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12
docs/cscs-userlab/index.md
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@@ -45,13 +45,13 @@ For 2025 we can offer access to [CSCS Alps](https://www.cscs.ch/computers/alps)
* [CSCS User Portal](https://user.cscs.ch/)
* Documentation
* [CSCS Eiger CPU multicore cluster](https://docs.cscs.ch/clusters/eiger/)
* [CSCS Daint GPU cluster](https://docs.cscs.ch/clusters/daint/)
* [CSCS Eiger CPU multicore cluster](https://docs.cscs.ch/clusters/eiger/)
* [CSCS Daint GPU cluster](https://docs.cscs.ch/clusters/daint/)
## Contact information
* PSI Contacts:
* Mailing list contact: <psi-hpc-at-cscs-admin@lists.psi.ch>
* Marc Caubet Serrabou <marc.caubet@psi.ch>
* Derek Feichtinger <derek.feichtinger@psi.ch>
* Mailing list for receiving user notifications and survey information: psi-hpc-at-cscs@lists.psi.ch [(subscribe)](https://psilists.ethz.ch/sympa/subscribe/psi-hpc-at-cscs)
* Mailing list contact: <psi-hpc-at-cscs-admin@lists.psi.ch>
* Marc Caubet Serrabou <marc.caubet@psi.ch>
* Derek Feichtinger <derek.feichtinger@psi.ch>
* Mailing list for receiving user notifications and survey information: <psi-hpc-at-cscs@lists.psi.ch> [(subscribe)](https://psilists.ethz.ch/sympa/subscribe/psi-hpc-at-cscs)

10
docs/gmerlin6/cluster-introduction.md
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@@ -1,12 +1,4 @@
---
title: Introduction
#tags:
#keywords:
last_updated: 28 June 2019
#summary: "GPU Merlin 6 cluster overview"
sidebar: merlin6_sidebar
permalink: /gmerlin6/cluster-introduction.html
---
# Introduction
## About Merlin6 GPU cluster

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docs/gmerlin6/hardware-and-software-description.md
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@@ -1,12 +1,4 @@
---
title: Hardware And Software Description
#tags:
#keywords:
last_updated: 19 April 2021
#summary: ""
sidebar: merlin6_sidebar
permalink: /gmerlin6/hardware-and-software.html
---
# Hardware And Software Description
## Hardware
@@ -145,6 +137,7 @@ ibstat | grep Rate
In the Merlin6 GPU computing nodes, we try to keep software stack coherency with the main cluster [Merlin6](../merlin6/index.md).
Due to this, the Merlin6 GPU nodes run:
* [**RedHat Enterprise Linux 7**](https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/7/html/7.9_release_notes/index)
* [**Slurm**](https://slurm.schedmd.com/), we usually try to keep it up to date with the most recent versions.
* [**GPFS v5**](https://www.ibm.com/support/knowledgecenter/en/STXKQY_5.0.2/ibmspectrumscale502_welcome.html)

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docs/gmerlin6/slurm-configuration.md
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@@ -1,12 +1,4 @@
---
title: Slurm cluster 'gmerlin6'
#tags:
keywords: configuration, partitions, node definition, gmerlin6
last_updated: 29 January 2021
summary: "This document describes a summary of the Slurm 'configuration."
sidebar: merlin6_sidebar
permalink: /gmerlin6/slurm-configuration.html
---
# Slurm cluster 'gmerlin6'
This documentation shows basic Slurm configuration and options needed to run jobs in the GPU cluster.
@@ -49,30 +41,35 @@ Users might need to specify the Slurm partition. If no partition is specified, i
The table below resumes shows all possible partitions available to users:
| GPU Partition | Default Time | Max Time | PriorityJobFactor\* | PriorityTier\*\* |
| GPU Partition | Default Time | Max Time | PriorityJobFactor | PriorityTier |
|:---------------------: | :----------: | :--------: | :-----------------: | :--------------: |
| `gpu` | 1 day | 1 week | 1 | 1 |
| `gpu-short` | 2 hours | 2 hours | 1000 | 500 |
| `gwendolen` | 30 minutes | 2 hours | 1000 | 1000 |
| `gwendolen-long`\*\*\* | 30 minutes | 8 hours | 1 | 1 |
| `gwendolen-long` | 30 minutes | 8 hours | 1 | 1 |
\*The **PriorityJobFactor** value will be added to the job priority (*PARTITION* column in `sprio -l` ). In other words, jobs sent to higher priority
The **PriorityJobFactor** value will be added to the job priority (*PARTITION* column in `sprio -l` ). In other words, jobs sent to higher priority
partitions will usually run first (however, other factors such like **job age** or mainly **fair share** might affect to that decision). For the GPU
partitions, Slurm will also attempt first to allocate jobs on partitions with higher priority over partitions with lesser priority.
\*\*Jobs submitted to a partition with a higher **PriorityTier** value will be dispatched before pending jobs in partition with lower *PriorityTier* value
and, if possible, they will preempt running jobs from partitions with lower *PriorityTier* values.
Jobs submitted to a partition with a higher **PriorityTier** value will be dispatched before pending jobs in partition with lower *PriorityTier* value
and, if possible, they will preempt running jobs from partitions with lower **PriorityTier** values.
\*\*\***gwnedolen-long** is a special partition which is enabled during non-working hours only. As of _Nov 2023_, the current policy is to disable this partition from Mon to Fri, from 1am to 5pm. However, jobs can be submitted anytime, but can only be scheduled outside this time range.
**gwnedolen-long** is a special partition which is enabled during non-working
hours only. As of **Nov 2023**, the current policy is to disable this partition
from Mon to Fri, from 1am to 5pm. However, jobs can be submitted anytime, but
can only be scheduled outside this time range.
### Merlin6 GPU Accounts
Users need to ensure that the public **`merlin`** account is specified. No specifying account options would default to this account.
This is mostly needed by users which have multiple Slurm accounts, which may define by mistake a different account.
```bash
#SBATCH --account=merlin # Possible values: merlin, gwendolen
```
Not all the accounts can be used on all partitions. This is resumed in the table below:
| Slurm Account | Slurm Partitions |
@@ -86,10 +83,16 @@ Users only need to specify the `gwendolen` account when using the `gwendolen` or
#### The 'gwendolen' account
For running jobs in the **`gwendolen`/`gwendolen-long`** partitions, users must specify the **`gwendolen`** account.
The `merlin` account is not allowed to use the Gwendolen partitions.
For running jobs in the **`gwendolen`/`gwendolen-long`** partitions, users must
specify the **`gwendolen`** account. The `merlin` account is not allowed to
use the Gwendolen partitions.
Gwendolen is restricted to a set of users belonging to the **`unx-gwendolen`** Unix group. If you belong to a project allowed to use **Gwendolen**, or you are a user which would like to have access to it, please request access to the **`unx-gwendolen`** Unix group through [PSI Service Now](https://psi.service-now.com/): the request will be redirected to the responsible of the project (Andreas Adelmann).
Gwendolen is restricted to a set of users belonging to the **`unx-gwendolen`**
Unix group. If you belong to a project allowed to use **Gwendolen**, or you are
a user which would like to have access to it, please request access to the
**`unx-gwendolen`** Unix group through [PSI Service
Now](https://psi.service-now.com/): the request will be redirected to the
responsible of the project (Andreas Adelmann).
### Slurm GPU specific options
@@ -119,10 +122,14 @@ This is detailed in the below table.
#### Constraint / Features
Instead of specifying the GPU **type**, sometimes users would need to **specify the GPU by the amount of memory available in the GPU** card itself.
This has been defined in Slurm with **Features**, which is a tag which defines the GPU memory for the different GPU cards.
Users can specify which GPU memory size needs to be used with the `--constraint` option. In that case, notice that *in many cases
there is not need to specify `[<type>:]`* in the `--gpus` option.
Instead of specifying the GPU **type**, sometimes users would need to **specify
the GPU by the amount of memory available in the GPU** card itself.
This has been defined in Slurm with **Features**, which is a tag which defines
the GPU memory for the different GPU cards. Users can specify which GPU memory
size needs to be used with the `--constraint` option. In that case, notice that
*in many cases there is not need to specify `[<type>:]`* in the `--gpus`
option.
```bash
#SBATCH --contraint=<Feature> # Possible values: gpumem_8gb, gpumem_11gb, gpumem_24gb, gpumem_40gb
@@ -172,6 +179,7 @@ The table below shows the available **Features** and which GPU card models and G
#### Other GPU options
Alternative Slurm options for GPU based jobs are available. Please refer to the **man** pages
for each Slurm command for further information about it (`man salloc`, `man sbatch`, `man srun`).
Below are listed the most common settings:
@@ -192,6 +200,7 @@ Please, notice that when defining `[<type>:]` once, then all other options must
#### Dealing with Hyper-Threading
The **`gmerlin6`** cluster contains the partitions `gwendolen` and `gwendolen-long`, which have a node with Hyper-Threading enabled.
In that case, one should always specify whether to use Hyper-Threading or not. If not defined, Slurm will
generally use it (exceptions apply). For this machine, generally HT is recommended.
@@ -219,24 +228,28 @@ Limits are defined using QoS, and this is usually set at the partition level. Li
| **gwendolen-long** | `gwendolen` | No limits, active from 9pm to 5:30am |
* With the limits in the public `gpu` and `gpu-short` partitions, a single job using the `merlin` acccount
(default account) can not use more than 40 CPUs, more than 8 GPUs or more than 200GB.
Any job exceeding such limits will stay in the queue with the message **`QOSMax[Cpu|GRES|Mem]PerJob`**.
As there are no more existing QoS during the week temporary overriding job limits (this happens for
instance in the CPU **daily** partition), the job needs to be cancelled, and the requested resources
must be adapted according to the above resource limits.
(default account) can not use more than 40 CPUs, more than 8 GPUs or more than 200GB.
Any job exceeding such limits will stay in the queue with the message **`QOSMax[Cpu|GRES|Mem]PerJob`**.
As there are no more existing QoS during the week temporary overriding job limits (this happens for
instance in the CPU **daily** partition), the job needs to be cancelled, and the requested resources
must be adapted according to the above resource limits.
* The **gwendolen** and **gwendolen-long** partitions are two special partitions for a **[NVIDIA DGX A100](https://www.nvidia.com/en-us/data-center/dgx-a100/)** machine.
Only users belonging to the **`unx-gwendolen`** Unix group can run in these partitions. No limits are applied (machine resources can be completely used).
Only users belonging to the **`unx-gwendolen`** Unix group can run in these partitions. No limits are applied (machine resources can be completely used).
* The **`gwendolen-long`** partition is available 24h. However,
* from 5:30am to 9pm the partition is `down` (jobs can be submitted, but can not run until the partition is set to `active`).
* from 9pm to 5:30am jobs are allowed to run (partition is set to `active`).
* from 5:30am to 9pm the partition is `down` (jobs can be submitted, but can not run until the partition is set to `active`).
* from 9pm to 5:30am jobs are allowed to run (partition is set to `active`).
### Per user limits for GPU partitions
These limits apply exclusively to users. In other words, there is a maximum of resources a single user can use.
Limits are defined using QoS, and this is usually set at the partition level. Limits are described in the table below with the format: `SlurmQoS(limits)`
(possible `SlurmQoS` values can be listed with the command `sacctmgr show qos`):
These limits apply exclusively to users. In other words, there is a maximum of
resources a single user can use. Limits are defined using QoS, and this is
usually set at the partition level. Limits are described in the table below
with the format: `SlurmQoS(limits)` (possible `SlurmQoS` values can be listed
with the command `sacctmgr show qos`):
| Partition | Slurm Account | Mon-Sun 0h-24h |
|:------------------:| :----------------: | :---------------------------------------------: |
@@ -246,12 +259,17 @@ Limits are defined using QoS, and this is usually set at the partition level. Li
| **gwendolen-long** | `gwendolen` | No limits, active from 9pm to 5:30am |
* With the limits in the public `gpu` and `gpu-short` partitions, a single user can not use more than 80 CPUs, more than 16 GPUs or more than 400GB.
Jobs sent by any user already exceeding such limits will stay in the queue with the message **`QOSMax[Cpu|GRES|Mem]PerUser`**.
In that case, job can wait in the queue until some of the running resources are freed.
Jobs sent by any user already exceeding such limits will stay in the queue
with the message **`QOSMax[Cpu|GRES|Mem]PerUser`**. In that case, job can
wait in the queue until some of the running resources are freed.
* Notice that user limits are wider than job limits. In that way, a user can run up to two 8 GPUs based jobs, or up to four 4 GPUs based jobs, etc.
Please try to avoid occupying all GPUs of the same type for several hours or multiple days, otherwise it would block other users needing the same
type of GPU.
!!! warning
Please try to avoid occupying all GPUs of the same type for several hours or
multiple days, otherwise it would block other users needing the same type of
GPU.
## Advanced Slurm configuration
@@ -265,4 +283,8 @@ For understanding the Slurm configuration setup in the cluster, sometimes may be
* ``/etc/slurm/cgroup.conf`` - can be found in the computing nodes, is also propagated to login nodes for user read access.
The previous configuration files which can be found in the login nodes, correspond exclusively to the **merlin6** cluster configuration files.
Configuration files for the old **merlin5** cluster or for the **gmerlin6** cluster must be checked directly on any of the **merlin5** or **gmerlin6** computing nodes (in example, by login in to one of the nodes while a job or an active allocation is running).
Configuration files for the old **merlin5** cluster or for the **gmerlin6**
cluster must be checked directly on any of the **merlin5** or **gmerlin6**
computing nodes (in example, by login in to one of the nodes while a job or an
active allocation is running).

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@@ -6,9 +6,9 @@ hide:
# HPCE User Documentation
![The HPCE clusters](images/front_page.png){ width="500" }
![The HPCE clusters](images/merlin_cave.png){ width="650px" }
/// caption
The magical trio 🪄
_Within his lair, the wizard ever strives for the perfection of his art._
///
The [HPCE
@@ -16,11 +16,7 @@ group](https://www.psi.ch/en/awi/high-performance-computing-and-emerging-technol
is part of the [PSI Center for Scientific Computing, Theory and
Data](https://www.psi.ch/en/csd) at [Paul Scherrer
Institute](https://www.psi.ch). It provides a range of HPC services for PSI
scientists, such as the Merlin series of HPC clusters, and also engages in
research activities on technologies (data analysis and machine learning
technologies) used on these systems.
## Quick Links
- user support
- news
researchers, staff, and external collaborators, such as the Merlin series of
HPC clusters. Furthermore the HPCE group engages in research activities on
technologies (data analysis and machine learning technologies) used on these
systems.

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@@ -15,8 +15,8 @@ Welcome to the official documentation for migrating experiment data from **MEG**
| merlin7 | /data/user/`$USER` | /data/user/`$USER` | /data/project/meg | |
* The **Merlin6 home and user data directores have been merged** into the single new home directory `/data/user/$USER` on Merlin7.
* This is the same for the home directory in the meg cluster, which has to be merged into `/data/user/$USER` on Merlin7.
* Users are responsible for moving the data.
* This is the same for the home directory in the meg cluster, which has to be merged into `/data/user/$USER` on Merlin7.
* Users are responsible for moving the data.
* The **experiment directory has been integrated into `/data/project/meg`**.
### Recommended Cleanup Actions
@@ -38,16 +38,17 @@ A `experiment_migration.setup` migration script must be executed from **any MeG
* The script **must be executed after every reboot** of the destination nodes.
* **Reason:** On Merlin7, the home directory for the `root` user resides on ephemeral storage (no physical disk).
After a reboot, this directory is cleaned, so **SSH keys need to be redeployed** before running the migration again.
#### When using a PSI Active Directory (AD) account
* Applicable accounts include, for example:
* `gac-meg2_data`
* `gac-meg2`
* `gac-meg2_data`
* `gac-meg2`
* The script only needs to be executed **once**, provided that:
* The home directory for the AD account is located on a shared storage area.
* This shared storage is accessible from the node executing the transfer.
* The home directory for the AD account is located on a shared storage area.
* This shared storage is accessible from the node executing the transfer.
* **Reason:** On Merlin7, these accounts have their home directories on persistent shared storage, so the SSH keys remain available across reboots.
To run it:
@@ -71,25 +72,29 @@ If you are stuck, email: [merlin-admins@lists.psi.ch](mailto:merlin-admins@lists
### Migration Procedure
1. **Run an initial sync**, ideally within a `tmux` session
* This copies the bulk of the data from MeG to Merlin7.
* **IMPORTANT: Do not modify the destination directories**
* Please, before starting the transfer ensure that:
* The source and destination directories are correct.
* The destination directories exist.
* This copies the bulk of the data from MeG to Merlin7.
* **IMPORTANT: Do not modify the destination directories**
* Please, before starting the transfer ensure that:
* The source and destination directories are correct.
* The destination directories exist.
2. **Run additional syncs if needed**
* Subsequent syncs can be executed to transfer changes.
* Ensure that **only one sync for the same directory runs at a time**.
* Multiple syncs are often required since the first one may take several hours or even days.
* Subsequent syncs can be executed to transfer changes.
* Ensure that **only one sync for the same directory runs at a time**.
* Multiple syncs are often required since the first one may take several hours or even days.
3. Schedule a date for the final migration:
* Any activity must be stopped on the source directory.
* In the same way, no activity must be done on the destination until the migration is complete.
* Any activity must be stopped on the source directory.
* In the same way, no activity must be done on the destination until the migration is complete.
4. **Perform a final sync with the `-E` option** (if it applies)
* Use `-E` **only if you need to delete files on the destination that were removed from the source.**
* This ensures the destination becomes an exact mirror of the source.
* **Never use `-E` after the destination has gone into production**, as it will delete new data created there.
* Use `-E` **only if you need to delete files on the destination that were removed from the source.**
* This ensures the destination becomes an exact mirror of the source.
* **Never use `-E` after the destination has gone into production**, as it will delete new data created there.
5. Disable access on the source folder.
6. Enable access on the destination folder.
* At this point, **no new syncs have to be performed.**
* At this point, **no new syncs have to be performed.**
!!! note "Important"
@@ -196,5 +201,5 @@ This command initiates the migration of the directory, by creating the destinati
```
* Runs FPSYNC with 10 threads and N parts of max 20000 files or 100G files:
* Source: `/meg/data1/shared/subprojects/meg1`
* Destination: `login002.merlin7.psi.ch:/data/project/meg/data1/shared/subprojects/meg1`
* Source: `/meg/data1/shared/subprojects/meg1`
* Destination: `login002.merlin7.psi.ch:/data/project/meg/data1/shared/subprojects/meg1`

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@@ -1,22 +1,15 @@
---
title: Hardware And Software Description
#tags:
#keywords:
last_updated: 09 April 2021
#summary: ""
sidebar: merlin6_sidebar
permalink: /merlin5/hardware-and-software.html
---
# Hardware And Software Description
## Hardware
### Computing Nodes
Merlin5 is built from recycled nodes, and hardware will be decomissioned as soon as it fails (due to expired warranty and age of the cluster).
* Merlin5 is based on the [**HPE c7000 Enclosure**](https://h20195.www2.hpe.com/v2/getdocument.aspx?docname=c04128339) solution, with 16 x [**HPE ProLiant BL460c Gen8**](https://h20195.www2.hpe.com/v2/getdocument.aspx?docname=c04123239) nodes per chassis.
* Connectivity is based on Infiniband **ConnectX-3 QDR-40Gbps**
* 16 internal ports for intra chassis communication
* 2 connected external ports for inter chassis communication and storage access.
* 16 internal ports for intra chassis communication
* 2 connected external ports for inter chassis communication and storage access.
The below table summarizes the hardware setup for the Merlin5 computing nodes:
@@ -91,6 +84,7 @@ However, this is an old version of Infiniband which requires older drivers and s
In Merlin5, we try to keep software stack coherency with the main cluster [Merlin6](../merlin6/index.md).
Due to this, Merlin5 runs:
* [**RedHat Enterprise Linux 7**](https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/7/html/7.9_release_notes/index)
* [**Slurm**](https://slurm.schedmd.com/), we usually try to keep it up to date with the most recent versions.
* [**GPFS v5**](https://www.ibm.com/support/knowledgecenter/en/STXKQY_5.0.2/ibmspectrumscale502_welcome.html)

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@@ -1,12 +1,4 @@
---
title: Slurm Configuration
#tags:
keywords: configuration, partitions, node definition
last_updated: 20 May 2021
summary: "This document describes a summary of the Merlin5 Slurm configuration."
sidebar: merlin6_sidebar
permalink: /merlin5/slurm-configuration.html
---
# Slurm Configuration
This documentation shows basic Slurm configuration and options needed to run jobs in the Merlin5 cluster.
@@ -28,7 +20,6 @@ consider the memory as a *consumable resource*. Hence, users can *oversubscribe*
this legacy configuration has been kept to ensure that old jobs can keep running in the same way they did a few years ago.
If you know that this might be a problem for you, please, always use Merlin6 instead.
## Running jobs in the 'merlin5' cluster
In this chapter we will cover basic settings that users need to specify in order to run jobs in the Merlin5 CPU cluster.

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@@ -1,12 +1,4 @@
---
title: Downtimes
#tags:
#keywords:
last_updated: 28 June 2019
#summary: "Merlin 6 cluster overview"
sidebar: merlin6_sidebar
permalink: /merlin6/downtimes.html
---
# Downtimes
On the first Monday of each month the Merlin6 cluster might be subject to interruption due to maintenance.
Users will be informed with at least one week in advance when a downtime is scheduled for the next month.
@@ -22,7 +14,9 @@ Scheduled downtimes mostly affecting the storage and Slurm configurantions may r
When this is required, users will be informed accordingly. Two different types of draining are possible:
* **soft drain**: new jobs may be queued on the partition, but queued jobs may not be allocated nodes and run from the partition.
Jobs already running on the partition continue to run. This will be the **default** drain method.
* **hard drain**: no new jobs may be queued on the partition (job submission requests will be denied with an error message),
but jobs already queued on the partition may be allocated to nodes and run.

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@@ -1,12 +1,4 @@
---
title: Past Downtimes
#tags:
#keywords:
last_updated: 03 September 2019
#summary: "Merlin 6 cluster overview"
sidebar: merlin6_sidebar
permalink: /merlin6/past-downtimes.html
---
# Past Downtimes
## Past Downtimes: Log Changes

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@@ -1,12 +1,4 @@
---
title: Contact
#tags:
keywords: contact, support, snow, service now, mailing list, mailing, email, mail, merlin-admins@lists.psi.ch, merlin-users@lists.psi.ch, merlin users
last_updated: 07 September 2022
#summary: ""
sidebar: merlin6_sidebar
permalink: /merlin6/contact.html
---
# Contact
## Support

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@@ -1,14 +1,4 @@
---
title: FAQ
#tags:
keywords: faq, frequently asked questions, support
last_updated: 27 October 2022
#summary: ""
sidebar: merlin6_sidebar
permalink: /merlin6/faq.html
---
{%include toc.html %}
# FAQ
## How do I register for Merlin?
@@ -35,7 +25,7 @@ How to install depends a bit on the software itself. There are three common inst
2. *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.
3. *conda environment*. This is now becoming standard for python-based software, including lots of the AI tools. First follow the [initial setup instructions](../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

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@@ -1,12 +1,4 @@
---
title: Known Problems
#tags:
keywords: "known problems, troubleshooting, illegal instructions, paraview, ansys, shell, opengl, mesa, vglrun, module: command not found, error"
last_updated: 07 September 2022
#summary: ""
sidebar: merlin6_sidebar
permalink: /merlin6/known-problems.html
---
# Known Problems
## Common errors
@@ -72,7 +64,6 @@ 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
@@ -84,7 +75,6 @@ In this example, by setting an environment variable SRUN_CPUS_PER_TASK
{1, 2, 3, 4, 45, 46, 47, 48}
```
## General topics
### Default SHELL

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@@ -1,12 +1,4 @@
---
title: Migration From Merlin5
#tags:
keywords: merlin5, merlin6, migration, rsync, archive, archiving, lts, long-term storage
last_updated: 07 September 2022
#summary: ""
sidebar: merlin6_sidebar
permalink: /merlin6/migrating.html
---
# Migration From Merlin5
## Directories
@@ -30,9 +22,10 @@ where:
* **Block** is capacity size in GB and TB
* **Files** is number of files + directories in Millions (M)
* **Quota types** are the following:
* **USR**: Quota is setup individually per user name
* **GRP**: Quota is setup individually per Unix Group name
* **Fileset**: Quota is setup per project root directory.
* **USR**: Quota is setup individually per user name
* **GRP**: Quota is setup individually per Unix Group name
* **Fileset**: Quota is setup per project root directory.
* User data directory ``/data/user`` has a strict user block quota limit policy. If more disk space is required, 'project' must be created.
* Soft quotas can be exceeded for short periods of time. Hard quotas cannot be exceeded.

10
docs/merlin6/99-support/troubleshooting.md
View File

@@ -1,12 +1,4 @@
---
title: Troubleshooting
#tags:
keywords: troubleshooting, problems, faq, known problems
last_updated: 07 September 2022
#summary: ""
sidebar: merlin6_sidebar
permalink: /merlin6/troubleshooting.html
---
# Troubleshooting
For troubleshooting, please contact us through the official channels. See [Contact](contact.md)
for more information.

22
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@@ -1,25 +1,19 @@
---
title: Hardware And Software Description
#tags:
#keywords:
last_updated: 13 June 2019
#summary: ""
sidebar: merlin6_sidebar
permalink: /merlin6/hardware-and-software.html
---
# Hardware And Software Description
## Hardware
### Computing Nodes
The new Merlin6 cluster contains a solution based on **four** [**HPE Apollo k6000 Chassis**](https://h20195.www2.hpe.com/v2/getdocument.aspx?docname=a00016641enw)
* *Three* of them contain 24 x [**HP Apollo XL230K Gen10**](https://h20195.www2.hpe.com/v2/GetDocument.aspx?docname=a00016634enw) blades.
* A *fourth* chassis was purchased on 2021 with [**HP Apollo XL230K Gen10**](https://h20195.www2.hpe.com/v2/GetDocument.aspx?docname=a00016634enw) blades dedicated to few experiments. Blades have slighly different components depending on specific project requirements.
The connectivity for the Merlin6 cluster is based on **ConnectX-5 EDR-100Gbps**, and each chassis contains:
* 1 x [HPE Apollo InfiniBand EDR 36-port Unmanaged Switch](https://h20195.www2.hpe.com/v2/getdocument.aspx?docname=a00016643enw)
* 24 internal EDR-100Gbps ports (1 port per blade for internal low latency connectivity)
* 12 external EDR-100Gbps ports (for external for internal low latency connectivity)
* 24 internal EDR-100Gbps ports (1 port per blade for internal low latency connectivity)
* 12 external EDR-100Gbps ports (for external for internal low latency connectivity)
<table>
<thead>
@@ -142,6 +136,7 @@ The connectivity is based on **ConnectX-5 EDR-100Gbps** for the new login nodes,
### Storage
The storage node is based on the [Lenovo Distributed Storage Solution for IBM Spectrum Scale](https://lenovopress.com/lp0626-lenovo-distributed-storage-solution-for-ibm-spectrum-scale-x3650-m5).
* 2 x **Lenovo DSS G240** systems, each one composed by 2 IO Nodes **ThinkSystem SR650** mounting 4 x **Lenovo Storage D3284 High Density Expansion** enclosures.
* Each IO node has a connectivity of 400Gbps (4 x EDR 100Gbps ports, 2 of them are **ConnectX-5** and 2 are **ConnectX-4**).
@@ -151,11 +146,13 @@ The storage solution is connected to the HPC clusters through 2 x **Mellanox SB7
Merlin6 cluster connectivity is based on the [**Infiniband**](https://en.wikipedia.org/wiki/InfiniBand) technology. This allows fast access with very low latencies to the data as well as running
extremely efficient MPI-based jobs:
* Connectivity amongst different computing nodes on different chassis ensures up to 1200Gbps of aggregated bandwidth.
* Inter connectivity (communication amongst computing nodes in the same chassis) ensures up to 2400Gbps of aggregated bandwidth.
* Communication to the storage ensures up to 800Gbps of aggregated bandwidth.
Merlin6 cluster currently contains 5 Infiniband Managed switches and 3 Infiniband Unmanaged switches (one per HP Apollo chassis):
* 1 x **MSX6710** (FDR) for connecting old GPU nodes, old login nodes and MeG cluster to the Merlin6 cluster (and storage). No High Availability mode possible.
* 2 x **MSB7800** (EDR) for connecting Login Nodes, Storage and other nodes in High Availability mode.
* 3 x **HP EDR Unmanaged** switches, each one embedded to each HP Apollo k6000 chassis solution.
@@ -164,8 +161,9 @@ Merlin6 cluster currently contains 5 Infiniband Managed switches and 3 Infiniban
## Software
In Merlin6, we try to keep the latest software stack release to get the latest features and improvements. Due to this, **Merlin6** runs:
* [**RedHat Enterprise Linux 7**](https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/7/html/7.9_release_notes/index)
* [**Slurm**](https://slurm.schedmd.com/), we usually try to keep it up to date with the most recent versions.
* [**GPFS v5**](https://www.ibm.com/support/knowledgecenter/en/STXKQY_5.0.2/ibmspectrumscale502_welcome.html)
* [**MLNX_OFED LTS v.5.2-2.2.0.0 or newer**](https://www.mellanox.com/products/infiniband-drivers/linux/mlnx_ofed) for all **ConnectX-5** or superior cards.
* [MLNX_OFED LTS v.4.9-2.2.4.0](https://www.mellanox.com/products/infiniband-drivers/linux/mlnx_ofed) is installed for remaining **ConnectX-3** and **ConnectIB** cards.
* [MLNX_OFED LTS v.4.9-2.2.4.0](https://www.mellanox.com/products/infiniband-drivers/linux/mlnx_ofed) is installed for remaining **ConnectX-3** and **ConnectIB** cards.

23
docs/merlin6/how-to-use-merlin/archive.md
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@@ -41,20 +41,21 @@ Archiving can be done from any node accessible by the users (usually from the lo
Below are the main steps for using the Data Catalog.
* Ingest the dataset into the Data Catalog. This makes the data known to the Data Catalog system at PSI:
* Prepare a metadata file describing the dataset
* Run **`datasetIngestor`** script
* If necessary, the script will copy the data to the PSI archive servers
* Prepare a metadata file describing the dataset
* Run **`datasetIngestor`** script
* If necessary, the script will copy the data to the PSI archive servers
* Usually this is necessary when archiving from directories other than **`/data/user`** or
**`/data/project`**. It would be also necessary when the Merlin export server (**`merlin-archive.psi.ch`**)
is down for any reason.
* Archive the dataset:
* Visit [https://discovery.psi.ch](https://discovery.psi.ch)
* Click **`Archive`** for the dataset
* The system will now copy the data to the PetaByte Archive at CSCS
* Visit [<https://discovery.psi.ch](https://discovery.psi.ch>)
* Click **`Archive`** for the dataset
* The system will now copy the data to the PetaByte Archive at CSCS
* Retrieve data from the catalog:
* Find the dataset on [https://discovery.psi.ch](https://discovery.psi.ch) and click **`Retrieve`**
* Wait for the data to be copied to the PSI retrieval system
* Run **`datasetRetriever`** script
* Find the dataset on [<https://discovery.psi.ch](https://discovery.psi.ch>) and click **`Retrieve`**
* Wait for the data to be copied to the PSI retrieval system
* Run **`datasetRetriever`** script
Since large data sets may take a lot of time to transfer, some steps are
designed to happen in the background. The discovery website can be used to
@@ -246,7 +247,7 @@ step will take a long time and may appear to have hung. You can check what files
where UID is the dataset ID (12345678-1234-1234-1234-123456789012) and PATH is the absolute path to your data. Note that rsync creates directories first and that the transfer order is not alphabetical in some cases, but it should be possible to see whether any data has transferred.
* There is currently a limit on the number of files per dataset (technically, the limit is from the total length of all file paths). It is recommended to break up datasets into 300'000 files or less.
* If it is not possible or desirable to split data between multiple datasets, an alternate work-around is to package files into a tarball. For datasets which are already compressed, omit the -z option for a considerable speedup:
* If it is not possible or desirable to split data between multiple datasets, an alternate work-around is to package files into a tarball. For datasets which are already compressed, omit the -z option for a considerable speedup:
```bash
tar -f [output].tar [srcdir]
@@ -266,7 +267,6 @@ step will take a long time and may appear to have hung. You can check what files
/data/project/bio/myproject/archive $ datasetIngestor -copy -autoarchive -allowexistingsource -ingest metadata.json
2019/11/06 11:04:43 Latest version: 1.1.11
2019/11/06 11:04:43 Your version of this program is up-to-date
2019/11/06 11:04:43 You are about to add a dataset to the === production === data catalog environment...
2019/11/06 11:04:43 Your username:
@@ -316,7 +316,6 @@ user_n@pb-archive.psi.ch's password:
2019/11/06 11:05:04 The source folder /data/project/bio/myproject/archive is not centrally available (decentral use case).
The data must first be copied to a rsync cache server.
2019/11/06 11:05:04 Do you want to continue (Y/n)?
Y
2019/11/06 11:05:09 Created dataset with id 12.345.67890/12345678-1234-1234-1234-123456789012

10
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@@ -1,12 +1,4 @@
---
title: Connecting from a MacOS Client
#tags:
keywords: MacOS, mac os, mac, connecting, client, configuration, SSH, X11
last_updated: 07 September 2022
summary: "This document describes a recommended setup for a MacOS client."
sidebar: merlin6_sidebar
permalink: /merlin6/connect-from-macos.html
---
# Connecting from a MacOS Client
## SSH without X11 Forwarding

11
docs/merlin6/how-to-use-merlin/connect-from-windows.md
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@@ -1,11 +1,4 @@
---
title: Connecting from a Windows Client
keywords: microsoft, mocosoft, windows, putty, xming, connecting, client, configuration, SSH, X11
last_updated: 07 September 2022
summary: "This document describes a recommended setup for a Windows client."
sidebar: merlin6_sidebar
permalink: /merlin6/connect-from-windows.html
---
# Connecting from a Windows Client
## SSH with PuTTY without X11 Forwarding
@@ -13,6 +6,7 @@ PuTTY is one of the most common tools for SSH.
Check, if the following software packages are installed on the Windows workstation by
inspecting the *Start* menu (hint: use the *Search* box to save time):
* PuTTY (should be already installed)
* *[Optional]* Xming (needed for [SSH with X11 Forwarding](#ssh-with-putty-with-x11-forwarding))
@@ -28,7 +22,6 @@ If they are missing, you can install them using the Software Kiosk icon on the D
![Create Merlin Session](../../images/PuTTY/Putty_Session.png)
## SSH with PuTTY with X11 Forwarding
Official X11 Forwarding support is through NoMachine. Please follow the document

22
docs/merlin6/how-to-use-merlin/kerberos.md
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@@ -1,12 +1,4 @@
---
title: Kerberos and AFS authentication
#tags:
keywords: kerberos, AFS, kinit, klist, keytab, tickets, connecting, client, configuration, slurm
last_updated: 07 September 2022
summary: "This document describes how to use Kerberos."
sidebar: merlin6_sidebar
permalink: /merlin6/kerberos.html
---
# Kerberos and AFS authentication
Projects and users have their own areas in the central PSI AFS service. In order
to access to these areas, valid Kerberos and AFS tickets must be granted.
@@ -20,7 +12,6 @@ time is 10 hours. It means than one needs to constantly renew (`krenew` command)
granting tickets, and their validity can not be extended longer than 7 days. At this point,
one needs to obtain new granting tickets.
## Obtaining granting tickets with username and password
As already described above, the most common use case is to obtain Kerberos and AFS granting tickets
@@ -28,6 +19,7 @@ by introducing username and password:
* When login to Merlin through SSH protocol, if this is done with username + password authentication,
tickets for Kerberos and AFS will be automatically obtained.
* When login to Merlin through NoMachine, no Kerberos and AFS are granted. Therefore, users need to
run `kinit` (to obtain a granting Kerberos ticket) followed by `aklog` (to obtain a granting AFS ticket).
See further details below.
@@ -49,16 +41,16 @@ klist
```bash
krenew
```
* Keep in mind that the maximum lifetime for granting tickets is 7 days, therefore `krenew` can not be used beyond that limit,
* Keep in mind that the maximum lifetime for granting tickets is 7 days, therefore `krenew` can not be used beyond that limit,
and then `kinit` should be used instead.
## Obtanining granting tickets with keytab
Sometimes, obtaining granting tickets by using password authentication is not possible. An example are user Slurm jobs
requiring access to private areas in AFS. For that, there's the possibility to generate a **keytab** file.
Be aware that the **keytab** file must be **private**, **fully protected** by correct permissions and not shared with any
other users.
### Creating a keytab file
@@ -70,6 +62,7 @@ For generating a **keytab**, one has to:
module load krb5/1.20
```
2. Create a private directory for storing the Kerberos **keytab** file
```bash
mkdir -p ~/.k5
```
@@ -78,6 +71,7 @@ mkdir -p ~/.k5
ktutil
```
4. In the `ktutil` console, one has to generate a **keytab** file as follows:
```bash
# Replace $USER by your username
add_entry -password -k 0 -f -p $USER
@@ -85,6 +79,7 @@ wkt /psi/home/$USER/.k5/krb5.keytab
exit
```
Notice that you will need to add your password once. This step is required for generating the **keytab** file.
5. Once back to the main shell, one has to ensure that the file contains the proper permissions:
```bash
chmod 0600 ~/.k5/krb5.keytab
@@ -112,14 +107,17 @@ The steps should be the following:
export KRB5CCNAME="$(mktemp "$HOME/.k5/krb5cc_XXXXXX")"
```
* To obtain a Kerberos5 granting ticket, run `kinit` by using your keytab:
```bash
kinit -kt "$HOME/.k5/krb5.keytab" $USER@D.PSI.CH
```
* To obtain a granting AFS ticket, run `aklog`:
```bash
aklog
```
* At the end of the job, you can remove destroy existing Kerberos tickets.
```bash
kdestroy
```

4
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View File

@@ -103,5 +103,5 @@ These settings prevent "bluriness" at the cost of some performance! (You might w
* Display > Resize remote display (forces 1:1 pixel sizes)
* Display > Change settings > Quality: Choose Medium-Best Quality
* Display > Change settings > Modify advanced settings
* Check: Disable network-adaptive display quality (diables lossy compression)
* Check: Disable client side image post-processing
* Check: Disable network-adaptive display quality (diables lossy compression)
* Check: Disable client side image post-processing

26
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@@ -1,13 +1,4 @@
---
title: Configuring SSH Keys in Merlin
#tags:
keywords: linux, connecting, client, configuration, SSH, Keys, SSH-Keys, RSA, authorization, authentication
last_updated: 15 Jul 2020
summary: "This document describes how to deploy SSH Keys in Merlin."
sidebar: merlin6_sidebar
permalink: /merlin6/ssh-keys.html
---
# Configuring SSH Keys in Merlin
Merlin users sometimes will need to access the different Merlin services without being constantly requested by a password.
One can achieve that with Kerberos authentication, however in some cases some software would require the setup of SSH Keys.
@@ -28,8 +19,9 @@ ls ~/.ssh/id*
For creating **SSH RSA Keys**, one should:
1. Run `ssh-keygen`, a password will be requested twice. You **must remember** this password for the future.
* Due to security reasons, ***always try protecting it with a password***. There is only one exception, when running ANSYS software, which in general should not use password to simplify the way of running the software in Slurm.
* This will generate a private key **id_rsa**, and a public key **id_rsa.pub** in your **~/.ssh** directory.
* Due to security reasons, ***always try protecting it with a password***. There is only one exception, when running ANSYS software, which in general should not use password to simplify the way of running the software in Slurm.
* This will generate a private key **id_rsa**, and a public key **id_rsa.pub** in your **~/.ssh** directory.
2. Add your public key to the **`authorized_keys`** file, and ensure proper permissions for that file, as follows:
```bash
cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys
@@ -61,12 +53,12 @@ By default, when accessing the login node via SSH (with `ForwardAgent=yes`), it
SSH Keys to the authentication agent. Hence, no actions should not be needed by the user. One can configure
`ForwardAgent=yes` as follows:
* **(Recommended)** In your local Linux (workstation, laptop or desktop) add the following line in the
* **(Recommended)** In your local Linux (workstation, laptop or desktop) add the following line in the
`$HOME/.ssh/config` (or alternatively in `/etc/ssh/ssh_config`) file:
```
ForwardAgent yes
```
* Alternatively, on each SSH you can add the option `ForwardAgent=yes` in the SSH command. In example:
* Alternatively, on each SSH you can add the option `ForwardAgent=yes` in the SSH command. In example:
```bash
ssh -XY -o ForwardAgent=yes merlin-l-001.psi.ch
```
@@ -74,12 +66,12 @@ SSH Keys to the authentication agent. Hence, no actions should not be needed by
If `ForwardAgent` is not enabled as shown above, one needs to run the authentication agent and then add your key
to the **ssh-agent**. This must be done once per SSH session, as follows:
* Run `eval $(ssh-agent -s)` to run the **ssh-agent** in that SSH session
* Check whether the authentication agent has your key already added:
* Run `eval $(ssh-agent -s)` to run the **ssh-agent** in that SSH session
* Check whether the authentication agent has your key already added:
```bash
ssh-add -l | grep "/psi/home/$(whoami)/.ssh"
```
* If no key is returned in the previous step, you have to add the private key identity to the authentication agent.
* If no key is returned in the previous step, you have to add the private key identity to the authentication agent.
You will be requested for the **passphrase** of your key, and it can be done by running:
```bash
ssh-add

19
docs/merlin6/how-to-use-merlin/storage.md
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@@ -7,7 +7,8 @@ This document describes the different directories of the Merlin6 cluster.
### User and project data
* ***Users are responsible for backing up their own data***. Is recommended to backup the data on third party independent systems (i.e. LTS, Archive, AFS, SwitchDrive, Windows Shares, etc.).
* **`/psi/home`**, as this contains a small amount of data, is the only directory where we can provide daily snapshots for one week. This can be found in the following directory **`/psi/home/.snapshot/`**
* **`/psi/home`**, as this contains a small amount of data, is the only directory where we can provide daily snapshots for one week. This can be found in the following directory **`/psi/home/.snapshot/`**
* ***When a user leaves PSI, she or her supervisor/team are responsible to backup and move the data out from the cluster***: every few months, the storage space will be recycled for those old users who do not have an existing and valid PSI account.
!!! warning
@@ -31,13 +32,15 @@ merlin_quotas
Merlin6 offers the following directory classes for users:
* ``/psi/home/<username>``: Private user **home** directory
* ``/data/user/<username>``: Private user **data** directory
* ``/data/project/general/<projectname>``: Shared **Project** directory
* For BIO experiments, a dedicated ``/data/project/bio/$projectname`` exists.
* For BIO experiments, a dedicated ``/data/project/bio/$projectname`` exists.
* ``/scratch``: Local *scratch* disk (only visible by the node running a job).
* ``/shared-scratch``: Shared *scratch* disk (visible from all nodes).
* ``/export``: Export directory for data transfer, visible from `ra-merlin-01.psi.ch`, `ra-merlin-02.psi.ch` and Merlin login nodes.
* Refer to **[Transferring Data](../how-to-use-merlin/transfer-data.md)** for more information about the export area and data transfer service.
* Refer to **[Transferring Data](../how-to-use-merlin/transfer-data.md)** for more information about the export area and data transfer service.
!!! tip
@@ -94,7 +97,8 @@ quota -s
* Read **[Important: Code of Conduct](../quick-start-guide/code-of-conduct.md)** for more information about Merlin6 policies.
* Is **forbidden** to use the home directories for IO intensive tasks
* Use `/scratch`, `/shared-scratch`, `/data/user` or `/data/project` for this purpose.
* Use `/scratch`, `/shared-scratch`, `/data/user` or `/data/project` for this purpose.
* Users can retrieve up to 1 week of their lost data thanks to the automatic **daily snapshots for 1 week**.
Snapshots can be accessed at this path:
@@ -121,7 +125,8 @@ mmlsquota -u <username> --block-size auto merlin-user
* Read **[Important: Code of Conduct](../quick-start-guide/code-of-conduct.md)** for more information about Merlin6 policies.
* Is **forbidden** to use the data directories as ``scratch`` area during a job runtime.
* Use ``/scratch``, ``/shared-scratch`` for this purpose.
* Use ``/scratch``, ``/shared-scratch`` for this purpose.
* No backup policy is applied for user data directories: users are responsible for backing up their data.
### Project data directory
@@ -178,7 +183,7 @@ The properties of the available scratch storage spaces are given in the followin
* Read **[Important: Code of Conduct](../quick-start-guide/code-of-conduct.md)** for more information about Merlin6 policies.
* By default, *always* use **local** first and only use **shared** if your specific use case requires it.
* Temporary files *must be deleted at the end of the job by the user*.
* Remaining files will be deleted by the system if detected.
* Remaining files will be deleted by the system if detected.
* Files not accessed within 28 days will be automatically cleaned up by the system.
* If for some reason the scratch areas get full, admins have the rights to cleanup the oldest data.
@@ -190,6 +195,6 @@ Please read **[Transferring Data](../how-to-use-merlin/transfer-data.md)** for m
#### Export directory policy
* Temporary files *must be deleted at the end of the job by the user*.
* Remaining files will be deleted by the system if detected.
* Remaining files will be deleted by the system if detected.
* Files not accessed within 28 days will be automatically cleaned up by the system.
* If for some reason the export area gets full, admins have the rights to cleanup the oldest data

36
docs/merlin6/how-to-use-merlin/transfer-data.md
View File

@@ -1,12 +1,4 @@
---
title: Transferring Data
#tags:
keywords: transferring data, data transfer, rsync, winscp, copy data, copying, sftp, import, export, hopx, vpn
last_updated: 24 August 2023
#summary: ""
sidebar: merlin6_sidebar
permalink: /merlin6/transfer-data.html
---
# Transferring Data
## Overview
@@ -24,7 +16,6 @@ visibility.
- Systems on the internet can access the [PSI Data Transfer](https://www.psi.ch/en/photon-science-data-services/data-transfer) service
`datatransfer.psi.ch`, using ssh-based protocols and [Globus](https://www.globus.org/)
## Direct transfer via Merlin6 login nodes
The following methods transfer data directly via the [login
@@ -50,7 +41,6 @@ rsync -avAHXS ~/localdata user@merlin-l-01.psi.ch:/data/project/general/myprojec
You can resume interrupted transfers by simply rerunning the command. Previously
transferred files will be skipped.
### WinSCP
The WinSCP tool can be used for remote file transfer on Windows. It is available
@@ -83,10 +73,12 @@ Notice that `datatransfer.psi.ch` does not allow SSH login, only `rsync`, `scp`
The following filesystems are mounted:
* `/merlin/export` which points to the `/export` directory in Merlin.
* `/merlin/data/experiment/mu3e` which points to the `/data/experiment/mu3e` directories in Merlin.
* Mu3e sub-directories are mounted in RW (read-write), except for `data` (read-only mounted)
* Mu3e sub-directories are mounted in RW (read-write), except for `data` (read-only mounted)
* `/merlin/data/project/general` which points to the `/data/project/general` directories in Merlin.
* Owners of Merlin projects should request explicit access to it.
* Currently, only `CSCS` is available for transferring files between PizDaint/Alps and Merlin
* Owners of Merlin projects should request explicit access to it.
* Currently, only `CSCS` is available for transferring files between PizDaint/Alps and Merlin
* `/merlin/data/project/bio` which points to the `/data/project/bio` directories in Merlin.
* `/merlin/data/user` which points to the `/data/user` directories in Merlin.
@@ -120,16 +112,17 @@ Transferring big amounts of data from outside PSI to Merlin is always possible t
##### Exporting data from Merlin
For exporting data from Merlin to outside PSI by using `/export`, one has to:
* From a Merlin login node, copy your data from any directory (i.e. `/data/project`, `/data/user`, `/scratch`) to
* From a Merlin login node, copy your data from any directory (i.e. `/data/project`, `/data/user`, `/scratch`) to
`/export`. Ensure to properly secure your directories and files with proper permissions.
* Once data is copied, from **`datatransfer.psi.ch`**, copy the data from `/merlin/export` to outside PSI
* Once data is copied, from **`datatransfer.psi.ch`**, copy the data from `/merlin/export` to outside PSI
##### Importing data to Merlin
For importing data from outside PSI to Merlin by using `/export`, one has to:
* From **`datatransfer.psi.ch`**, copy the data from outside PSI to `/merlin/export`.
* From **`datatransfer.psi.ch`**, copy the data from outside PSI to `/merlin/export`.
Ensure to properly secure your directories and files with proper permissions.
* Once data is copied, from a Merlin login node, copy your data from `/export` to any directory (i.e. `/data/project`, `/data/user`, `/scratch`).
* Once data is copied, from a Merlin login node, copy your data from `/export` to any directory (i.e. `/data/project`, `/data/user`, `/scratch`).
#### Request access to your project directory
@@ -144,10 +137,10 @@ Merlin6 is fully accessible from within the PSI network. To connect from outside
- [VPN](https://www.psi.ch/en/computing/vpn) ([alternate instructions](https://intranet.psi.ch/BIO/ComputingVPN))
- [SSH hopx](https://www.psi.ch/en/computing/ssh-hop)
* Please avoid transferring big amount data through **hopx**
* Please avoid transferring big amount data through **hopx**
- [No Machine](nomachine.md)
* Remote Interactive Access through [**'rem-acc.psi.ch'**](https://www.psi.ch/en/photon-science-data-services/remote-interactive-access)
* Please avoid transferring big amount of data through **NoMachine**
* Remote Interactive Access through [**'rem-acc.psi.ch'**](https://www.psi.ch/en/photon-science-data-services/remote-interactive-access)
* Please avoid transferring big amount of data through **NoMachine**
## Connecting from Merlin6 to outside file shares
@@ -161,5 +154,4 @@ provides a helpful wrapper over the Gnome storage utilities, and provides suppor
- FTP, SFTP
- [others](https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/8/html/using_the_desktop_environment_in_rhel_8/managing-storage-volumes-in-gnome_using-the-desktop-environment-in-rhel-8#gvfs-back-ends_managing-storage-volumes-in-gnome)
[More instruction on using `merlin_rmount`](../software-support/merlin-rmount.md)

9
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View File

@@ -1,12 +1,3 @@
---
#tags:
keywords: Pmodules, software, stable, unstable, deprecated, overlay, overlays, release stage, module, package, packages, library, libraries
last_updated: 07 September 2022
#summary: ""
sidebar: merlin6_sidebar
permalink: /merlin6/using-modules.html
---
# Using PModules
## Environment Modules

6
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@@ -5,15 +5,17 @@
* The new Slurm CPU cluster is called **`merlin6`**.
* The new Slurm GPU cluster is called [**`gmerlin6`**](../gmerlin6/cluster-introduction.md)
* The old Slurm *merlin* cluster is still active and best effort support is provided.
The cluster, was renamed as [**merlin5**](../merlin5/cluster-introduction.md).
From July 2019, **`merlin6`** becomes the **default Slurm cluster** and any job submitted from the login node will be submitted to that cluster if not .
From July 2019, **`merlin6`** becomes the **default Slurm cluster** and any job submitted from the login node will be submitted to that cluster if not.
* Users can keep submitting to the old *`merlin5`* computing nodes by using the option ``--cluster=merlin5``.
* Users submitting to the **`gmerlin6`** GPU cluster need to specify the option ``--cluster=gmerlin6``.
### Slurm 'merlin6'
**CPU nodes** are configured in a **Slurm** cluster, called **`merlin6`**, and
this is the _**default Slurm cluster**_. Hence, by default, if no Slurm cluster is
this is the ***default Slurm cluster***. Hence, by default, if no Slurm cluster is
specified (with the `--cluster` option), this will be the cluster to which the jobs
will be sent.

6
docs/merlin6/quick-start-guide/accessing-interactive-nodes.md
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@@ -7,10 +7,10 @@ applications (e.g. a text editor, but for more performant graphical access, refe
in the login nodes and X11 forwarding can be used for those users who have properly configured X11 support in their desktops, however:
* Merlin6 administrators **do not offer support** for user desktop configuration (Windows, MacOS, Linux).
* Hence, Merlin6 administrators **do not offer official support** for X11 client setup.
* Nevertheless, a generic guide for X11 client setup (*Linux*, *Windows* and *MacOS*) is provided below.
* Hence, Merlin6 administrators **do not offer official support** for X11 client setup.
* Nevertheless, a generic guide for X11 client setup (*Linux*, *Windows* and *MacOS*) is provided below.
* PSI desktop configuration issues must be addressed through **[PSI Service Now](https://psi.service-now.com/psisp)** as an *Incident Request*.
* Ticket will be redirected to the corresponding Desktop support group (Windows, Linux).
* Ticket will be redirected to the corresponding Desktop support group (Windows, Linux).
### Accessing from a Linux client

22
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@@ -10,25 +10,27 @@ The basic principle is courtesy and consideration for other users.
## Interactive nodes
* The interactive nodes (also known as login nodes) are for development and quick testing:
* It is **strictly forbidden to run production jobs** on the login nodes. All production jobs must
* It is **strictly forbidden to run production jobs** on the login nodes. All production jobs must
be submitted to the batch system.
* It is **forbidden to run long processes** occupying big parts of a login node's resources.
* According to the previous rules, **misbehaving running processes will have to be killed.**
* It is **forbidden to run long processes** occupying big parts of a login node's resources.
* According to the previous rules, **misbehaving running processes will have to be killed.**
in order to keep the system responsive for other users.
## Batch system
* Make sure that no broken or run-away processes are left when your job is done. Keep the process space clean on all nodes.
* During the runtime of a job, it is mandatory to use the ``/scratch`` and ``/shared-scratch`` partitions for temporary data:
* It is **forbidden** to use the ``/data/user``, ``/data/project`` or ``/psi/home/`` for that purpose.
* Always remove files you do not need any more (e.g. core dumps, temporary files) as early as possible. Keep the disk space clean on all nodes.
* Prefer ``/scratch`` over ``/shared-scratch`` and use the latter only when you require the temporary files to be visible from multiple nodes.
* It is **forbidden** to use the ``/data/user``, ``/data/project`` or ``/psi/home/`` for that purpose.
* Always remove files you do not need any more (e.g. core dumps, temporary files) as early as possible. Keep the disk space clean on all nodes.
* Prefer ``/scratch`` over ``/shared-scratch`` and use the latter only when you require the temporary files to be visible from multiple nodes.
* Read the description in **[Merlin6 directory structure](../how-to-use-merlin/storage.md#merlin6-directories)** for learning about the correct usage of each partition type.
## User and project data
* ***Users are responsible for backing up their own data***. Is recommended to backup the data on third party independent systems (i.e. LTS, Archive, AFS, SwitchDrive, Windows Shares, etc.).
* **`/psi/home`**, as this contains a small amount of data, is the only directory where we can provide daily snapshots for one week. This can be found in the following directory **`/psi/home/.snapshot/`**
* **`/psi/home`**, as this contains a small amount of data, is the only directory where we can provide daily snapshots for one week. This can be found in the following directory **`/psi/home/.snapshot/`**
* ***When a user leaves PSI, she or her supervisor/team are responsible to backup and move the data out from the cluster***: every few months, the storage space will be recycled for those old users who do not have an existing and valid PSI account.
!!! warning
@@ -41,8 +43,8 @@ The basic principle is courtesy and consideration for other users.
* The system administrator has the right to temporarily block the access to
Merlin6 for an account violating the Code of Conduct in order to maintain the
efficiency and stability of the system.
* Repetitive violations by the same user will be escalated to the user's supervisor.
* Repetitive violations by the same user will be escalated to the user's supervisor.
* The system administrator has the right to delete files in the **scratch** directories
* after a job, if the job failed to clean up its files.
* during the job in order to prevent a job from destabilizing a node or multiple nodes.
* after a job, if the job failed to clean up its files.
* during the job in order to prevent a job from destabilizing a node or multiple nodes.
* The system administrator has the right to kill any misbehaving running processes.

8
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View File

@@ -9,8 +9,8 @@ At present, the **Merlin local HPC cluster** contains _two_ generations of it:
* the old **Merlin5** cluster (`merlin5` Slurm cluster), and
* the newest generation **Merlin6**, which is divided in two Slurm clusters:
* `merlin6` as the Slurm CPU cluster
* `gmerlin6` as the Slurm GPU cluster.
* `merlin6` as the Slurm CPU cluster
* `gmerlin6` as the Slurm GPU cluster.
Access to the different Slurm clusters is possible from the [**Merlin login nodes**](accessing-interactive-nodes.md),
which can be accessed through the [SSH protocol](accessing-interactive-nodes.md#ssh-access) or the [NoMachine (NX) service](../how-to-use-merlin/nomachine.md).
@@ -42,9 +42,9 @@ by the BIO Division and by Deep Leaning project.
These computational resources are split into **two** different **[Slurm](https://slurm.schedmd.com/overview.html)** clusters:
* The Merlin6 CPU nodes are in a dedicated **[Slurm](https://slurm.schedmd.com/overview.html)** cluster called [**`merlin6`**](../slurm-configuration.md).
* This is the **default Slurm cluster** configured in the login nodes: any job submitted without the option `--cluster` will be submited to this cluster.
* This is the **default Slurm cluster** configured in the login nodes: any job submitted without the option `--cluster` will be submited to this cluster.
* The Merlin6 GPU resources are in a dedicated **[Slurm](https://slurm.schedmd.com/overview.html)** cluster called [**`gmerlin6`**](../../gmerlin6/slurm-configuration.md).
* Users submitting to the **`gmerlin6`** GPU cluster need to specify the option ``--cluster=gmerlin6``.
* Users submitting to the **`gmerlin6`** GPU cluster need to specify the option ``--cluster=gmerlin6``.
### Merlin5

162
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@@ -1,12 +1,4 @@
---
title: Slurm Configuration
#tags:
keywords: configuration, partitions, node definition
last_updated: 29 January 2021
summary: "This document describes a summary of the Merlin6 configuration."
sidebar: merlin6_sidebar
permalink: /merlin6/slurm-configuration.html
---
# Slurm Configuration
This documentation shows basic Slurm configuration and options needed to run jobs in the Merlin6 CPU cluster.
@@ -28,6 +20,7 @@ If nothing is specified, by default each core will use up to 8GB of memory. Memo
In **`merlin6`**, Memory is considered a Consumable Resource, as well as the CPU. Hence, both resources will account when submitting a job,
and by default resources can not be oversubscribed. This is a main difference with the old **`merlin5`** cluster, when only CPU were accounted,
and memory was by default oversubscribed.
!!! tip "Check Configuration"
@@ -66,12 +59,12 @@ The following *partitions* (also known as *queues*) are configured in Slurm:
| **asa-ansys** | 1 hour | 90 days | unlimited | 1000 | 4 | 15600 |
| **mu3e** | 1 day | 7 days | unlimited | 1000 | 4 | 3712 |
\*The **PriorityJobFactor** value will be added to the job priority (*PARTITION* column in `sprio -l` ). In other words, jobs sent to higher priority
The **PriorityJobFactor** value will be added to the job priority (**PARTITION** column in `sprio -l` ). In other words, jobs sent to higher priority
partitions will usually run first (however, other factors such like **job age** or mainly **fair share** might affect to that decision). For the GPU
partitions, Slurm will also attempt first to allocate jobs on partitions with higher priority over partitions with lesser priority.
**\*\***Jobs submitted to a partition with a higher **PriorityTier** value will be dispatched before pending jobs in partition with lower *PriorityTier* value
and, if possible, they will preempt running jobs from partitions with lower *PriorityTier* values.
Jobs submitted to a partition with a higher **PriorityTier** value will be dispatched before pending jobs in partition with lower *PriorityTier* value
and, if possible, they will preempt running jobs from partitions with lower **PriorityTier** values.
* The **`general`** partition is the **default**. It can not have more than 50 nodes running jobs.
* For **`daily`** this limitation is extended to 67 nodes.
@@ -79,11 +72,18 @@ and, if possible, they will preempt running jobs from partitions with lower *Pri
* **`asa-general`,`asa-daily`,`asa-ansys`,`asa-visas` and `mu3e`** are **private** partitions, belonging to different experiments owning the machines. **Access is restricted** in all cases. However, by agreement with the experiments, nodes are usually added to the **`hourly`** partition as extra resources for the public resources.
!!! tip "Partition Selection"
Jobs which would run for less than one day should be always sent to **daily**, while jobs that would run for less than one hour should be sent to **hourly**. This would ensure that you have highest priority over jobs sent to partitions with less priority, but also because **general** has limited the number of nodes that can be used for that. The idea behind that, is that the cluster can not be blocked by long jobs and we can always ensure resources for shorter jobs.
Jobs which would run for less than one day should be always sent to
**daily**, while jobs that would run for less than one hour should be sent
to **hourly**. This would ensure that you have highest priority over jobs
sent to partitions with less priority, but also because **general** has
limited the number of nodes that can be used for that. The idea behind
that, is that the cluster can not be blocked by long jobs and we can always
ensure resources for shorter jobs.
### Merlin5 CPU Accounts
Users need to ensure that the public **`merlin`** account is specified. No specifying account options would default to this account.
This is mostly needed by users which have multiple Slurm accounts, which may define by mistake a different account.
```bash
@@ -100,16 +100,14 @@ Not all the accounts can be used on all partitions. This is resumed in the table
#### Private accounts
* The *`gfa-asa`* and *`mu3e`* accounts are private accounts. These can be used for accessing dedicated
partitions with nodes owned by different groups.
* The *`gfa-asa`* and *`mu3e`* accounts are private accounts. These can be used for accessing dedicated partitions with nodes owned by different groups.
### Slurm CPU specific options
Some options are available when using CPUs. These are detailed here.
Alternative Slurm options for CPU based jobs are available. Please refer to the **man** pages
for each Slurm command for further information about it (`man salloc`, `man sbatch`, `man srun`).
Below are listed the most common settings:
Alternative Slurm options for CPU based jobs are available. Please refer to the
**man** pages for each Slurm command for further information about it (`man
salloc`, `man sbatch`, `man srun`). Below are listed the most common settings:
```bash
#SBATCH --hint=[no]multithread
@@ -125,8 +123,9 @@ Below are listed the most common settings:
#### Enabling/Disabling Hyper-Threading
The **`merlin6`** cluster contains nodes with Hyper-Threading enabled. One should always specify
whether to use Hyper-Threading or not. If not defined, Slurm will generally use it (exceptions apply).
The **`merlin6`** cluster contains nodes with Hyper-Threading enabled. One
should always specify whether to use Hyper-Threading or not. If not defined,
Slurm will generally use it (exceptions apply).
```bash
#SBATCH --hint=multithread # Use extra threads with in-core multi-threading.
@@ -138,7 +137,7 @@ whether to use Hyper-Threading or not. If not defined, Slurm will generally use
Slurm allows to define a set of features in the node definition. This can be used to filter and select nodes according to one or more
specific features. For the CPU nodes, we have the following features:
```
```text
NodeName=merlin-c-[001-024,101-124,201-224] Features=mem_384gb,xeon-gold-6152
NodeName=merlin-c-[301-312] Features=mem_768gb,xeon-gold-6240r
NodeName=merlin-c-[313-318] Features=mem_768gb,xeon-gold-6240r
@@ -149,26 +148,36 @@ Therefore, users running on `hourly` can select which node they want to use (fat
This is possible by using the option `--constraint=<feature_name>` in Slurm.
Examples:
1. Select nodes with 48 cores only (nodes with [2 x Xeon Gold 6240R](https://ark.intel.com/content/www/us/en/ark/products/199343/intel-xeon-gold-6240r-processor-35-75m-cache-2-40-ghz.html)):
```
sbatch --constraint=xeon-gold-6240r ...
```
2. Select nodes with 44 cores only (nodes with [2 x Xeon Gold 6152](https://ark.intel.com/content/www/us/en/ark/products/120491/intel-xeon-gold-6152-processor-30-25m-cache-2-10-ghz.html)):
```
sbatch --constraint=xeon-gold-6152 ...
```
3. Select fat memory nodes only:
```
sbatch --constraint=mem_768gb ...
```
4. Select regular memory nodes only:
```
sbatch --constraint=mem_384gb ...
```
5. Select fat memory nodes with 48 cores only:
```
sbatch --constraint=mem_768gb,xeon-gold-6240r ...
```
```bash
sbatch --constraint=xeon-gold-6240r ...
```
1. Select nodes with 44 cores only (nodes with [2 x Xeon Gold 6152](https://ark.intel.com/content/www/us/en/ark/products/120491/intel-xeon-gold-6152-processor-30-25m-cache-2-10-ghz.html)):
```bash
sbatch --constraint=xeon-gold-6152 ...
```
1. Select fat memory nodes only:
```bash
sbatch --constraint=mem_768gb ...
```
1. Select regular memory nodes only:
```bash
sbatch --constraint=mem_384gb ...
```
1. Select fat memory nodes with 48 cores only:
```bash
sbatch --constraint=mem_768gb,xeon-gold-6240r ...
```
Detailing exactly which type of nodes you want to use is important, therefore, for groups with private accounts (`mu3e`,`gfa-asa`) or for
public users running on the `hourly` partition, *constraining nodes by features is recommended*. This becomes even more important when
@@ -190,14 +199,24 @@ Hence, there is a need of setting up wise limits and to ensure that there is a f
of the cluster while allowing jobs of different nature and sizes (it is, **single core** based **vs parallel jobs** of different sizes) to run.
!!! warning "Resource Limits"
Wide limits are provided in the **daily** and **hourly** partitions, while for **general** those limits are more restrictive. However, we kindly ask users to inform the Merlin administrators when there are plans to send big jobs which would require a massive draining of nodes for allocating such jobs. This would apply to jobs requiring the **unlimited** QoS (see below "Per job limits").
Wide limits are provided in the **daily** and **hourly** partitions, while
for **general** those limits are more restrictive. However, we kindly ask
users to inform the Merlin administrators when there are plans to send big
jobs which would require a massive draining of nodes for allocating such
jobs. This would apply to jobs requiring the **unlimited** QoS (see below
"Per job limits").
!!! tip "Custom Requirements"
If you have different requirements, please let us know, we will try to accommodate or propose a solution for you.
If you have different requirements, please let us know, we will try to
accommodate or propose a solution for you.
#### Per job limits
These are limits which apply to a single job. In other words, there is a maximum of resources a single job can use. Limits are described in the table below with the format: `SlurmQoS(limits)` (possible `SlurmQoS` values can be listed with the command `sacctmgr show qos`). Some limits will vary depending on the day and time of the week.
These are limits which apply to a single job. In other words, there is a
maximum of resources a single job can use. Limits are described in the table
below with the format: `SlurmQoS(limits)` (possible `SlurmQoS` values can be
listed with the command `sacctmgr show qos`). Some limits will vary depending
on the day and time of the week.
| Partition | Mon-Fri 0h-18h | Sun-Thu 18h-0h | From Fri 18h to Mon 0h |
|:----------: | :------------------------------: | :------------------------------: | :------------------------------: |
@@ -205,18 +224,29 @@ These are limits which apply to a single job. In other words, there is a maximum
| **daily** | daytime(cpu=704,mem=2750G) | nighttime(cpu=1408,mem=5500G) | unlimited(cpu=2200,mem=8593.75G) |
| **hourly** | unlimited(cpu=2200,mem=8593.75G) | unlimited(cpu=2200,mem=8593.75G) | unlimited(cpu=2200,mem=8593.75G) |
By default, a job can not use more than 704 cores (max CPU per job). In the same way, memory is also proportionally limited. This is equivalent as
running a job using up to 8 nodes at once. This limit applies to the **general** partition (fixed limit) and to the **daily** partition (only during working hours).
Limits are softed for the **daily** partition during non working hours, and during the weekend limits are even wider.
By default, a job can not use more than 704 cores (max CPU per job). In the
same way, memory is also proportionally limited. This is equivalent as running
a job using up to 8 nodes at once. This limit applies to the **general**
partition (fixed limit) and to the **daily** partition (only during working
hours).
For the **hourly** partition, **despite running many parallel jobs is something not desirable** (for allocating such jobs it requires massive draining of nodes),
wider limits are provided. In order to avoid massive nodes drain in the cluster, for allocating huge jobs, setting per job limits is necessary. Hence, **unlimited** QoS
mostly refers to "per user" limits more than to "per job" limits (in other words, users can run any number of hourly jobs, but the job size for such jobs is limited
with wide values).
Limits are softed for the **daily** partition during non working hours, and
during the weekend limits are even wider. For the **hourly** partition,
**despite running many parallel jobs is something not desirable** (for
allocating such jobs it requires massive draining of nodes), wider limits are
provided. In order to avoid massive nodes drain in the cluster, for allocating
huge jobs, setting per job limits is necessary. Hence, **unlimited** QoS mostly
refers to "per user" limits more than to "per job" limits (in other words,
users can run any number of hourly jobs, but the job size for such jobs is
limited with wide values).
#### Per user limits for CPU partitions
These limits which apply exclusively to users. In other words, there is a maximum of resources a single user can use. Limits are described in the table below with the format: `SlurmQoS(limits)` (possible `SlurmQoS` values can be listed with the command `sacctmgr show qos`). Some limits will vary depending on the day and time of the week.
These limits which apply exclusively to users. In other words, there is a
maximum of resources a single user can use. Limits are described in the table
below with the format: `SlurmQoS(limits)` (possible `SlurmQoS` values can be
listed with the command `sacctmgr show qos`). Some limits will vary depending
on the day and time of the week.
| Partition | Mon-Fri 0h-18h | Sun-Thu 18h-0h | From Fri 18h to Mon 0h |
|:-----------:| :----------------------------: | :---------------------------: | :----------------------------: |
@@ -224,15 +254,22 @@ These limits which apply exclusively to users. In other words, there is a maximu
| **daily** | daytime(cpu=1408,mem=5500G) | nighttime(cpu=2112,mem=8250G) | unlimited(cpu=6336,mem=24750G) |
| **hourly** | unlimited(cpu=6336,mem=24750G) | unlimited(cpu=6336,mem=24750G)| unlimited(cpu=6336,mem=24750G) |
By default, users can not use more than 704 cores at the same time (max CPU per user). Memory is also proportionally limited in the same way. This is
equivalent to 8 exclusive nodes. This limit applies to the **general** partition (fixed limit) and to the **daily** partition (only during working hours).
For the **hourly** partition, there are no limits restriction and user limits are removed. Limits are softed for the **daily** partition during non
working hours, and during the weekend limits are removed.
By default, users can not use more than 704 cores at the same time (max CPU per
user). Memory is also proportionally limited in the same way. This is
equivalent to 8 exclusive nodes. This limit applies to the **general**
partition (fixed limit) and to the **daily** partition (only during working
hours).
For the **hourly** partition, there are no limits restriction and user limits
are removed. Limits are softed for the **daily** partition during non working
hours, and during the weekend limits are removed.
## Advanced Slurm configuration
Clusters at PSI use the [Slurm Workload Manager](http://slurm.schedmd.com/) as the batch system technology for managing and scheduling jobs.
Slurm has been installed in a **multi-clustered** configuration, allowing to integrate multiple clusters in the same batch system.
Clusters at PSI use the [Slurm Workload Manager](http://slurm.schedmd.com/) as
the batch system technology for managing and scheduling jobs. Slurm has been
installed in a **multi-clustered** configuration, allowing to integrate
multiple clusters in the same batch system.
For understanding the Slurm configuration setup in the cluster, sometimes may be useful to check the following files:
@@ -240,5 +277,10 @@ For understanding the Slurm configuration setup in the cluster, sometimes may be
* ``/etc/slurm/gres.conf`` - can be found in the GPU nodes, is also propgated to login nodes and computing nodes for user read access.
* ``/etc/slurm/cgroup.conf`` - can be found in the computing nodes, is also propagated to login nodes for user read access.
The previous configuration files which can be found in the login nodes, correspond exclusively to the **merlin6** cluster configuration files.
Configuration files for the old **merlin5** cluster or for the **gmerlin6** cluster must be checked directly on any of the **merlin5** or **gmerlin6** computing nodes (in example, by login in to one of the nodes while a job or an active allocation is running).
The previous configuration files which can be found in the login nodes,
correspond exclusively to the **merlin6** cluster configuration files.
Configuration files for the old **merlin5** cluster or for the **gmerlin6**
cluster must be checked directly on any of the **merlin5** or **gmerlin6**
computing nodes (in example, by login in to one of the nodes while a job or an
active allocation is running).

17
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View File

@@ -249,7 +249,6 @@ sview
!['sview' graphical user interface](../../images/slurm/sview.png)
## General Monitoring
The following pages contain basic monitoring for Slurm and computing nodes.
@@ -262,17 +261,17 @@ support:
### Merlin6 Monitoring Pages
* Slurm monitoring:
* ***[Merlin6 Slurm Statistics - XDMOD](https://merlin-slurmmon01.psi.ch/)***
* [Merlin6 Slurm Live Status](https://hpc-monitor02.psi.ch/d/QNcbW1AZk/merlin6-slurm-live-status?orgId=1&refresh=10s)
* [Merlin6 Slurm Overview](https://hpc-monitor02.psi.ch/d/94UxWJ0Zz/merlin6-slurm-overview?orgId=1&refresh=10s)
* ***[Merlin6 Slurm Statistics - XDMOD](https://merlin-slurmmon01.psi.ch/)***
* [Merlin6 Slurm Live Status](https://hpc-monitor02.psi.ch/d/QNcbW1AZk/merlin6-slurm-live-status?orgId=1&refresh=10s)
* [Merlin6 Slurm Overview](https://hpc-monitor02.psi.ch/d/94UxWJ0Zz/merlin6-slurm-overview?orgId=1&refresh=10s)
* Nodes monitoring:
* [Merlin6 CPU Nodes Overview](https://hpc-monitor02.psi.ch/d/JmvLR8gZz/merlin6-computing-cpu-nodes?orgId=1&refresh=10s)
* [Merlin6 GPU Nodes Overview](https://hpc-monitor02.psi.ch/d/gOo1Z10Wk/merlin6-computing-gpu-nodes?orgId=1&refresh=10s)
* [Merlin6 CPU Nodes Overview](https://hpc-monitor02.psi.ch/d/JmvLR8gZz/merlin6-computing-cpu-nodes?orgId=1&refresh=10s)
* [Merlin6 GPU Nodes Overview](https://hpc-monitor02.psi.ch/d/gOo1Z10Wk/merlin6-computing-gpu-nodes?orgId=1&refresh=10s)
### Merlin5 Monitoring Pages
* Slurm monitoring:
* [Merlin5 Slurm Live Status](https://hpc-monitor02.psi.ch/d/o8msZJ0Zz/merlin5-slurm-live-status?orgId=1&refresh=10s)
* [Merlin5 Slurm Overview](https://hpc-monitor02.psi.ch/d/eWLEW1AWz/merlin5-slurm-overview?orgId=1&refresh=10s)
* [Merlin5 Slurm Live Status](https://hpc-monitor02.psi.ch/d/o8msZJ0Zz/merlin5-slurm-live-status?orgId=1&refresh=10s)
* [Merlin5 Slurm Overview](https://hpc-monitor02.psi.ch/d/eWLEW1AWz/merlin5-slurm-overview?orgId=1&refresh=10s)
* Nodes monitoring:
* [Merlin5 CPU Nodes Overview](https://hpc-monitor02.psi.ch/d/ejTyWJAWk/merlin5-computing-cpu-nodes?orgId=1&refresh=10s)
* [Merlin5 CPU Nodes Overview](https://hpc-monitor02.psi.ch/d/ejTyWJAWk/merlin5-computing-cpu-nodes?orgId=1&refresh=10s)

21
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View File

@@ -5,19 +5,19 @@
Before starting using the cluster, please read the following rules:
1. To ease and improve *scheduling* and *backfilling*, always try to **estimate and** to **define a proper run time** of your jobs:
* Use `--time=<D-HH:MM:SS>` for that.
* For very long runs, please consider using ***[Job Arrays with Checkpointing](#array-jobs-running-very-long-tasks-with-checkpoint-files)***
* Use `--time=<D-HH:MM:SS>` for that.
* For very long runs, please consider using ***[Job Arrays with Checkpointing](#array-jobs-running-very-long-tasks-with-checkpoint-files)***
2. Try to optimize your jobs for running at most within **one day**. Please, consider the following:
* Some software can simply scale up by using more nodes while drastically reducing the run time.
* Some software allow to save a specific state, and a second job can start from that state: ***[Job Arrays with Checkpointing](#array-jobs-running-very-long-tasks-with-checkpoint-files)*** can help you with that.
* Jobs submitted to **`hourly`** get more priority than jobs submitted to **`daily`**: always use **`hourly`** for jobs shorter than 1 hour.
* Jobs submitted to **`daily`** get more priority than jobs submitted to **`general`**: always use **`daily`** for jobs shorter than 1 day.
* Some software can simply scale up by using more nodes while drastically reducing the run time.
* Some software allow to save a specific state, and a second job can start from that state: ***[Job Arrays with Checkpointing](#array-jobs-running-very-long-tasks-with-checkpoint-files)*** can help you with that.
* Jobs submitted to **`hourly`** get more priority than jobs submitted to **`daily`**: always use **`hourly`** for jobs shorter than 1 hour.
* Jobs submitted to **`daily`** get more priority than jobs submitted to **`general`**: always use **`daily`** for jobs shorter than 1 day.
3. Is **forbidden** to run **very short jobs** as they cause a lot of overhead but also can cause severe problems to the main scheduler.
* ***Question:*** Is my job a very short job? ***Answer:*** If it lasts in few seconds or very few minutes, yes.
* ***Question:*** How long should my job run? ***Answer:*** as the *Rule of Thumb*, from 5' would start being ok, from 15' would preferred.
* Use ***[Packed Jobs](#packed-jobs-running-a-large-number-of-short-tasks)*** for running a large number of short tasks.
* ***Question:*** Is my job a very short job? ***Answer:*** If it lasts in few seconds or very few minutes, yes.
* ***Question:*** How long should my job run? ***Answer:*** as the *Rule of Thumb*, from 5' would start being ok, from 15' would preferred.
* Use ***[Packed Jobs](#packed-jobs-running-a-large-number-of-short-tasks)*** for running a large number of short tasks.
4. Do not submit hundreds of similar jobs!
* Use ***[Array Jobs](#array-jobs-launching-a-large-number-of-related-jobs)*** for gathering jobs instead.
* Use ***[Array Jobs](#array-jobs-launching-a-large-number-of-related-jobs)*** for gathering jobs instead.
!!! tip
Having a good estimation of the *time* needed by your jobs, a proper way for
@@ -37,6 +37,7 @@ Before starting using the cluster, please read the following rules:
## Basic settings
For a complete list of options and parameters available is recommended to use the **man pages** (i.e. `man sbatch`, `man srun`, `man salloc`).
Please, notice that behaviour for some parameters might change depending on the command used when running jobs (in example, `--exclusive` behaviour in `sbatch` differs from `srun`).
In this chapter we show the basic parameters which are usually needed in the Merlin cluster.

1
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@@ -251,7 +251,6 @@ The `%1` in the `#SBATCH --array=1-10%1` statement defines that only 1 subjob ca
this will result in subjob n+1 only being started when job n has finished. It will read the checkpoint file
if it is present.
### Packed jobs: running a large number of short tasks
Since the launching of a Slurm job incurs some overhead, you should not submit each short task as a separate

1
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@@ -116,6 +116,7 @@ fi
In the above example, one can increase the number of *nodes* and/or *ntasks* if needed and combine it
with `--exclusive` whenever needed. In general, **no hypertheading** is recommended for MPI based jobs.
Also, one can combine it with `--exclusive` when necessary. Finally, one can change the MPI technology in `-start-method`
(check CFX documentation for possible values).

18
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@@ -75,10 +75,10 @@ To setup HFSS RSM for using it with the Merlin cluster, it must be done from the
![RSM_Remote_Scheduler](../../images/ANSYS/HFSS/02_Select_Scheduler_RSM_Remote.png)
* **Select Scheduler**: `Remote RSM`.
* **Server**: Add a Merlin login node.
* **User name**: Add your Merlin username.
* **Password**: Add you Merlin username password.
* **Select Scheduler**: `Remote RSM`.
* **Server**: Add a Merlin login node.
* **User name**: Add your Merlin username.
* **Password**: Add you Merlin username password.
Once *refreshed*, the **Scheduler info** box must provide **Slurm**
information of the server (see above picture). If the box contains that
@@ -92,7 +92,7 @@ To setup HFSS RSM for using it with the Merlin cluster, it must be done from the
![Product_Path](../../images/ANSYS/HFSS/05_Submit_Job_Product_Path.png)
* In example, for **ANSYS/2022R1**, the location is `/data/software/pmodules/Tools/ANSYS/2021R1/v211/AnsysEM21.1/Linux64/ansysedt.exe`.
* In example, for **ANSYS/2022R1**, the location is `/data/software/pmodules/Tools/ANSYS/2021R1/v211/AnsysEM21.1/Linux64/ansysedt.exe`.
### HFSS Slurm (from login node only)
@@ -118,10 +118,10 @@ Desktop** to submit to Slurm. This can set as follows:
![RSM_Remote_Scheduler](../../images/ANSYS/HFSS/03_Select_Scheduler_Slurm.png)
* **Select Scheduler**: `Slurm`.
* **Server**: must point to `localhost`.
* **User name**: must be empty.
* **Password**: must be empty.
* **Select Scheduler**: `Slurm`.
* **Server**: must point to `localhost`.
* **User name**: must be empty.
* **Password**: must be empty.
The **Server, User name** and **Password** boxes can't be modified, but if
value do not match with the above settings, they should be changed by

4
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@@ -1,6 +1,4 @@
---
title: ANSYS - MAPDL
---
# ANSYS - MAPDL
# ANSYS - Mechanical APDL

24
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View File

@@ -57,24 +57,24 @@ The different steps and settings required to make it work are that following:
![Adding a new HPC Resource](../../images/ANSYS/rsm-1-add_hpc_resource.png)
3. In the **HPC Resource** tab, fill up the corresponding fields as follows:
![HPC Resource](../../images/ANSYS/rsm-2-add_cluster.png)
* **"Name"**: Add here the preffered name for the cluster. In example: `Merlin6 cluster - merlin-l-001`
* **"HPC Type"**: Select `SLURM`
* **"Submit host"**: Add one of the login nodes. In example `merlin-l-001`.
* **"Slurm Job submission arguments (optional)"**: Add any required Slurm options for running your jobs.
* **"Name"**: Add here the preffered name for the cluster. In example: `Merlin6 cluster - merlin-l-001`
* **"HPC Type"**: Select `SLURM`
* **"Submit host"**: Add one of the login nodes. In example `merlin-l-001`.
* **"Slurm Job submission arguments (optional)"**: Add any required Slurm options for running your jobs.
* In general, `--hint=nomultithread` should be at least present.
* Check **"Use SSH protocol for inter and intra-node communication (Linux only)"**
* Select **"Able to directly submit and monitor HPC jobs"**.
* **"Apply"** changes.
* Check **"Use SSH protocol for inter and intra-node communication (Linux only)"**
* Select **"Able to directly submit and monitor HPC jobs"**.
* **"Apply"** changes.
4. In the **"File Management"** tab, fill up the corresponding fields as follows:
![File Management](../../images/ANSYS/rsm-3-add_scratch_info.png)
* Select **"RSM internal file transfer mechanism"** and add **`/shared-scratch`** as the **"Staging directory path on Cluster"**
* Select **"Scratch directory local to the execution node(s)"** and add **`/scratch`** as the **HPC scratch directory**.
* **Never check** the option "Keep job files in the staging directory when job is complete" if the previous
* Select **"RSM internal file transfer mechanism"** and add **`/shared-scratch`** as the **"Staging directory path on Cluster"**
* Select **"Scratch directory local to the execution node(s)"** and add **`/scratch`** as the **HPC scratch directory**.
* **Never check** the option "Keep job files in the staging directory when job is complete" if the previous
option "Scratch directory local to the execution node(s)" was set.
* **"Apply"** changes.
* **"Apply"** changes.
5. In the **"Queues"** tab, use the left button to auto-discover partitions
![Queues](../../images/ANSYS/rsm-4-get_slurm_queues.png)
* If no authentication method was configured before, an authentication window will appear. Use your
* If no authentication method was configured before, an authentication window will appear. Use your
PSI account to authenticate. Notice that the **`PSICH\`** prefix **must not be added**.
![Authenticating](../../images/ANSYS/rsm-5-authenticating.png)
* From the partition list, select the ones you want to typically use.

1
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@@ -62,6 +62,7 @@ option. This will show the location of the different ANSYS releases as follows:
### ANSYS RSM
**ANSYS Remote Solve Manager (RSM)** is used by ANSYS Workbench to submit computational jobs to HPC clusters directly from Workbench on your desktop.
Therefore, PSI workstations with direct access to Merlin can submit jobs by using RSM.
For further information, please visit the **[ANSYS RSM](ansys-rsm.md)** section.

7
docs/merlin7/01-Quick-Start-Guide/accessing-interactive-nodes.md
View File

@@ -7,10 +7,10 @@ applications (e.g. a text editor, but for more performant graphical access, refe
in the login nodes and X11 forwarding can be used for those users who have properly configured X11 support in their desktops, however:
* Merlin7 administrators **do not offer support** for user desktop configuration (Windows, MacOS, Linux).
* Hence, Merlin7 administrators **do not offer official support** for X11 client setup.
* Nevertheless, a generic guide for X11 client setup (*Linux*, *Windows* and *MacOS*) is provided below.
* Hence, Merlin7 administrators **do not offer official support** for X11 client setup.
* Nevertheless, a generic guide for X11 client setup (*Linux*, *Windows* and *MacOS*) is provided below.
* PSI desktop configuration issues must be addressed through **[PSI Service Now](https://psi.service-now.com/psisp)** as an *Incident Request*.
* Ticket will be redirected to the corresponding Desktop support group (Windows, Linux).
* Ticket will be redirected to the corresponding Desktop support group (Windows, Linux).
### Accessing from a Linux client
@@ -27,6 +27,7 @@ Refer to [{How To Use Merlin -> Accessing from MacOS Clients}](../02-How-To-Use-
## NoMachine Remote Desktop Access
X applications are supported in the login nodes and can run efficiently through a **NoMachine** client. This is the officially supported way to run more demanding X applications on Merlin7.
* For PSI Windows workstations, this can be installed from the Software Kiosk as 'NX Client'. If you have difficulties installing, please request support through **[PSI Service Now](https://psi.service-now.com/psisp)** as an *Incident Request*.
* For other workstations The client software can be downloaded from the [Nomachine Website](https://www.nomachine.com/product&p=NoMachine%20Enterprise%20Client).

10
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@@ -1,12 +1,4 @@
---
title: Accessing Slurm Cluster
#tags:
keywords: slurm, batch system, merlin5, merlin7, gmerlin7, cpu, gpu
last_updated: 07 September 2022
#summary: ""
sidebar: merlin7_sidebar
permalink: /merlin7/slurm-access.html
---
# Accessing Slurm Cluster
## The Merlin Slurm clusters

22
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@@ -1,12 +1,4 @@
---
title: Code Of Conduct
#tags:
keywords: code of conduct, rules, principle, policy, policies, administrator, backup
last_updated: 07 September 2022
#summary: ""
sidebar: merlin7_sidebar
permalink: /merlin7/code-of-conduct.html
---
# Code Of Conduct
## The Basic principle
@@ -18,9 +10,9 @@ The basic principle is courtesy and consideration for other users.
## Interactive nodes
* The interactive nodes (also known as login nodes) are for development and quick testing:
* It is **strictly forbidden to run production jobs** on the login nodes. All production jobs must be submitted to the batch system.
* It is **forbidden to run long processes** occupying big parts of a login node's resources.
* According to the previous rules, **misbehaving running processes will have to be killed.**
* It is **strictly forbidden to run production jobs** on the login nodes. All production jobs must be submitted to the batch system.
* It is **forbidden to run long processes** occupying big parts of a login node's resources.
* According to the previous rules, **misbehaving running processes will have to be killed.**
in order to keep the system responsive for other users.
## Batch system
@@ -46,8 +38,8 @@ The basic principle is courtesy and consideration for other users.
## System Administrator Rights
* The system administrator has the right to temporarily block the access to Merlin7 for an account violating the Code of Conduct in order to maintain the efficiency and stability of the system.
* Repetitive violations by the same user will be escalated to the user's supervisor.
* Repetitive violations by the same user will be escalated to the user's supervisor.
* The system administrator has the right to delete files in the **scratch** directories
* after a job, if the job failed to clean up its files.
* during the job in order to prevent a job from destabilizing a node or multiple nodes.
* after a job, if the job failed to clean up its files.
* during the job in order to prevent a job from destabilizing a node or multiple nodes.
* The system administrator has the right to kill any misbehaving running processes.

16
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@@ -1,14 +1,4 @@
---
title: Introduction
#tags:
keywords: introduction, home, welcome, architecture, design
last_updated: 07 September 2022
sidebar: merlin7_sidebar
permalink: /merlin7/introduction.html
redirect_from:
- /merlin7
- /merlin7/index.html
---
# Introduction
## About Merlin7
@@ -56,9 +46,9 @@ The appliance is built of several storage servers:
With effective storage capacity of:
* 10 PB HDD
* value visible on linux: HDD 9302.4 TiB
* value visible on linux: HDD 9302.4 TiB
* 162 TB SSD
* value visible on linux: SSD 151.6 TiB
* value visible on linux: SSD 151.6 TiB
* 23.6 TiB on Metadata
The storage is directly connected to the cluster (and each individual node) through the Slingshot NIC.

10
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@@ -1,12 +1,4 @@
---
title: Requesting Merlin Accounts
#tags:
keywords: registration, register, account, merlin5, merlin7, snow, service now
last_updated: 07 September 2022
#summary: ""
sidebar: merlin7_sidebar
permalink: /merlin7/request-account.html
---
# Requesting Merlin Accounts
## Requesting Access to Merlin7

15
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@@ -1,12 +1,4 @@
---
title: Requesting a Merlin Project
#tags:
keywords: merlin project, project, snow, service now
last_updated: 07 September 2022
#summary: ""
sidebar: merlin7_sidebar
permalink: /merlin7/request-project.html
---
# Requesting a Merlin Project
A project owns its own storage area in Merlin, which can be accessed by other group members.
@@ -30,8 +22,8 @@ In addition, a list of administrators can be set. The administrators, together w
is covered in the [Linux Documentation - Services Admin Guides: Unix Groups / Group Management](https://linux.psi.ch/admin-guide/configuration/basic/users_and_groups.html), managed by the Central Linux Team.
To gran access to specific Merlin project directories, some users may require to be added to some specific **Unix groups**:
* Each Merlin project (i.e. `/data/project/{bio|general}/$projectname`) or experiment (i.e. `/data/experiment/$experimentname`) directory has access restricted by ownership and group membership (with a very few exceptions allowing public access).
* Users requiring access to a specific restricted project or experiment directory have to request membership for the corresponding Unix group owning the directory.
* Each Merlin project (i.e. `/data/project/{bio|general}/$projectname`) or experiment (i.e. `/data/experiment/$experimentname`) directory has access restricted by ownership and group membership (with a very few exceptions allowing public access).
* Users requiring access to a specific restricted project or experiment directory have to request membership for the corresponding Unix group owning the directory.
### Requesting a new Unix group
@@ -62,6 +54,7 @@ The owner of the group is the person who will be allowed to modify the group.
### Requesting Unix group membership
Existing Merlin projects have already a Unix group assigned. To have access to a project, users must belong to the proper **Unix group** owning that project.
Supervisors should inform new users which extra groups are needed for their project(s). If this information is not known, one can check the permissions for that directory. In example:
```bash
(base) ❄ [caubet_m@merlin-l-001:/data/user/caubet_m]# ls -ltrhd /data/project/general/$projectname

39
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@@ -1,12 +1,4 @@
---
title: Archive & PSI Data Catalog
#tags:
keywords: linux, archive, data catalog, archiving, lts, tape, long term storage, ingestion, datacatalog
last_updated: 31 January 2020
summary: "This document describes how to use the PSI Data Catalog for archiving Merlin7 data."
sidebar: merlin7_sidebar
permalink: /merlin7/archive.html
---
# Archive & PSI Data Catalog
## PSI Data Catalog as a PSI Central Service
@@ -48,20 +40,20 @@ Archiving can be done from any node accessible by the users (usually from the lo
Below are the main steps for using the Data Catalog.
* Ingest the dataset into the Data Catalog. This makes the data known to the Data Catalog system at PSI:
* Prepare a metadata file describing the dataset
* Run **``datasetIngestor``** script
* If necessary, the script will copy the data to the PSI archive servers
* Usually this is necessary when archiving from directories other than **``/data/user``** or
* Prepare a metadata file describing the dataset
* Run **``datasetIngestor``** script
* If necessary, the script will copy the data to the PSI archive servers
* Usually this is necessary when archiving from directories other than **``/data/user``** or
**``/data/project``**. It would be also necessary when the Merlin export server (**``merlin-archive.psi.ch``**)
is down for any reason.
* Archive the dataset:
* Visit [https://discovery.psi.ch](https://discovery.psi.ch)
* Click **``Archive``** for the dataset
* The system will now copy the data to the PetaByte Archive at CSCS
* Visit [<https://discovery.psi.ch](https://discovery.psi.ch>)
* Click **``Archive``** for the dataset
* The system will now copy the data to the PetaByte Archive at CSCS
* Retrieve data from the catalog:
* Find the dataset on [https://discovery.psi.ch](https://discovery.psi.ch) and click **``Retrieve``**
* Wait for the data to be copied to the PSI retrieval system
* Run **``datasetRetriever``** script
* Find the dataset on [<https://discovery.psi.ch](https://discovery.psi.ch>) and click **``Retrieve``**
* Wait for the data to be copied to the PSI retrieval system
* Run **``datasetRetriever``** script
Since large data sets may take a lot of time to transfer, some steps are designed to happen in the
background. The discovery website can be used to track the progress of each step.
@@ -179,6 +171,7 @@ datasetIngestor --token $SCICAT_TOKEN --ingest --autoarchive metadata.json
You will be asked whether you want to copy the data to the central system:
* If you are on the Merlin cluster and you are archiving data from ``/data/user`` or ``/data/project``, answer 'no' since the data catalog can
directly read the data.
* If you are on a directory other than ``/data/user`` and ``/data/project, or you are on a desktop computer, answer 'yes'. Copying large datasets
to the PSI archive system may take quite a while (minutes to hours).
@@ -188,7 +181,7 @@ This is important, since the next step is for the system to copy all the data to
this process may take several days, and it will fail if any modifications are detected.
If using the ``--autoarchive`` option as suggested above, your dataset should now be in the queue. Check the data catalog:
[https://discovery.psi.ch](https://discovery.psi.ch). Your job should have status 'WorkInProgress'. You will receive an email when the ingestion
[<https://discovery.psi.ch](https://discovery.psi.ch>). Your job should have status 'WorkInProgress'. You will receive an email when the ingestion
is complete.
If you didn't use ``--autoarchive``, you need to manually move the dataset into the archive queue. From **discovery.psi.ch**, navigate to the 'Archive'
@@ -250,7 +243,7 @@ step will take a long time and may appear to have hung. You can check what files
where UID is the dataset ID (12345678-1234-1234-1234-123456789012) and PATH is the absolute path to your data. Note that rsync creates directories first and that the transfer order is not alphabetical in some cases, but it should be possible to see whether any data has transferred.
* There is currently a limit on the number of files per dataset (technically, the limit is from the total length of all file paths). It is recommended to break up datasets into 300'000 files or less.
* If it is not possible or desirable to split data between multiple datasets, an alternate work-around is to package files into a tarball. For datasets which are already compressed, omit the -z option for a considerable speedup:
* If it is not possible or desirable to split data between multiple datasets, an alternate work-around is to package files into a tarball. For datasets which are already compressed, omit the -z option for a considerable speedup:
```
tar -f [output].tar [srcdir]
@@ -271,7 +264,6 @@ step will take a long time and may appear to have hung. You can check what files
/data/project/bio/myproject/archive $ datasetIngestor -copy -autoarchive -allowexistingsource -ingest metadata.json
2019/11/06 11:04:43 Latest version: 1.1.11
2019/11/06 11:04:43 Your version of this program is up-to-date
2019/11/06 11:04:43 You are about to add a dataset to the === production === data catalog environment...
2019/11/06 11:04:43 Your username:
@@ -321,7 +313,6 @@ user_n@pb-archive.psi.ch's password:
2019/11/06 11:05:04 The source folder /data/project/bio/myproject/archive is not centrally available (decentral use case).
The data must first be copied to a rsync cache server.
2019/11/06 11:05:04 Do you want to continue (Y/n)?
Y
2019/11/06 11:05:09 Created dataset with id 12.345.67890/12345678-1234-1234-1234-123456789012
@@ -359,7 +350,7 @@ user_n@pb-archive.psi.ch's password:
### Publishing
After datasets are are ingested they can be assigned a public DOI. This can be included in publications and will make the datasets on http://doi.psi.ch.
After datasets are are ingested they can be assigned a public DOI. This can be included in publications and will make the datasets on <http://doi.psi.ch>.
For instructions on this, please read the ['Publish' section in the ingest manual](https://scicatproject.github.io/documentation/Ingestor/ingestManual.html#sec-8).

10
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@@ -1,12 +1,4 @@
---
title: Connecting from a Linux Client
#tags:
keywords: linux, connecting, client, configuration, SSH, X11
last_updated: 07 September 2022
summary: "This document describes a recommended setup for a Linux client."
sidebar: merlin7_sidebar
permalink: /merlin7/connect-from-linux.html
---
# Connecting from a Linux Client
## SSH without X11 Forwarding

10
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@@ -1,12 +1,4 @@
---
title: Connecting from a MacOS Client
#tags:
keywords: MacOS, mac os, mac, connecting, client, configuration, SSH, X11
last_updated: 07 September 2022
summary: "This document describes a recommended setup for a MacOS client."
sidebar: merlin7_sidebar
permalink: /merlin7/connect-from-macos.html
---
# Connecting from a MacOS Client
## SSH without X11 Forwarding

2
docs/merlin7/02-How-To-Use-Merlin/connect-from-windows.md
View File

@@ -6,6 +6,7 @@ PuTTY is one of the most common tools for SSH.
Check, if the following software packages are installed on the Windows workstation by
inspecting the *Start* menu (hint: use the *Search* box to save time):
* PuTTY (should be already installed)
* *[Optional]* Xming (needed for [SSH with X11 Forwarding](#ssh-with-putty-with-x11-forwarding))
@@ -21,7 +22,6 @@ If they are missing, you can install them using the Software Kiosk icon on the D
![Create Merlin Session](../../images/PuTTY/Putty_Session.png)
## SSH with PuTTY with X11 Forwarding
Official X11 Forwarding support is through NoMachine. Please follow the document

16
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@@ -1,12 +1,4 @@
---
title: Kerberos and AFS authentication
#tags:
keywords: kerberos, AFS, kinit, klist, keytab, tickets, connecting, client, configuration, slurm
last_updated: 07 September 2022
summary: "This document describes how to use Kerberos."
sidebar: merlin7_sidebar
permalink: /merlin7/kerberos.html
---
# Kerberos and AFS authentication
Projects and users have their own areas in the central PSI AFS service. In order
to access to these areas, valid Kerberos and AFS tickets must be granted.
@@ -58,7 +50,7 @@ Kerberos ticket is mandatory.
krenew
```
* Keep in mind that the maximum lifetime for granting tickets is 7 days, therefore `krenew` can not be used beyond that limit,
* Keep in mind that the maximum lifetime for granting tickets is 7 days, therefore `krenew` can not be used beyond that limit,
and then `kinit` should be used instead.
## Obtanining granting tickets with keytab
@@ -95,8 +87,8 @@ For generating a **keytab**, one has to:
```
Please note:
* That you will need to add your password once. This step is required for generating the **keytab** file.
* `ktutil`does **not** report an error if you enter a wrong password! You can test with the `kinit` command documented below. If `kinit` fails with an error message like "pre-authentication failed", this is usually due to a wrong password/key in the keytab file. In this case **you have to remove the keytab file** and re-run the `ktutil` command. See "Updating the keytab file" in the section below.
* That you will need to add your password once. This step is required for generating the **keytab** file.
* `ktutil`does **not** report an error if you enter a wrong password! You can test with the `kinit` command documented below. If `kinit` fails with an error message like "pre-authentication failed", this is usually due to a wrong password/key in the keytab file. In this case **you have to remove the keytab file** and re-run the `ktutil` command. See "Updating the keytab file" in the section below.
### Updating an existing keytab file

5
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@@ -10,10 +10,8 @@ provides a helpful wrapper over the Gnome storage utilities (GIO and GVFS), and
- FTP, SFTP
- [complete list](https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/8/html/using_the_desktop_environment_in_rhel_8/managing-storage-volumes-in-gnome_using-the-desktop-environment-in-rhel-8#gvfs-back-ends_managing-storage-volumes-in-gnome)
## Usage
### Start a session
First, start a new session. This will start a new bash shell in the current terminal where you can add further commands.
@@ -47,7 +45,6 @@ Other endpoints can be mounted using the `merlin_rmount --mount <endpoint>` comm
![merlin_rmount --mount](../../images/rmount/mount.png)
### Accessing Files
After mounting a volume the script will print the mountpoint. It should be of the form
@@ -67,7 +64,6 @@ ln -s ~/mnt /run/user/$UID/gvfs
Files are accessible as long as the `merlin_rmount` shell remains open.
### Disconnecting
To disconnect, close the session with one of the following:
@@ -78,7 +74,6 @@ To disconnect, close the session with one of the following:
Disconnecting will unmount all volumes.
## Alternatives
### Thunar

11
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@@ -1,12 +1,4 @@
---
title: Merlin7 Tools
#tags:
keywords: merlin_quotas
#last_updated: 07 September 2022
#summary: ""
sidebar: merlin7_sidebar
permalink: /merlin7/tools.html
---
# Merlin7 Tools
## About
@@ -105,4 +97,3 @@ If you are added/removed from a project, you can update this config file by
calling `merlin_quotas genconf --force` (notice the `--force`, which will overwrite
your existing config file) or by editing the file by hand (*not recommended*).

12
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@@ -1,10 +1,4 @@
---
title: Remote Desktop Access to Merlin7
keywords: NX, NoMachine, remote desktop access, login node, login001, login002, merlin7-nx-01, merlin7-nx, nx.psi.ch, VPN, browser access
last_updated: 07 August 2024
sidebar: merlin7_sidebar
permalink: /merlin7/nomachine.html
---
# Remote Desktop Access to Merlin7
## Overview
@@ -21,7 +15,7 @@ If you are inside the PSI network, you can directly connect to the Merlin7 NoMac
#### Method 1: Using a Web Browser
Open your web browser and navigate to [https://merlin7-nx.psi.ch:4443](https://merlin7-nx.psi.ch:4443).
Open your web browser and navigate to <https://merlin7-nx.psi.ch:4443>.
#### Method 2: Using the NoMachine Client
@@ -42,7 +36,7 @@ Documentation about the `nx.psi.ch` service can be found [here](https://www.psi.
##### Using a Web Browser
Open your web browser and navigate to [https://nx.psi.ch](https://nx.psi.ch).
Open your web browser and navigate to <https://nx.psi.ch>.
##### Using the NoMachine Client

10
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@@ -1,12 +1,4 @@
---
title: Software repositories
#tags:
keywords: modules, software, stable, unstable, deprecated, spack, repository, repositories
last_updated: 16 January 2024
summary: "This page contains information about the different software repositories"
sidebar: merlin7_sidebar
permalink: /merlin7/software-repositories.html
---
# Software repositories
## Module Systems in Merlin7

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@@ -1,13 +1,4 @@
---
title: Configuring SSH Keys in Merlin
#tags:
keywords: linux, connecting, client, configuration, SSH, Keys, SSH-Keys, RSA, authorization, authentication
last_updated: 15 Jul 2020
summary: "This document describes how to deploy SSH Keys in Merlin."
sidebar: merlin7_sidebar
permalink: /merlin7/ssh-keys.html
---
# Configuring SSH Keys in Merlin
Merlin users sometimes will need to access the different Merlin services without being constantly requested by a password.
One can achieve that with Kerberos authentication, however in some cases some software would require the setup of SSH Keys.
@@ -28,8 +19,8 @@ ls ~/.ssh/id*
For creating **SSH RSA Keys**, one should:
1. Run `ssh-keygen`, a password will be requested twice. You **must remember** this password for the future.
* Due to security reasons, ***always try protecting it with a password***. There is only one exception, when running ANSYS software, which in general should not use password to simplify the way of running the software in Slurm.
* This will generate a private key **id_rsa**, and a public key **id_rsa.pub** in your **~/.ssh** directory.
* Due to security reasons, ***always try protecting it with a password***. There is only one exception, when running ANSYS software, which in general should not use password to simplify the way of running the software in Slurm.
* This will generate a private key **id_rsa**, and a public key **id_rsa.pub** in your **~/.ssh** directory.
2. Add your public key to the **`authorized_keys`** file, and ensure proper permissions for that file, as follows:
```bash

15
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@@ -1,13 +1,4 @@
---
title: Merlin7 Storage
#tags:
keywords: storage, /data/user, /data/software, /data/project, /scratch, /data/scratch/shared, quota, export, user, project, scratch, data, data/scratch/shared, merlin_quotas
#last_updated: 07 September 2022
#summary: ""
sidebar: merlin7_sidebar
redirect_from: /merlin7/data-directories.html
permalink: /merlin7/storage.html
---
# Merlin7 Storage
## Introduction
@@ -151,7 +142,7 @@ Directory policies:
* Read **[Important: Code of Conduct](../01-Quick-Start-Guide/code-of-conduct.md)** for more information about Merlin7 policies.
* It is **forbidden** to use the data directories as `/scratch` area during a job's runtime, i.e. for high throughput I/O for a job's temporary files.
* Please Use `/scratch`, `/data/scratch/shared` for this purpose.
* Please Use `/scratch`, `/data/scratch/shared` for this purpose.
* No backups: users are responsible for managing the backups of their data directories.
#### Dedicated project directories
@@ -190,6 +181,6 @@ Scratch directories policies:
* Read **[Important: Code of Conduct](../01-Quick-Start-Guide/code-of-conduct.md)** for more information about Merlin7 policies.
* By default, *always* use **local** first and only use **shared** if your specific use case requires it.
* Temporary files *must be deleted at the end of the job by the user*.
* Remaining files will be deleted by the system if detected.
* Remaining files will be deleted by the system if detected.
* Files not accessed within 28 days will be automatically cleaned up by the system.
* If for some reason the scratch areas get full, admins have the rights to cleanup the oldest data.

96
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@@ -1,26 +1,19 @@
---
title: Transferring Data
#tags:
keywords: transferring data, data transfer, rsync, winscp, copy data, copying, sftp, import, export, hop, vpn
last_updated: 24 August 2023
#summary: ""
sidebar: merlin7_sidebar
permalink: /merlin7/transfer-data.html
---
# Transferring Data
## Overview
Most data transfer methods support both sending and receiving, so you may initiate the transfer from either **Merlin** or the other system — depending on **network visibility**.
- **From PSI Network to Merlin:** Merlin login nodes are visible from the PSI network, so direct transfers using `rsync`, or **ftp** are generally preferable. Transfers **from Merlin7 to PSI may require special firewall rules**.
- **From Merlin to the Internet:** Merlin login nodes can access the internet with a **limited set of protocols**:
- HTTP-based protocols on ports `80` or `445` (e.g., HTTPS, WebDAV).
- Other protocols (e.g., SSH, FTP, rsync daemon mode) require admin configuration, may only work with specific hosts, and might need new firewall rules.
- **From the Internet to PSI:** Systems outside PSI can access the [PSI Data Transfer Service](https://www.psi.ch/en/photon-science-data-services/data-transfer) at `datatransfer.psi.ch` using SSH-based protocols or [Globus](https://www.globus.org/).
> SSH-based protocols using port `22` **to most PSI servers** are generally **not permitted**.
> * However, **transfers from any PSI host to Merlin7 using port 22 are allowed**.
>
> Port `21` is also available for FTP transfers from PSI to Merlin7.
* **From PSI Network to Merlin:** Merlin login nodes are visible from the PSI network, so direct transfers using `rsync`, or **ftp** are generally preferable. Transfers **from Merlin7 to PSI may require special firewall rules**.
* **From Merlin to the Internet:** Merlin login nodes can access the internet with a **limited set of protocols**:
* HTTP-based protocols on ports `80` or `445` (e.g., HTTPS, WebDAV).
* Other protocols (e.g., SSH, FTP, rsync daemon mode) require admin configuration, may only work with specific hosts, and might need new firewall rules.
* **From the Internet to PSI:** Systems outside PSI can access the [PSI Data Transfer Service](https://www.psi.ch/en/photon-science-data-services/data-transfer) at `datatransfer.psi.ch` using SSH-based protocols or [Globus](https://www.globus.org/).
!!! note
SSH-based protocols using port `22` **to most PSI servers** are generally **not permitted**.
However, **transfers from any PSI host to Merlin7 using port 22 are allowed**.
Port `21` is also available for FTP transfers from PSI to Merlin7.
### Choosing the best transfer method
@@ -46,6 +39,7 @@ The following methods transfer data directly via the [login nodes](../01-Quick-S
### Rsync (Recommended for Linux/macOS)
Rsync is the **preferred** method for small datasets from Linux/macOS systems. It supports **resuming interrupted transfers** and **skips already transferred files**. Syntax:
```bash
rsync -avAHXS <src> <dst>
```
@@ -65,12 +59,15 @@ rsync -avAHXS ~/localdata $USER@login001.merlin7.psi.ch:/data/project/general/my
### SCP
SCP works similarly to `rsync` but **does not support resuming** interrupted transfers. It may be used for quick one-off transfers. Example:
```bash
scp ~/localfile.txt $USER@login001.merlin7.psi.ch:/data/project/general/myproject/
```
### Secure FTP
A `vsftpd` service is available on the login nodes, providing high-speed transfers. Choose the server based on your **speed vs. encryption** needs:
* **`login001.merlin7.psi.ch`:** Encrypted control & data channels.
**Use if your data is sensitive**. **Slower**, but secure.
* **`service03.merlin7.psi.ch`**: Encrypted control channel only.
@@ -80,14 +77,16 @@ A `vsftpd` service is available on the login nodes, providing high-speed transfe
The **control channel** is always **encrypted**, therefore, authentication is encrypted and secured.
## UI-based Clients for Data Transfer
### WinSCP (Windows)
Available in the **Software Kiosk** on PSI Windows machines.
* Using your PSI credentials, connect to
* when using port 22, connect to `login001.merlin7.psi.ch` or `login002.merlin7.psi.ch`.
* when using port 21, connect to:
* `ftp-encrypted.merlin7.psi.ch`: **Fast** transfer rates. **Both** control and data **channels encrypted**.
* `service03.merlin7.psi.ch`: **Fastest** transfer rates, but **data channel not encrypted**.
* when using port 22, connect to `login001.merlin7.psi.ch` or `login002.merlin7.psi.ch`.
* when using port 21, connect to:
* `ftp-encrypted.merlin7.psi.ch`: **Fast** transfer rates. **Both** control and data **channels encrypted**.
* `service03.merlin7.psi.ch`: **Fastest** transfer rates, but **data channel not encrypted**.
* Drag and drop files between your PC and Merlin.
* FTP (port 21)
@@ -95,30 +94,34 @@ Available in the **Software Kiosk** on PSI Windows machines.
### FileZilla (Linux/MacOS/Windows)
Download from [FileZilla Project](https://filezilla-project.org/), or install from your Linux software repositories if available.
* Using your PSI credentials, connect to
* when using port 22, connect to `login001.merlin7.psi.ch` or `login002.merlin7.psi.ch`.
* when using port 21, connect to:
* `ftp-encrypted.merlin7.psi.ch`: **Fast** transfer rates. **Both** control and data **channels encrypted**.
* `service03.merlin7.psi.ch`: **Fastest** transfer rates, but **data channel not encrypted**.
* when using port 22, connect to `login001.merlin7.psi.ch` or `login002.merlin7.psi.ch`.
* when using port 21, connect to:
* `ftp-encrypted.merlin7.psi.ch`: **Fast** transfer rates. **Both** control and data **channels encrypted**.
* `service03.merlin7.psi.ch`: **Fastest** transfer rates, but **data channel not encrypted**.
* Supports drag-and-drop file transfers.
## Sharing Files with SWITCHfilesender
**[SWITCHfilesender](https://filesender.switch.ch/filesender2/?s=upload)** is a Swiss-hosted installation of the [FileSender](https://filesender.org/) project — a web-based application that allows authenticated users to securely and easily send **arbitrarily large files** to other users. Features:
- **Secure large file transfers:** Send files that exceed normal email attachment limits.
- **Time-limited availability:** Files are automatically deleted after the chosen expiration date or number of downloads.
- **Voucher system:** Authenticated users can send upload vouchers to external recipients without an account.
- **Designed for research & education:** Developed to meet the needs of universities and research institutions.
* **Secure large file transfers:** Send files that exceed normal email attachment limits.
* **Time-limited availability:** Files are automatically deleted after the chosen expiration date or number of downloads.
* **Voucher system:** Authenticated users can send upload vouchers to external recipients without an account.
* **Designed for research & education:** Developed to meet the needs of universities and research institutions.
About the authentication:
- It uses **SimpleSAMLphp**, supporting multiple authentication mechanisms: SAML2, LDAP, RADIUS and more.
- It's fully integrated with PSI's **Authentication and Authorization Infrastructure (AAI)**.
- PSI employees can log in using their PSI account:
* It uses **SimpleSAMLphp**, supporting multiple authentication mechanisms: SAML2, LDAP, RADIUS and more.
* It's fully integrated with PSI's **Authentication and Authorization Infrastructure (AAI)**.
* PSI employees can log in using their PSI account:
1. Open [SWITCHfilesender](https://filesender.switch.ch/filesender2/?s=upload).
2. Select **PSI** as the institution.
3. Authenticate with your PSI credentials.
The service is designed to **send large files for temporary availability**, not as a permanent publishing platform. Typical use case:
1. Upload a file.
2. Share the download link with a recipient.
3. File remains available until the specified **expiration date** is reached, or the **download limit** is reached.
@@ -134,6 +137,7 @@ From August 2024, Merlin is connected to the **[PSI Data Transfer](https://www.p
[reported](../99-support/contact.md) to the Merlin administrators, which will forward the request if necessary.
The PSI Data Transfer servers supports the following protocols:
* Data Transfer - SSH (scp / rsync)
* Data Transfer - Globus
@@ -150,27 +154,25 @@ Therefore, having the Microsoft Authenticator App is required as explained [here
## Connecting to Merlin7 from outside PSI
Merlin7 is fully accessible from within the PSI network. To connect from outside you can use:
- [VPN](https://www.psi.ch/en/computing/vpn) ([alternate instructions](https://intranet.psi.ch/BIO/ComputingVPN))
- [SSH hopx](https://www.psi.ch/en/computing/ssh-hop)
* Please avoid transferring big amount data through **hop**
- [No Machine](nomachine.md)
* Remote Interactive Access through [**'nx.psi.ch'**](https://www.psi.ch/en/photon-science-data-services/remote-interactive-access)
* Please avoid transferring big amount of data through **NoMachine**
{% comment %}
* [VPN](https://www.psi.ch/en/computing/vpn) ([alternate instructions](https://intranet.psi.ch/BIO/ComputingVPN))
* [SSH hopx](https://www.psi.ch/en/computing/ssh-hop)
* Please avoid transferring big amount data through **hop**
* [No Machine](nomachine.md)
* Remote Interactive Access through [**'nx.psi.ch'**](https://www.psi.ch/en/photon-science-data-services/remote-interactive-access)
* Please avoid transferring big amount of data through **NoMachine**
## Connecting from Merlin7 to outside file shares
### `merlin_rmount` command
Merlin provides a command for mounting remote file systems, called `merlin_rmount`. This
provides a helpful wrapper over the Gnome storage utilities, and provides support for a wide range of remote file formats, including
- SMB/CIFS (Windows shared folders)
- WebDav
- AFP
- FTP, SFTP
- [others](https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/8/html/using_the_desktop_environment_in_rhel_8/managing-storage-volumes-in-gnome_using-the-desktop-environment-in-rhel-8#gvfs-back-ends_managing-storage-volumes-in-gnome)
* SMB/CIFS (Windows shared folders)
* WebDav
* AFP
* FTP, SFTP
* [others](https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/8/html/using_the_desktop_environment_in_rhel_8/managing-storage-volumes-in-gnome_using-the-desktop-environment-in-rhel-8#gvfs-back-ends_managing-storage-volumes-in-gnome)
[More instruction on using `merlin_rmount`](merlin-rmount.md)
{% endcomment %}

1
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@@ -119,6 +119,7 @@ how to connect to the **NoMachine** service in the Merlin cluster.
For other non officially supported graphical access (X11 forwarding):
* For Linux clients, please follow [{How To Use Merlin -> Accessing from Linux Clients}](../02-How-To-Use-Merlin/connect-from-linux.md)
* For Windows clients, please follow [{How To Use Merlin -> Accessing from Windows Clients}](../02-How-To-Use-Merlin/connect-from-windows.md)
* For MacOS clients, please follow [{How To Use Merlin -> Accessing from MacOS Clients}](../02-How-To-Use-Merlin/connect-from-macos.md)

22
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@@ -1,12 +1,4 @@
---
title: Slurm cluster 'merlin7'
#tags:
keywords: configuration, partitions, node definition
#last_updated: 24 Mai 2023
summary: "This document describes a summary of the Merlin7 configuration."
sidebar: merlin7_sidebar
permalink: /merlin7/merlin7-configuration.html
---
# Slurm cluster 'merlin7'
This documentation shows basic Slurm configuration and options needed to run jobs in the Merlin7 cluster.
@@ -14,10 +6,10 @@ This documentation shows basic Slurm configuration and options needed to run job
### Hardware
* 2 CPU-only login nodes
* 77 CPU-only compute nodes
* 5 GPU A100 nodes
* 8 GPU Grace Hopper nodes
* 2 CPU-only login nodes
* 77 CPU-only compute nodes
* 5 GPU A100 nodes
* 8 GPU Grace Hopper nodes
The specification of the node types is:
@@ -51,9 +43,9 @@ The appliance is built of several storage servers:
With effective storage capacity of:
* 10 PB HDD
* value visible on linux: HDD 9302.4 TiB
* value visible on linux: HDD 9302.4 TiB
* 162 TB SSD
* value visible on linux: SSD 151.6 TiB
* value visible on linux: SSD 151.6 TiB
* 23.6 TiB on Metadata
The storage is directly connected to the cluster (and each individual node) through the Slingshot NIC.

24
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@@ -1,12 +1,4 @@
---
title: Slurm merlin7 Configuration
#tags:
keywords: configuration, partitions, node definition
#last_updated: 24 Mai 2023
summary: "This document describes a summary of the Merlin7 Slurm CPU-based configuration."
sidebar: merlin7_sidebar
permalink: /merlin7/slurm-configuration.html
---
# Slurm merlin7 Configuration
This documentation shows basic Slurm configuration and options needed to run jobs in the Merlin7 cluster.
@@ -53,6 +45,7 @@ However, when necessary, one can specify the cluster as follows:
### CPU general configuration
The **Merlin7 CPU cluster** is configured with the **`CR_CORE_MEMORY`** and **`CR_ONE_TASK_PER_CORE`** options.
* This configuration treats both cores and memory as consumable resources.
* Since the nodes are running with **hyper-threading** enabled, each core thread is counted as a CPU
to fulfill a job's resource requirements.
@@ -75,8 +68,8 @@ scripts accordingly.
Notes on memory configuration:
* **Memory allocation options:** To request additional memory, use the following options in your submission script:
* **`--mem=<mem_in_MB>`**: Allocates memory per node.
* **`--mem-per-cpu=<mem_in_MB>`**: Allocates memory per CPU (equivalent to a core thread).
* **`--mem=<mem_in_MB>`**: Allocates memory per node.
* **`--mem-per-cpu=<mem_in_MB>`**: Allocates memory per CPU (equivalent to a core thread).
The total memory requested cannot exceed the **`MaxMemPerNode`** value.
* **Impact of disabling Hyper-Threading:** Using the **`--hint=nomultithread`** option disables one thread per core,
@@ -223,12 +216,14 @@ For submittng jobs to the GPU cluster, **the cluster name `gmerlin7` must be spe
### GPU general configuration
The **Merlin7 GPU cluster** is configured with the **`CR_CORE_MEMORY`**, **`CR_ONE_TASK_PER_CORE`**, and **`ENFORCE_BINDING_GRES`** options.
* This configuration treats both cores and memory as consumable resources.
* Since the nodes are running with **hyper-threading** enabled, each core thread is counted as a CPU
to fulfill a job's resource requirements.
* Slurm will allocate the CPUs to the selected GPU.
By default, Slurm will allocate one task per core, which means:
* For hyper-threaded nodes (NVIDIA A100-based nodes), each task will consume 2 **CPUs**, regardless of whether both threads are actively used by the job.
* For the NVIDIA GraceHopper-based nodes, each task will consume 1 **CPU**.
@@ -247,10 +242,11 @@ scripts accordingly.
Notes on memory configuration:
* **Memory allocation options:** To request additional memory, use the following options in your submission script:
* **`--mem=<mem_in_MB>`**: Allocates memory per node.
* **`--mem-per-cpu=<mem_in_MB>`**: Allocates memory per CPU (equivalent to a core thread).
* **`--mem=<mem_in_MB>`**: Allocates memory per node.
* **`--mem-per-cpu=<mem_in_MB>`**: Allocates memory per CPU (equivalent to a core thread).
The total memory requested cannot exceed the **`MaxMemPerNode`** value.
* **Impact of disabling Hyper-Threading:** Using the **`--hint=nomultithread`** option disables one thread per core,
effectively halving the number of available CPUs. Consequently, memory allocation will also be halved unless explicitly
adjusted.
@@ -278,7 +274,9 @@ effectively.
To implement these limits, **we utilize Quality of Service (QoS)**. Different QoS policies are defined and applied
**to specific partitions** in line with the established resource allocation policies. The table below outlines the
various QoS definitions applicable to the merlin7 CPU-based cluster. Here:
* `MaxTRES` specifies resource limits per job.
* `MaxTRESPU` specifies resource limits per user.

10
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@@ -1,12 +1,4 @@
---
title: Slurm Examples
#tags:
keywords: slurm example, template, examples, templates, running jobs, sbatch, single core based jobs, HT, multithread, no-multithread, mpi, openmp, packed jobs, hands-on, array jobs, gpu
last_updated: 24 Mai 2023
summary: "This document shows different template examples for running jobs in the Merlin cluster."
sidebar: merlin7_sidebar
permalink: /merlin7/slurm-examples.html
---
# Slurm Examples
## Single core based job examples

10
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@@ -1,12 +1,4 @@
---
title: Jupyterhub on Merlin7
#tags:
keywords: jupyterhub, jupyter, jupyterlab, notebook, notebooks
last_updated: 24 July 2025
summary: "Jupyterhub service description"
sidebar: merlin7_sidebar
permalink: /merlin7/jupyterhub.html
---
# Jupyterhub on Merlin7
Jupyterhub provides [jupyter notebooks](https://jupyter.org/) that are launched on
cluster nodes of merlin and can be accessed through a web portal.

19
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@@ -1,12 +1,4 @@
---
title: ANSYS RSM (Remote Resolve Manager)
#tags:
keywords: software, ansys, rsm, slurm, interactive, rsm, windows
last_updated: 23 August 2024
summary: "This document describes how to use the ANSYS Remote Resolve Manager service in the Merlin7 cluster"
sidebar: merlin7_sidebar
permalink: /merlin7/ansys-rsm.html
---
# ANSYS RSM (Remote Resolve Manager)
## ANSYS Remote Resolve Manager
@@ -34,11 +26,12 @@ The different steps and settings required to make it work are that following:
3. In the **HPC Resource** tab, fill up the corresponding fields as follows:
![HPC Resource](../../images/ANSYS/merlin7/rsm-2-add_cluster.png)
* **"Name"**: Add here the preffered name for the cluster. For example: `Merlin7 cluster`
* **"HPC Type"**: Select `SLURM`
* **"Submit host"**: `service03.merlin7.psi.ch`
* **"Slurm Job submission arguments (optional)"**: Add any required Slurm options for running your jobs.
* `--hint=nomultithread` must be present.
* `--exclusive` must also be present for now, due to a bug in the `Slingshot` interconnect which does not allow running shared nodes.
* `--hint=nomultithread` must be present.
* `--exclusive` must also be present for now, due to a bug in the `Slingshot` interconnect which does not allow running shared nodes.
* Check **"Use SSH protocol for inter and intra-node communication (Linux only)"**
* Select **"Able to directly submit and monitor HPC jobs"**.
* **"Apply"** changes.
@@ -55,8 +48,8 @@ option "Scratch directory local to the execution node(s)" was set.
PSI account to authenticate. Notice that the **`PSICH\`** prefix **must not be added**.
![Authenticating](../../images/ANSYS/merlin7/rsm-5-authenticating.png)
* From the partition list, select the ones you want to typically use.
* In general, standard Merlin users must use **`hourly`**, **`daily`** and **`general`** only.
* Other partitions are reserved for allowed users only.
* In general, standard Merlin users must use **`hourly`**, **`daily`** and **`general`** only.
* Other partitions are reserved for allowed users only.
* **"Apply"** changes.
![Select partitions](../../images/ANSYS/merlin7/rsm-6-selected-partitions.png)
6. *[Optional]* You can perform a test by submitting a test job on each partition by clicking on the **Submit** button

12
docs/merlin7/05-Software-Support/ansys.md
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@@ -1,12 +1,4 @@
---
title: ANSYS
#tags:
keywords: software, ansys, slurm, interactive, rsm, pmodules, overlay, overlays
last_updated: 23 August 2024
summary: "This document describes how to load and use ANSYS in the Merlin7 cluster"
sidebar: merlin7_sidebar
permalink: /merlin7/ansys.html
---
# ANSYS
This document describes generic information of how to load and run ANSYS software in the Merlin cluster
@@ -22,7 +14,6 @@ Merlin high performance storage and we have made it available from Pmodules.
### Loading Merlin7 ANSYS
```bash
module purge
module use unstable # Optional
@@ -69,7 +60,6 @@ ANSYS/2025R2:
</pre>
</details>
!!! tip
Please always run **ANSYS/2024R2 or superior**.

12
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@@ -1,11 +1,4 @@
---
title: CP2k
keywords: CP2k software, compile
summary: "CP2k is a quantum chemistry and solid state physics software package"
sidebar: merlin7_sidebar
toc: false
permalink: /merlin7/cp2k.html
---
# CP2k
## CP2k
@@ -131,14 +124,13 @@ module purge
module use Spack unstable
module load gcc/12.3 openmpi/5.0.8-r5lz-A100-gpu dbcsr/2.8.0-3r22-A100-gpu-omp cosma/2.7.0-y2tr-gpu cuda/12.6.0-3y6a dftd4/3.7.0-4k4c-omp elpa/2025.01.002-bovg-A100-gpu-omp fftw/3.3.10-syba-omp hdf5/1.14.6-pcsd libint/2.11.1-3lxv libxc/7.0.0-u556 libxsmm/1.17-2azz netlib-scalapack/2.2.2-rmcf openblas/0.3.30-ynou-omp plumed/2.9.2-47hk py-fypp/3.1-z25p py-numpy/2.3.2-45ay python/3.13.5-qivs sirius/develop-qz4c-A100-gpu-omp spglib/2.5.0-jl5l-omp spla/1.6.1-hrgf-gpu cmake/3.31.8-j47l ninja/1.12.1-afxy
git clone https://github.com/cp2k/cp2k.git
git clone <https://github.com/cp2k/cp2k.git>
cd cp2k
mkdir build && cd build
CC=mpicc CXX=mpic++ FC=mpifort cmake -GNinja -DCMAKE_CUDA_HOST_COMPILER=mpicc -DCP2K_USE_LIBXC=ON -DCP2K_USE_LIBINT2=ON -DCP2K_USE_SPGLIB=ON -DCP2K_USE_ELPA=ON -DCP2K_USE_SPLA=ON -DCP2K_USE_SIRIUS=ON -DCP2K_USE_PLUMED=ON -DCP2K_USE_DFTD4=ON -DCP2K_USE_COSMA=ON -DCP2K_USE_ACCEL=CUDA -DCMAKE_CUDA_ARCHITECTURES=80 -DCP2K_USE_FFTW3=ON ..
ninja -j 16
```
#### GH200
[![Pipeline](https://gitea.psi.ch/HPCE/spack-psi/actions/workflows/cp2k_gh_merlin7.yml/badge.svg?branch=main)](https://gitea.psi.ch/HPCE/spack-psi)

12
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@@ -1,12 +1,4 @@
---
title: Cray Programming Environment
#tags:
keywords: cray, module
last_updated: 24 Mai 2023
summary: "This document describes how to use the Cray Programming Environment on Merlin7."
sidebar: merlin7_sidebar
permalink: /merlin7/cray-module-env.html
---
# Cray Programming Environment
## Loading the Cray module
@@ -38,7 +30,7 @@ as a whole called Programming Environment. In the Cray Programming Environment,
* `cray-libsci` is a collection of numerical routines tuned for performance on Cray systems.
* `libfabric` is an important low-level library that allows you to take advantage of the high performance Slingshot network.
* `cray-mpich` is a CUDA-aware MPI implementation, optimized for Cray systems.
* `cce` is the compiler from Cray. C/C++ compilers are based on Clang/LLVM while Fortran supports Fortran 2018 standard. More info: https://user.cscs.ch/computing/compilation/cray/
* `cce` is the compiler from Cray. C/C++ compilers are based on Clang/LLVM while Fortran supports Fortran 2018 standard. More info: <https://user.cscs.ch/computing/compilation/cray/>
You can switch between different programming environments. You can check the available module with the `module avail` command, as follows:

9
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@@ -1,11 +1,4 @@
---
title: GROMACS
keywords: GROMACS software, compile
summary: "GROMACS (GROningen Machine for Chemical Simulations) is a versatile and widely-used open source package to perform molecular dynamics"
sidebar: merlin7_sidebar
toc: false
permalink: /merlin7/gromacs.html
---
# GROMACS
## GROMACS

9
docs/merlin7/05-Software-Support/ippl.md
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@@ -1,11 +1,4 @@
---
title: IPPL
keywords: IPPL software, compile
summary: "Independent Parallel Particle Layer (IPPL) is a performance portable C++ library for Particle-Mesh methods"
sidebar: merlin7_sidebar
toc: false
permalink: /merlin7/ippl.html
---
# IPPL
## IPPL

9
docs/merlin7/05-Software-Support/lammps.md
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@@ -1,11 +1,4 @@
---
title: LAMMPS
keywords: LAMMPS software, compile
summary: "LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state"
sidebar: merlin7_sidebar
toc: false
permalink: /merlin7/lammps.html
---
# LAMMPS
## LAMMPS

9
docs/merlin7/05-Software-Support/opal-x.md
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@@ -1,11 +1,4 @@
---
title: OPAL-X
keywords: OPAL-X software, compile
summary: "OPAL (Object Oriented Particle Accelerator Library) is an open source C++ framework for general particle accelerator simulations including 3D space charge, short range wake fields and particle matter interaction."
sidebar: merlin7_sidebar
toc: false
permalink: /merlin7/opal-x.html
---
# OPAL-X
## OPAL

10
docs/merlin7/05-Software-Support/openmpi.md
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@@ -1,12 +1,4 @@
---
title: OpenMPI Support
#tags:
last_updated: 15 January 2025
keywords: software, openmpi, slurm
summary: "This document describes how to use OpenMPI in the Merlin7 cluster"
sidebar: merlin7_sidebar
permalink: /merlin7/openmpi.html
---
# OpenMPI Support
## Introduction

26
docs/merlin7/05-Software-Support/pmodules.md
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@@ -1,12 +1,4 @@
---
title: PSI Modules
#tags:
keywords: Pmodules, software, stable, unstable, deprecated, overlay, overlays, release stage, module, package, packages, library, libraries
last_updated: 07 September 2022
#summary: ""
sidebar: merlin7_sidebar
permalink: /merlin7/pmodules.html
---
# PSI Modules
## PSI Environment Modules
@@ -22,25 +14,25 @@ If you miss any package/versions or a software with a specific missing feature,
To ensure proper software lifecycle management, PModules uses three release stages: unstable, stable, and deprecated.
1. **Unstable Release Stage:**
* Contains experimental or under-development software versions.
* Not visible to users by default. Use explicitly:
* Contains experimental or under-development software versions.
* Not visible to users by default. Use explicitly:
```bash
module use unstable
```
* Software is promoted to **stable** after validation.
* Software is promoted to **stable** after validation.
2. **Stable Release Stage:**
* Default stage, containing fully tested and supported software versions.
* Recommended for all production workloads.
* Default stage, containing fully tested and supported software versions.
* Recommended for all production workloads.
3. **Deprecated Release Stage:**
* Contains software versions that are outdated or discontinued.
* These versions are hidden by default but can be explicitly accessed:
* Contains software versions that are outdated or discontinued.
* These versions are hidden by default but can be explicitly accessed:
```bash
module use deprecated
```
* Deprecated software can still be loaded directly without additional configuration to ensure user transparency.
* Deprecated software can still be loaded directly without additional configuration to ensure user transparency.
## PModules commands

10
docs/merlin7/05-Software-Support/quantum-espresso.md
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@@ -1,11 +1,4 @@
---
title: Quantum Espresso
keywords: Quantum Espresso software, compile
summary: "Quantum Espresso code for electronic-structure calculations and materials modeling at the nanoscale"
sidebar: merlin7_sidebar
toc: false
permalink: /merlin7/quantum-espresso.html
---
# Quantum Espresso
## Quantum ESPRESSO
@@ -135,7 +128,6 @@ module purge
module use Spack unstable
module load nvhpc/25.3 openmpi/5.0.7-e3bf-GH200-gpu fftw/3.3.10-sfpw-omp hdf5/develop-2.0-ztvo nvpl-blas/0.4.0.1-3zpg nvpl-lapack/0.3.0-ymy5 netlib-scalapack/2.2.2-qrhq cmake/3.31.6-5dl7
cd <path to QE source directory>
mkdir build
cd build

9
docs/merlin7/05-Software-Support/spack.md
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@@ -1,11 +1,4 @@
---
title: Spack
keywords: spack, python, software, compile
summary: "Spack the HPC package manager documentation"
sidebar: merlin7_sidebar
toc: false
permalink: /merlin7/spack.html
---
# Spack
For Merlin7 the *package manager for supercomputing* [Spack](https://spack.io/) is available. It is meant to compliment the existing PModules
solution, giving users the opertunity to manage their own software environments.

12
docs/merlin7/99-support/contact.md
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@@ -1,12 +1,4 @@
---
title: Contact
#tags:
keywords: contact, support, snow, service now, mailing list, mailing, email, mail, merlin-admins@lists.psi.ch, merlin-users@lists.psi.ch, merlin users
last_updated: 15. Jan 2025
#summary: ""
sidebar: merlin7_sidebar
permalink: /merlin7/contact.html
---
# Contact
## Support
@@ -16,10 +8,10 @@ Support can be asked through:
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 incident 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).

40
docs/merlin7/99-support/migration-from-merlin6.md
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@@ -1,12 +1,3 @@
---
#tags:
keywords: merlin6, merlin7, migration, fpsync, rsync
#summary: ""
sidebar: merlin7_sidebar
last_updated: 28 May 2025
permalink: /merlin7/migrating.html
---
# Merlin6 to Merlin7 Migration Guide
Welcome to the official documentation for migrating your data from **Merlin6** to **Merlin7**. Please follow the instructions carefully to ensure a smooth and secure transition.
@@ -59,8 +50,8 @@ for further information.
* The **home directory and user data directory have been merged** into the single new home directory`/data/user/$USER`.
* The **experiments directory has been integrated into `/data/project/`**:
* `/data/project/general` contains general Merlin7 projects.
* Other subdirectories are used for large-scale projects such as CLS division, Mu3e, and MeG.
* `/data/project/general` contains general Merlin7 projects.
* Other subdirectories are used for large-scale projects such as CLS division, Mu3e, and MeG.
---
@@ -70,13 +61,15 @@ Before starting the migration, make sure you:
* are **registered on Merlin7**.
* If not yet registered, please do so following [these instructions](../01-Quick-Start-Guide/requesting-accounts.md)
* If not yet registered, please do so following [these instructions](../01-Quick-Start-Guide/requesting-accounts.md)
* **have cleaned up your data to reduce migration time and space usage**.
* **For the user data migration**, ensure your total usage on Merlin6 (`/psi/home`+`/data/user`) is **well below the 1 TB quota** (use the `merlin_quotas` command). Remember:
* **Merlin7 also has a 1 TB quota on your home directory**, and you might already have data there.
* If your usage exceeds this during the transfer, the process might fail.
* **Merlin7 also has a 1 TB quota on your home directory**, and you might already have data there.
* If your usage exceeds this during the transfer, the process might fail.
* No activity should be running / performed on Merlin6 when the transfer process is ongoing.
### Recommended Cleanup Actions
@@ -85,13 +78,13 @@ Before starting the migration, make sure you:
* Archive large, inactive data sets.
* Delete or clean up unused `conda` or `virtualenv` Python environments:
* These are often large and may not work as-is on Merlin7.
* You can export your conda environment description to a file with:
* These are often large and may not work as-is on Merlin7.
* You can export your conda environment description to a file with:
```bash
conda env export -n myenv > $HOME/myenv.yml
```
* Then recreate them later on Merlin7 from these files.
* Then recreate them later on Merlin7 from these files.
> 🧹 For the **user data**, you can always remove more old data **after** migration — it will be copied into `~/merlin6data` and `~/merlin6home` on Merlin7.
@@ -113,10 +106,11 @@ This script will:
* Configure and check that your environment is ready for transferring files via Slurm job.
* **Create two directories:**
* `~/merlin6data` → copy of your old /data/user
* `~/merlin6home` → copy of your old home
* `~/merlin6data` → copy of your old /data/user
* `~/merlin6home` → copy of your old home
> ⚠️ **Important:** If `~/merlin6home` or `~/merlin6data` already exist on Merlin7, the script will exit.
> **Please remove them or contact support**.
If there are issues, the script will:
@@ -159,9 +153,9 @@ If a problem occurs during the migration process:
* 🔍 **Check the job log files** mentioned in the script output. They contain detailed messages that explain what failed and why.
* 🛠️ **Fix the root cause** on the source system. Common issues include:
* Files with incorrect permissions
* Ownership mismatches
* Disk quota exceeded on Merlin7
* Files with incorrect permissions
* Ownership mismatches
* Disk quota exceeded on Merlin7
* 📚 Refer to the [⚠️ Common rsync/fpsync Migration Issues](#common-rsyncfpsync-migration-issues) section below for detailed explanations and solutions.
> ℹ️ **Important:** If `migrate_merlin6data.batch` fails, the migration process will automatically cancel `migrate_merlin6home.batch` to avoid ending in an inconsistent state.
@@ -287,7 +281,7 @@ Further instructions will be sent via email once the owning team is contacted by
* **Cause**: Source files are owned by another user (e.g. root or a collaborator).
* **Solution**:
* Change ownership before migration:
* Change ownership before migration:
```bash
chown -R $USER /path/to/file

6
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View File

@@ -181,10 +181,10 @@ nav:
- merlin6/99-support/known-problems.md
- merlin6/99-support/migration-from-merlin5.md
- merlin6/99-support/troubleshooting.md
- PSI@CSCS:
- cscs-userlab/index.md
- cscs-userlab/transfer-data.md
- MeG:
- meg/index.md
- meg/contact.md
- meg/migration-to-merlin7.md
- PSI@CSCS:
- cscs-userlab/index.md
- cscs-userlab/transfer-data.md