Software Build Documentation

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(shiny-server/1.4.4.802)
(shiny-server/1.4.4.802)
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== shiny-server/1.4.4.802 ==
== shiny-server/1.4.4.802 ==
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# <code>module load cmake/3.7.0-rc1</code>
+
<ol>
-
# <code>mkdir  <i>build-dir</i>/tmp</code>
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<li><code>module load cmake/3.7.0-rc1</code>
-
# <code>pushd <i>build-dir</i>/tmp</code>
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<li><code>mkdir  <i>build-dir</i>/tmp</code>
-
# <code>cmake -DCMAKE_INSTALL_PREFIX=${BCCD_SW}/shiny-server/1.4.4.802/${ARCHPATH} ../</code>
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<li><code>pushd <i>build-dir</i>/tmp</code>
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# <code>nice make -j3</code>
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<li><code>cmake -DCMAKE_INSTALL_PREFIX=${BCCD_SW}/shiny-server/1.4.4.802/${ARCHPATH} ../</code></li>
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# Edit <code>cmake_install.cmake</code>, and change in the block <code>file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/shiny-server" TYPE DIRECTORY FILES</code>
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<li><code>nice make -j3</code></li>
-
## Remove <code><i>build-dir</i>/build</code>
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<li>Edit <code>cmake_install.cmake</code>, and change in the block <code>file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/shiny-server" TYPE DIRECTORY FILES</code></li>
-
## Remove <code><i>build-dir</i>/node_modules</code>
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<ol>
-
# <code>module load shiny-server/1.4.4.802</code>
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  <li>Remove <code><i>build-dir</i>/build</code></li>
-
# Install needed Node.js packages: <code>sudo $(which npm) install log4j client-sessions posix</code>
+
  <li>Remove <code><i>build-dir</i>/node_modules</code></li>
-
# Fix the references to the <code>posix</code> module: <code>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/)</code>
+
</ol>
-
# Set to run as <code>bccd</code> user: <code>sudo perl -wpl -i -e 's!^run_as shiny$!run_as bccd!g' /etc/shiny-server/shiny-server.conf</code>
+
<li><code>module load shiny-server/1.4.4.802</code></li>
-
# <code>sudo cp -R node_modules /bccd/software/shiny-server/1.4.4.802/Linux/BCCD/x86_64</code>
+
<li>Install needed Node.js packages: <code>sudo $(which npm) install log4j client-sessions posix</code></li>
 +
<li>Fix the references to the <code>posix</code> module: <code>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/)</code></li>
 +
<li>Set to run as <code>bccd</code> user: <code>sudo perl -wpl -i -e 's!^run_as shiny$!run_as bccd!g' /etc/shiny-server/shiny-server.conf</code></li>
 +
<li>Add to the init script:</li>
 +
<ol>
 +
  <li>Modules (before <code>NAME</code>):
 +
<pre>
 +
# Modules
 +
. /usr/local/Modules/3.2.10/init/bash
 +
module load modules shiny-server/1.4.4.802
 +
</pre></li>
 +
  <li>
 +
</ol>
 +
<li><code>sudo cp -R node_modules /bccd/software/shiny-server/1.4.4.802/Linux/BCCD/x86_64</code></li>
 +
</ol>
= BCCD 3.4.0 =
= BCCD 3.4.0 =

Revision as of 03:03, 18 October 2016

Contents

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. 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
  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

See Software Build

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