Made significant improvements to the Docker, Apptainer, and Singulari…

…ty containers.

Dockerfile

@@ -163,7 +163,12 @@ RUN echo 'find_path(NETCDF_INCLUDE_DIR NAMES netcdf.mod HINTS ENV NETCDF_FORTRAN
 
 # Production container
 FROM continuumio/miniconda3 
-COPY ./python/. /opt/conda/pkgs/swiftest/python/
+SHELL ["/bin/bash", "--login", "-c"]
+ENV SHELL="/bin/bash"
+ENV PATH="/opt/conda/bin:${PATH}"
+ENV LD_LIBRARY_PATH="/usr/local/lib"
+
+COPY environment.yml .
 
 RUN apt-get update && apt-get upgrade -y && \
   DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
@@ -172,27 +177,28 @@ RUN apt-get update && apt-get upgrade -y && \
   conda update --all -y && \
   conda install conda-libmamba-solver -y && \
   conda config --set solver libmamba && \
-  conda install -c conda-forge conda-build numpy scipy matplotlib pandas xarray astropy astroquery tqdm x264 bottleneck ffmpeg h5netcdf netcdf4 dask -y && \
-  conda update --all -y && \
-  cd /opt/conda/pkgs/swiftest/python/swiftest && conda develop . && \
-  conda clean --all -y 
+  conda env create -f environment.yml && \
+  conda init bash && \
+  echo "conda activate swiftest-env" >> ~/.bashrc 
 
-ENV LD_LIBRARY_PATH="/usr/local/lib"
-ENV SHELL="/bin/bash"
-COPY --from=build /opt/intel/oneapi/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libicaf.so /usr/local/lib/
-COPY --from=build /opt/intel/oneapi/mpi/2021.9.0//lib/release/libmpi.so.12 /usr/local/lib/
-COPY --from=build /opt/intel/oneapi/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libintlc.so.5 /usr/local/lib/
-COPY --from=build /opt/intel/oneapi/mpi/latest/bin/mpiexec.hydra  /usr/local/bin/
-COPY --from=build /usr/local/bin/swiftest_driver /usr/local/bin
-COPY --from=build /usr/local/bin/swiftest_driver_caf /usr/local/bin/
+COPY ./python/. /opt/conda/pkgs/
+COPY --from=build /usr/local/bin/swiftest_driver /opt/conda/envs/swiftest-env/bin/
+COPY --from=build /usr/local/bin/swiftest_driver /opt/conda/bin/
+COPY --from=build /usr/local/bin/swiftest_driver_caf /opt/conda/envs/swiftest-env/bin/
+COPY --from=build /opt/intel/oneapi/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libicaf.so /opt/conda/envs/swiftest-env/lib/
+COPY --from=build /opt/intel/oneapi/mpi/2021.9.0//lib/release/libmpi.so.12 /opt/conda/envs/swiftest-env/lib/
+COPY --from=build /opt/intel/oneapi/compiler/2023.1.0/linux/compiler/lib/intel64_lin/libintlc.so.5 /opt/conda/envs/swiftest-env/lib/
+COPY --from=build /opt/intel/oneapi/mpi/latest/bin/mpiexec.hydra  /opt/conda/envs/swiftest-env/bin/
 
-RUN mkdir -p /.astropy && \
+# Start new shell to activate the environment and install Swiftest
+RUN cd /opt/conda/pkgs/swiftest && conda develop . && \
+  conda clean --all -y && \
+  mkdir -p /.astropy && \
   chmod -R 777 /.astropy && \
   mkdir -p /.cache/matplotlib && \
   mkdir -p /.config/matplotlib && \
   chmod -R 777 /.cache/matplotlib && \
   chmod -R 777 /.config/matplotlib && \
-  mkdir -p /opt/conda/pkgs/swiftest/bin && \
-  ln -s /usr/local/bin/swiftest_driver /opt/conda/pkgs/swiftest/bin/swiftest_driver 
+  ln -s /opt/conda/bin/swiftest_driver /opt/conda/bin/driver
 
-ENTRYPOINT ["/opt/conda/bin/python"]
+ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "swiftest-env"]

apptainer/.gitignore

@@ -1,5 +1,4 @@
 !bin/
 !bin/swiftest_driver
-!bin/swiftest_python
+!bin/swiftest
 !install.sh
-!setenv.sh

apptainer/bin/swiftest_python → apptainer/bin/swiftest

@@ -1,2 +1,4 @@
 #!/bin/sh --
+OMP_NUM_THREADS=${OMP_NUM_THREADS:-`nproc --all`}
+FOR_COARRAY_NUM_IMAGES=${FOR_COARRAY_NUM_IMAGES:-1}
 apptainer run --bind $(pwd):$(pwd) --env OMP_NUM_THREADS=${OMP_NUM_THREADS},FOR_COARRAY_NUM_IMAGES=${FOR_COARRAY_NUM_IMAGES} ${SWIFTEST_SIF} "$@"

apptainer/bin/swiftest_driver

@@ -1,2 +1,4 @@
 #!/bin/sh --
+OMP_NUM_THREADS=${OMP_NUM_THREADS:-`nproc --all`}
+FOR_COARRAY_NUM_IMAGES=${FOR_COARRAY_NUM_IMAGES:-1}
 apptainer exec --bind $(pwd):$(pwd) --env OMP_NUM_THREADS=${OMP_NUM_THREADS},FOR_COARRAY_NUM_IMAGES=${FOR_COARRAY_NUM_IMAGES} ${SWIFTEST_SIF} swiftest_driver "$@"

apptainer/install.sh

@@ -1,11 +1,21 @@
 #!/bin/sh --
-# This will install the Singularity container version of the swiftest_driver in place of the native compiled version into ../bin. 
-# In order to use the executable script, the SWIFTEST_SIF environment variable must be set to point to the location of swiftest.sif, which requires this script to be called via source:
-# $ . ./install.sh
+# This will install the Apptainer version of the swiftest_driver in place of the native compiled version into ../bin as 
+# well as the swiftest_python script that is used to execute a Python input file.
+# The swiftest.sif file will be copied to the SIF_DIR directory. The default location is ${HOME}/.apptainer. 
+# To change this, just set environment variable SIF_DIR prior to running this script.
+# 
+# The script takes an optional argument "tag" if you want to pull a container other than "latest".
 # 
-tag=${1:-latest}
-echo "Installing swiftest.sif Singularity container and executable script from swiftest:${tag} Docker container"
-apptainer pull --force swiftest.sif docker://daminton/swiftest:${tag}
+# In order to use one executable script, the SWIFTEST_SIF environment variable must be set to point to the location of swiftest.sif, 
+# which requires this script to be called via source:
+# $ source ./install.sh
+# or 
+# $ . ./install.sh
+TAG=${1:-latest}
+
+SIF_DIR=${SIF_DIR:-${HOME}/.apptainer}
+echo "Installing ${SIF_DIR}/swiftest.sif container from mintongroup/swiftest:${TAG} Docker container"
+apptainer pull --force ${SIF_DIR}/swiftest.sif docker://mintongroup/swiftest:${TAG}
+cp -rf bin/swiftest ../bin/
 cp -rf bin/swiftest_driver ../bin/
-cp -rf bin/swiftest_python ../bin/
-source ./setenv.sh
+export SWIFTEST_SIF=${SIF_DIR}/swiftest.sif

docker/.gitignore

@@ -2,5 +2,5 @@
 !.gitignore
 !install.sh
 !bin
-!bin/swiftest_python
+!bin/swiftest
 !bin/swiftest_driver

docker/bin/swiftest

@@ -0,0 +1,4 @@
+#!/bin/sh --
+OMP_NUM_THREADS=${OMP_NUM_THREADS:-`nproc --all`}
+FOR_COARRAY_NUM_IMAGES=${FOR_COARRAY_NUM_IMAGES:-1}
+docker run -v $(pwd):$(pwd) -w $(pwd) --user "$(id -u):$(id -g)" -ti -e OMP_NUM_THREADS -e FOR_COARRAY_NUM_IMAGES mintongroup/swiftest "$@"

docker/bin/swiftest_driver

@@ -1,2 +1,4 @@
 #!/bin/sh --
-docker run -v $(pwd):$(pwd) -w $(pwd) --user "$(id -u):$(id -g)" -ti --entrypoint /usr/local/bin/swiftest_driver -e OMP_NUM_THREADS -e FOR_COARRAY_NUM_IMAGES swiftest:1.0.0  "$@"
+OMP_NUM_THREADS=${OMP_NUM_THREADS:-`nproc --all`}
+FOR_COARRAY_NUM_IMAGES=${FOR_COARRAY_NUM_IMAGES:-1}
+docker run -v $(pwd):$(pwd) -w $(pwd) --user "$(id -u):$(id -g)" -ti --entrypoint /usr/local/bin/swiftest_driver -e OMP_NUM_THREADS -e FOR_COARRAY_NUM_IMAGES MintonGroup/swiftest  "$@"

docker/install.sh

@@ -1,5 +1,6 @@
 #!/bin/sh --
 tag=${1:-latest}
 echo "Installing swiftest:${tag} Docker container and executable script"
-docker pull daminton/swiftest:${tag}
-cp -rf bin/swiftest ../bin/
+docker pull mintongroup/swiftest:${tag}
+cp -rf bin/swiftest ../bin/
+cp -rf bin/swiftest_driver ../bin/

python/swiftest/swiftest/simulation_class.py

@@ -470,6 +470,9 @@ def _type_scrub(output_data):
                     sys.exit()
         except:
             warnings.warn(f"Error executing main swiftest_driver program", stacklevel=2)
+            res = p.communicate()
+            for line in res[1]:
+                print(line, end='')
             sys.exit()
 
         pbar.close()
@@ -502,11 +505,9 @@ def run(self,dask: bool = False, **kwargs):
 
         if not self.binary_source.exists():
             msg = "Path to swiftest_driver has not been set!"
-            msg += f"\nMake sure swiftest_driver is compiled and the executable is in {str(self.binary_path)}"
+            msg += f"\nMake sure swiftest_driver is compiled and the executable is in {str(self.binary_source.parent)}"
             warnings.warn(msg,stacklevel=2)
             return
-        else:
-            shutil.copy2(self.binary_source, self.driver_executable) 
 
         if not self.restart:
             self.clean()
@@ -942,16 +943,15 @@ def set_integrator(self,
             update_list.append("codename")
             if self.codename == "Swiftest":
                 self.binary_source = Path(_pyfile).parent.parent.parent.parent / "bin" / "swiftest_driver"
-                self.binary_path = self.simdir.resolve()
-                self.driver_executable = self.binary_path / "swiftest_driver"
+                self.driver_executable = self.binary_source
                 if not self.binary_source.exists():
-                    warnings.warn(f"Cannot find the Swiftest driver in {str(self.binary_path)}",stacklevel=2)
+                    warnings.warn(f"Cannot find the Swiftest driver at {str(self.binary_source)}",stacklevel=2)
                     self.driver_executable = None
                 else:
-                    if self.binary_path.exists():
+                    if self.binary_source.exists():
                         self.driver_executable.resolve()
             else:
-                self.binary_path = "NOT IMPLEMENTED FOR THIS CODE"
+                self.binary_source = "NOT IMPLEMENTED FOR THIS CODE"
                 self.driver_executable = None
             update_list.append("driver_executable")
 
@@ -1200,8 +1200,6 @@ def set_feature(self,
                     msg = f"Cannot create the {self.simdir.resolve()} directory: File exists."
                     msg += "\nDelete the file or change the location of param_file"
                     raise NotADirectoryError(msg)
-            self.binary_path = self.simdir.resolve()
-            self.driver_executable = self.binary_path / "swiftest_driver"
             self.param_file = Path(kwargs.pop("param_file","param.in"))
 
         if self.codename == "Swiftest": 
@@ -2754,7 +2752,6 @@ def write_param(self,
         self.driver_script = os.path.join(self.simdir, "swiftest_driver.sh")
         with open(self.driver_script, 'w') as f:
             f.write(f"#{self._shell_full}\n")
-            #f.write(f"source ~/.{self._shell}rc\n")
             f.write(f"cd {self.simdir}\n")
             f.write(f"{str(self.driver_executable)} {self.integrator} {str(self.param_file)} compact\n")
 
@@ -2991,11 +2988,9 @@ def save(self,
             self.write_param(param_file=param_file,**kwargs)
             if not self.binary_source.exists():
                 msg = "Path to swiftest_driver has not been set!"
-                msg += f"\nMake sure swiftest_driver is compiled and the executable is in {str(self.binary_path)}"
+                msg += f"\nMake sure swiftest_driver is compiled and the executable is in {str(self.binary_source.parent)}"
                 warnings.warn(msg,stacklevel=2)
                 return
-            else:
-                shutil.copy2(self.binary_source, self.driver_executable)  
         elif codename == "Swifter":
             swifter_param = io.swiftest2swifter_param(param)
             if "rhill" in self.data:

singularity/.gitignore

@@ -2,4 +2,3 @@
 !bin/swiftest_driver
 !bin/swiftest_python
 !install.sh
-!setenv.sh

singularity/bin/swiftest_driver

@@ -1,2 +1,4 @@
 #!/bin/sh --
+OMP_NUM_THREADS=${OMP_NUM_THREADS:-`nproc --all`}
+FOR_COARRAY_NUM_IMAGES=${FOR_COARRAY_NUM_IMAGES:-1}
 singularity exec --bind $(pwd):$(pwd) --env OMP_NUM_THREADS=${OMP_NUM_THREADS},FOR_COARRAY_NUM_IMAGES=${FOR_COARRAY_NUM_IMAGES} ${SWIFTEST_SIF} swiftest_driver "$@"

singularity/install.sh

@@ -1,11 +1,21 @@
 #!/bin/sh --
-# This will install the Singularity container version of the swiftest_driver in place of the native compiled version into ../bin. 
-# In order to use the executable script, the SWIFTEST_SIF environment variable must be set to point to the location of swiftest.sif, which requires this script to be called via source:
-# $ . ./install.sh
+# This will install the Singularity version of the swiftest_driver in place of the native compiled version into ../bin as 
+# well as the swiftest_python script that is used to execute a Python input file.
+# The swiftest.sif file will be copied to the SIF_DIR directory. The default location is ${HOME}/.singularity. 
+# To change this, just set environment variable SIF_DIR prior to running this script.
+# 
+# The script takes an optional argument "tag" if you want to pull a container other than "latest".
 # 
-tag=${1:-latest}
-echo "Installing swiftest.sif Singularity container and executable script from swiftest:${tag} Docker container"
-singularity pull --force swiftest.sif docker://daminton/swiftest:${tag}
+# In order to use one executable script, the SWIFTEST_SIF environment variable must be set to point to the location of swiftest.sif, 
+# which requires this script to be called via source:
+# $ source ./install.sh
+# or 
+# $ . ./install.sh
+TAG=${1:-latest}
+
+SIF_DIR=${SIF_DIR:-${HOME}/.singularity}
+echo "Installing ${SIF_DIR}/swiftest.sif container from mintongroup/swiftest:${TAG} Docker container"
+singularity pull --force ${SIF_DIR}/swiftest.sif docker://mintongroup/swiftest:${TAG}
+cp -rf bin/swiftest ../bin/
 cp -rf bin/swiftest_driver ../bin/
-cp -rf bin/swiftest_python ../bin/
-source ./setenv.sh
+export SWIFTEST_SIF=${SIF_DIR}/swiftest.sif