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Merge pull request #8 from DouglasNeuroInformatics/initial-docs
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gdevenyi committed Jun 17, 2021
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2 changes: 1 addition & 1 deletion docs/Makefile
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# You can set these variables from the command line, and also
# from the environment for the first two.
SPHINXOPTS ?=
SPHINXOPTS ?= -n -v -j auto
SPHINXBUILD ?= sphinx-build
SOURCEDIR = .
BUILDDIR = _build
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128 changes: 10 additions & 118 deletions docs/about_the_platform/index.md
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Expand Up @@ -5,6 +5,8 @@ computer system. Originally the computing platform of the Douglas Cerebral
Imaging Center (CIC), it has grown and generalized to meet the informatics
needs of the Douglas Research Center as a whole.

## Hardware

The system itself consists (as of mid-2021) of Linux-based single-sign-on
user management system, along with a 1 PB storage system, ~40 8-12 core
workstations with 16-32 GB of RAM, and a 10-node compute cluster of
Expand All @@ -18,7 +20,14 @@ scheduling on workstations.
Entry-level GPU computation is available on workstations to provide CUDA
and OpenCL acceleration suitable applications.

# Filesystem layout
## Software

The platform workstations run Ubuntu Linux variants, with full productivity
software (LibreOffice, GIMP, Inkscape, etc), modern web browsers (Chrome, Firefox),
and a large suite of scientific software. Scientific software is avaialble in the
{ref}`software quarantine<doing_things/index:accessing scientific software (quarantine aka modules)>`.

## Filesystem layout

Each computer in the system has access to two system-wide network filesystems.
User home directories `$HOME` are mounted from the user server (currently `cicus03`).
Expand All @@ -29,120 +38,3 @@ All users have access to scratch storage at `/data/scratch`, which is suitable
for storing data during processing. Scratch does not keep any historical versions
and is not backed up, so it should not be relied upon for long-term storage. In
the future it is expected a date-based deletion policy will be implemented.

## Accessing Human MRI Scanner DICOMS

The Siemens MAGNETOM Prisma Human MRI scanner sends collected data to `cicus03`
which acts a pseudo-PACS system, collecting the files and storing them at
`/home/cic/dicom/transfers` accessible for 14 calendar days before being moved
to long-term cold storage. Users are expected to access their data during that
time and copy it to appropriate long term storage.

# Accessing Scientific Software (quarantine aka modules)

All computer systems have installed a standard suite of desktop productivity software
(office, image maniupuation, web browser, etc.). If a readily available productivity
software package is not installed and you wish to use it, please contact us to request
installation.

Scientific sofware is deployed across all computers in the platform via shared network
drive, ensuring the same version of software is run on all machines during any kind of
cluster processing. To make multiple versions of software available, software is isolated
in seperate installation directories and access is managed via the `module` system.
The `module` system allows for multiple versions to live side-by-side, for dependencies
between software to be specified, and for conflicting versions to be specified.

The obtain a list of available software, run `module avail`, below is an example generated
on 2021-06-09, the format of the naming below is `<modulename>/<moduleversion>`:
```
-------------------------------------------------------------------------------------------- /opt/quarantine/modules ---------------------------------------------------------------------------------------------
ACVD/20161025 jmrui/6.0beta pyminc/0.41
AFNI/2014.09.08.21.47EDT mango/3.8 pyminc/0.42b
AFNI/2017.03.30.07.57EDT mango/4.0.1 pyminc/0.46
AllenGeneMNI/dev matlab/R2012a pyminc/0.47
anaconda/2.0.1 matlab/R2014a pyminc/0.48
anaconda/2019.03-python3 matlab/R2015aSP1 pyminc/0.49
anaconda/2.1.0 matlab/R2016a pyminc/0.51
anaconda/2.3 matlab/R2018b PyQC/1.0
anaconda/2.5 mi-brain/2020.04.09 qbatch/2.1.3
anaconda/4.1.1 MIDER/v2 qbatch/2.1.5
anaconda/4.2.0-python3 minclaplace/a280379ff13d8265a9ca342cfa6f4510c24d26b8 qbatch/2.2
anaconda/4.3.0-python2.7(default) minc-stuffs/0.1.12^minc-toolkit-1.9.10 quarantine
anaconda/5.0.1-python3 minc-stuffs/0.1.12^minc-toolkit-1.9.11 R/3.1.1
anaconda/5.1.0-python3 minc-stuffs/0.1.15a^minc-toolkit-1.9.11 R/3.2.1
anaconda/miniconda3 minc-stuffs/0.1.16^minc-toolkit-1.9.11 R/3.2.4
ANTs/20190211 minc-stuffs/0.1.20^minc-toolkit-1.9.11 R/3.3.3
ANTs/20191007 minc-stuffs/0.1.20^minc-toolkit-1.9.15 R/3.4.0
ANTs/20191119 minc-stuffs/0.1.21^minc-toolkit-1.9.15 R/3.5.0
ANTs/20200104 minc-stuffs/0.1.22^minc-toolkit-1.9.16 R/3.5.1
ANTs/20200227 minc-stuffs/0.1.24^minc-toolkit-1.9.16 remotemesa/1.0
ANTs/20200410 minc-stuffs/0.1.24^minc-toolkit-1.9.17 R-extras/3.1.1
ANTs/2.1.0 minc-stuffs/0.1.4^minc-toolkit-1.0.01 R-extras/3.2.1
ANTs/2.1.0rc3 minc-stuffs/0.1.7^minc-toolkit-1.0.01 R-extras/3.2.3
ANTs/2.2 minc-stuffs/0.1.9^minc-toolkit-1.9.10 R-extras/3.2.4
ANTs/2.3.1 minc-toolkit/1.0.01 R-extras/3.3.3
bpipe/0.9.8.6 minc-toolkit/1.0.04 R-extras/3.4.0
bpipe/0.9.8.7 minc-toolkit/1.0.07 RMINC/1.2.4.5^minc-toolkit-1.0.01^R-3.1.1
bpipe/0.9.9 minc-toolkit/1.9.10 RMINC/1.2.4.7^minc-toolkit-1.0.01^R-3.1.1
bpipe/0.9.9.2 minc-toolkit/1.9.10.1 RMINC/1.2.4.9^minc-toolkit-1.9.10^R-3.2.1
bpipe/0.9.9.3 minc-toolkit/1.9.11 RMINC/1.3.0.0^minc-toolkit-1.9.10^R-3.2.1
bpipe/0.9.9.4 minc-toolkit/1.9.15 RMINC/1.3.0.0^minc-toolkit-1.9.11^R-3.2.4
bpipe/0.9.9.5 minc-toolkit/1.9.16 RMINC/1.4.0.0^minc-toolkit-1.9.11^R-3.2.4
bpipe/0.9.9.6 minc-toolkit/1.9.17 RMINC/1.4.0.3^minc-toolkit-1.9.11^R-3.2.4
BrainExplorer/2 minc-toolkit-extras/1.0 RMINC/1.4.1.1^minc-toolkit-1.9.11^R-3.2.4
braingl/0.0-1 miniconda/2020-03 RMINC/1.4.2.0^minc-toolkit-1.9.11^R-3.2.4
braingl/dev MIPAV/6.0.1 RMINC/1.4.3.0^minc-toolkit-1.9.11^R-3.2.4
brain-view2/1.0^minc-toolkit-1.0.01 MIPAV/7.1.1 RMINC/1.4.3.1^minc-toolkit-1.9.11^R-3.2.4
brain-view2/1.0^minc-toolkit-1.9.10 MIPAV/7.2.0 RMINC/1.4.3.2^minc-toolkit-1.9.11^R-3.2.4
Bru2Nii/1.0.20170707 mni.cortical.statistics/0.9.4 RMINC/1.4.3.3^minc-toolkit-1.9.11^R-3.2.4
c3d/2015.06.22 mountainlab/20171005 RMINC/1.4.3.4^minc-toolkit-1.9.11^R-3.2.4
CIVET/1.1.10 mricrogl/12-February-2016 RMINC/1.4.4.0^minc-toolkit-1.9.15^R-3.3.3
CIVET/1.1.12 mricrogl/12-June-2015 RMINC/1.5.0.0^minc-toolkit-1.9.15^R-3.4.0
CIVET/2.1.0 mricron/1JUNE2015 RMINC/1.5.1.0^minc-toolkit-1.9.16^R-3.4.0
CIVET-extras/1.0 mricron/22DEC2015 RMINC/1.5.2.0^minc-toolkit-1.9.16^R-3.5.0
cmake/3.10.2 MRO/3.2.3 RMINC/1.5.2.1^minc-toolkit-1.9.16^R-3.5.0
cmake/3.13.1 mrtrix3/3.0_rc3_30c24e3 RMINC/1.5.2.1^minc-toolkit-1.9.16^R-3.5.1
dcm2niix/1.0.20171215 mrtrix3/d861bbe6 RMINC/1.5.2.2^minc-toolkit-1.9.17^R-3.5.1
dcm2niix/1.0.20181125 MVGC/1.0 RMINC/1.5.2.3^minc-toolkit-1.9.17^R-3.5.1
dcm2niix/1.0.20190902 niak/v0.13.5 rstudio/0.98.1103
dcm2niix/1.0.20200331 niftimatlib/1.2 rstudio/0.99.491
DKE/2015.10.28 NODDI_toolbox/0.9 rstudio/0.99.896
DKE-ft/2015.10.26 octave/4.0.2 rstudio/0.99.903
fmristat/2006.06.06 paraview/5.0.0 rstudio/1.0.136
freesurfer/5.3.0 PLINK/1.0.7 rstudio/1.0.143
freesurfer/6.0 PLINK/201502 rstudio/1.1.383
FSL/5.0.6 PLS/6.1311050 rstudio/1.1.453
FSL/5.0.7 PLS/6.15 rstudio/1.1.463
FSL/5.0.8 pvconv/0.57 SGE-extras/1.0
FSL/5.0.9 pycharm/2017.2.1 shapeit/2r790
FSL/6.0.2 pydpiper/1.10 singularity/2.6.1
gcc/4.1.2 pydpiper/1.11 snptest/2.5
gift/4.0a pydpiper/1.13.1 SPAMS/2.5
git/2.1.0 pydpiper/1.14-beta1 SPM/12b_r6080
git/2.3.0 pydpiper/1.14-beta2 SPM/12b_r6225
gradunwarp/1.0.2 pydpiper/1.15 SPM/8_r5236
GreatApes/dev pydpiper/1.18 SPM12/r6080
GTOOL/0.7.5 pydpiper/2.0.1 SPM12/r6225
HCP_ConnectomeWorkbench/1.3.2 pydpiper/2.0.10 SPM12/r6685
ilastik/1.3.3post3 pydpiper/2.0.12 SPM12/r7219
ILT/4bc2d846 pydpiper/2.0.13 SPM8/r5236
impute/2.3.2 pydpiper/2.0.3 SPM8/r6313
itksnap/3.2.0 pydpiper/2.0.5 torch/d3b017d2aba6a865f44caf1b8e5f07996c26d4c0
itksnap/3.4.0-minc pydpiper/2.0.6 webp/1.1.0
itksnap/3.6.0 pydpiper/2.0.8
java/8u171-32bit pyminc/0.4
```

To load a module, use the load command, `module load <modulename>` which will load the deafault version `(D)` if it is specified in the module
system, otherwise it will load the latest version. To load a specific version of a module, specify the version during loading,
`module load <modulename>/<moduleversion>`.

:::{note}
If you try to load a module which has dependencies you have not yet satisfied, you will receive an error that will specify the dependencie and
modules available that would satisfy it, each missing depndency stops the module loading so this may occur several times as you load all dependencies:
```bash
$ module load pyminc
pyminc/0.51(7):ERROR:151: Module 'pyminc/0.51' depends on one of the module(s) 'anaconda/miniconda3 anaconda/5.1.0-python3 anaconda/5.0.1-python3 anaconda/4.3.0-python2.7 anaconda/4.2.0-python3 anaconda/4.1.1 anaconda/2019.03-python3 anaconda/2.5 anaconda/2.3 anaconda/2.1.0 anaconda/2.0.1'
pyminc/0.51(7):ERROR:102: Tcl command execution failed: prereq anaconda
```
:::
6 changes: 5 additions & 1 deletion docs/conf.py
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extensions = [
"myst_parser",
"sphinx.ext.githubpages",
"sphinx_rtd_dark_mode"
"sphinx_rtd_dark_mode",
"sphinx.ext.autosectionlabel"
]

# Make sure the target is unique
autosectionlabel_prefix_document = True

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']

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