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ZIH
hpcsupport
hpc-compendium
Commits
523fafa6
Commit
523fafa6
authored
3 years ago
by
Jan Frenzel
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Merge branch 'rotscher--tu-dresden.de-preview-patch-54625' into 'preview'
Rotscher tu dresden.de preview patch 54625 Closes
#303
See merge request
!533
parents
6a1c6606
a4732279
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1 merge request
!555
Added process of incorporating MR from forked repo into
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doc.zih.tu-dresden.de/docs/software/containers.md
+10
-7
10 additions, 7 deletions
doc.zih.tu-dresden.de/docs/software/containers.md
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doc.zih.tu-dresden.de/docs/software/containers.md
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523fafa6
...
...
@@ -46,7 +46,7 @@ instructions from the official documentation to install Singularity.
1.
Check if
`go`
is installed by executing
`go version`
. If it is
**not**
:
```console
marie@local$ wget
<
https://storage.googleapis.com/golang/getgo/installer_linux
>
&& chmod +x
marie@local$ wget
'
https://storage.googleapis.com/golang/getgo/installer_linux
'
&& chmod +x
installer_linux && ./installer_linux && source $HOME/.bash_profile
```
...
...
@@ -88,7 +88,9 @@ instructions from the official documentation to install Singularity.
There are two possibilities:
1.
Create a new container on your local workstation (where you have the necessary privileges), and
then copy the container file to ZIH systems for execution.
then copy the container file to ZIH systems for execution. Therefore you also have to install
[
Singularity
](
https://sylabs.io/guides/3.0/user-guide/quick_start.html#quick-installation-steps
)
on your local workstation.
1.
You can, however, import an existing container from, e.g., Docker.
Both methods are outlined in the following.
...
...
@@ -103,10 +105,11 @@ You can create a new custom container on your workstation, if you have root righ
which is different to the x86 architecture in common computers/laptops. For that you can use
the [VM Tools](singularity_power9.md).
Creating a container is done by writing a
**definition file**
and passing it to
Creating a container is done by writing a definition file, such as
`myDefinition.def`
, and passing
it to
`singularity`
via
```
console
marie@local$
singularity build myContainer.sif
<
myDefinition.def
>
marie@local$
singularity build myContainer.sif myDefinition.def
```
A definition file contains a bootstrap
...
...
@@ -167,7 +170,7 @@ https://github.com/singularityware/singularity/tree/master/examples.
You can import an image directly from the Docker repository (Docker Hub):
```
console
marie@lo
cal
$
singularity build my-container.sif docker://ubuntu:latest
marie@lo
gin
$
singularity build my-container.sif docker://ubuntu:latest
```
Creating a singularity container directly from a local docker image is possible but not
...
...
@@ -284,7 +287,7 @@ While the `shell` command can be useful for tests and setup, you can also launch
inside the container directly using "exec":
```console
marie@login$ singularity exec my-container.
img
/opt/myapplication/bin/run_myapp
marie@login$ singularity exec my-container.
sif
/opt/myapplication/bin/run_myapp
```
This can be useful if you wish to create a wrapper script that transparently calls a containerized
...
...
@@ -299,7 +302,7 @@ if [ "z$X" = "z" ] ; then
exit 1
fi
singularity exec /
scratch/p_myproject
/my-container.sif /opt/myapplication/run_myapp "$@"
singularity exec /
projects/p_number_crunch
/my-container.sif /opt/myapplication/run_myapp "$@"
```
The better approach is to use `
singularity run
`, which executes whatever was set in the `
%runscript
`
...
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