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Vlastimil Holer edited this page May 11, 2018 · 4 revisions

All site specific configuration is in gromacs-inputs.yaml.m4. It's a combination of YAML key-value parameters and only a few m4 configurable definitions. Each parameter is documented right in the file. We'll highlight here only a few parameters you'll most likely need to modify for your needs.

OCCI

  • occi_endpoint configure the remote OCCI server URL. Set to your provider's endpoint.
  • occi_user_cred change the absolute path to your VOMS proxy certificate (the VOMS proxy was created as the last step of Security setup.

Default authentication type is x509 VOMS. The rest occi_ prefixed parameters can be used to change the other connection parameters (e.g. authentication type, user name, password, CA certificates path). These parameters are handed over to the OCCI CLI, you can run occi --help for more information.

Host Pool

Instead of OCCI provisioner, you can use a pool of predeployed hosts provided by Host Pool service. You need the service deployed and configured with a set of available hosts, obviously you need to have these hosts already running. Then you have to switch from OCCI to Host Pool provisioner in the gromacs-inputs.yaml.m4 via following parameters:

  • _PROVISIONER_ change to hostpool,
  • hostpool_service_url configure with your Host Pool service address

Deployment parameters

There are 2 types of nodes - main portal node, and workers. Each type has its parameter for the option type.

  • olin_os_tpl and worker_os_tpl - operating system template. You need to fill both with the suitable name of the CentOS 7 image template. To get the name, you have to use the OCCI CLI. See examples below.

  • olin_resource_tpl and worker_resource_tpl - instance type (sizing). You need to fill both parameters with a valid instance type name, which matches at least the minimum requirements. To get the names, please use the OCCI CLI as described on the example below.

Instance type Minimum Recommended
OLIN (portal, batch) 4 GiB RAM, 1 core 4 GiB RAM, 2 cores
Worker 2 GiB RAM, 1 core 8 GiB RAM, 8 cores, NVIDIA GPU

  • olin_availability_zone and worker_availability_zone - site availability zone. This can be a different a different cluster or data center. List of availability zones can be get with the OCCI CLI, see the example below.

  • olin_scratch_size and worker_scratch_size - scratch space to be available for the computation in GB.

Worker nodes count

  • _WORKERS_ - initial number of deployed worker nodes

For the advanced deployment with the Cloudify Manager, auto scaling functionality is available, and following parameters set the scaling limits:

  • _WORKERS_MIN_ - minimum number of running worker nodes
  • _WORKERS_MAX_ - maximum number of running worker nodes

OCCI CLI examples

Operating system template

Get list of OS template URLs (for the default connection parameters provided in gromacs-inputs.yaml.m4):

$ occi --endpoint=https://carach5.ics.muni.cz:11443 \
    --auth=x509 --user-cred=/tmp/x509up_u1000 --voms \
    --action list --resource os_tpl
http://occi.carach5.ics.muni.cz/occi/infrastructure/os_tpl#uuid_1cc39672_0f09_51da_b232_17722be1c583_warg_default_shared_198
http://occi.carach5.ics.muni.cz/occi/infrastructure/os_tpl#uuid_4c566580_0d9f_5b79_91e0_0b65bc4eceff_warg_default_shared_199
http://occi.carach5.ics.muni.cz/occi/infrastructure/os_tpl#uuid_55f38ac1_ff24_5bd5_acea_a9668c7b04da_warg_default_shared_201
http://occi.carach5.ics.muni.cz/occi/infrastructure/os_tpl#uuid_51149658_e395_5971_b235_dcfd4d1db873_warg_default_shared_202
http://occi.carach5.ics.muni.cz/occi/infrastructure/os_tpl#uuid_bf5b76c9_d3f3_5cda_908d_e5f5e8d103cf_warg_default_shared_203

Walk through the URLs to find a suitable CentOS 7 image, e.g.:

$ occi --endpoint=https://carach5.ics.muni.cz:11443 \
    --auth=x509 --user-cred=/tmp/x509up_u1000 --voms \
    --action describe --resource http://occi.carach5.ics.muni.cz/occi/infrastructure/os_tpl#uuid_55f38ac1_ff24_5bd5_acea_a9668c7b04da_warg_default_shared_201
###############################################################################
[[ http://occi.carach5.ics.muni.cz/occi/infrastructure/os_tpl#uuid_55f38ac1_ff24_5bd5_acea_a9668c7b04da_warg_default_shared_201 ]]
title:        Image for EGI CentOS 7 [CentOS/7/VirtualBox]
term:         uuid_55f38ac1_ff24_5bd5_acea_a9668c7b04da_warg_default_shared_201
location:     /mixin/os_tpl/uuid_55f38ac1_ff24_5bd5_acea_a9668c7b04da_warg_default_shared_201/
###############################################################################

The term attribute (or URL part after # hash) is the required operating system template name.

Instance type

Get list of instance type URLs (for the default connection parameters provided in gromacs-inputs.yaml.m4):

$ occi --endpoint=https://carach5.ics.muni.cz:11443 \
    --auth=x509 --user-cred=/tmp/x509up_u1000 --voms \
    --action list --resource resource_tpl
http://schemas.fedcloud.egi.eu/occi/infrastructure/resource_tpl#extra_large
http://fedcloud.egi.eu/occi/compute/flavour/1.0#medium
http://fedcloud.egi.eu/occi/compute/flavour/1.0#mem_medium
http://fedcloud.egi.eu/occi/compute/flavour/1.0#small
http://fedcloud.egi.eu/occi/compute/flavour/1.0#large

Walk through the URLs to find a suitable instance type, e.g.:

$ occi --endpoint=https://carach5.ics.muni.cz:11443 \
    --auth=x509 --user-cred=/tmp/x509up_u1000 --voms \
    --action describe --resource http://fedcloud.egi.eu/occi/compute/flavour/1.0#large
###############################################################################
[[ http://fedcloud.egi.eu/occi/compute/flavour/1.0#large ]]
title:        Large Instance - 4 cores and 4 GB RAM
term:         large
location:     /mixin/resource_tpl/large/
###############################################################################

The term attribute (or URL part after # hash) is the required instance type name.

Availability zone

Get list of availability zones URLs (for the default connection parameters provided in gromacs-inputs.yaml.m4):

$ occi --endpoint=https://carach5.ics.muni.cz:11443 \
    --auth=x509 --user-cred=/tmp/x509up_u1000 --voms \
    --action list --resource availability_zone
http://occi.carach5.ics.muni.cz/occi/infrastructure/availability_zone#uuid_fedcloud_warg_101
http://occi.carach5.ics.muni.cz/occi/infrastructure/availability_zone#uuid_fedcloud_cerit_sc_103

The URL part after # hash is the required availability zone.

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