created the .def file that builds a minimal singularity image in which all the...

created the .def file that builds a minimal singularity image in which all the mp-tmcode codes can be run, including all the needed runtime files

.gitignore

@@ -3,4 +3,4 @@ build/cluster/*
 build/sphere/*
 build/trapping/*
 doc/build/*
-
+containers/singularity/*.sif

containers/singularity/README.md

+# Singularity support for the NP-TMcode project
+
+This `np-tmcode-run.def` file allows to create a np-tmcode-run image, that contains only the pre-built executables, python test scripts, compiled documentation, and the minimal runtime to run them
+
+In order for the singularity build to create the image, singularity build must be invoked from this directory as:
+
+   > singularity build \<image name\> np-tmcode-run.def
+
+where `<image name>` is the name one wants to give to the image, e.g. `np-tmcode-run.sif`. Depending on the singularity installation, the additional `--fakeroot` option may be needed (see singularity documentation).
+
+The image thus built can be run either as
+
+   > singularity run \<image name\> \<np-tmcode command\>
+
+or directly as
+
+   > \<full path to image name\> \<np-tmcode command\>
+
+where `<full path to image name>` is the name of the sif image, including full or relative path to it, and `<np-tmcode command>` is one of the executables built in np-tmcode project, or the `pycompare.py` script used to compare results between the Fortran and C++ versions of the code. These executables, as well as the minimum runtime for them to execute correctly, are embedded in the image, and "see" the current directory the image is run in (which technically is automatically bind-mounted by singularity in the running image instance).
\ No newline at end of file

containers/singularity/np-tmcode-run.def

+Bootstrap: docker
+From: debian:bookworm-slim
+Stage: np-tmcode-run-dev
+
+%files
+	../../src /usr/local/np-tmcode/src
+	../../doc /usr/local/np-tmcode/doc
+	../../build /usr/local/np-tmcode/build
+	../../test_data /usr/local/np-tmcode/test_data
+
+%post
+	apt update
+	apt -y upgrade
+	apt -y install g++ gfortran make gcc-offload-nvptx libhdf5-dev
+	apt -y install python3 python-is-python3 python3-regex
+	apt -y install doxygen
+	apt -y install texlive-latex-base texlive-latex-recommended texlive-latex-extra texlive-font-utils
+	rm -rf /var/lib/apt/lists/*
+	cd /usr/local/np-tmcode/src
+	make wipe
+	make -j
+	make docs -j && make -C ../doc/build/latex -j
+
+
+Bootstrap: docker
+From: debian:bookworm-slim
+Stage: np-tmcode-run-minimal
+
+%files from np-tmcode-run-dev
+       /usr/local/np-tmcode /usr/local/np-tmcode
+
+%post
+	apt update
+	apt -y upgrade
+	apt -y install libgfortran5 libgcc-s1 libhdf5-103-1 libstdc++6 libssl3 libcurl4 libsz2 zlib1g libnghttp2-14 libidn2-0 librtmp1 libssh2-1 libpsl5 libgssapi-krb5-2 libldap-2.5-0 libzstd1 libbrotli1 libaec0 libunistring2 libgmp10 libkrb5-3 libk5crypto3 libcom-err2 libkrb5support0 libsasl2-2 libp11-kit0 libtasn1-6 libkeyutils1 libffi8 python3 python-is-python3 python3-regex
+	rm -rf /var/lib/apt/lists/*
+	cd /usr/local/np-tmcode
+	find build -name "*.o" -exec rm -v \{\} \;
+	find build -name "*.gcno" -exec rm -v \{\} \;
+	cd src
+	rm -rvf cluster libnptm trapping include sphere Makefile make.inc README.md
+	cd ..
+	rm -rvf containers
+	cd doc
+	rm -rvf src/cluster /src/include /src/libntpm /src/sphere /src/trapping /src/Makefile /src/make.inc
+	cd build/latex
+	rm -rvf *.tex *.out *.sty *.ind *.log *.toc *.ilg *.idx *.aux *.eps Makefile class*.pdf
+	cp -a /usr/bin/ld.so /usr/bin/sh /usr/bin/dash /usr/bin/mkdir /usr/bin/rm /usr/bin/cp /usr/bin/python* /usr/local/bin/
+	rm -rvf /bin/* /usr/bin/* /sbin /usr/sbin /usr/games /usr/local/games
+	/usr/local/bin/mkdir -p /bin
+	/usr/local/bin/cp -av /usr/local/bin/* /bin/
+	rm -rvf /usr/local/bin/* /bin/cp /bin/rm /bin/mkdir
+
+
+Bootstrap: scratch
+Stage: np-tmcode-run
+
+%files from np-tmcode-run-minimal
+       / /
+
+%runscript
+	PATH=/bin:/usr/local/np-tmcode/src/scripts:/usr/local/np-tmcode/build/trapping:/usr/local/np-tmcode/build/cluster:/usr/local/np-tmcode/build/sphere $*