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Updated interactive jobs

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caubet_m
2019-11-05 16:25:03 +01:00
parent a2aaf3f2bb
commit 520d861191
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pages/merlin6/03 Job Submission/interactive-jobs.md
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@ -51,35 +51,79 @@ merlin-c-103.psi.ch
### salloc
``salloc`` is used to obtain a Slurm job allocation (a set of nodes). Once job is allocated,
**``salloc``** is used to obtain a Slurm job allocation (a set of nodes). Once job is allocated,
users are able to execute interactive command(s). Once finished (``exit`` or ``Ctrl+D``),
the allocation is released.
the allocation is released. **``salloc``** is a blocking command, it is, command will be blocked
until the requested resources are allocated.
Please, not that ``salloc`` is by default a blocking process, and once the resources get
allocated user gets the bash prompt back. Once prompt is back, a new bash shell is created,
and user can run any ``srun`` commands, which will run tasks on the allocated resources. Once
finished, exiting the bash shell will release the allocation.
When running **``salloc``**, once the resources get allocated, *by default* the user will get
a ***new shell on one of the allocated resources*** (if a user has requested few nodes, it will
prompt a new shell in the first allocated node). This is thanks to the default command
``srun -n1 -N1 --mem-per-cpu=0 --gres=gpu:0 --pty --preserve-env --mpi=none $SHELL`` which will run
in the background (users do not need to specify any ``srun`` command). However, this behaviour can
be changed by running a different command after the **``salloc``** command, and someone can replace
the default ``srun`` command. In example:
```bash
# Typical 'salloc' call
# - Same as running:
# 'salloc --clusters=merlin6 -N 2 -n 2 srun -n1 -N1 --mem-per-cpu=0 --gres=gpu:0 --pty --preserve-env --mpi=none $SHELL'
salloc --clusters=merlin6 -N 2 -n 2
# Custom 'salloc' call
# - $SHELL will open a shell locally on the machine running 'salloc' (login node shell)
salloc --clusters=merlin6 -N 2 -n 2 $SHELL
```
<details>
<summary>[Show 'salloc' example]: Allocating 2 cores (1 task/core) in 2 nodes (1 core/node)</summary>
<summary>[Show 'salloc' example]: Allocating 2 cores (1 task/core) in 2 nodes (1 core/node) - <i>Default</i></summary>
<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
(base) [caubet_m@merlin-l-001 ~]$ salloc --clusters=merlin6 --ntasks=2 --nodes=2
salloc: Pending job allocation 135087844
salloc: job 135087844 queued and waiting for resources
salloc: job 135087844 has been allocated resources
salloc: Granted job allocation 135087844
salloc: Pending job allocation 135171306
salloc: job 135171306 queued and waiting for resources
salloc: job 135171306 has been allocated resources
salloc: Granted job allocation 135171306
(base) [caubet_m@merlin-l-001 ~]$ srun hostname
merlin-c-120.psi.ch
merlin-c-119.psi.ch
(base) [caubet_m@merlin-c-213 ~]$ srun hostname
merlin-c-213.psi.ch
merlin-c-214.psi.ch
(base) [caubet_m@merlin-c-119 ~]$ exit
logout
Connection to merlin-c-119 closed.
(base) [caubet_m@merlin-l-001 ~]$ exit
(base) [caubet_m@merlin-c-213 ~]$ exit
exit
salloc: Relinquishing job allocation 135087844
salloc: Relinquishing job allocation 135171306
(base) [caubet_m@merlin-l-001 ~]$ salloc --clusters=merlin6 -N 2 -n 2 srun -n1 -N1 --mem-per-cpu=0 --gres=gpu:0 --pty --preserve-env --mpi=none $SHELL
salloc: Pending job allocation 135171342
salloc: job 135171342 queued and waiting for resources
salloc: job 135171342 has been allocated resources
salloc: Granted job allocation 135171342
(base) [caubet_m@merlin-c-021 ~]$ srun hostname
merlin-c-021.psi.ch
merlin-c-022.psi.ch
(base) [caubet_m@merlin-c-021 ~]$ exit
exit
salloc: Relinquishing job allocation 135171342
</pre>
</details>
<details>
<summary>[Show 'salloc' example]: Allocating 2 cores (1 task/core) in 2 nodes (1 core/node) - <i>$SHELL</i></summary>
<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
(base) [caubet_m@merlin-export-01 ~]$ salloc --clusters=merlin6 --ntasks=2 --nodes=2 $SHELL
salloc: Pending job allocation 135171308
salloc: job 135171308 queued and waiting for resources
salloc: job 135171308 has been allocated resources
salloc: Granted job allocation 135171308
(base) [caubet_m@merlin-export-01 ~]$ srun hostname
merlin-c-218.psi.ch
merlin-c-117.psi.ch
(base) [caubet_m@merlin-export-01 ~]$ exit
exit
salloc: Relinquishing job allocation 135171308
</pre>
</details>
@ -162,7 +206,7 @@ Once RSA keys are setup, you can run any windows based application. For that, yo
add the option ``--x11`` to the ``srun`` command. In example:
```bash
srun --x11 xclock
srun --clusters=merlin6 --x11 xclock
```
will popup a X11 based clock.
@ -172,19 +216,19 @@ to add the option ``--pty`` to the ``srun --x11`` command. Once resource is allo
there you can interactively run X11 and non-X11 based commands.
```bash
srun --x11 --pty bash
srun --clusters=merlin6 --x11 --pty bash
```
<details>
<summary>[Show 'srun' with X11 support examples]</summary>
<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
(base) [caubet_m@merlin-l-001 ~]$ srun --x11 xclock
(base) [caubet_m@merlin-l-001 ~]$ srun --clusters=merlin6 --x11 xclock
srun: job 135095591 queued and waiting for resources
srun: job 135095591 has been allocated resources
(base) [caubet_m@merlin-l-001 ~]$
(base) [caubet_m@merlin-l-001 ~]$ srun --x11 --pty bash
(base) [caubet_m@merlin-l-001 ~]$ srun --clusters=merlin6 --x11 --pty bash
srun: job 135095592 queued and waiting for resources
srun: job 135095592 has been allocated resources
@ -197,3 +241,51 @@ This was an example
exit
</pre>
</details>
### 'salloc' with x11 support
Once RSA keys are setup, you can run any windows based application. For that, you need to
add the option ``--x11`` to the ``salloc`` command. In example:
```bash
salloc --clusters=merlin6 --x11 xclock
```
will popup a X11 based clock.
In the same manner, you can create a bash shell with x11 support. For doing that, you need
to add to run just ``salloc --clusters=merlin6 --x11``. Once resource is allocated, from
there you can interactively run X11 and non-X11 based commands.
```bash
salloc --clusters=merlin6 --x11
```
<details>
<summary>[Show 'salloc' with X11 support examples]</summary>
<pre class="terminal code highlight js-syntax-highlight plaintext" lang="plaintext" markdown="false">
(base) [caubet_m@merlin-l-001 ~]$ salloc --clusters=merlin6 --x11 xclock
salloc: Pending job allocation 135171355
salloc: job 135171355 queued and waiting for resources
salloc: job 135171355 has been allocated resources
salloc: Granted job allocation 135171355
salloc: Relinquishing job allocation 135171355
(base) [caubet_m@merlin-l-001 ~]$ salloc --clusters=merlin6 --x11
salloc: Pending job allocation 135171349
salloc: job 135171349 queued and waiting for resources
salloc: job 135171349 has been allocated resources
salloc: Granted job allocation 135171349
salloc: Waiting for resource configuration
salloc: Nodes merlin-c-117 are ready for job
(base) [caubet_m@merlin-c-117 ~]$ xclock
(base) [caubet_m@merlin-c-117 ~]$ echo "This was an example"
This was an example
(base) [caubet_m@merlin-c-117 ~]$ exit
exit
salloc: Relinquishing job allocation 135171349
</pre>
</details>