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ZIH
hpcsupport
hpc-compendium
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29d58273
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29d58273
authored
1 year ago
by
Natalie Breidenbach
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Update containers.md
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29d58273
...
@@ -101,7 +101,7 @@ You can create a new custom container on your workstation, if you have root righ
...
@@ -101,7 +101,7 @@ You can create a new custom container on your workstation, if you have root righ
!!! attention "Respect the micro-architectures"
!!! attention "Respect the micro-architectures"
You cannot create containers for the
partition `ml
`, as it bases on Power9 micro-architecture
You cannot create containers for the
cluster `Power
`, as it bases on Power9 micro-architecture
which is different to the x86 architecture in common computers/laptops. For that you can use
which is different to the x86 architecture in common computers/laptops. For that you can use
the [VM Tools](singularity_power9.md).
the [VM Tools](singularity_power9.md).
...
@@ -260,12 +260,12 @@ marie@compute$ singularity shell my-container.sif
...
@@ -260,12 +260,12 @@ marie@compute$ singularity shell my-container.sif
automatically and instead set up your binds manually via `-B` parameter. Example:
automatically and instead set up your binds manually via `-B` parameter. Example:
```console
```console
marie@compute$ singularity shell --contain -B /
scratch
,/my/folder-on-host:/folder-in-container my-container.sif
marie@compute$ singularity shell --contain -B /
data/horse
,/my/folder-on-host:/folder-in-container my-container.sif
```
```
You can write into those folders by default. If this is not desired, add an
`:ro`
for read-only to
You can write into those folders by default. If this is not desired, add an
`:ro`
for read-only to
the bind specification (e.g.
`-B /
scratch:/scratch
:ro\`). Note that we already defined bind paths
the bind specification (e.g.
`-B /
data/horse:/data/horse
:ro\`). Note that we already defined bind paths
for `
/
scratch
`, `
/projects
` and `
/sw
` in our global `
singularity.conf
`, so you needn't use the `
-B
`
for `
/
data/horse
`, `
/projects
` and `
/sw
` in our global `
singularity.conf
`, so you needn't use the `
-B
`
parameter for those.
parameter for those.
If you wish to install additional packages, you have to use the `
-w
` parameter to
If you wish to install additional packages, you have to use the `
-w
` parameter to
...
@@ -280,7 +280,7 @@ Singularity.my-container.sif> yum install htop
...
@@ -280,7 +280,7 @@ Singularity.my-container.sif> yum install htop
The `
-w
` parameter should only be used to make permanent changes to your container, not for your
The `
-w
` parameter should only be used to make permanent changes to your container, not for your
productive runs (it can only be used writable by one user at the same time). You should write your
productive runs (it can only be used writable by one user at the same time). You should write your
output to the usual ZIH filesystems like `
/
scratch
`. Launching applications in your container
output to the usual ZIH filesystems like `
/
data/horse
`. Launching applications in your container
#### Run a Command Inside the Container
#### Run a Command Inside the Container
...
@@ -351,9 +351,9 @@ One common use-case for containers is that you need an operating system with a n
...
@@ -351,9 +351,9 @@ One common use-case for containers is that you need an operating system with a n
[glibc](https://www.gnu.org/software/libc/) version than what is available on ZIH systems. E.g., the
[glibc](https://www.gnu.org/software/libc/) version than what is available on ZIH systems. E.g., the
bullx Linux on ZIH systems used to be based on RHEL 6 having a rather dated glibc version 2.12, some
bullx Linux on ZIH systems used to be based on RHEL 6 having a rather dated glibc version 2.12, some
binary-distributed applications didn't work on that anymore. You can use one of our pre-made CentOS
binary-distributed applications didn't work on that anymore. You can use one of our pre-made CentOS
7 container images (`
/
scratch
/singularity/centos7.img
`) to circumvent this problem. Example:
7 container images (`
/
data/horse
/singularity/centos7.img
`) to circumvent this problem. Example:
```console
```console
marie@compute$ singularity exec /
scratch
/singularity/centos7.img ldd --version
marie@compute$ singularity exec /
data/horse
/singularity/centos7.img ldd --version
ldd (GNU libc) 2.17
ldd (GNU libc) 2.17
``
`
``
`
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