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Add FAQ and Known problems entries

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2022-12-14 18:01:32 +01:00
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15
pages/merlin6/99-support/faq.md
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@ -10,10 +10,21 @@ permalink: /merlin6/faq.html
{%include toc.html %}
## How do I register for merlin?
## How do I register for Merlin?
See [Requesting Accounts](/merlin6/request-account.html).
## How do I get information about downtimes and updates?
See [Get updated through the Merlin User list!](/merlin6/contact.html#get-updated-through-the-merlin-user-list)
## How can I request access to a Merlin project directory?
Merlin projects are placed in the `/data/project` directory. Access to each project is controlled by Unix group membership.
If you require access to an existing project, please request group membership as described in [Requesting extra Unix groups](/merlin6/request-account.html#requesting-extra-unix-groups).
Your project leader or project colleagues will know what Unix group you should belong to. Otherwise, you can check what Unix group is allowed to access that project directory (simply run `ls -ltrha`).
## Can I install software myself?
Most software can be installed in user directories without any special permissions. We recommend using `/data/user/$USER/bin` for software since home directories are fairly small. For software that will be used by multiple groups/users you can also [request the admins](/merlin6/contact.html) install it as a [module](/merlin6/using-modules.html).
@ -34,3 +45,5 @@ conda create --name myenv python==3.9 ...
conda activate myenv
```
## I have problems with Slurm

127
pages/merlin6/99-support/known-problems.md
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@ -8,17 +8,86 @@ sidebar: merlin6_sidebar
permalink: /merlin6/known-problems.html
---
## Known Problems Summary
## Common errors
| Topic |
|:----------------------------------------------------------------------------------------- |
| [Default Shell](/merlin6/known-problems.html#default-shell) |
| [OpenGL vs Mesa](/merlin6/known-problems.html#opengl-vs-mesa) |
| [Paraview](/merlin6/known-problems.html#OpenGL) |
| [ANSYS](/merlin6/known-problems.html#opengl-support-paraview-ansys-etc) |
| [Illegal instructions error](i/merlin6/known-problems.html#illegal-instructions) |
### Illegal instruction error
## Default SHELL
It may happened that your code, compiled on one machine will not be executed on another throwing exception like **"(Illegal instruction)"**.
This is usually because the software was compiled with a set of instructions newer than the ones available in the node where the software runs,
and it mostly depends on the processor generation.
In example, `merlin-l-001` and `merlin-l-002` contain a newer generation of processors than the old GPUs nodes, or than the Merlin5 cluster.
Hence, unless one compiles the software with compatibility with set of instructions from older processors, it will not run on old nodes.
Sometimes, this is properly set by default at the compilation time, but sometimes is not.
For GCC, please refer to [GCC x86 Options](https://gcc.gnu.org/onlinedocs/gcc/x86-Options.html) for compiling options. In case of doubts, contact us.
## Slurm
### sbatch using one core despite setting -c/--cpus-per-task
From **Slurm v22.05.6**, the behavior of `srun` has changed. Merlin has been updated to this version since *Tuesday 13.12.2022*.
`srun` will no longer read in `SLURM_CPUS_PER_TASK`, which is typically set when defining `-c/--cpus-per-task` in the `sbatch` command.
This means you will implicitly have to specify `-c\--cpus-per-task` also on your `srun` calls, or set the new `SRUN_CPUS_PER_TASK` environment variable to accomplish the same thing.
Therefore, unless this is implicitly specified, `srun` will use only one Core per task (resulting in 2 CPUs per task when multithreading is enabled)
An example for setting up `srun` with `-c\--cpus-per-task`:
```bash
(base) ❄ [caubet_m@merlin-l-001:/data/user/caubet_m]# cat mysbatch_method1
#!/bin/bash
#SBATCH -n 1
#SBATCH --cpus-per-task=8
echo 'From Slurm v22.05.8 srun does not inherit $SLURM_CPUS_PER_TASK'
srun python -c "import os; print(os.sched_getaffinity(0))"
echo 'One has to implicitly specify $SLURM_CPUS_PER_TASK'
echo 'In this example, by setting -c/--cpus-per-task in srun'
srun --cpus-per-task=$SLURM_CPUS_PER_TASK python -c "import os; print(os.sched_getaffinity(0))"
(base) ❄ [caubet_m@merlin-l-001:/data/user/caubet_m]# sbatch mysbatch_method1
Submitted batch job 8000813
(base) ❄ [caubet_m@merlin-l-001:/data/user/caubet_m]# cat slurm-8000813.out
From Slurm v22.05.8 srun does not inherit $SLURM_CPUS_PER_TASK
{1, 45}
One has to implicitly specify $SLURM_CPUS_PER_TASK
In this example, by setting -c/--cpus-per-task in srun
{1, 2, 3, 4, 45, 46, 47, 48}
```
An example to accomplish the same thing with the `SRUN_CPUS_PER_TASK` environment variable:
```bash
(base) ❄ [caubet_m@merlin-l-001:/data/user/caubet_m]# cat mysbatch_method2
#!/bin/bash
#SBATCH -n 1
#SBATCH --cpus-per-task=8
echo 'From Slurm v22.05.8 srun does not inherit $SLURM_CPUS_PER_TASK'
srun python -c "import os; print(os.sched_getaffinity(0))"
echo 'One has to implicitly specify $SLURM_CPUS_PER_TASK'
echo 'In this example, by setting an environment variable SRUN_CPUS_PER_TASK'
export SRUN_CPUS_PER_TASK=$SLURM_CPUS_PER_TASK
srun python -c "import os; print(os.sched_getaffinity(0))"
(base) ❄ [caubet_m@merlin-l-001:/data/user/caubet_m]# sbatch mysbatch_method2
Submitted batch job 8000815
(base) ❄ [caubet_m@merlin-l-001:/data/user/caubet_m]# cat slurm-8000815.out
From Slurm v22.05.8 srun does not inherit $SLURM_CPUS_PER_TASK
{1, 45}
One has to implicitly specify $SLURM_CPUS_PER_TASK
In this example, by setting an environment variable SRUN_CPUS_PER_TASK
{1, 2, 3, 4, 45, 46, 47, 48}
```
## General topics
### Default SHELL
In general, **`/bin/bash` is the recommended default user's SHELL** when working in Merlin.
@ -53,7 +122,7 @@ Notice that available *shells* can be found in the following file:
cat /etc/shells
```
## OpenGL vs Mesa
### 3D acceleration: OpenGL vs Mesa
Some applications can run with OpenGL support. This is only possible when the node contains a GPU card.
@ -64,16 +133,20 @@ module load paraview
paraview-mesa paraview # 'paraview --mesa' for old releases
```
However, if one needs to run with OpenGL support, this is still possible by running `vglrun`. Officially, the supported method is
NoMachine remote desktop (SSH with X11 Forwarding is slow, but also needs to properly setup the client -desktop or laptop-, where
Merlin admins have no access or rights to it). In example, for running Paraview:
However, if one needs to run with OpenGL support, this is still possible by running `vglrun`. In example, for running Paraview:
```bash
module load paraview
vglrun paraview
```
## ANSYS
Officially, the supported method for running `vglrun` is by using the [NoMachine remote desktop](/merlin6/nomachine.html).
Running `vglrun` it's also possible using SSH with X11 Forwarding. However, it's very slow and it's only recommended when running
in Slurm (from [NoMachine](/merlin6/nomachine.html)). Please, avoid running `vglrun` over SSH from a desktop or laptop.
## Software
### ANSYS
Sometimes, running ANSYS/Fluent requires X11 support. For that, one should run fluent as follows.
@ -82,27 +155,7 @@ module load ANSYS
fluent -driver x11
```
## Paraview
### Paraview
For running Paraview, one can run it with Mesa support or OpenGL support.
```bash
module load paraview
# Run with Mesa support (nodes without GPU)
paraview-mesa paraview # 'paraview --mesa' for old releases
# Run with OpenGL support (nodes with GPU)
vglrun paraview
```
## Illegal instructions
It may happened that your code, compiled on one machine will not be executed on another throwing exception like **"(Illegal instruction)"**.
This is usually because the software was compiled with a set of instructions newer than the ones available in the node where the software runs,
and it mostly depends on the processor generation.
In example, `merlin-l-001` and `merlin-l-002` contain a newer generation of processors than the old GPUs nodes, or than the Merlin5 cluster.
Hence, unless one compiles the software with compatibility with set of instructions from older processors, it will not run on old nodes.
Sometimes, this is properly set by default at the compilation time, but sometimes is not.
For GCC, please refer to https://gcc.gnu.org/onlinedocs/gcc/x86-Options.html for compiling options. In case of doubts, contact us.
For running Paraview, one can run it with Mesa support or OpenGL support. Please refer to [OpenGL vs Mesa](/merlin6/known-problems.html#opengl-vs-mesa) for
further information about how to run it.