azurehpc/tutorials/oil_and_gas_opm

Build a PBS compute cluster with a Windows visualization node to run OPM and ResInsight

Visualisation: config.json

This example will create an HPC cluster with a CentOS 7.6 headnode running PBS Pro 19.1 exporting a 4TB NFS space and multiple CentOS 7.6 HB60rs compute nodes; and a Windows visualization node. This tutorial uses NFS and RDP for simplicity but you can also easily set it up with an alternate storage or visualization solution using the examples here.

NOTE:

• MAKE SURE you have followed the steps in prerequisite before proceeding here

First initialise a new project. AZHPC provides the azhpc-init command that will help here. Running with the -s parameter will show all the variables that need to be set, e.g.

azhpc-init -c $azhpc_dir/tutorials/oil_and_gas_opm -d oil_and_gas_opm -s

The variables can be set with the -v option where variables are comma separated. The -d option is required and will create a new directory name for you.

azhpc-init -c $azhpc_dir/tutorials/oil_and_gas_opm -d oil_and_gas_opm -v location=southcentralus,resource_group=azhpc-cluster,win_password=[password or secret.azhpc-vault.winadmin-secret]

Create the cluster

cd oil_and_gas_opm
azhpc-build

Allow ~10 minutes for deployment.

To check the status of the VMs run

azhpc-status

Connect to the headnode and check PBS and NFS

$ azhpc-connect -u hpcuser headnode
Fri Jun 28 09:18:04 UTC 2019 : logging in to headnode (via headnode6cfe86.westus2.cloudapp.azure.com)
[hpcuser@headnode ~]$ pbsnodes -avS
vnode           state           OS       hardware host            queue        mem     ncpus   nmics   ngpus  comment
--------------- --------------- -------- -------- --------------- ---------- -------- ------- ------- ------- ---------
compuc407000003 free            --       --       10.2.4.8        --            224gb      60       0       0 --
compuc407000002 free            --       --       10.2.4.7        --            224gb      60       0       0 --
[hpcuser@headnode ~]$ sudo exportfs -v
/share/apps     <world>(sync,wdelay,hide,no_subtree_check,sec=sys,rw,secure,root_squash,no_all_squash)
/share/data     <world>(sync,wdelay,hide,no_subtree_check,sec=sys,rw,secure,root_squash,no_all_squash)
/share/home     <world>(sync,wdelay,hide,no_subtree_check,sec=sys,rw,secure,root_squash,no_all_squash)
/mnt/resource/scratch
                <world>(sync,wdelay,hide,no_subtree_check,sec=sys,rw,secure,root_squash,no_all_squash)
[hpcuser@headnode ~]$

To check the state of the cluster you can run the following commands
azhpc-connect -u hpcuser headnode
qstat -Q
pbsnodes -avS
df -h

Return to the deployment node to install applications

exit

Install applications

First copy the apps directory to the cluster. The azhpc-scp can be used to do this:

azhpc-scp -r $azhpc_dir/apps hpcuser@headnode:.

Alternatively you can checkout the azurehpc repository but you will need to update the paths to apps directory according to where you put it.

Install OPM

Run the install script:

azhpc-run -u hpcuser apps/opm/install_opm.sh

Note: this can be run when on the cluster

OPM requires that lapack be installed on all of the compute nodes. The scripts/app_opm_req.sh script was created and has been added as an install step in the config.json.

The full_install_opm.sh can be used to build everything from source.

ResInsight Installation

Run the install script:

azhpc-run -u hpcuser apps/resinsight/install_resinsight_v2019.04.sh

Connect to the headnode

azhpc-connect -u hpcuser headnode

Run the OPM norne scenario

To run on a single node with 30 cores run

qsub -l select=1:ncpus=30:mpiprocs=30,place=scatter:excl $HOME/apps/opm/flow_norne.sh

To run on two node with 30 cores run

qsub -l select=2:ncpus=15:mpiprocs=15,place=scatter:excl $HOME/apps/opm/flow_norne.sh

Notes:

• The job outputs files will be stored in \data\opm-data\norne\out_parallel.

Remote Visualization

Connect to the viznode using RDB (get the RDP file for nvnode from the Azure Portal)

• Username: hpcadmin
• Password:

Check that Y: and Z: drives are mapped to the NFS server

Note : Y: and Z: drives appears as disconnected while they are not.

Launch ResInsight from the Y: drive (Y:\resinsight\ResInsight-2019.04.0_oct-4.0.0_souring_win64\ResInsight) and then, from ResInsight, click import eclipse file. The result file is located on the Z: drive (Z:\opm-data\norne\out_parallel\NORNE_ATW2013.EGRID)