SPECFEM3D_GLOBE
- - Running SPECFEM3D_GLOBE on the Strasbourg HPC cluster with gnu 4.8 and cuda 7.5
  - Running SEM simulations in parallel
    - Preparing the input files
    - Running the simulations in parallel

SPECFEM3D_GLOBE

Running SPECFEM3D_GLOBE on the Strasbourg HPC cluster with gnu 4.8 and cuda 7.5

Setup the environment

Load modules and declare environment variables as follows:

module purge
module load batch/slurm
module load compilers/cuda-7.5
export CUDA_INC=/usr/local/cuda/cuda-7.5/include
export CUDA_LIB=/usr/local/cuda/cuda-7.5/lib64
export PATH=/rpriv/ipgs/zac/openmpi-1.10.7/bin:$PATH
export LD_LIBRARY_PATH=/rpriv/ipgs/zac/openmpi-1.10.7/lib:$LD_LIBRARY_PATH

Notice that we use default gnu compiler of the operating system:

$ gfortran --version
GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)

Compilation

Before compilation, make sure that required modules are loaded and CUDA_LIB, CUDA_INC environment variables are declared (see previous section). Create a run directory including directories DATABASE_MPI, OUTPUT_FILES, bin and DATA. In the directory DATA, create CMTSOLUTION, Par_file and STATIONS file (cf., SPECFEM3D_GLOBE documentation).

Change directory to the main specfem3D_globe directory. Copy the Par_file of the run directory into DATA of the main specfem3D_globe directory. You can then run configure:

./configure -with-cuda=cuda5

(the cuda5 option will enable more recent GPU compute capabilities).

Then compile the code:

make clean
make all

Copy binaries to the run directory and backup setup files:

cp bin/xmeshfem3D $rundir/bin
cp bin/xspecfem3D $rundir/bin
cp setup/* $rundir/OUTPUT_FILES/
cp DATA/Par_file $rundir/OUTPUT_FILES/

Link model directories. For example with s362ani:

ln -s DATA/crust2.0   $rundir/DATA/crust2.0
ln -s DATA/s362ani    $rundir/DATA/s362ani
ln -s DATA/QRFSI12    $rundir/DATA/QRFSI12
ln -s DATA/topo_bathy $rundir/DATA/topo_bathy

Below is a script doing all the configuration and compilation:

#!/bin/bash

# Load modules 
module purge
module load batch/slurm
module load compilers/cuda-7.5
module load mpi/openmpi-basic
export CUDA_LIB=/usr/local/cuda/cuda-7.5/lib64
export CUDA_INC=/usr/local/cuda/cuda-7.5/include

# source directory
rootdir=/b/home/ipgs/cmorales/specfem3d_globe

# setting up run directory
currentdir=`pwd`

mkdir -p DATABASES_MPI
mkdir -p OUTPUT_FILES

rm -rf DATABASES_MPI/*
rm -rf OUTPUT_FILES/*

# configure and compile in the source directory
cd $rootdir

# configure
./configure -with-cuda=cuda5

# compiles for a forward simulation
cp $currentdir/DATA/Par_file DATA/Par_file
make clean
make all

# backup of constants setup
cp setup/* $currentdir/OUTPUT_FILES/
cp DATA/Par_file $currentdir/OUTPUT_FILES/

# Copy executables/Model in the current directory
cd $currentdir

# copy executables
mkdir -p bin
cp $rootdir/bin/xmeshfem3D ./bin/
cp $rootdir/bin/xspecfem3D ./bin/

# Links data necessary directories 
# The example below is for s362ani... this part should be changed if another model is used
cd DATA/
ln -s $rootdir/DATA/crust2.0
ln -s $rootdir/DATA/s362ani
ln -s $rootdir/DATA/QRFSI12
ln -s $rootdir/DATA/topo_bathy
cd ../

Run with CPU

Example of slurm script (number of CPU cores should be adapted to NPROC_XI and NPROC_ETA:

#!/bin/bash
#SBATCH -p grant -A g2016a68   # Partition / Account
#SBATCH -n 96                  # Number of CPU cores
#SBATCH --job-name=SPECFEM
#SBATCH -t 23:00:00            # Wall time

# Load modules 
module purge
module load batch/slurm
module load mpi/openmpi-basic

# 
echo Master on host `hostname`
echo Time is `date`

# Start time
begin=`date +"%s"`

# Run
BASEMPIDIR=`grep LOCAL_PATH DATA/Par_file | cut -d = -f 2 `
NPROC_XI=`grep NPROC_XI DATA/Par_file   | cut -d = -f 2 `
NPROC_ETA=`grep NPROC_ETA DATA/Par_file  | cut -d = -f 2`
NCHUNKS=`grep NCHUNKS DATA/Par_file    | cut -d = -f 2 `
numcpus=$(( $NCHUNKS * $NPROC_XI * $NPROC_ETA ))

# numcpus should be consistent with the -n option

mkdir -p OUTPUT_FILES
# backup files used for this simulation
cp DATA/Par_file OUTPUT_FILES/
cp DATA/STATIONS OUTPUT_FILES/
cp DATA/CMTSOLUTION OUTPUT_FILES/

##
## mesh generation
##
sleep 2

echo
echo `date`
echo "starting MPI mesher on $numcpus processors"
echo 

mpirun -np $numcpus bin/xmeshfem3D

echo "  mesher done: `date`"
echo

# backup important files addressing.txt and list*.txt 
cp OUTPUT_FILES/*.txt $BASEMPIDIR/

##
## forward simulation
##

# set up addressing
#cp $BASEMPIDIR/addr*.txt OUTPUT_FILES/
#cp $BASEMPIDIR/list*.txt OUTPUT_FILES/

sleep 2

echo
echo `date`
echo starting run in current directory $PWD
echo 

mpirun -np $numcpus bin/xspecfem3D
/bin/rm -rf DATABASES_MPI

echo "finished successfully"
echo `date`

# Print time after running
echo Time is `date`
echo Walltime : $(expr `date +"%s"` - $begin)          # Seconds
echo CPUtime  : $(squeue -j $SLURM_JOBID -o "%M" -h)   # HH:MM:SS

Run with GPU

Example of slurm script (number of nodes should be adapted to the number of GPU per nodes and to NPROC_XI and NPROC_ETA:

#!/bin/bash
#SBATCH -p pri2015gpu -A eost
#SBATCH -N 3-3                 # Will use 3 nodes
#SBATCH --tasks-per-node 8     # 8 tasks per node
#SBATCH --gres=gpu:8           # We only want nodes with 8 GPUs
#SBATCH --job-name=SPECFEM      
#SBATCH -t 12:00:00            # Wall time
#SBATCH --cpu_bind=verbose 

# Load modules 
module purge
module load batch/slurm
module load compilers/cuda-7.5
module load mpi/openmpi-basic

# ID of each GPU (should be adapted if using a different number of GPUs)
export CUDA_VISIBLE_DEVICES=0,1,2,3,4,5,6,7  

echo Master on host `hostname`
echo Time is `date`

# Start time
begin=`date +"%s"`

# Run
BASEMPIDIR=`grep LOCAL_PATH DATA/Par_file | cut -d = -f 2 `
NPROC_XI=`grep NPROC_XI DATA/Par_file   | cut -d = -f 2 `
NPROC_ETA=`grep NPROC_ETA DATA/Par_file  | cut -d = -f 2`
NCHUNKS=`grep NCHUNKS DATA/Par_file    | cut -d = -f 2 `
numgpus=$(( $NCHUNKS * $NPROC_XI * $NPROC_ETA ))

mkdir -p OUTPUT_FILES

# backup files used for this simulation
cp -pf DATA/Par_file OUTPUT_FILES/
cp -pf DATA/STATIONS OUTPUT_FILES/
cp -pf DATA/CMTSOLUTION OUTPUT_FILES/

##
## mesh generation
##
sleep 2

echo
echo `date`
echo "starting MPI mesher on $numgpus processors"
echo 

mpirun -np $numgpus bin/xmeshfem3D

echo "  mesher done: `date`"
echo

# backup important files addressing.txt and list*.txt 
cp OUTPUT_FILES/*.txt $BASEMPIDIR/

##
## forward simulation
##

# set up addressing
#cp $BASEMPIDIR/addr*.txt OUTPUT_FILES/
#cp $BASEMPIDIR/list*.txt OUTPUT_FILES/

sleep 2

echo
echo `date`
echo starting run in current directory $PWD
echo 

mpirun -np $numgpus bin/xspecfem3D
/bin/rm -rf DATABASES_MPI

echo "finished successfully"
echo `date`

# Print time after running
echo Time is `date`
echo Walltime : $(expr `date +"%s"` - $begin)          # Seconds
echo CPUtime  : $(squeue -j $SLURM_JOBID -o "%M" -h)   # HH:MM:SS

Running SEM simulations in parallel

Some instructions to use custom scripts enabling parallel SEM simulations on the HPC cluster

Preparing the input files

First, create an event list “Events.txt” with 3 collumns:

1st column: event_id (will also be the name of the run directory)
2nd column: path to CMTSOLUTION file for this event
3nd column: path to STATION file for this event (can be the same for all events)

Then you must setup a Par_file (be careful to use a version of Par_file that is compatible with your SEM version)

Finally, you must setup hostfiles named nodelistN files where N=0,…,Np-1 (Np, the number of parallel SEM simulations). These files must specify host names and number of slots per node. Here is an example:

$ cat nodelist0 
hpc-n443 slots=8
hpc-n444 slots=8
hpc-n445 slots=8

(see /b/home/eost/zac/jobs/specfem/parallelSEM/nodelist0)

Running the simulations in parallel

Parallel SEM simulations are handled using 3 scripts:

parallelSEM.sh: is the main script, that compiles the code and run the simulations
run_gpu_nodelist.sh is the script used to run the mesher and solver
sleep.slurm is a script to reserve the GPU nodes

All these scripts are available in /b/home/eost/zac/jobs/specfem/parallelSEM

Before running your job, make sure that the input parameters in parallelSEM.sh are consistent with the input parameters stated above (see INPUT PARAMS in the main script). Specifically:

SPECFEMDIR: path to SPECFEM3D_GLOBE directory
Par_file: path to the Par_file used in simulations
Nparallel: Number of SEM simulations in parallel (make sure enough GPUs are available)
event_list: List of events with the format given above

Then run your simulations:

./parallelSEM.sh

The script will make sure that the GPU nodes are available before launching SPECFEM3D_GLOBE.

Table of Contents