Compiling RAxML and ExaML

RAxML and ExaML are phylogenetic inferences codes.[1]

Compiling RAxML

We will compile the AVX-enabled, threaded, non-MPI version using GCC.

First, create a directory for the source:

[juser@proteusa01 ~]$ cd [juser@proteusa01 ~]$ mkdir src [juser@proteusa01 ~]$ cd src

Download from github by cloning the repository. At https://github.com/stamatak/standard-RAxML the clone link is in the right sidebar, towards the bottom:

This creates the directory standard-RAxML

Make sure these are the loaded modules:

Currently Loaded Modulefiles: 1) shared 2) proteus 3) sge/univa 4) gcc/4.8.1

Clear any environment variables:

[juser@proteusa01 ~]$ unset CFLAGS CXXFLAGS

NOTE Do not use AVX2 - none of the compute nodes in Proteus support AVX2.

Build:

[juser@proteusa01 src]$ cd standard-RAxML [juser@proteusa01 src]$ make -f Makefile.AVX.PTHREADS.gcc -j 16 > & Make.out &

This creates the executable

raxmlHPC-PTHREADS-AVX

We will compile with GCC and OpenMPI.

First, create a directory for the source:

[juser@proteusa01 ~]$ cd [juser@proteusa01 ~]$ mkdir src [juser@proteusa01 ~]$ cd src

Download from the github repository: https://github.com/stamatak/ExaML

This creates the directory named ExaML.

These are the loaded modules:

Currently Loaded Modulefiles: 1) shared 3) sge/univa 5) proteus-openmpi/gcc/64 2) proteus 4) gcc/4.8.1

Clear any environment variables:

[juser@proteusa01 ~]$ unset CFLAGS CXXFLAGS

[juser@proteusa01 src]$ cd ExaML/examl [juser@proteusa01 examl]$ make -f Makefile.AVX.gcc -j 16 >& Make.out &

This produces the executable:

examl-AVX

Since this is an MPI program, it must be run in a parallel environment, and using mpirun:

#$ -pe openmpi_ib 512 ... module load gcc module load proteus-openmpi/gcc ... mpirun -n $NSLOTS examl-AVXargs`` ``...