Software Build Documentation

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BCCD 3.1.1

      1. module unload openmpi
      2. CC=$(which icc) CXX=$(which icpc) F77=$(which ifort) ./configure --prefix=${BCCD_SW}/mpich2/1.4.1p1/${ARCHPATH} --enable-fc --enable-cxx --enable-mpe --enable-strict --enable-shared --enable-sharedlibs=gcc --enable-dependencies --disable-checkpointing --with-mpe --disable-checkpointing --with-pm=mpd && make
      3. Delete share/{doc,examples*}
      4. Delete etc/mpd.conf symlink
      5. gzip share/man/man*/*

BCCD 3.2.1

BCCD 3.3.0

R/3.3.1

  1. Build zlib-1.2.8 and associated module (zlib 1.2.3.4 is too old and according to config.log a hack from Debian anyways)
    1. ruby1.9.1 /var/lib/gems/1.9.1/gems/fpm-1.4.0/bin/fpm -n zlib -v 1.2.8~v334 -a amd64 -s dir -t deb ${BCCD_SW}/zlib/1.2.8/${ARCHPATH} /usr/local/etc/modules/zlib/1.2.8
  2. Build bzip2-1.0.6 and associated module (again, Debian is too old)
    1. Add -fPIC to CFLAGS in Makefile
    2. ruby1.9.1 /var/lib/gems/1.9.1/gems/fpm-1.4.0/bin/fpm -n bzip2 -v 1.0.6~v334 -a amd64 -s dir -t deb ${BCCD_SW}/bzip2/1.0.6/${ARCHPATH} /usr/local/etc/modules/bzip2/1.0.6
  3. Build xz-5.2.2 and associated module (same story)
    1. ruby1.9.1 /var/lib/gems/1.9.1/gems/fpm-1.4.0/bin/fpm -n xz -v 5.2.2~v334 -a amd64 -s dir -t deb ${BCCD_SW}/xz/5.2.2/${ARCHPATH} /usr/local/etc/modules/xz/5.2.2

  1. Build pcre-8.39 and associated module
    1. ./configure --prefix=${BCCD_SW}/pcre/8.39/${ARCHPATH} --enable-utf
    2. ruby1.9.1 /var/lib/gems/1.9.1/gems/fpm-1.4.0/bin/fpm -n pcre -v 8.3.9~v334 -a amd64 -s dir -t deb ${BCCD_SW}/pcre/8.39/${ARCHPATH} /usr/local/etc/modules/pcre/8.39
  2. Build curl-7.50.8 (for HTTPS support)
    1. ruby1.9.1 /var/lib/gems/1.9.1/gems/fpm-1.4.0/bin/fpm -n curl -v 7.50.3~v334 -a amd64 -s dir -t deb ${BCCD_SW}/curl/7.50.3/${ARCHPATH} /usr/local/etc/modules/curl/7.50.3
  3. Install texinfo and texlive-latex-extra packages
    1. Touch docs/NEWS.pdf if you don't want to wait
  4. CFLAGS=F77=gfortran FC=gfortran CC=gcc CXX=g++ ./configure --prefix=${BCCD_SW}/R/3.3.1/${ARCHPATH} --enable-R-shlib --with-system-zlib --with-system-bzlib --with-system-pcre && make && make install
  5. ruby1.9.1 /var/lib/gems/1.9.1/gems/fpm-1.4.0/bin/fpm -n r -v 3.3.1~v334 -a amd64 -s dir -t deb -d 'bzip2 (>= 1.0.6~v334)' -d 'xz (>= 5.2.2~v334)' -d 'pcre (>= 8.3.9~v334)' -d 'curl (>= 7.5.0.3~v334)' -d 'zlib (>=1.2.8~v334)' ${BCCD_SW}/R/3.3.1/${ARCHPATH} /usr/local/etc/modules/R/3.3.1

cmake/3.7.0-rc1

  1. ./configure --prefix=${BCCD_SW}/cmake/3.7.0-rc1/${ARCHPATH} && make -j3 && make install
  2. ruby1.9.1 /var/lib/gems/1.9.1/gems/fpm-1.4.0/bin/fpm -n cmake -v 3.7.0-rc1 -a amd64 -s dir -t deb ${BCCD_SW}/cmake/3.7.0-rc1/${ARCHPATH} /usr/local/etc/modules/cmake/3.7.0-rc1

shiny-server/1.4.4.802

  1. module load cmake/3.7.0-rc1
  2. mkdir build-dir/tmp
  3. pushd build-dir/tmp
  4. cmake -DCMAKE_INSTALL_PREFIX=${BCCD_SW}/shiny-server/1.4.4.802/${ARCHPATH} ../
  5. nice make -j3
  6. Edit cmake_install.cmake, and change in the block file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/shiny-server" TYPE DIRECTORY FILES
    1. Remove build-dir/build
    2. Remove build-dir/node_modules
  7. module load shiny-server/1.4.4.802
  8. Install needed Node.js packages: sudo $(which npm) install log4j client-sessions posix
  9. Fix the references to the posix module: sudo perl -wpl -i -e 's!../../build/Release/posix!posix!g' $(grep -lr './../build/Release/posix' ${BCCD_SW}/shiny-server/1.4.4.802/${ARCHPATH}/shiny-server/)
  10. Edit the config file:
    1. Set to run as bccd user: sudo perl -wpl -i -e 's!^run_as shiny$!run_as bccd!g' /etc/shiny-server/shiny-server.conf
    2. Change site_dir to point to the BCCD user home directory: perl -wpl -i -e 's!site_dir /srv!site_dir /home/bccd!g' /etc/shiny-server/shiny-server.conf
  11. Add to the init script:
    1. Modules (before NAME):
      # Modules
      . /usr/local/Modules/3.2.10/init/bash
      module load modules shiny-server/1.4.4.802
      
  12. sudo cp -R node_modules /bccd/software/shiny-server/1.4.4.802/Linux/BCCD/x86_64

BCCD 3.4.0

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