software:specfem
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software:specfem [2017/03/29 13:41] wphase |
software:specfem [2018/03/05 16:06] (current) wphase |
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| ====== SPECFEM3D_GLOBE ====== | ====== SPECFEM3D_GLOBE ====== | ||
| + | |||
| ==== Running SPECFEM3D_GLOBE on the Strasbourg HPC cluster with gnu 4.8 and cuda 7.5 ==== | ==== Running SPECFEM3D_GLOBE on the Strasbourg HPC cluster with gnu 4.8 and cuda 7.5 ==== | ||
| Line 9: | Line 10: | ||
| module load batch/slurm | module load batch/slurm | ||
| module load compilers/cuda-7.5 | module load compilers/cuda-7.5 | ||
| - | module load mpi/openmpi-basic | + | export CUDA_INC=/usr/local/cuda/cuda-7.5/include |
| export CUDA_LIB=/usr/local/cuda/cuda-7.5/lib64 | export CUDA_LIB=/usr/local/cuda/cuda-7.5/lib64 | ||
| - | export CUDA_INC=/usr/local/cuda/cuda-7.5/include | + | 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 | ||
| </code> | </code> | ||
| Notice that we use default gnu compiler of the operating system: | Notice that we use default gnu compiler of the operating system: | ||
| Line 20: | Line 22: | ||
| === Compilation === | === Compilation === | ||
| - | Before compilation, make sure that you are logged in hpc-n523 (the frontal node is not yet migrated on the new OS): | + | 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''. |
| - | <code> | + | |
| - | ssh hpc-n523 | + | |
| - | </code> | + | |
| - | + | ||
| - | First 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). | In the directory ''DATA'', create ''CMTSOLUTION'', ''Par_file'' and ''STATIONS'' file (cf., SPECFEM3D_GLOBE documentation). | ||
| Line 59: | Line 56: | ||
| <code> | <code> | ||
| #!/bin/bash | #!/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 | # source directory | ||
| Line 76: | Line 81: | ||
| # configure | # configure | ||
| - | ./configure -with-gpu=cuda5 | + | ./configure -with-cuda=cuda5 |
| # compiles for a forward simulation | # compiles for a forward simulation | ||
| Line 116: | Line 121: | ||
| #SBATCH -t 23:00:00 # Wall time | #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 Master on host `hostname` | ||
| echo Time is `date` | echo Time is `date` | ||
| Line 196: | Line 207: | ||
| #SBATCH -t 12:00:00 # Wall time | #SBATCH -t 12:00:00 # Wall time | ||
| #SBATCH --cpu_bind=verbose | #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) | # ID of each GPU (should be adapted if using a different number of GPUs) | ||
| Line 264: | Line 281: | ||
| echo CPUtime : $(squeue -j $SLURM_JOBID -o "%M" -h) # HH:MM:SS | echo CPUtime : $(squeue -j $SLURM_JOBID -o "%M" -h) # HH:MM:SS | ||
| </code> | </code> | ||
| + | |||
| + | |||
| + | |||
| + | ==== 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: | ||
| + | <code> | ||
| + | $ cat nodelist0 | ||
| + | hpc-n443 slots=8 | ||
| + | hpc-n444 slots=8 | ||
| + | hpc-n445 slots=8 | ||
| + | </code> | ||
| + | (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: | ||
| + | <code> | ||
| + | ./parallelSEM.sh | ||
| + | </code> | ||
| + | The script will make sure that the GPU nodes are available before launching SPECFEM3D_GLOBE. | ||
| + | |||
| + | |||
| + | |||
| + | |||
software/specfem.1490787713.txt.gz · Last modified: 2017/03/29 13:41 by wphase
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