Installing WRF and WPS

2018-08-07T12:51:26Z

Danie010:

==General config==
The following setup works for WRF version 4.0!

To install WRF download the WRF and WPS source code from
http://www2.mmm.ucar.edu/wrf/users/download/get_source.html
and untar into your directory

load the following modules:

* GCC OR INTEL
* HDF5
* NETCDF
* OpenMPI
* JasPER

Known good versions:

* gcc:
** jasper/gcc/64/1.900.1
** gcc/6.3.0
** hdf5/gcc/64/1.10.1
** netcdf/gcc/64/4.6.1
** openmpi/gcc/64/3.1.1

==WRF==

Run ./configure and choose the (dmpar) GNU (gfortran/gcc) option (34?)

Compile WRF as needed (em_real is used for model runs with real data, e.g. ERA-Interim, ECMWF, etc)

==WPS==

Run ./configure and choose the Linux x86_64, gfortran (serial) option (1?)

WPS Will attempt to find WRF in ../WRFv3. Override this with setting WRF_DIR.

Compile WPS

In namelist.wps edit the geog_data_path to

/lustre/backup/WUR/ESG/data/MODEL_DATA/WRF/geog_v4.0 (still needs to be created)

Installing WRF and WPS

2018-08-07T12:12:32Z

Danie010:

The following setup works for WRF version 4.0!

To install WRF download the WRF and WPS source code from
http://www2.mmm.ucar.edu/wrf/users/download/get_source.html
and untar into your directory

load the following modules:

1) shared

2) slurm/16.05.8

3) jasper/gcc/64/1.900.1

4) gcc/6.3.0

5) hdf5/gcc/64/1.10.1

6) netcdf/gcc/64/4.6.1

7) openmpi/gcc/64/3.1.1

In /WRF run ./configure and choose the (dmpar) GNU (gfortran/gcc) option (34?)

Compile WRF as needed

In /WPS run ./configure and choose the Linux x86_64, gfortran (serial) option (1?)

Compile WPS

In namelist.wps edit the geog_data_path to

/lustre/backup/WUR/ESG/data/MODEL_DATA/WRF/geog_v4.0 (still needs to be created)

Installing WRF and WPS

2018-08-07T12:10:38Z

Danie010: Created page with "The following setup works for WRF version 4.0! To install WRF download the WRF and WPS source code from http://www2.mmm.ucar.edu/wrf/users/download/get_source.html and untar..."

The following setup works for WRF version 4.0!

To install WRF download the WRF and WPS source code from
http://www2.mmm.ucar.edu/wrf/users/download/get_source.html
and untar into your directory

load the following modules:
1) shared
2) slurm/16.05.8
3) jasper/gcc/64/1.900.1
4) gcc/6.3.0
5) hdf5/gcc/64/1.10.1
6) netcdf/gcc/64/4.6.1
7) openmpi/gcc/64/3.1.1

In /WRF run ./configure and choose the (dmpar) GNU (gfortran/gcc) option (34?)
Compile WRF as needed

In /WPS run ./configure and choose the Linux x86_64, gfortran (serial) option (1?)
Compile WPS
In namelist.wps edit the geog_data_path to
/lustre/backup/WUR/ESG/data/MODEL_DATA/WRF/geog_v4.0 (still needs to be created)

Main Page

2018-08-07T12:02:24Z

Danie010: /* Installation of software by users */

The Agrogenomics cluster is a [http://en.wikipedia.org/wiki/High-performance_computing High Performance Computer] (HPC) infrastructure hosted by [http://www.wageningenur.nl/nl/activiteit/Opening-High-Performance-Computing-cluster-HPC.htm Wageningen University & Research Centre]. It is open for use for all WUR research groups as well as other organizations, including companies, that have collaborative projects with WUR.

The Agrogenomics HPC was an initiative of the [http://www.breed4food.com/en/breed4food.htm Breed4Food] (B4F) consortium, consisting of the [[About_ABGC | Animal Breeding and Genomics Centre]] (WU-Animal Breeding and Genomics and Wageningen Livestock Research) and four major breeding companies: [http://www.cobb-vantress.com Cobb-Vantress], [https://www.crv4all.nl CRV], [http://www.hendrix-genetics.com Hendrix Genetics], and [http://www.topigs.com TOPIGS]. Currently, in addition to the original partners, the HPC (HPC-Ag) is used by other groups from Wageningen UR (Bioinformatics, Centre for Crop Systems Analysis, Environmental Sciences Group, and Plant Research International) and plant breeding industry (Rijk Zwaan).

= Using the HPC-Ag =
== Gaining access to the HPC-Ag ==
Access to the cluster and file transfer are traditionally done via [http://en.wikipedia.org/wiki/Secure_Shell SSH and SFTP].
* [[log_in_to_B4F_cluster | Logging into cluster using ssh and file transfer]]
* [[Services | Alternative access methods, and extra features and services on the HPC]]
* [[Filesystems | Accessible storage methods on the HPC]]

== Access Policy ==
[[Access_Policy | Main Article: Access Policy]]

Access needs to be granted actively (by creation of an account on the cluster by FB-IT). Use of resources is limited by the scheduler. Depending on availability of queues ('partitions') granted to a user, priority to the system's resources is regulated. Note that the use of the HPC-Ag is not free of charge. List price of CPU time and storage, and possible discounts on that list price for your organisation, can be retrieved from CAT-AGRO or FB-ICT.

= Events =
* [[Courses]] that have happened and are happening
* [[Downtime]] that will affect all users
* [[Meetings]] that may affect the policies of the HPC

= Other Software =

== Cluster Management Software and Scheduler ==
The HPC-Ag uses Bright Cluster Manager software for overall cluster management, and Slurm as job scheduler.
* [[BCM_on_B4F_cluster | Monitor cluster status with BCM]]
* [[SLURM_on_B4F_cluster | Submit jobs with Slurm]]
* [[node_usage_graph | Be aware of how much work the cluster is under right now with 'node_usage_graph']]
* [[SLURM_Compare | Rosetta Stone of Workload Managers]]

== Installation of software by users ==

* [[Domain_specific_software_on_B4Fcluster_installation_by_users | Installing domain specific software: installation by users]]
* [[Setting local variables]]
* [[Installing_R_packages_locally | Installing R packages locally]]
* [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]
* [[Virtual_environment_Python_3.4_or_higher | Setting up and using a virtual environment for Python3.4 or higher ]]
* [[Installing WRF and WPS]]

== Installed software ==

* [[Globally_installed_software | Globally installed software]]
* [[ABGC_modules | ABGC specific modules]]

= Useful Notes =

== Being in control of Environment parameters ==

* [[Using_environment_modules | Using environment modules]]
* [[Setting local variables]]
* [[Setting_TMPDIR | Set a custom temporary directory location]]
* [[Installing_R_packages_locally | Installing R packages locally]]
* [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]

== Controlling costs ==

* [[SACCT | using SACCT to see your costs]]
* [[get_my_bill | using the "get_my_bill" script to estimate costs]]

== Management ==
[[HPC_management | Main Article: HPC management]]

Project Leader of the HPC is Stephen Janssen (Wageningen UR,FB-IT, Service Management). [[User:lith010 | Jan van Lith (Wageningen UR,FB-IT, Infrastructure)]] and [[User:dawes001 | Gwen Dawes (Wageningen UR, FB-IT, Infrastructure)]] are responsible for [[Maintenance_and_Management | Maintenance and Management]].

= Miscellaneous =
* [[Mailinglist | Electronic mail discussion lists]]
* [[History_of_the_Cluster | Historical information on the startup of the HPC]]
* [[Bioinformatics_tips_tricks_workflows | Bioinformatics tips, tricks, and workflows]]
* [[Parallel_R_code_on_SLURM | Running parallel R code on SLURM]]
* [[Convert_between_MediaWiki_and_other_formats | Convert between MediaWiki format and other formats]]
* [[Manual GitLab | GitLab: Create projects and add scripts]]

= See also =
* [[Maintenance_and_Management | Maintenance and Management]]
* [[BCData | BCData]]
* [[Mailinglist | Electronic mail discussion lists]]
* [[About_ABGC | About ABGC]]
* [[Computer_cluster | High Performance Computing @ABGC]]
* [[Lustre_PFS_layout | Lustre Parallel File System layout]]

= External links =
{| width="90%"
|- valign="top"
| width="30%" |
* [http://www.breed4food.com/en/show/Breed4Food-initiative-reinforces-the-Netherlands-position-as-an-innovative-country-in-animal-breeding-and-genomics.htm Breed4Food programme]
* [http://www.wageningenur.nl/en/Expertise-Services/Facilities/CATAgroFood-3/CATAgroFood-3/Our-facilities/Show/High-Performance-Computing-Cluster-HPC.htm CATAgroFood offers a HPC facilty]
* [http://www.cobb-vantress.com Cobb-Vantress homepage]

| width="30%" |
* [https://www.crv4all.nl CRV homepage]
* [http://www.hendrix-genetics.com Hendrix Genetics homepage]
* [http://www.topigs.com TOPIGS homepage]
| width="30%" |
* [http://en.wikipedia.org/wiki/Scientific_Linux Scientific Linux]
* [http://en.wikipedia.org/wiki/Help:Cheatsheet Help with editing Wiki pages]
|}

HPCwiki - User contributions [en]

Installing WRF and WPS

Installing WRF and WPS

Installing WRF and WPS

Main Page