title: Installing Rmpi on centos with intel mpi
body: <p>I am trying to install Rmpi in package in R, with intel mpi installed. First I downloaded Rmpi, and the processed by following comand:</p>
  
  <p><strong>Command line</strong></p>
  
  <pre><code>R CMD INSTALL --configure-args="--with-mpi=/opt/intel_2015/impi/5.0.1.035/intel64/" Rmpi_0.6-5.tar.gz
  </code></pre>
  
  <p>But it didn't install, instead it shows the following result:</p>
  
  <p><strong>Log</strong></p>
  
  <pre><code>* installing to library ‘/home/user/R/x86_64-pc-linux-gnu-library/3.2’
  * installing *source* package ‘Rmpi’ ...
  ** package ‘Rmpi’ successfully unpacked and MD5 sums checked
  checking for gcc... icc -std=gnu99
  checking whether the C compiler works... yes
  checking for C compiler default output file name... a.out
  checking for suffix of executables... 
  checking whether we are cross compiling... no
  checking for suffix of object files... o
  checking whether we are using the GNU C compiler... yes
  checking whether icc -std=gnu99 accepts -g... yes
  checking for icc -std=gnu99 option to accept ISO C89... none needed
  Trying to find mpi.h ...
  Found in /opt/intel_2015/impi/5.0.1.035/intel64//include
  Trying to find libmpi.so or libmpich.a ...
  Found libmpi in /opt/intel_2015/impi/5.0.1.035/intel64//lib
  checking for openpty in -lutil... yes
  checking for main in -lpthread... yes
  configure: error: Unknown type of mpi: use --with-Rmpi-type or RMPI_TYPE to specify it
  ERROR: configuration failed for package ‘Rmpi’
  * removing ‘/home/user/R/x86_64-pc-linux-gnu-library/3.2/Rmpi’
  * restoring previous ‘/home/user/R/x86_64-pc-linux-gnu-library/3.2/Rmpi’
  </code></pre>
  
  <p>Then I used <code>--with-Rmpi-type='MPI2CH'</code> and <code>--with-Rmpi-type='OPENMPI'</code> Nothing worked, I know It must be the mpi type problem. But I tried everything I can find, still can't figure it out. 
  <strong>Architecture</strong></p>
  
  <ul>
  <li>Centos 6.7 final  </li>
  <li>R-3.2.3</li>
  <li>Rmpi_0.6-5</li>
  </ul>
  
  <p>Following is my <code>.bashrc</code> file of intel</p>
  
  <pre><code>source /opt/intel_2015/bin/compilervars.sh intel64
  source /opt/intel_2015/impi/5.0.1.035/bin64/mpivars.sh
  source /opt/intel_2015/composer_xe_2015.0.090/mkl/bin/mklvars.sh intel64
  source /opt/intel_2015/bin/iccvars.sh intel64
  </code></pre>
  
  <p>After I tried the following command:</p>
  
  <pre><code>R CMD INSTALL --configure-args="\
  --with-Rmpi-include='/opt/intel_2015/impi/5.0.1.035/intel64/include' \
  --with-Rmpi-libpath='/opt/intel_2015/impi/5.0.1.035/intel64/lib' \
  --with-mpi='/opt/intel_2015/impi/5.0.1.035/intel64' \
  --with-Rmpi-type='OPENMPI' " Rmpi_0.6-5.tar.gz
  </code></pre>
  
  <p>It shows the following result, still something wrong, but promising:</p>
  
  <pre><code>* installing *source* package ‘Rmpi’ ...
  ** package ‘Rmpi’ successfully unpacked and MD5 sums checked
  checking for openpty in -lutil... no
  checking for main in -lpthread... no
  configure: creating ./config.status
  config.status: creating src/Makevars
  ** libs
  icc -std=gnu99 -I/opt/R-3.2.3MKL/lib64/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/opt/intel_2015/impi/5.0.1.035/intel64/include  -DMPI2 -DOPENMPI -I/usr/local/include    -fpic  -ip -O3 -opt-mem-layout-trans=3 -xHost -march=core-avx2 -wd188 -fp-model precise  -c Rmpi.c -o Rmpi.o
  icc -std=gnu99 -I/opt/R-3.2.3MKL/lib64/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/opt/intel_2015/impi/5.0.1.035/intel64/include  -DMPI2 -DOPENMPI -I/usr/local/include    -fpic  -ip -O3 -opt-mem-layout-trans=3 -xHost -march=core-avx2 -wd188 -fp-model precise  -c conversion.c -o conversion.o
  icc -std=gnu99 -I/opt/R-3.2.3MKL/lib64/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/opt/intel_2015/impi/5.0.1.035/intel64/include  -DMPI2 -DOPENMPI -I/usr/local/include    -fpic  -ip -O3 -opt-mem-layout-trans=3 -xHost -march=core-avx2 -wd188 -fp-model precise  -c internal.c -o internal.o
  icc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so Rmpi.o conversion.o internal.o -L/opt/intel_2015/impi/5.0.1.035/intel64/lib -lmpi
  installing to /home/user/R/x86_64-pc-linux-gnu-library/3.2/Rmpi/libs
  ** R
  ** demo
  ** inst
  ** preparing package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded
  * DONE (Rmpi)
  </code></pre>