Commit c21769d7 authored by Josef Hrabal's avatar Josef Hrabal
Browse files

Update singularity-it4i.md

parent d018d998
......@@ -35,7 +35,7 @@ For better user experience with singularity containers we prepared several wrapp
* image-update
Listed wrappers helps you to use prepared singularity images loaded as modules. You can easily load singularity image like any other module on the cluster
by `ml OS/version` command. After first module load, the prepared image is copied into your home folder and is prepared for use. When you load the module
by `ml OS/version` command. After the module is loaded for the first time, the prepared image is copied into your home folder and is ready for use. When you load the module
next time, the version of image is checked and image update (if exists) is offered. Then you can update your copy of image by the `image-update` command.
!!! warning
......@@ -56,7 +56,7 @@ This command has the same parameters as the `mpirun`. Thanks to that, there is n
## Examples
In next examples, we will be use Singularity images on IT4Innovations clusters.
In the examples, we will use the prepared Singularity images.
### Load Image
......@@ -66,13 +66,13 @@ Your image of CentOS/6.9 is at location: /home/login/.singularity/images/CentOS-
```
!!! tip
First usage module with singularity image, copy singularity image from /apps/all/OS/... to your /home (.singularity/images)
After the module is loaded for the first time, the prepared image is copied into your home folder to the *.singularity/images* subfolder.
### Wrappers
**image-exec**
Open the image and run the command inside the image.
Executes the given command inside the Singularity image. The container is in this case started, then the command is executed and the container is stopped.
```console
$ ml CentOS/7.3
......@@ -87,11 +87,11 @@ MPI wrapper. More in the chapter [Examples MPI](#mpi).
**image-run**
Run the subscript inside image.
This command runs the runscript inside the Singularity image. Note, that the prepared images don't contain a runscript.
**image-shell**
Start the shell inside image.
Invokes an interactive shell inside the Singularity image.
```console
$ ml CentOS/7.3
......@@ -103,7 +103,7 @@ Singularity CentOS-7.3_20180220104046.img:~>
### Update Image
If a new image (version) exists, informs the user and offers an update image.
This command is for updating your local copy of the Singularity image. The local copy is in this case overridden.
```console
$ ml CentOS/6.9
......@@ -123,12 +123,12 @@ New version is ready. (/home/login/.singularity/images/CentOS-6.9_20180220092823
### Intel Xeon Phi Cards - MIC
For example submit job `qsub -A PROJECT -q qprod -l select=1:mpiprocs=24:accelerator=true -I`
In the following example, we are using a job submitted by the command: `qsub -A PROJECT -q qprod -l select=1:mpiprocs=24:accelerator=true -I`
!!! info
MIC image was prepared for only Salomon cluster
The MIC image was prepared only for the Salomon cluster
**Code for testing offload**
**Code for the offload test**
```c
#include <stdio.h>
......@@ -173,10 +173,10 @@ Hello world from MIC, #of cores: 244
### GPU Image
For example submit job `qsub -A PROJECT -q qnvidia -l select=1:ncpus=16:mpiprocs=16 -l walltime=01:00:00 -I`
In the following example, we are using a job submitted by the command: `qsub -A PROJECT -q qnvidia -l select=1:ncpus=16:mpiprocs=16 -l walltime=01:00:00 -I`
!!! note
GPU image was prepared for only Anselm cluster
GPU image was prepared only for the Anselm cluster
**Checking nvidia driver inside image**
......@@ -208,7 +208,7 @@ Mon Mar 12 07:07:53 2018
### MPI
For example submit job `qsub -A PROJECT -q qprod -l select=2:mpiprocs=24 -l walltime=00:30:00 -I`
In the following example, we are using a job submitted by the command: `qsub -A PROJECT -q qprod -l select=2:mpiprocs=24 -l walltime=00:30:00 -I`
!!! note
We have seen no major performance impact from running a job in a Singularity container.
......
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