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Commits (2)
......@@ -15,9 +15,7 @@
"\n",
"Let's begin by pulling our first container from [Singularity-Hub](https://singularity-hub.org/).\n",
"\n",
"This singularity image contains the tool [neurodebian](http://neuro.debian.net/).\n",
"\n",
"NeuroDebian provides a large collection of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives."
"The [neurodebian](http://neuro.debian.net/) singularity image contains a large collection of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives."
]
},
{
......@@ -66,7 +64,7 @@
"metadata": {},
"source": [
"Now, we'll try to execute a command from within the container. \n",
"__exec__ parameter allows you to achieve this functionality. Let's list the content of you /home/$USER directory"
"__exec__ parameter allows you to achieve this functionality. Let's list the content of your /home/$USER directory"
]
},
{
......@@ -82,7 +80,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"Now, that we have the container pulled, we can use it for running the actual tool that we wanted to use, the reason for actually downloading the container in the first place: [dcm2nii](https://www.nitrc.org/projects/mricron)"
"Now that we have the container pulled onto the cluster, we can use it for running an actual neuro-imaging tool that we wanted to use: [dcm2nii](https://www.nitrc.org/projects/mricron)"
]
},
{
......@@ -226,7 +224,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"Now like mentioned earlier during the security considerations of Singularity in a HPC environment, all the sigularity runs adhere to the user level permissions, from the host system. So I would get a permission denied issue if I try to list William's directory content."
"Now like mentioned earlier during the security considerations of Singularity in a HPC environment, all the sigularity runs adhere to the user level permissions, from the host system. So I would get a permission denied error if I try to list directories to which I don't have access. In this example William's directory contents."
]
},
{
......@@ -242,7 +240,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"Now that we know how to bind paths from the host machine to the container image, I would be able to use __dcm2nii__ tool with my raw files available in my DATA_USER location.\n",
"Now that we know how to bind paths from the host machine to the container image, we will be able to use __dcm2nii__ tool with our raw files available in our DATA_USER location.\n",
"\n",
"\n",
"We'll take a look at how to use it within a job script in the next section."
......@@ -254,7 +252,7 @@
"source": [
"## Job Script with containers\n",
"\n",
"Using Singularity container with [SLURM job script](https://docs.uabgrid.uab.edu/wiki/Slurm) is very easy, as the containers run as a process on the host machine. You just need to load Singularity in your job script and run the singularity process. Here's an example job script below:"
"Using Singularity container with [SLURM job script](https://docs.uabgrid.uab.edu/wiki/Slurm) is very easy, as the containers run as a process on the host machine, just like any other command in a batch script. You just need to load Singularity in your job script and run the command via a singularity process. Here's an example job script below:"
]
},
{
......@@ -264,7 +262,7 @@
"```\n",
"#!/bin/bash\n",
"#\n",
"#SBATCH --job-name=test\n",
"#SBATCH --job-name=test-singularity\n",
"#SBATCH --output=res.out\n",
"#SBATCH --error=res.err\n",
"#\n",
......@@ -288,7 +286,7 @@
"#Set your environment here\n",
"module load Singularity/2.5.2-GCC-5.4.0-2.26\n",
"\n",
"#Run your commands here\n",
"#Run your singularity or any other commands here\n",
"singularity exec -B /data/user/$USER /data/user/$USER/rc-training-sessions/neurodebian-neurodebian-master-latest.simg dcm2nii PATH_TO_YOUR_DICOM_FILES\n",
"```"
]
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