add bdas (#19)

Signed-off-by: vsoch <[email protected]>
Co-authored-by: vsoch <[email protected]>

.github/workflows/docker-builds.yaml

@@ -23,6 +23,7 @@ jobs:
                ["ovis-hpc", "ghcr.io/converged-computing/metric-ovis-hpc:latest"],
                ["kripke", "ghcr.io/converged-computing/metric-kripke:latest"],
                ["hpctoolkit", "ghcr.io/converged-computing/metric-hpctoolkit:latest"],
+               ["bdas", "ghcr.io/converged-computing/metric-bdas:latest"],
                ["laghos", "ghcr.io/converged-computing/metric-laghos:latest"],
                ["nekbone", "ghcr.io/converged-computing/metric-nekbone:latest"],
                ["lammps", "ghcr.io/converged-computing/metric-lammps:latest"],

bdas/Dockerfile

@@ -0,0 +1,51 @@
+ARG tag=latest
+FROM ubuntu:${tag}
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Example commands
+# mpirun -np num_ranks ./source/cxx/build/princomp num_local_rows num_global_cols
+# mpirun -np num_ranks Rscript princomp.r num_local_rows num_global_cols
+# 16 ranks, 50 total columns, and a total of 16,000 rows (local number of rows 1000)
+# mpirun -np 16 princomp 1000 50
+
+RUN apt-get update && \
+    apt-get install -y fftw3-dev fftw3 pdsh libfabric-dev libfabric1 \
+        openssh-client openssh-server \
+        dnsutils telnet strace cmake git g++ \
+        r-base r-base-dev \
+        unzip bzip2 \
+        openmpi-bin openmpi-common libopenmpi-dev libgtk2.0-dev \
+        libopenmpi-dev
+
+WORKDIR /opt
+RUN wget https://asc.llnl.gov/sites/asc/files/2020-09/BDAS_b4bcf27_0.zip && \
+    unzip BDAS_b4bcf27_0.zip && \
+    rm -rf __MACOSX && \
+    rm BDAS_b4bcf27_0.zip && \
+    path=$(ls .) && \
+    mv $path bdas && \
+    cd bdas/source/cxx && \
+    mkdir build && \
+    cd build && \
+    cmake ../ && \
+    make 
+
+WORKDIR /opt/bdas/source/r
+COPY ./install.R ./install.R
+RUN R CMD INSTALL rlecuyer_0.3-4.tar.gz && \
+    Rscript ./install.R && \
+    # This does not work
+    # R CMD INSTALL pbdMPI_0.3-3.tar.gz && \
+    R CMD INSTALL kazaam_0.2-0.tar.gz
+
+# Hack for ssh for now...
+RUN echo "        LogLevel ERROR" >> /etc/ssh/ssh_config && \
+    echo "        StrictHostKeyChecking no" >> /etc/ssh/ssh_config && \
+    echo "        UserKnownHostsFile=/dev/null" >> /etc/ssh/ssh_config && \
+    cd /root && \
+    mkdir -p /run/sshd && \
+    ssh-keygen -t rsa -N "" -f /root/.ssh/id_rsa && chmod og+rX . && \
+    cd .ssh && cat id_rsa.pub > authorized_keys && chmod 644 authorized_keys
+
+EXPOSE 22
+WORKDIR /opt/bdas

bdas/install.R

@@ -0,0 +1,2 @@
+install.packages('remotes')
+remotes::install_github("RBigData/pbdMPI")