Skip to content
Snippets Groups Projects
Commit 4dfa42c6 authored by Krish Moodbidri's avatar Krish Moodbidri
Browse files

edited IGV app template to work with CoD cluster

parent f6d1d408
No related branches found
No related tags found
No related merge requests found
--- ---
cluster: "owens" cluster: "CoD"
form:
- version
- bc_account
- bc_num_hours
- bc_num_slots
- num_cores
- node_type
- bc_vnc_resolution
- bc_email_on_started
attributes: attributes:
num_cores: bc_num_hours:
widget: "number_field" value: 1
label: "Number of cores"
bc_num_slots:
label: Number of CPU
value: 1 value: 1
help: | min: 1
Number of cores on node type (4 GB per core unless requesting whole max: 24
node). Leave blank if requesting full node.
min: 0
max: 48
step: 1 step: 1
id: 'num_cores'
bc_num_slots: "1" bc_num_mems:
bc_vnc_resolution: widget: "number_field"
required: true label: Memory per CPU (GB)
bc_account: value: 4
label: "Project" min: 1
help: "You can leave this blank if **not** in multiple projects." max: 128
node_type: step: 1
bc_partition:
widget: select widget: select
label: "Node type" label: Partition
help: |
- **any** - (*1-28 cores*) Use any available Owens node. This reduces the
wait time as there are no node requirements.
- **hugemem** - (*48 cores*) Use an Owens node that has 1.5TB of
available RAM as well as 48 cores. There are 16 of these nodes on
Owens. Requesting hugemem nodes allocates entire nodes.
- **vis** - (*1-28 cores*) Use an Owens node that has an [NVIDIA Tesla P100
GPU](http://www.nvidia.com/object/tesla-p100.html) with an X server
running in the background. This utilizes the GPU for hardware
accelerated 3D visualization. There are 160 of these nodes on Owens.
options: options:
- [ "any", "" ] - [ "express", "express" ]
- [ "hugemem", ":hugemem" ] - [ "short", "short" ]
- [ "vis", ":vis:gpus=1" ] - [ "medium", "medium" ]
- [ "long", "long" ]
- [ "interactive", "interactive" ]
- [ "pascalnodes", "pascalnodes" ]
- [ "pascalnodes-medium", "pascalnodes-medium" ]
- [ "largemem", "largemem" ]
- [ "largemem-long", "largemem-long" ]
- [ "amd-hdr100", "amd-hdr100" ]
version: version:
widget: select widget: select
label: "MATLAB version" label: "IGV version"
help: "This defines the version of MATLAB you want to load." help: "This defines the version of IGV you want to load."
options: options:
- [ "R2018b", "matlab/r2018b" ] - [ "2.12.2-Java-11", "IGV/2.12.2-Java-11" ]
- [ "R2018a", "matlab/r2018a" ]
- [ "R2017a", "matlab/r2017a" ] form:
- [ "R2016b", "matlab/r2016b" ] - version
- [ "R2015b", "matlab/r2015b" ] - bc_num_hours
- bc_partition
- bc_num_slots
- bc_num_mems
- bc_email_on_started
#!/usr/bin/env bash
# Clean the environment
module reset
# Set working directory to home directory
cd "${HOME}"
#
# Launch Xfce Window Manager and Panel
#
(
export SEND_256_COLORS_TO_REMOTE=1
export XDG_CONFIG_HOME="<%= session.staged_root.join("config") %>"
export XDG_DATA_HOME="<%= session.staged_root.join("share") %>"
export XDG_CACHE_HOME="$(mktemp -d)"
module restore
set -x
xfwm4 --compositor=off --daemon --sm-client-disable
xsetroot -solid "#D3D3D3"
xfsettingsd --sm-client-disable
xfce4-panel --sm-client-disable
) &
#
# Start Integrative Genomics Viewer
#
# Load the required environment
module load <%= context.version %>
# Launch IGV
module list
set -x
igvtools_gui.command &
igv.sh
---
batch_connect:
template: "vnc"
script:
native:
- "-N 1"
- "-n <%= bc_num_slots.blank? ? 1 : bc_num_slots.to_i %>"
- "--mem-per-cpu=<%= bc_num_mems.blank? ? 4 : bc_num_mems.to_i %>G"
- "--partition=<%= bc_partition %>"
- "--time=<%= bc_num_hours.blank? ? 1 : bc_num_hours.to_i %>:00:00"
- "--job-name=ood-{{ igv_module_name|lower }}"
<%- if bc_partition.include? "pascalnodes" -%>
- "--gres=gpu:1"
<%- end -%>
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment