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+title = "Running OGS With MPI for parallel computing"
+date = "2022-05-06T11:20:34+02:00"
+author = "Wenqing Wang"
+weight = 2
+
+[menu]
+ [menu.userguide]
+ parent = "basics"
++++
+
+The executable OGS for MPI parallel computing is compiled with special
+ build configuration. If you need to compile the source code, please read
+ [Build configuration for MPI and PETSc]({{<ref "configure_for_mpi_and_petsc.md">}}).
+
+To conduct DDC enabled parallel computing with OGS, following steps are required:
+
+### 1. Prepare input data
+#### 1.1 Partition mesh
+For the domain decomposition approach, an application of OGS using METIS as a node wise
+ mesh topology partitioner, [`partmesh`]({{<ref
+"mesh-partition">}}), is provided to partition meshes by node. An example of how
+ to partition meshes is available in a workflow documentation on how to [create a simple parallel model]({{<ref
+"create-a-simple-parallel-model">}}). You can type `partmesh --help` for the detailed
+command line options.
+
+The partitioned meshes are written in binary files for a fast parallel reading
+ in ogs.
+
+#### 1.2 Configure PETSc solver in project file
+
+Setting PETSc solver is the only change in project file for running parallel ogs with PETSc.
+For linear solver, it is done by adding a tag of `petsc` inside `linear_solver` tag,
+ e.g:
+```
+ <linear_solvers>
+ <linear_solver>
+ <name>linear_solver</name>
+ <eigen>
+ <solver_type>SparseLU</solver_type>
+ <scaling>true</scaling>
+ </eigen>
+ <petsc>
+ <parameters>-ksp_type bcgs
+ -pc_type jacobi
+ -ksp_rtol 1.e-16 -ksp_atol 1.e-12
+ -ksp_max_it 4000
+ </parameters>
+ </petsc>
+ </linear_solver>
+ </linear_solvers>
+```
+If tag of `petsc` is not given in project file, the default setting of PETSc
+ linear solver will be taken, which uses the solver type of `cg` and
+ the preconditioner type of `jacobi`.
+
+For the simulation of coupled processes with the staggered scheme, a prefix
+can be used by tag `prefix` to set PETSc solver for each process, individually.
+ For example:
+```
+ <linear_solvers>
+ <linear_solver>
+ <name>linear_solver_T</name>
+ <petsc>
+ <prefix>T</prefix>
+ <parameters>-T_ksp_type bcgs
+ -T_pc_type bjacobi
+ -T_ksp_rtol 1e-16
+ -T_ksp_max_it 3000
+ </parameters>
+ </petsc>
+ </linear_solver>
+ <linear_solver>
+ <name>linear_solver_H</name>
+ <petsc>
+ <prefix>H</prefix>
+ <parameters>-H_ksp_type bcgs
+ -H_pc_type mg
+ -H_ksp_rtol 1e-12
+ -H_ksp_max_it 4000
+ </parameters>
+ </petsc>
+ </linear_solver>
+ </linear_solvers>
+```
+The above example shows that once a prefix is given for PETSc linear solver
+ settings, the original prefix of PETSc
+ keyword, `-`, can be replaced with a new prefix, `-[given prefix string]_`. In the
+above example, `-`, is replaced with `-T_` and `-H_`, respectively.
+
+A introduction and a list of of PETSc ksp solvers and preconditioners can be found by
+[this link](https://petsc.org/main/docs/manual/ksp/).
+
+### 2. Launch MPI OGS
+For MPI launcher, either *mpiexec* or *mpirun* can be used to run OGS.
+ Preferably, *mpiexec* is recommended because it is defined in the MPI standard.
+The number of processes to run of *mpiexec* must be identical to the number of
+ mesh partitions.
+For example, if the meshes of a project, foo.prj, are partitioned into 5 partitions,
+ OGS can be launched in MPI as
+```
+mpiexec -n 5 ogs foo.prj -o [path to the output directory]
+```
+
+Running PETSc enabled OGS with one compute thread does not need mesh partitioning.
+ However, the MPI launcher mpiexc or mpirun is required, e.g.:
+```
+mpiexec -n 1 ogs ...
+```
+
+Additional PETSc command line options can be given as unlabelled arguments at the end of the ogs run command preceded by two minus-signs
+(`... ogs ... -- [PETSc options]`).
+
+With PETSc command line options, you can
+* monitor ksp solver convergence status, e.g.
+```
+ mpiexec -n 5 ogs foo.prj -o output -- -ksp_converged_reason -ksp_monitor_true_residual
+```
+* change ksp solver setting, e.g.:
+```
+ mpiexec -n 5 ogs foo.prj -o output -- -ksp_type gmres -ksp_rtol 1e-16 -ksp_max_it 2000
+```
+* or use other PETSc command line options.
+
+For Linux clusters or supercomputer, computation job has to be submitted to
+ queue and job management system, which may provide a special command to
+ launch MPI job. A job script for such
+ queue system is required.
+
+The cluster system EVE of UFZ uses SLURM
+ (Simple Linux Utility for Resource Management) to manage computing jobs.
+Here is an example of job script for the SLURM system on EVE:
+```
+#!/bin/bash
+#SBATCH --job-name=ARESH_HM_3D_20
+#SBATCH --chdir=/home/wwang/data_D/project/AREHS/HM_3D
+#SBATCH --output=/home/wwang/data_D/project/AREHS/HM_3D/output/log_%x_%j.txt
+#SBATCH --error=/home/wwang/data_D/project/AREHS/HM_3D/output/err_%x_%j.txt
+#SBATCH --time=0-48:00:00
+#SBATCH -n 20
+#SBATCH --mem-per-cpu=4G
+
+#SBATCH --mail-user=wenqing.wang@ufz.de
+#SBATCH --mail-type=BEGIN,END
+
+###source /etc/profile.d/000-modules.sh
+export MODULEPATH="/software/easybuild-broadwell/modules/all/Core:/software/modulefiles"
+module load foss/2020b petsc-bilke/3.16.5_foss2020b
+module load OpenMPI/4.0.5 HDF5/1.10.7 GMP/6.2.0
+
+APP="/home/wwang/code/ogs6/exe_petsc/bin/ogs"
+/bin/echo In directory: `pwd`
+/bin/echo Number of CPUs: $SLURM_CPUS_PER_TASK
+/bin/echo File name: $1
+
+##load $APP
+
+srun -n "$SLURM_NTASKS" $APP /home/wwang/data_D/project/AREHS/HM_3D/simHM_glaciation.prj -o /home/wwang/data_D/project/AREHS/HM_3D/output
+```
+In the job script for EVE, `module load foss/2020b` must be presented, and
+ srun is a sort of MPI job launcher.
+ If a job fails with an error message about shared library not found, you can check
+ the EVE modules specified in the files in source code directory:
+ *scripts/env/eve*, and add the corresponding modules to the load list
+in the job script.
+
+Once the the job script is ready, you can
+ - submit the job by command, `sbatch [job script name]`,
+ - check the job status by command `squeue`,
+ - or cancel the job by command `scancel [job ID]`.
+
+
+For the detailed syntax of job script of SLURM for EVE, please visit https://wiki.ufz.de/eve/
+(user login required).
+
+### 3. Check results
+There are two output types available, VTK and XMDF.
+In the project file, output type can be specified in `type` tag of `output` tag,
+for example:
+```
+ <output>
+ <type>VTK</type>
+ ...
+ </output>
+```
+or
+```
+ <output>
+ <type>XDMF</type>
+ ...
+ </output>
+```
+
+#### 3.1 VTK output
+The results are output in the partitioned vtu files, which are governed by
+ a pvtu file. The data in the ghost cells of vtu files are overlapped.
+An OGS utility, *RemoveGhostData*, is available to merge the partition vtu files into one vtu file,
+meanwhile to eliminate the data overlapping. Here is an example to use that utility:
+```
+RemoveGhostData -i foo.pvtu -o foo.vtu
+```
+where the input file name is the name of pvtu file.
+
+#### 3.2 XMDF output
+With XMDF, ogs gives two files, one XMDF file and one HDF5 file with file name
+ extension of `h5`. You can use ParaView to open the XDMF file by selecting
+ `Xdmf3ReaderS` or `Xdmf3ReaderT`. The XMDF output is highly recommended for
+ running OGS with a large mesh, especially on supercomputers.
+