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merge and move support pages

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this are now under the /support path, meaning that this is unified for
all clusters.
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---
title: "FAQ"
---
# Frequently Asked Questions
## How do I register for Merlin?
See [Requesting Merlin Access](../merlin7/01-Quick-Start-Guide/requesting-accounts.md).
## How do I get information about downtimes and updates?
See [Get updated through the Merlin User list!](index.md#merlin-user-mailing-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 Unix Group Membership](../merlin7/01-Quick-Start-Guide/requesting-projects.md#requesting-unix-group-membership).
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 -ltrhd` for the project directory).
## Can I install software myself?
Most software can be installed in user directories without any special
permissions. We recommend using `/data/user/$USER/bin` for software since home
directories are fairly small. For software that will be used by multiple
groups/users you can also [request the admins](index.md) install it as a
[module](../merlin7/05-Software-Support/pmodules.md).
How to install depends a bit on the software itself. There are three common
installation procedures:
* *binary distributions*. These are easy; just put them in a directory (eg
`/data/user/$USER/bin`) and add that to your PATH.
* *source compilation* using make/cmake/autoconfig/etc. Usually the
compilation scripts accept a `--prefix=/data/user/$USER` directory for where
to install it. Then they place files under `<prefix>/bin`, `<prefix>/lib`,
etc. The exact syntax should be documented in the installation instructions.
!!! note inline end
The following is based on `merlin6`, but should still be valid for `merlin7`.
* *conda environment*. This is now becoming standard for python-based
software, including lots of the AI tools. First follow the [initial setup
instructions](../merlin6/software-support/python.md#anaconda) to configure conda to
use /data/user instead of your home directory. Then you can create
environments like:
```bash
module load anaconda/2019.07
# if they provide environment.yml
conda env create -f environment.yml
# or to create manually
conda create --name myenv python==3.9 ...
conda activate myenv
```
## Something doesn't work
Check the list of [known problems](known-problems.md) to see if a solution is known.
If not, please [contact the admins](index.md).

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# Getting Support
!!! tip
It is strongly recommended that users subscribe to the [user mailing
list](#merlin-user-mailing-list), that way you will receive the newest
announcements concerning the status of the clusters, information regarding
maintenance actions, and other tasks that might affect your work.
There are several channels you can use to get support:
* the **preferred** choice is to submit a ticket with [PSI Service Now](https://psi.service-now.com/psisp), alternatively
* you can also us our [user mailing list](#merlin-user-mailing-list), or lastly
* you can email the Admins directly <merlin-admins@lists.psi.ch>
!!! info
Basic contact information is also displayed on every shell login to the
system using the *Message of the Day* mechanism.
## PSI Service Now
[PSI Service Now](https://psi.service-now.com/psisp) is the official tool for
opening tickets and requests.
* PSI HelpDesk will redirect the incident to the corresponding department, or
* you can always assign it directly by checking the box `I know which service
is affected` and providing the service name `Local HPC Resources (e.g.
Merlin) [CF]` (just type in `Local` and you should get the valid
completions).
## Merlin User mailing list
This mailing list is the official channel used by Merlin administrators to inform users about downtimes,
interventions or problems. Users can be subscribed in two ways:
* *Preferred way*: Self-registration through [Sympa](https://psilists.ethz.ch/sympa/info/merlin-users)
* If you need to subscribe many people (e.g. your whole group) by sending a
request to the admin list <merlin-admins@lists.psi.ch>
and providing a list of email addresses.
## Email the Admins
This is the official way to contact Merlin Administrators for discussions which
do not fit well into the incident category. Do not hesitate to contact us for
such cases.
**E-Mail**: <merlin-admins@lists.psi.ch>
---
## Who are we?
The PSI Merlin clusters are managed by the **[High Performance Computing and
Emerging technologies Group](https://www.psi.ch/de/lsm/hpce-group)**, which is
part of the [Science IT Infrastructure, and Services department
(AWI)](https://www.psi.ch/en/awi) in PSI's [Center for Scientific Computing,
Theory and Data (SCD)](https://www.psi.ch/en/csd).

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# Known Problems
## Common errors
### Illegal instruction error
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.
Some users might notice that BASH is not the default SHELL when logging in to Merlin systems, or they might need to run a different SHELL.
This is probably because when the PSI account was requested, no SHELL description was specified or a different one was requested explicitly by the requestor.
Users can check which is the default SHELL specified in the PSI account with the following command:
```bash
getent passwd $USER | awk -F: '{print $NF}'
```
If SHELL does not correspond to the one you need to use, you should request a central change for it.
This is because Merlin accounts are central PSI accounts. Hence, **change must be requested** via [PSI Service Now](index.md#psi-service-now).
Alternatively, if you work on other PSI Linux systems but for Merlin you need a different SHELL type, a temporary change can be performed during login startup.
You can update one of the following files:
* `~/.login`
* `~/.profile`
* Any `rc` or `profile` file in your home directory (i.e. `.cshrc`, `.bashrc`, `.bash_profile`, etc.)
with the following lines:
```bash
# Replace MY_SHELL with the bash type you need
MY_SHELL=/bin/bash
exec $MY_SHELL -l
```
Notice that available *shells* can be found in the following file:
```bash
cat /etc/shells
```
### 3D acceleration: OpenGL vs Mesa
Some applications can run with OpenGL support. This is only possible when the node contains a GPU card.
In general, X11 with Mesa Driver is the recommended method as it will work in all cases (no need of GPUs). In example, for ParaView:
```bash
module load paraview
paraview-mesa paraview # 'paraview --mesa' for old releases
```
However, if one needs to run with OpenGL support, this is still possible by running `vglrun`. In example, for running Paraview:
```bash
module load paraview
vglrun paraview
```
Officially, the supported method for running `vglrun` is by using the [NoMachine remote desktop](../merlin7/02-How-To-Use-Merlin/nomachine.md).
Running `vglrun` it's also possible using SSH with X11 Forwarding. However, it's very slow and it's only recommended when running
in Slurm (from [NoMachine](../merlin7/02-How-To-Use-Merlin/nomachine.md)). Please, avoid running `vglrun` over SSH from a desktop or laptop.
## Software
### ANSYS
Sometimes, running ANSYS/Fluent requires X11 support. For that, one should run fluent as follows.
```bash
module load ANSYS
fluent -driver x11
```
### Paraview
For running Paraview, one can run it with Mesa support or OpenGL support. Please refer to [OpenGL vs Mesa](#3d-acceleration-opengl-vs-mesa) for
further information about how to run it.
### Module command not found
In some circumstances the module command may not be initialized properly. For instance, you may see the following error upon logon:
```
bash: module: command not found
```
The most common cause for this is a custom `.bashrc` file which fails to source the global `/etc/bashrc` responsible for setting up PModules in some OS versions. To fix this, add the following to `$HOME/.bashrc`:
```bash
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
```
It can also be fixed temporarily in an existing terminal by running `. /etc/bashrc` manually.

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# Troubleshooting
For troubleshooting, please contact us through the official channels. See
[here](index.md) for more information.
## Known Problems
Before contacting us for support, please check the [Known
Problems](known-problems.md) page to see if there is an existing workaround for
your specific problem.
## Troubleshooting Slurm Jobs
If you want to report a problem or request for help when running jobs, please
**always provide** the following information:
1. Provide your batch script or, alternatively, the path to your batch script.
2. Add **always** the following commands to your batch script
```bash
echo "User information:"; who am i
echo "Running hostname:"; hostname
echo "Current location:"; pwd
echo "User environment:"; env
echo "List of PModules:"; module list
```
3. Whenever possible, provide the Slurm JobID.
Providing this information is **extremely important** in order to ease
debugging, otherwise only with the description of the issue or just the error
message is completely insufficient in most cases.
## Troubleshooting SSH
Use the ssh command with the "-vvv" option and copy and paste the text
(**please don't send us screenshots**) the output to your request in
Service-Now. Example:
```bash
ssh -Y -vvv $username@<hostname>
```