest pytest-cov pytest-randomly coverage black
         # TODO: Add pynn once we switch from our custom to the official release
         pip3 install numpy scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo==0.12.0 cython psutil future requests elephant pytest-xdist pytest-timeout junitparser numba numpyencoder sphinx imageio

diff --git a/.github/workflows/fast-model-mpi.yml b/.github/workflows/fast-model-mpi.yml
@@ -12,11 +12,11 @@ jobs:
     - name: Pytest Unit Tests
       uses: actions/setup-python@v2
       with:
-        python-version: '3.9'
+        python-version: '3.12'
     - name: Install prerequisites
       run: |
         sudo apt-get update
-        sudo apt-get install python3-setuptools subversion git libopenmpi-dev g++ libjpeg8 libjpeg8-dev libfreetype6 libfreetype6-dev zlib1g-dev libpng++-dev libncurses5 libncurses5-dev libreadline-dev liblapack-dev libblas-dev gfortran libgsl0-dev openmpi-bin python-tk cmake
+        sudo apt-get install python3 python3-dev python3-pip python3-setuptools subversion git libopenmpi-dev g++ libjpeg8 libjpeg8-dev libfreetype6 libfreetype6-dev zlib1g-dev libpng++-dev libncurses5-dev libreadline-dev liblapack-dev libblas-dev gfortran libgsl0-dev openmpi-bin python-tk cmake libboost-all-dev
         pip3 install pytest pytest-cov pytest-randomly coverage black
         # TODO: Add pynn once we switch from our custom to the official release
         pip3 install numpy scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo==0.12.0 cython psutil future requests elephant pytest-xdist pytest-timeout junitparser numba numpyencoder sphinx imageio

diff --git a/.github/workflows/fast-model-stepcurrentmodule.yml b/.github/workflows/fast-model-stepcurrentmodule.yml
@@ -11,11 +11,11 @@ jobs:
     - name: Pytest Unit Tests
       uses: actions/setup-python@v2
       with:
-        python-version: '3.9'
+        python-version: '3.12'
     - name: Install prerequisites
       run: |
         sudo apt-get update
-        sudo apt-get install python3-setuptools subversion git libopenmpi-dev g++ libjpeg8 libjpeg8-dev libfreetype6 libfreetype6-dev zlib1g-dev libpng++-dev libncurses5 libncurses5-dev libreadline-dev liblapack-dev libblas-dev gfortran libgsl0-dev openmpi-bin python-tk cmake
+        sudo apt-get install python3 python3-dev python3-pip python3-setuptools subversion git libopenmpi-dev g++ libjpeg8 libjpeg8-dev libfreetype6 libfreetype6-dev zlib1g-dev libpng++-dev libncurses5-dev libreadline-dev liblapack-dev libblas-dev gfortran libgsl0-dev openmpi-bin python-tk cmake libboost-all-dev
         pip3 install pytest pytest-cov pytest-randomly coverage black
         # TODO: Add pynn once we switch from our custom to the official release
         pip3 install numpy scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo==0.12.0 cython psutil future requests elephant pytest-xdist pytest-timeout junitparser numba numpyencoder sphinx imageio

diff --git a/.github/workflows/fast-model.yml b/.github/workflows/fast-model.yml
@@ -11,11 +11,11 @@ jobs:
     - name: Pytest Unit Tests
       uses: actions/setup-python@v2
       with:
-        python-version: '3.9'
+        python-version: '3.12'
     - name: Install prerequisites
       run: |
         sudo apt-get update
-        sudo apt-get install python3-setuptools subversion git libopenmpi-dev g++ libjpeg8 libjpeg8-dev libfreetype6 libfreetype6-dev zlib1g-dev libpng++-dev libncurses5 libncurses5-dev libreadline-dev liblapack-dev libblas-dev gfortran libgsl0-dev openmpi-bin python-tk cmake
+        sudo apt-get install python3 python3-dev python3-pip python3-setuptools subversion git libopenmpi-dev g++ libjpeg8 libjpeg8-dev libfreetype6 libfreetype6-dev zlib1g-dev libpng++-dev libncurses5-dev libreadline-dev liblapack-dev libblas-dev gfortran libgsl0-dev openmpi-bin python-tk cmake libboost-all-dev
         pip3 install pytest pytest-cov pytest-randomly coverage black
         # TODO: Add pynn once we switch from our custom to the official release
         pip3 install numpy scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo==0.12.0 cython psutil future requests elephant pytest-xdist pytest-timeout junitparser numba numpyencoder sphinx imageio

diff --git a/.github/workflows/lsv1m-model.yml b/.github/workflows/lsv1m-model.yml
@@ -11,11 +11,11 @@ jobs:
     - name: Pytest Unit Tests
       uses: actions/setup-python@v2
       with:
-        python-version: '3.9'
+        python-version: '3.12'
     - name: Install prerequisites
       run: |
         sudo apt-get update
-        sudo apt-get install python3-setuptools subversion git libopenmpi-dev g++ libjpeg8 libjpeg8-dev libfreetype6 libfreetype6-dev zlib1g-dev libpng++-dev libncurses5 libncurses5-dev libreadline-dev liblapack-dev libblas-dev gfortran libgsl0-dev openmpi-bin python-tk cmake
+        sudo apt-get install python3 python3-dev python3-pip python3-setuptools subversion git libopenmpi-dev g++ libjpeg8 libjpeg8-dev libfreetype6 libfreetype6-dev zlib1g-dev libpng++-dev libncurses5-dev libreadline-dev liblapack-dev libblas-dev gfortran libgsl0-dev openmpi-bin python-tk cmake libboost-all-dev
         pip3 install pytest pytest-cov pytest-randomly coverage black
         # TODO: Add pynn once we switch from our custom to the official release
         pip3 install numpy scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo==0.12.0 cython psutil future requests elephant pytest-xdist pytest-timeout junitparser numba numpyencoder sphinx imageio

diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml
@@ -11,11 +11,11 @@ jobs:
     - name: Pytest Unit Tests
       uses: actions/setup-python@v2
       with:
-        python-version: '3.9'
+        python-version: '3.12'
     - name: Install prerequisites
       run: |
         sudo apt-get update
-        sudo apt-get install python3-setuptools subversion git libopenmpi-dev g++ libjpeg8 libjpeg8-dev libfreetype6 libfreetype6-dev zlib1g-dev libpng++-dev libncurses5 libncurses5-dev libreadline-dev liblapack-dev libblas-dev gfortran libgsl0-dev openmpi-bin python-tk cmake
+        sudo apt-get install python3 python3-dev python3-pip python3-setuptools subversion git libopenmpi-dev g++ libjpeg8 libjpeg8-dev libfreetype6 libfreetype6-dev zlib1g-dev libpng++-dev libncurses5-dev libreadline-dev liblapack-dev libblas-dev gfortran libgsl0-dev openmpi-bin python-tk cmake libboost-all-dev
         pip3 install pytest pytest-cov pytest-randomly coverage black
         # TODO: Add pynn once we switch from our custom to the official release
         pip3 install numpy scipy mpi4py matplotlib quantities lazyarray interval Pillow param==1.5.1 parameters neo==0.12.0 cython psutil future requests elephant pytest-xdist pytest-timeout junitparser numba numpyencoder sphinx imageio

diff --git a/README.rst b/README.rst
@@ -15,7 +15,7 @@ fresh installation of current Ubuntu system.
 
 First the list of ubuntu package dependencies::
 
-  sudo apt-get install python3 python3-dev python3-pip python3-setuptools python3-tk python-nose subversion git libopenmpi-dev g++ libjpeg8 libjpeg8-dev libfreetype6 libfreetype6-dev zlib1g-dev libpng++-dev libncurses5 libncurses5-dev libreadline-dev liblapack-dev libblas-dev gfortran libgsl0-dev openmpi-bin python-tk cmake libboost-all-dev
+  sudo apt-get install python3 python3-dev python3-pip python3-setuptools subversion git libopenmpi-dev g++ libjpeg8 libjpeg8-dev libfreetype6 libfreetype6-dev zlib1g-dev libpng++-dev libncurses5-dev libreadline-dev liblapack-dev libblas-dev gfortran libgsl0-dev openmpi-bin python-tk cmake libboost-all-dev
 
 
 Virtual env

diff --git a/mozaik/meta_workflow/parameter_search.py b/mozaik/meta_workflow/parameter_search.py
@@ -115,7 +115,7 @@ def execute_job(self,run_script,simulator_name,parameters_url,parameters,simulat
                             '#SBATCH -c ' + str(self.num_threads),
                             'source ' + str(self.path_to_mozaik_env),
                             'cd ' + os.getcwd(),
-                            ' '.join(["srun","--mpi=pmix_v3","python",run_script, simulator_name, str(self.num_threads) ,parameters_url]+modified_parameters+[simulation_run_name]+['>']  + [parameters['results_dir'][1:-1] +'/OUTFILE'+str(time.time())]),
+                            ' '.join(["srun","--mpi=pmix_v5","python",run_script, simulator_name, str(self.num_threads) ,parameters_url]+modified_parameters+[simulation_run_name]+['>']  + [parameters['results_dir'][1:-1] +'/OUTFILE'+str(time.time())]),
                         ]) 
          print(p.communicate(input=data)[0])
          print(data)