wip: getting started on gromacs

gromacs/Dockerfile

@@ -0,0 +1,33 @@
+ARG tag=latest
+FROM ubuntu:${tag}
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && \
+    apt-get install -y fftw3-dev fftw3 pdsh libfabric-dev libfabric1 \
+        dnsutils telnet strace cmake git g++ \
+        mpich wget curl unzip vim ffmpeg python3-pip \
+        build-essential openssh-server libxml2-dev
+
+# llvm https://apt.llvm.org/
+RUN /bin/bash -c "wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | apt-key add -" && \
+    apt-get update && \
+    apt-get install -y clang-format clang-tidy clang-tools clang clangd libc++-dev libc++1 libc++abi-dev libc++abi1 libclang-dev libclang1 liblldb-dev libllvm-ocaml-dev libomp-dev libomp5 lld lldb llvm-dev llvm-runtime llvm python3-clang
+
+ENV GROMACS_VERSION=5.1.2
+WORKDIR /opt
+RUN wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-${GROMACS_VERSION}.tar.gz && \
+    tar zxvf gromacs-${GROMACS_VERSION}.tar.gz
+COPY ./CMakeLists.txt /opt/gromacs-${GROMACS_VERSION}/CMakeLists.txt
+RUN git clone https://github.com/compor/llvm-ir-cmake-utils /tmp/cmake-utils && \
+    cd gromacs-${GROMACS_VERSION} && \
+    cp /tmp/cmake-utils/cmake/* /opt/gromacs-${GROMACS_VERSION}/cmake && \
+    mkdir build && \
+    cd build && \
+# Note there is an error here for libgromacs
+# Attempt to add a custom rule to output
+# /opt/gromacs-5.1.2/build/llvm-ir/libgromacs_bc/md5.c.bc.rule
+# which already has a custom rule.
+    cmake .. -DGMX_BUILD_OWN_FFTW=ON -Wno-dev -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_C_FLAGS="-O0 -fPIC" -DCMAKE_CXX_FLAGS="-O0 -fPIC" -DLINKER_LANGUAGE=C -DCMAKE_CXX_COMPILER=clang -DCMAKE_C_COMPILER=clang && \
+    cmake --build . --target gmx_bc libgromacs_bc && \
+    cd ./llvm-ir/gmx_bc && \
+    llvm-dis ./*.bc 

gromacs/README.md

@@ -0,0 +1,17 @@
+# Half Baked Gromacs
+
+Let's build the half baked image, manually first. This is going to use [llvm-ir-cmake-utils](https://github.com/compor/llvm-ir-cmake-utils).
+
+```bash
+docker build -t half-baked-gromacs .
+```
+
+Build the image, then inside at `/opt/gromacs-5.1.2/build/llvm-ir/gmx_bc`. Note that this is only possible
+if you disable libgromacs.
+
+```bash
+for filename in $(ls *.ll); do
+    llc -filetype=obj -O0 --relocation-model=pic --runtime-counter-relocation --relax-elf-relocations  $filename -o $filename.o
+done
+clang -lstdc++ -lm *.o -o gmx
+```