Refactor Dockerfile to use multi-stage builds for PISCAL, separating build and runtime stages.

Dockerfile

@@ -1,56 +1,77 @@
-#Download base image
-FROM ubuntu:latest
+# Multi-stage Dockerfile for PISCAL
+# Stage 1: Build stage - Compile PISCAL executable from Fortran sources
+FROM ubuntu:latest AS builder
 
-# Install and update software
+# Install build dependencies
 RUN set -xe \
 	&& apt-get update \
-	&& apt-get upgrade -y \
-	# SSHD install
-	&& apt-get install --no-install-recommends -y openssh-server sudo \
-	# Piscal reqs
-	&& apt-get install make -y \
-	&& apt-get install xutils-dev -y \
-	&& apt-get install gfortran -y \
-	&& apt-get install libopenmpi-dev -y \
-	# utils
-	&& apt-get install iproute2 -y \
-	&& apt-get install vim -y \
-	# cleanup
+	&& apt-get install --no-install-recommends -y \
+		make \
+		xutils-dev \
+		gfortran \
 	&& apt-get autoclean -y \
 	&& apt-get autoremove -y
 
-# configure sshd, copied from wataken44/ubuntu-latest-sshd
+# Copy source files from multiple directories
+COPY leafres/testarea/ /build/leafres/testarea/
+COPY dataassim/math/optimization/ /build/dataassim/math/optimization/
+COPY dataassim/math/othersupmath/ /build/dataassim/math/othersupmath/
+COPY dataassim/math/algebra/ /build/dataassim/math/algebra/
+COPY dataassim/math/specialfuncs/ /build/dataassim/math/specialfuncs/
+COPY dataassim/math/nonlinsystems/ /build/dataassim/math/nonlinsystems/
+COPY leafres/testrun/Makefile /build/leafres/testrun/Makefile
+
+# Build the executable
+WORKDIR /build/leafres/testrun
+RUN make clean || true
+RUN make
+
+# Stage 2: Runtime stage - Create minimal application container
+FROM ubuntu:latest
+
+# Install runtime dependencies only
 RUN set -xe \
-    && groupadd launcher \
-    && useradd -g launcher -G sudo -m -s /bin/bash launcher \
-    && echo 'launcher:launcher' | chpasswd
+	&& apt-get update \
+	&& apt-get upgrade -y \
+	&& apt-get install --no-install-recommends -y \
+		openssh-server \
+		sudo \
+		iproute2 \
+		vim \
+		libgfortran5 \
+	&& apt-get autoclean -y \
+	&& apt-get autoremove -y
+
+# Configure SSH server
+RUN set -xe \
+	&& groupadd launcher \
+	&& useradd -g launcher -G sudo -m -s /bin/bash launcher \
+	&& echo 'launcher:launcher' | chpasswd
 
 RUN set -xe \
-    && sed -i -e 's/#PasswordAuthentication.*/PasswordAuthentication yes/g' /etc/ssh/sshd_config \
-    && sed -i -e 's/UsePAM yes/UsePAM no/g' /etc/ssh/sshd_config \
-    && sed 's@session\s*required\s*pam_loginuid.so@session optional pam_loginuid.so@g' -i /etc/pam.d/sshd
+	&& sed -i -e 's/#PasswordAuthentication.*/PasswordAuthentication yes/g' /etc/ssh/sshd_config \
+	&& sed -i -e 's/UsePAM yes/UsePAM no/g' /etc/ssh/sshd_config \
+	&& sed 's@session\s*required\s*pam_loginuid.so@session optional pam_loginuid.so@g' -i /etc/pam.d/sshd
 
 RUN set -xe \
-    && chown -R launcher:launcher /home/launcher 
+	&& chown -R launcher:launcher /home/launcher
 
-# fix for SSHD - "Missing privilege separation directory: /run/sshd"
+# Fix for SSHD - "Missing privilege separation directory: /run/sshd"
 RUN set -xe \
-    && mkdir /run/sshd
+	&& mkdir /run/sshd
 
-##### add user l2g
-# RUN set -xe \
-#     && groupadd l2g \
-#     && useradd -g l2g -G sudo -m -s /bin/bash l2g \
-#     && echo 'l2g:pwdpwd' | chpasswd
-# RUN set -xe \
-#     && chown -R l2g:l2g /home/l2g 
-# RUN set -xe \
-# 	&& apt-get install nano
-#####
+# Copy compiled executable from builder stage
+COPY --from=builder /build/leafres/testrun/piscal /srv/piscal
+
+# Copy piscal-manager scripts
+COPY piscal-manager /srv
+
+# Fix Windows line endings (CRLF -> LF) for scripts and config files, and make scripts executable
+RUN set -xe \
+	&& find /srv -name "*.sh" -type f -exec sed -i 's/\r$//' {} \; \
+	&& find /srv -name "*.cfg" -type f -exec sed -i 's/\r$//' {} \; \
+	&& chmod +x /srv/*.sh || true
 
-ADD piscal-manager /srv
-ADD leafres/testrun/piscal /srv
-#RUN chmod R +x /srv/*.sh
 WORKDIR /srv
 
 EXPOSE 22