diff --git a/form.yml b/form.yml index 37810473f4ecbcccf66b944cbae15bbba4d12662..b5d8df8fa64ee5009d6604b146d80428493c4787 100644 --- a/form.yml +++ b/form.yml @@ -1,56 +1,50 @@ --- -cluster: "owens" -form: - - version - - bc_account - - bc_num_hours - - bc_num_slots - - num_cores - - node_type - - bc_vnc_resolution - - bc_email_on_started +cluster: "CoD" attributes: - num_cores: - widget: "number_field" - label: "Number of cores" + bc_num_hours: + value: 1 + + bc_num_slots: + label: Number of CPU value: 1 - help: | - Number of cores on node type (4 GB per core unless requesting whole - node). Leave blank if requesting full node. - min: 0 - max: 48 + min: 1 + max: 24 step: 1 - id: 'num_cores' - bc_num_slots: "1" - bc_vnc_resolution: - required: true - bc_account: - label: "Project" - help: "You can leave this blank if **not** in multiple projects." - node_type: + + bc_num_mems: + widget: "number_field" + label: Memory per CPU (GB) + value: 4 + min: 1 + max: 128 + step: 1 + + bc_partition: widget: select - label: "Node type" - 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. + label: Partition options: - - [ "any", "" ] - - [ "hugemem", ":hugemem" ] - - [ "vis", ":vis:gpus=1" ] + - [ "express", "express" ] + - [ "short", "short" ] + - [ "medium", "medium" ] + - [ "long", "long" ] + - [ "interactive", "interactive" ] + - [ "pascalnodes", "pascalnodes" ] + - [ "pascalnodes-medium", "pascalnodes-medium" ] + - [ "largemem", "largemem" ] + - [ "largemem-long", "largemem-long" ] + - [ "amd-hdr100", "amd-hdr100" ] + version: widget: select - label: "MATLAB version" - help: "This defines the version of MATLAB you want to load." + label: "IGV version" + help: "This defines the version of IGV you want to load." options: - - [ "R2018b", "matlab/r2018b" ] - - [ "R2018a", "matlab/r2018a" ] - - [ "R2017a", "matlab/r2017a" ] - - [ "R2016b", "matlab/r2016b" ] - - [ "R2015b", "matlab/r2015b" ] + - [ "2.12.2-Java-11", "IGV/2.12.2-Java-11" ] + +form: + - version + - bc_num_hours + - bc_partition + - bc_num_slots + - bc_num_mems + - bc_email_on_started diff --git a/script.sh.erb b/script.sh.erb new file mode 100644 index 0000000000000000000000000000000000000000..3d1c1e5aa106e30602994ba574c9a037565ba8d6 --- /dev/null +++ b/script.sh.erb @@ -0,0 +1,37 @@ +#!/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 diff --git a/submit.yml.erb b/submit.yml.erb new file mode 100644 index 0000000000000000000000000000000000000000..d32e9497cf242cf154007b8b5bcf3d031f113427 --- /dev/null +++ b/submit.yml.erb @@ -0,0 +1,14 @@ +--- +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 -%>