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---
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#tags:
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keywords: merlin6, merlin7, migration, fpsync, rsync
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#summary: ""
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sidebar: merlin7_sidebar
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last_updated: 28 May 2025
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permalink: /merlin7/migrating.html
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---
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# Merlin6 to Merlin7 Migration Guide
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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.
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## 📅 Migration Schedule
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### Phase 1: Users without Projects — **Deadline: July 11**
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If you **do not belong to any Merlin project**, i.e for
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* Users not in any group project (`/data/projects/general`)
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* Users not in BIO, MEG, Mu3e
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* Users not part of PSI-owned private Merlin nodes (ASA, MEG, Mu3e)
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You must complete your migration **before July 11**. You just need to migrate your personal */data/user/$USER* and */home/psi/$USER* directories.
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Users are responsible for initiating and completing the migration process as lined out below.
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Contact the Merlin support team [merlin-admins@lists.psi.ch](mailto:merlin-admins@lists.psi.ch) if you need help.
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> ⚠️ In this phase, **it's important that you don't belong to any project**.
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> Once the migration is finished, **access to Merlin6 will be no longer possible.**
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Please refer to the [Phase 1: Step-by-Step Migration Instructions](/merlin7/migrating.html#phase-1-step-by-step-migration-instructions) section
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for detailed information about user data migration.
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### Phase 2: Project Members and Owners — **Start Before August 1**
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For users in active projects:
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* Project **owners and members will be contacted by the Merlin admins**.
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* Migration will be **scheduled individually per project**.
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* Expect contact **before August 1**.
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> ⚠️ In this phase, **data and home directories of group owners and members will be also requested to be migrated in parallel.**
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Please refer to the [Phase 2: Migration Instructions](/merlin7/migrating.html#phase-2-migration-instructions) section
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for further information.
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---
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## Directory Structure Changes
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### Merlin6 vs Merlin7
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| Cluster | Home Directory | User Data Directory | Projects | Experiments |
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| ------- | :----------------- | :------------------ | -------------- | ----------------- |
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| merlin6 | /psi/home/`$USER` | /data/user/`$USER` | /data/project/ | /data/experiments |
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| merlin7 | /data/user/`$USER` | /data/user/`$USER` | /data/project/ | /data/project/ |
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* The **home directory and user data directory have been merged** into the single new home directory`/data/user/$USER`.
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* The **experiments directory has been integrated into `/data/project/`**:
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* `/data/project/general` contains general Merlin7 projects.
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* Other subdirectories are used for large-scale projects such as CLS division, Mu3e, and MeG.
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---
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## 📋 Prerequisites and Preparation
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Before starting the migration, make sure you:
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* are **registered on Merlin7**.
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* If not yet registered, please do so following [these instructions](../merlin7/request-account.html)
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* **have cleaned up your data to reduce migration time and space usage**.
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* **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:
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* **Merlin7 also has a 1 TB quota on your home directory**, and you might already have data there.
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* If your usage exceeds this during the transfer, the process might fail.
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### Recommended Cleanup Actions
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* Remove unused files and datasets.
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* Archive large, inactive data sets.
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* Delete or clean up unused `conda` or `virtualenv` Python environments:
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* These are often large and may not work as-is on Merlin7.
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* You can export your conda environment description to a file with:
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```bash
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conda env export -n myenv > $HOME/myenv.yml
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```
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* Then recreate them later on Merlin7 from these files.
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> 🧹 For the **user data**, you can always remove more old data **after** migration — it will be copied into `~/merlin6data` and `~/merlin6home` on Merlin7.
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---
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## Phase 1: Step-by-Step Migration Instructions
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### Step 1: Run `merlin7_migration.setup`
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Log into any **Merlin6 login node** (`merlin-l-001.psi.ch`, `merlin-l-002.psi.ch`, `merlin-l-01.psi.ch`) and run:
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```bash
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merlin7_migration.setup
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```
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This script will:
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* Check that you have an account on Merlin7.
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* Configure and check that your environment is ready for transferring files via Slurm job.
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* **Create two directories:**
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* `~/merlin6data` → copy of your old /data/user
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* `~/merlin6home` → copy of your old home
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> ⚠️ **Important:** If `~/merlin6home` or `~/merlin6data` already exist on Merlin7, the script will exit.
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> **Please remove them or contact support**.
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If there are issues, the script will:
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* Print clear diagnostic output
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* Give you some hints to resolve the issue
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If you are stuck, email: [merlin-admins@lists.psi.ch](mailto:merlin-admins@lists.psi.ch)
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---
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### Step 2: Run `merlin7_migration.start`
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After setup completes, start the migration by running:
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```bash
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merlin7_migration.start
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```
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This script will:
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* Check the status of your quota on Merlin6.
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* Submit **SLURM batch jobs** to the **`xfer`** partition
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* Queue two jobs:
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* `migrate_merlin6data.batch` (data dir)
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* `migrate_merlin6home.batch` (home dir)
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* This job will only start if `migrate_merlin6data.batch` has successfully
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finished.
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* Automatically track the job IDs
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* Print log file locations for the different jobs
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> ⚠️ **Once both transfers succeed, your access to Merlin6 will be revoked.**
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> Do **not** attempt to reconnect to Merlin6 after this.
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#### ❗ If Something Goes Wrong
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If a problem occurs during the migration process:
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* 🔍 **Check the job log files** mentioned in the script output. They contain detailed messages that explain what failed and why.
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* 🛠️ **Fix the root cause** on the source system. Common issues include:
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* Files with incorrect permissions
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* Ownership mismatches
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* Disk quota exceeded on Merlin7
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* 📚 Refer to the [⚠️ Common rsync/fpsync Migration Issues](/merlin7/migrating.html#%EF%B8%8F--common-rsyncfpsync-migration-issues) section below for detailed explanations and solutions.
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> ℹ️ **Important:** If `migrate_merlin6data.batch` fails, the migration process will automatically cancel `migrate_merlin6home.batch` to avoid ending in an inconsistent state.
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Once the problem is resolved, simply re-run the `merlin7_migration.start` script to resume the migration.
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---
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### Step 3: Monitor Transfer Jobs
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To monitor your transfer jobs, run:
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```bash
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squeue -M merlin6 -u $USER -p xfer
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```
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Check the output to ensure your jobs are:
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* Running (`R`) or completed (`CG` or removed from queue)
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* Not failed (`F`, `TO`, or stuck)
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You can also check logs (as printed by the script) to verify job completion.
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> ✅ When `/data/user/$USER` and `/psi/home/$USER` on Merlin6 are no longer accessible, migration is complete.
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---
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### Examples
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#### Setup the Migration
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```bash
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merlin7_migration.setup
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```
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*Expected output:*
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```bash
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✅ login002.merlin7.psi.ch
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✅ `$USER` is a member of svc-cluster_merlin7
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✅ Skipping key generation
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✅ SSH key already added to agent.
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✅ SSH ID successfully copied to login00[1|2].merlin7.psi.ch.
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✅ Test successful.
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✅ /data/software/xfer_logs/caubet_m created.
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✅ ~/merlin6data directory created.
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✅ ~/merlin6home directory created.
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```
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#### Start the Migration
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```bash
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merlin7_migration.start
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```
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*Expected output:*
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```bash
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(base) ❄ [caubet_m@merlin-l-001:/data/software/admin/scripts/merlin-user-tools/alps(master)]# ./merlin7_migration.start
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✅ Quota check passed.
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Used: 512 GB, 234001 files
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###################################################
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Submitting transfer jobs to Slurm
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Job logs can be found here:
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➡️ Directory '/data/user/caubet_m' does NOT have 000 permissions. Transfer pending, continuing...
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✅ Submitted DATA_MIGRATION job: 24688554. Sleeping 3 seconds...
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- /data/user transfer logs:
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- /data/software/xfer_logs/caubet_m/data-24688554.out
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- /data/software/xfer_logs/caubet_m/data-24688554.err
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➡️ Directory '/psi/home/caubet_m' does NOT have 000 permissions. Transfer pending, continuing...
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✅ Submitted HOME_MIGRATION job with dependency on 24688554: 24688555. Sleeping 3 seconds...
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- /psi/home transfer logs:
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- /data/software/xfer_logs/caubet_m/home-24688555.out
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- /data/software/xfer_logs/caubet_m/home-24688555.err
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✅ You can start manually a monitoring window with:
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tmux new-session -d -s "xfersession" "watch 'squeue -M merlin6 -u caubet_m -p xfer'"
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tmux attach -t "xfersession"
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✅ FINISHED - PLEASE CHECK JOB TRANSFER PROGRESS
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```
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#### Monitor Progress
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```bash
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squeue -M merlin6 -u $USER -p xfer
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```
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*Output:*
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```bash
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$ squeue -M merlin6 -u $USER -p xfer
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CLUSTER: merlin6
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JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
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24688581 xfer HOME_MIG caubet_m PD 0:00 1 (Dependency)
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24688580 xfer DATA_MIG caubet_m R 0:22 1 merlin-c-017
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```
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---
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## Phase 2: Migration Instructions
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Please refer to the [Prerequisites and Preparation](/merlin7/migrating.html#-prerequisites-and-preparation) section for initial setup steps.
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Further instructions will be sent via email once the owning team is contacted by the Merlin administrators.
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---
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## ⚠️ Common `rsync`/`fpsync` Migration Issues
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### File Permission Denied
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* **Cause**: Files or directories are not readable by the user running the transfer.
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* **Solution**: Fix source-side permissions:
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```bash
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chmod -R u+rX /path/to/file_or_dir
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```
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### Ownership Mismatches
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* **Cause**: Source files are owned by another user (e.g. root or a collaborator).
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* **Solution**:
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* Change ownership before migration:
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```bash
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chown -R $USER /path/to/file
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```
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### Special Files (e.g. device files, sockets)
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* **Cause**: `rsync` tries to copy UNIX sockets, device files, or FIFOs.
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* **Effect**: Errors or incomplete copies.
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* **Solution**: Avoid transferring such files entirely (by deleting them).
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### Exceeded Disk Quota
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* **Cause**: Combined size of existing + incoming data exceeds 1 TB quota on Merlin7.
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* **Effect**: Transfer stops abruptly.
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* **Solution**: Clean up or archive non-essential data before migration.
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### Very Small Files or Large Trees → Many Small rsync Calls
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* **Cause**: Directory with thousands/millions of small files.
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* **Effect**: Transfer is slow or hits process limits.
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* **Solution**: Consider archiving to `.tar.gz` before transferring:
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```bash
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tar -czf myenv.tar.gz myenv/
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```
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---
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## Need Help?
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If something doesn't work:
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* Re-run the scripts and check the logs carefully.
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* Use `less`, `cat`, or `tail -f` to view your job logs.
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* Contact the Merlin support team: 📧 [merlin-admins@lists.psi.ch](mailto:merlin-admins@lists.psi.ch)
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> We are here to help you migrate safely and efficiently.
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