Merge branch 'main' into issue-1153-additional-vader-workers

Author: LourensVeen

.github/ISSUE_TEMPLATE/bug_report.md

@@ -2,7 +2,7 @@
 name: Bug report
 about: Create a report to help us improve
 title: ''
-labels: bug
+labels: 'kind: bug'
 assignees: ''
 
 ---

.github/ISSUE_TEMPLATE/feature_request.md

@@ -2,7 +2,7 @@
 name: Feature request
 about: Suggest a feature or improvement for AMUSE
 title: ''
-labels: feature request
+labels: 'kind: feature request'
 assignees: ''
 
 ---

.github/ISSUE_TEMPLATE/question.md

@@ -2,7 +2,7 @@
 name: Question
 about: Ask an AMUSE-related question
 title: ''
-labels: question
+labels: 'kind: question'
 assignees: ''
 
 ---

.github/stale.yml

@@ -4,13 +4,13 @@ daysUntilStale: 365
 daysUntilClose: 365
 # Issues with these labels will never be considered stale
 exemptLabels:
-  - pinned
-  - security
-  - feature request
-  - keep-open
-  - bug
+  - 'status: pinned'
+  - 'kind: security'
+  - 'kind: feature request'
+  - 'status: keep-open'
+  - 'kind: bug'
 # Label to use when marking an issue as stale
-staleLabel: stale
+staleLabel: 'status: stale'
 # Comment to post when marking an issue as stale. Set to `false` to disable
 markComment: >
   This issue has been automatically marked as stale because it has not had

.github/workflows/test-framework.yml

@@ -37,19 +37,15 @@ jobs:
         conda info
         conda list
 
-    - name: Install dependencies
+    - name: Install dependencies (Linux)
+      if: ${{ startsWith(matrix.os, 'ubuntu') }}
       run: |
-        conda install c-compiler cxx-compiler fortran-compiler 'gfortran<14' python pkgconfig coreutils patch curl tar unzip gzip bzip2 xz perl bison make cmake openmpi gsl fftw gmp mpfr hdf5 netcdf4 libopenblas liblapack zlib pip wheel 'docutils>=0.6' 'mpi4py>=1.1.0' 'numpy>=1.2.2' 'h5py>=1.1.0' pytest
+        conda install c-compiler cxx-compiler fortran-compiler 'gfortran<14' python-gil pkgconfig coreutils patch curl tar unzip gzip bzip2 xz perl bison make cmake openmpi gsl fftw gmp mpfr hdf5 netcdf4 libopenblas liblapack zlib pip wheel 'docutils>=0.6' 'mpi4py>=1.1.0' 'numpy>=1.2.2' 'h5py>=1.1.0' pytest
 
-      # - name: Configure OpenMPI
-      #      run: |
-      #        mkdir -p "$HOME/.openmpi"
-      #        echo "rmaps_base_oversubscribe = true" >>"$HOME/.openmpi/mca-params.conf"
-      #        echo "mpi_yield_when_idle = true" >>"$HOME/.openmpi/mca-params.conf"
-      #        echo "btl_tcp_if_include = lo,eth0" >>"$HOME/.openmpi/mca-params.conf"
-      #        mkdir -p "$HOME/.prte"
-      #        echo "rmaps_default_mapping_policy = :oversubscribe" >>"$HOME/.prte/mca-params.conf"
-      #        echo "prte_if_include = lo,eth0" >>"$HOME/.prte/mca-params.conf"
+    - name: Install dependencies (macOS)
+      if: ${{ startsWith(matrix.os, 'macos') }}
+      run: |
+        conda install c-compiler cxx-compiler fortran-compiler 'gfortran<14' python-gil pkgconfig coreutils patch curl tar unzip gzip bzip2 xz perl bison make cmake mpich gsl fftw gmp mpfr hdf5 netcdf4 libopenblas liblapack zlib pip wheel 'docutils>=0.6' 'mpi4py>=1.1.0' 'numpy>=1.2.2' 'h5py>=1.1.0' pytest
 
     - name: Checkout
       uses: actions/checkout@v4
@@ -62,15 +58,16 @@ jobs:
         ./setup install amuse-framework
 
     - name: Test framework
-      #      env:
-      #        OMPI_MCA_rmaps_base_oversubscribe: 1
-      #        PRTE_MCA_rmaps_base_oversubscribe: 1
-      #        PRTE_MCA_rmaps_default_mapping_policy: ":oversubscribe"
-      #        OMPI_MCA_mpi_yield_when_idle: 1
-      #        OMPI_MCA_btl_tcp_if_include: lo,eth0
-      #        PRTE_MCA_btl_tcp_if_include: lo,eth0
-      #        PRTE_MCA_if_include: lo,eth0
-      #        OMPI_MCA_pmix_server_max_wait: 10
+      env:
+        OMPI_MCA_rmaps_base_oversubscribe: 1
+        PRTE_MCA_rmaps_base_oversubscribe: 1
+        PRTE_MCA_rmaps_default_mapping_policy: ":oversubscribe"
+        OMPI_MCA_mpi_yield_when_idle: 1
+        PRTE_MCA_mpi_yield_when_idle: 1
+        OMPI_MCA_btl_tcp_if_include: lo,eth0
+        PRTE_MCA_btl_tcp_if_include: lo,eth0
+        PRTE_MCA_if_include: lo,eth0
+        OMPI_MCA_pmix_server_max_wait: 10
       run: |
         ./setup test amuse-framework
 

.github/workflows/test-seba.yml

@@ -41,7 +41,7 @@ jobs:
 
     - name: Install dependencies
       run: |
-        conda install c-compiler cxx-compiler fortran-compiler 'gfortran<14' python pkgconfig coreutils patch curl tar unzip gzip bzip2 xz perl bison make cmake openmpi gsl fftw gmp mpfr hdf5 netcdf4 libopenblas liblapack zlib pip wheel 'docutils>=0.6' 'mpi4py>=1.1.0' 'numpy>=1.2.2' 'h5py>=1.1.0' pytest
+        conda install c-compiler cxx-compiler fortran-compiler 'gfortran<14' python-gil pkgconfig coreutils patch curl tar unzip gzip bzip2 xz perl bison make cmake openmpi gsl fftw gmp mpfr hdf5 netcdf4 libopenblas liblapack zlib pip wheel 'docutils>=0.6' 'mpi4py>=1.1.0' 'numpy>=1.2.2' 'h5py>=1.1.0' pytest
 
         #    - name: Configure OpenMPI
         #      run: |

examples/textbook/relax_gas_and_stars.py

@@ -1,11 +1,20 @@
 import numpy
 import pickle
-from amuse.lab import *
+
+from amuse.lab import (
+    units, nbody_system, 
+    new_plummer_model, write_set_to_file,
+    new_salpeter_mass_distribution, 
+)
 from amuse.community.fastkick.interface import FastKick
-from amuse.ext.relax_sph import relax
+from amuse.community.fi.interface import Fi
+from amuse.ext.relax_sph import relax, monitor_energy
 from amuse.ext.spherical_model import new_gas_plummer_distribution
 from amuse.community.fractalcluster.interface import new_fractal_cluster_model
 
+
+from prepare_figure import *
+
 ###BOOKLISTSTART1###
 def check_energy_conservation(system, i_step, time, n_steps):
     unit = units.J
@@ -163,7 +172,6 @@ def make_map(sph,N=100,L=1):
 def plot_hydro_and_stars(hydro, stars):
     x_label = "x [pc]"
     y_label = "y [pc]"
-    from prepare_figure import *
     fig = single_frame(x_label, y_label, logx=False, logy=False,
                        xsize=12, ysize=12)
 

lib/sapporo_light/dev_evaluate_gravity.cu

@@ -73,7 +73,11 @@ __device__ void body_body_interaction(float &ds_min,
 
   }
 
-  float inv_ds  = rsqrt(ds2 + EPS2) * (__float_as_int(pos_i.w.y) != __float_as_int(pos_j.w.y));
+  float inv_ds = 0.0f;
+  if (__float_as_int(pos_i.w.y) != __float_as_int(pos_j.w.y)) {
+      inv_ds = rsqrt(ds2 + EPS2);
+  }
+
   float mass    = pos_j.w.x;
   float inv_ds2 = inv_ds*inv_ds;                         // 1 FLOP
   float inv_ds3 = mass * inv_ds*inv_ds2;                 // 2 FLOP

lib/sapporo_light/send_fetch_data.cpp

@@ -23,7 +23,7 @@ void sapporo::free_cuda_memory(int ignore) {
     CUDA_SAFE_CALL(cudaFree( (void*)dev.ngb_list_i));
 
 
-    CUDA_SAFE_CALL(cudaThreadExit());
+    CUDA_SAFE_CALL(cudaDeviceReset());
     CUT_CHECK_ERROR("Failedn");
 }
 

lib/sapporo_light/support/configure

@@ -3934,11 +3934,11 @@ if test x$ac_prog_cxx_stdcxx = xno
 then :
   { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $CXX option to enable C++11 features" >&5
 printf %s "checking for $CXX option to enable C++11 features... " >&6; }
-if test ${ac_cv_prog_cxx_11+y}
+if test ${ac_cv_prog_cxx_cxx11+y}
 then :
   printf %s "(cached) " >&6
 else $as_nop
-  ac_cv_prog_cxx_11=no
+  ac_cv_prog_cxx_cxx11=no
 ac_save_CXX=$CXX
 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
@@ -3980,11 +3980,11 @@ if test x$ac_prog_cxx_stdcxx = xno
 then :
   { printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $CXX option to enable C++98 features" >&5
 printf %s "checking for $CXX option to enable C++98 features... " >&6; }
-if test ${ac_cv_prog_cxx_98+y}
+if test ${ac_cv_prog_cxx_cxx98+y}
 then :
   printf %s "(cached) " >&6
 else $as_nop
-  ac_cv_prog_cxx_98=no
+  ac_cv_prog_cxx_cxx98=no
 ac_save_CXX=$CXX
 cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */