Tested on (Requirements)

• OS base: CentOS (x86_64) \(\boldsymbol{\ge}\) 6.6 (Rocks 6.2)
• Compiler: Intel Parallel Studio XE Cluster Edition \(\boldsymbol{\ge}\) 17.0.1
• MPI: Intel MPI \(\boldsymbol{\ge}\) 17.0.1
• Scheduler: SLURM \(\boldsymbol{\ge}\) 16.05.6

Build process

1. Get source code from the github repository (RAxML Releases).

   cd ~/apps/raxml/src/intel
   wget https://github.com/stamatak/standard-RAxML/archive/v8.2.12.tar.gz
   tar -zxvf v8.2.12.tar.gz
   

2. To build RAxML follow next steps:

   Apolo II

   1. Create a new Makefile for your particular environment

      (i.e. AVX2 instruction set and the supported MPI implementation)

      # Go to source directory
      cd standard-RAxML-8.2.12
      # Load the necessary environment
      module load impi/2017_update-1
      # Create a new Makefile
      cp Makefile.AVX2.HYBRID.gcc Makefile.AVX2.HYBRID.icc
      

   2. Add Intel MPI support editing the Makefile (Makefile.AVX2.HYBRID.icc)

      # From
      CC = mpicc
      # To
      CC = mpiicc
      

   3. Build RAxML and deploy it

      make -f Makefile.AVX2.HYBRID.icc 2>&1 | tee raxml-make.log
      sudo mkdir -p /share/apps/raxml/8.2.12/intel-17.0.1/bin
      sudo cp raxmlHPC-HYBRID-AVX2 /share/apps/raxml/8.2.12/intel-17.0.1/bin
      

      Note

      If something goes wrong, check the raxml-make.log file to review the build process.

Cronos

1. Create a new Makefile for your particular environment

   (i.e. AVX instruction set and the supported MPI implementation)

   # Go to source directory
   cd standard-RAxML-8.2.12
   # Load the necessary environment
   module load impi/18.0.2
   # Create a new Makefile
   cp Makefile.AVX.HYBRID.gcc Makefile.AVX.HYBRID.icc
   

2. Add Intel MPI support editing the Makefile (Makefile.AVX.HYBRID.icc)

   # From
   CC = mpicc
   # To
   CC = mpiicc
   

3. Build RAxML and deploy it

   make -f Makefile.AVX.HYBRID.icc 2>&1 | tee raxml-make.log
   sudo mkdir -p /share/apps/raxml/8.2.12/intel-18.0.2/bin
   sudo cp raxmlHPC-HYBRID-AVX /share/apps/raxml/8.2.12/intel-18.0.2/bin
   

   Note

   If something goes wrong, check the raxml-make.log file to review the build process.

Modulefile

Apolo II

Module file

#%Module1.0####################################################################
##
## module load raxml/8.2.12_intel-17.0.1
##
## /share/apps/modules/raxml/8.2.12_intel-17.0.1
## Written by Mateo Gómez Zuluaga
##

proc ModulesHelp {} {
     global version modroot
     puts stderr "Sets the environment for using raxml 8.2.12\
		  \nin the shared directory \
		  \n/share/apps/raxml/8.2.12/intel-17.0.1\
		  \nbuilded with Intel Parallel Studio Cluster Edition XE 17.0.1\
		  \n"
}

module-whatis "(Name________) raxml"
module-whatis "(Version_____) 8.2.12"
module-whatis "(Compilers___) intel-17.0.1"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) "

# for Tcl script use only
set         topdir        /share/apps/raxml/8.2.12/intel-17.0.1
set         version       8.2.12
set         sys           x86_64-redhat-linux

conflict raxml
module load impi/2017_update-1
 
prepend-path	PATH			$topdir/bin

Cronos

Module file

#%Module1.0####################################################################
##
## module load raxml/8.2.12_intel-18.02
##
## /share/apps/modules/raxml/8.2.12_intel-18.02
## Written by Mateo Gómez Zuluaga
##

proc ModulesHelp {} {
     global version modroot
     puts stderr "Sets the environment for using raxml 8.2.12\
		  \nin the shared directory \
		  \n/share/apps/raxml/8.2.12/intel-18.02\
		  \nbuilded with Intel Parallel Studio Cluster Edition XE 18.02\
		  \n"
}

module-whatis "(Name________) raxml"
module-whatis "(Version_____) 8.2.12"
module-whatis "(Compilers___) intel-18.02"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) "

# for Tcl script use only
set         topdir        /share/apps/raxml/8.2.12/intel-18.02
set         version       8.2.12
set         sys           x86_64-redhat-linux

conflict raxml
module load impi/18.0.2
 
prepend-path	PATH			$topdir/bin