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29 container image for tracking memory usage (#40)
* Adding valgrind container * to revert - run build * completing exclusion criteria * fixing path to R installation * single include for valgrind * to revert - targeting only valgrind * fixing wrong R path * adding DrMemory * fixing path * minor cleaning up * make it executable
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| @@ -0,0 +1,119 @@ | ||
| # Before the build stage | ||
| ARG TARGET_OS | ||
| ARG COMPILER | ||
| ARG R_VERSION | ||
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| # For the valgrind container, target_os, compiler and r_vresion are not specified | ||
| # Hovever, the valgrind container is fedora, gcc, devel | ||
| # see https://r-hub.github.io/containers/containers.html#valgrind | ||
| FROM rhub/${TARGET_OS} | ||
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| # Build stage: ARGs need to be redeclared | ||
| ARG TARGET_OS | ||
| ARG COMPILER | ||
| ARG R_VERSION | ||
| # ARG PACKAGE | ||
| ARG PACKAGE_PATH | ||
| ARG REPO_PATH | ||
| ARG JAGS | ||
| ARG DRMEMORY | ||
| # # sets the date for the CRAN snapshot (e.g. BUILD_DATE=2023-12-20) | ||
| # ARG BUILD_DATE | ||
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| # Update package repositories | ||
| RUN dnf check-update && dnf -y install \ | ||
| openssl-devel \ | ||
| libcurl-devel | ||
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| # Install dependencies for DrMemory | ||
| RUN dnf -y install libunwind | ||
| # Install DrMemory | ||
| ADD https://github.com/DynamoRIO/drmemory/releases/download/release_$DRMEMORY/DrMemory-Linux-$DRMEMORY.tar.gz /tmp/drmemory.tar.gz | ||
| WORKDIR /tmp/ | ||
| RUN mkdir -p /opt/DrMemory | ||
| RUN tar -xf drmemory.tar.gz --directory /opt/DrMemory | ||
| RUN rm drmemory.tar.gz | ||
| # add DrMemory to PATH | ||
| RUN chmod 755 /opt/DrMemory/DrMemory-Linux-$DRMEMORY/bin/drmemory | ||
| ENV PATH="/opt/DrMemory/DrMemory-Linux-$DRMEMORY/bin:${PATH}" | ||
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| # add R to PATH | ||
| ENV PATH="/opt/R/devel-valgrind/bin:${PATH}" | ||
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| # diff to debian: /lib/ > /lib64/ | ||
| # ENV PATH "$PATH:/opt/R-devel/bin/" | ||
| # Set a mirror for CRAN | ||
| RUN RPATH=/opt/R/devel-valgrind \ | ||
| && echo 'options(repos =c(CRAN = "https://cran.rstudio.com"))' >> ${RPATH}/lib/R/library/base/R/Rprofile | ||
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| # rjags: | ||
| RUN dnf -y install \ | ||
| lapack* blas* atlas* | ||
| ADD https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/$JAGS.tar.gz/download /tmp/jags.tar.gz | ||
| WORKDIR /tmp/ | ||
| RUN tar -xf jags.tar.gz | ||
| RUN rm jags.tar.gz | ||
| WORKDIR /tmp/$JAGS | ||
| # Building JAGS requires the same environment that is then used to build rjags. | ||
| # To achieve this we follow the approach for building JAGS with Clang outlined | ||
| # in the JAGS installation guide | ||
| # (https://usermanual.wiki/Document/jagsinstallationmanual.880863585.pdf) | ||
| # and substitute the compilers with the specifics from the R installation that | ||
| # we can get by using the `R CMD config CC/CXX/BLAS_LIBS/LAPACK_LIBS' commands: | ||
| RUN if [ "$COMPILER" = "clang" ]; then RCC=/usr/bin/clang RCXX="/usr/bin/clang++ -std=gnu++17 -stdlib=libc++"; else RRCC=/usr/bin/gcc RCXX="/usr/bin/g++"; fi \ | ||
| && LD="llvm-ld" CC="${RCC}" CXX="${RCXX}" ./configure --with-blas="-L/opt/R/devel-valgrind/lib/R/lib -lRblas" --with-lapack="-L/opt/R/devel-valgrind/lib/R/lib -lRlapack" --libdir=/usr/local/lib && make && make install | ||
| RUN ls /tmp/$JAGS | ||
| # ENV PKG_CONFIG_PATH=/usr/local/lib/pkgconfig | ||
| # RUN R -e "install.packages('rjags')" | ||
| RUN R -e "install.packages('rjags', configure.args = '--enable-rpath')" | ||
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| # Get and install packages for local debugging | ||
| RUN R -e "install.packages('devtools')" \ | ||
| && R -e "install.packages('remotes')" \ | ||
| && R -e "install.packages('R.rsp')" \ | ||
| && R -e "install.packages('renv')" \ | ||
| && R -e "install.packages('desc')" | ||
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| # Prepare for potential check to be run | ||
| RUN R -e "install.packages('urlchecker')" | ||
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| # Install dependencies not managed by CRAN | ||
| # - lme4 and gsl: | ||
| RUN dnf -y install \ | ||
| gsl-devel \ | ||
| sqlite-devel \ | ||
| NLopt-devel | ||
| # RUN R -e "install.packages('lme4')" | ||
| # RUN R -e "install.packages('gsl')" | ||
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| # Graphviz | ||
| RUN R -e "install.packages('BiocManager')" \ | ||
| && R -e "BiocManager::install('Rgraphviz')" | ||
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| # INLA | ||
| # - sf | ||
| RUN dnf -y install \ | ||
| udunits2-devel gdal-devel geos-devel proj-devel | ||
| # RUN R -e "install.packages('sf')" | ||
| # - fmesher | ||
| RUN dnf -y install \ | ||
| udunits2-devel | ||
| # RUN R -e "install.packages('fmesher')" | ||
| # - INLA | ||
| RUN R -e "install.packages('INLA',repos=c(getOption('repos'),INLA='https://inla.r-inla-download.org/R/stable'), dep=TRUE)" | ||
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| ### | ||
| # install all package dependencies | ||
| ### | ||
| RUN dnf -y install \ | ||
| git \ | ||
| openssh-clients | ||
| WORKDIR /root/ | ||
| # get a shallow copy of the target repository | ||
| # # Note: If the repository is private you must use a deploy token here (ssh key) | ||
| # RUN --mount=type=secret,id=key,dst=/root/.ssh/key GIT_SSH_COMMAND="ssh -i /root/.ssh/key -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no" git clone --depth=1 git@$REPO_PATH target | ||
| RUN git clone --depth=1 https://$REPO_PATH target | ||
| WORKDIR target/ | ||
| # get a list of all dependencies; install remaining packages | ||
| # escape=\ | ||
| RUN R -e "renv::deactivate();pckgs<-unique(renv::dependencies('$PACKAGE_PATH')[,'Package']);pres_pckgs<-installed.packages()[,'Package'];install.packages(pckgs[!(pckgs %in% pres_pckgs)])" |