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RC Data Science
community-ood-sandbox
fsl
Commits
4dfa42c6
Commit
4dfa42c6
authored
2 years ago
by
Krish Moodbidri
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edited IGV app template to work with CoD cluster
parent
f6d1d408
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3 changed files
form.yml
+41
-47
41 additions, 47 deletions
form.yml
script.sh.erb
+37
-0
37 additions, 0 deletions
script.sh.erb
submit.yml.erb
+14
-0
14 additions, 0 deletions
submit.yml.erb
with
92 additions
and
47 deletions
form.yml
+
41
−
47
View file @
4dfa42c6
---
---
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
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script.sh.erb
0 → 100644
+
37
−
0
View file @
4dfa42c6
#!/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
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submit.yml.erb
0 → 100644
+
14
−
0
View file @
4dfa42c6
---
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
-%>
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