# Configuring Cylc on REANNZ/NeSI platform

**URL:** <https://cylc.discourse.group/t/configuring-cylc-on-reannz-nesi-platform/1259>\
**Category:** Cylc Support\
**Created:** [October 23, 2025, 11:51pm UTC](https://cylc.discourse.group/t/configuring-cylc-on-reannz-nesi-platform/1259 "2025-10-23T23:51:43Z")\
**Posts on this page:** 7\
**Page:** 1

<div class="post-metadata">

**Author:** ![pletzer](https://yyz2.discourse-cdn.com/free1/user_avatar/cylc.discourse.group/pletzer/32/553_2.png) [@pletzer](https://cylc.discourse.group/u/pletzer)\
**Post date:** [October 23, 2025, 11:51pm UTC](https://cylc.discourse.group/t/configuring-cylc-on-reannz-nesi-platform/1259/1 "2025-10-23T23:51:43Z")

</div>

Hi all,

On the new REANNZ platform, the cylc command is no longer available. Users must install Cylc using the Conda commands. I’m trying to configure Cylc. My global.cylc file is

```ini
#!Jinja2
[platforms]
[[mahuika-slurm]]
hosts = login01
job runner = slurm
global init-script = “”"
module load Miniforge3
conda activate /nesi/project/nesi99999/pletzera/environment/cylc-env
“”"
[[[meta]]]
description = “Submit SLURM jobs locally from login node with Conda environment.”
note = “Cylc and all dependencies are loaded via Conda.”

```

I get (note the cylc command was not found). As you can see above I used a “global init-script” to load the Conda environment. I’d be grateful for any pointers.

Thanks in advance. --Alex

```auto

(cylc-env)login03~/cylc_patterns/cylc-src/test$ cylc play -N test

▪ ■ Cylc Workflow Engine 8.6.0
██ Copyright (C) 2008-2025 NIWA
▝▘ & British Crown (Met Office) & Contributors
INFO - Extracting job.sh to /home/pletzera/cylc-run/test/run1/.service/etc/job.sh
INFO - Workflow: test/run1
INFO - Scheduler: url=tcp://login03.hpc.nesi.org.nz:43046 pid=2298870
INFO - Workflow publisher: url=tcp://login03.hpc.nesi.org.nz:43076
INFO - Run: (re)start number=1, log rollover=1
INFO - Cylc version: 8.6.0
INFO - Run mode: live
INFO - Initial point: 1
INFO - Final point: 1
INFO - Cold start from 1
INFO - New flow: 1 (original flow from 1) 2025-10-24T12:48:24
INFO - [1/a:waiting(runahead)] => waiting
INFO - [1/a:waiting] => waiting(queued)
INFO - [1/b:waiting(runahead)] => waiting
INFO - [1/b:waiting] => waiting(queued)
INFO - [1/a:waiting(queued)] => waiting
INFO - [1/b:waiting(queued)] => waiting
INFO - [1/a:waiting] => preparing
INFO - [1/b:waiting] => preparing
INFO - platform: mahuika-slurm - remote init (on login01)
ERROR - platform: mahuika-slurm - initialisation did not complete
COMMAND:
ssh -oBatchMode=yes -oConnectTimeout=10 login01 env 
CYLC_VERSION=8.6.0 bash --login -c ‘exec “$0” “$@”’ cylc 
remote-init mahuika-slurm $HOME/cylc-run/test/run1
RETURN CODE:
127
STDERR:
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
cylc: line 1: exec: cylc: not foundERROR - [jobs-submit cmd] (init login01)
[jobs-submit ret_code] 1
[jobs-submit err] REMOTE INIT FAILED
ERROR - [jobs-submit cmd] (remote init)
[jobs-submit ret_code] 1
ERROR - [1/a/01:preparing] submission failed
INFO - [1/a/01:preparing] => submit-failed
WARNING - [1/a/01:submit-failed] did not complete the required outputs:
⨯ ┆ succeeded
ERROR - [jobs-submit cmd] (init login01)
[jobs-submit ret_code] 1
[jobs-submit err] REMOTE INIT FAILED
ERROR - [jobs-submit cmd] (remote init)
[jobs-submit ret_code] 1
ERROR - [1/b/01:preparing] submission failed
INFO - [1/b/01:preparing] => submit-failed
WARNING - [1/b/01:submit-failed] did not complete the required outputs:
⨯ ┆ succeeded
ERROR - Incomplete tasks:
* 1/a did not complete the required outputs:
⨯ ┆ succeeded
* 1/b did not complete the required outputs:
⨯ ┆ succeeded
CRITICAL - Workflow stalled
WARNING - PT1H stall timer starts NOW

```

---

<div class="post-metadata">

**Author:** ![wxtim](https://yyz2.discourse-cdn.com/free1/user_avatar/cylc.discourse.group/wxtim/32/151_2.png) [@wxtim](https://cylc.discourse.group/u/wxtim)\
**Post date:** [October 24, 2025, 7:27am UTC](https://cylc.discourse.group/t/configuring-cylc-on-reannz-nesi-platform/1259/2 "2025-10-24T07:27:38Z")

</div>

That’s not going to work, because you need Cylc available on your remote platform to read the config to see the global init script.

As part of Cylc we provide a wrapper script designed to handle activating environments on remote machines. The instructions for using that are [here](https://cylc.github.io/cylc-doc/stable/html/installation.html#managing-environments). Let us know how you get on, so we can fine tune the instructions!

---

<div class="post-metadata">

**Author:** ![pletzer](https://yyz2.discourse-cdn.com/free1/user_avatar/cylc.discourse.group/pletzer/32/553_2.png) [@pletzer](https://cylc.discourse.group/u/pletzer)\
**Post date:** [October 30, 2025, 2:20am UTC](https://cylc.discourse.group/t/configuring-cylc-on-reannz-nesi-platform/1259/3 "2025-10-30T02:20:29Z")

</div>

Hi,

Thanks.

I still have issues running slurm tasks on a personal installation of cylc 8.6.0 on REANNZ’s platform. The error is

```auto
login03~/nesi99999$ cat /home/pletzera/cylc-run/slurm/run1/log/job/1/a/01/job-activity.log
[jobs-submit cmd] (init login01)
[jobs-submit ret_code] 1
[jobs-submit err] REMOTE INIT FAILED
[jobs-submit cmd] (remote init)
[jobs-submit ret_code] 1

```

I can ssh to login01 just fine…

My global.cylc file is

```auto
login03~/nesi99999$ cat ~/.cylc/flow/global.cylc
#!Jinja2
[platforms]
    [[mahuika-slurm]]
        hosts = login01
        job runner = slurm

```

The steps to install cylc are below

```auto
login03~/nesi99999$ cat install_cylc.sh 
export CYLC_HOME=/nesi/nobackup/nesi99999/pletzera/envs/cylc
ml Miniforge3
conda create --prefix $CYLC_HOME --yes
conda activate $CYLC_HOME
conda install -c conda-forge cylc-flow --yes
#
# call cylc through a wrapper
#
mkdir $CYLC_HOME/wrapper
# this will save $CYLC_HOME/wrapper/cylc
cylc get-resources cylc $CYLC_HOME/wrapper
chmod +x $CYLC_HOME/wrapper/cylc
cp $CYLC_HOME/wrapper/cylc $CYLC_HOME/wrapper/cylc.bak
sed -i "s|CYLC_HOME_ROOT=\"\${CYLC_HOME_ROOT:-/opt}\"|CYLC_HOME_ROOT=\"\${CYLC_HOME_ROOT:-${CYLC_HOME}}\"|" $CYLC_HOME/wrapper/cylc
# make sure the wrapper is in the PATH
export PATH=$CYLC_HOME/wrapper:$PATH

```

The flow.cylc file is

```auto
login03~/nesi99999$ cat cylc_patterns/cylc-src/slurm/flow.cylc 
[scheduling]
    [[graph]]
        R1 = """
            a & b
        """
[runtime]
    [[a]]
        platform = mahuika-slurm
        execution time limit = PT1M
        script = """
        echo "executing task A..."
        sleep 5
        echo "done with task A..."
        """
        [[[directives]]]
            --ntasks = 1
    [[b]]
        script = """
        echo "executing task B..."
        sleep 2
        echo "done with task B"
        """

```

Thanks in advance for any help…

---

<div class="post-metadata">

**Author:** ![oliver.sanders](https://yyz2.discourse-cdn.com/free1/user_avatar/cylc.discourse.group/oliver.sanders/32/110_2.png) [@oliver.sanders](https://cylc.discourse.group/u/oliver.sanders)\
**Post date:** [October 30, 2025, 11:23am UTC](https://cylc.discourse.group/t/configuring-cylc-on-reannz-nesi-platform/1259/4 "2025-10-30T11:23:15Z")

</div>

Your setup steps look good.

Assuming that the issue is that the `cylc` command cannot be found (the scheduler log might provide more debug info), the issue is likely that the wrapper script is not in the default `$PATH`.

I.E, this puts the wrapper in `$PATH` in your current session, but not in future sessions:

```auto
export PATH=$CYLC_HOME/wrapper:$PATH

```

Maybe copy this into your `.bash_profile` file.

---

<div class="post-metadata">

**Author:** ![pletzer](https://yyz2.discourse-cdn.com/free1/user_avatar/cylc.discourse.group/pletzer/32/553_2.png) [@pletzer](https://cylc.discourse.group/u/pletzer)\
**Post date:** [November 2, 2025, 9:36pm UTC](https://cylc.discourse.group/t/configuring-cylc-on-reannz-nesi-platform/1259/5 "2025-11-02T21:36:06Z")

</div>

Hi Oliver,

Thanks for your help.

I added login02 and login03 to the hosts in global.cylc

```auto
login03~/nesi99999/cylc_patterns/cylc-src/slurm$ cat ~/.cylc/flow/global.cylc
#!Jinja2

[platforms]
    [[mahuika-slurm]]
        hosts = login01,login02,login03
        job runner = slurm

```

and added

```auto
export CYLC_HOME=/nesi/nobackup/nesi99999/pletzera/envs/cylc
export PATH=$CYLC_HOME/wrapper:$PATH

```

to my `~/.bash_profile`.

This got me further but I’m still having an error… Note that I’m unable to clean the workflow, maybe the error is related to

```auto
login03~/nesi99999/cylc_patterns/cylc-src/slurm$ cylc clean slurm
Would clean the following workflows:
  slurm/run1
Remove these workflows (y/n): y
INFO - Cleaning slurm/run1 on install target: mahuika-slurm
INFO - [mahuika-slurm]
    INFO - Removing directory: /home/pletzera/cylc-run/slurm/run1
    INFO - Removing directory: /home/pletzera/cylc-run/slurm/_cylc-install
    INFO - Removing directory: /home/pletzera/cylc-run/slurm
ERROR - Failed to clean slurm/run1
    Error: /home/pletzera/cylc-run/slurm/run1
CylcError: Clean failed

```

Though it seems the directory was removed

```auto
login03~/nesi99999/cylc_patterns/cylc-src/slurm$ ls -ltr /home/pletzera/cylc-run/slurm/run1
ls: cannot access '/home/pletzera/cylc-run/slurm/run1': No such file or directory

```

```auto
login03~/nesi99999/cylc_patterns/cylc-src/slurm$ cylc vip .
$ cylc validate /nesi/nobackup/nesi99999/pletzera/cylc_patterns/cylc-src/slurm
Valid for cylc-8.6.0
$ cylc install /nesi/nobackup/nesi99999/pletzera/cylc_patterns/cylc-src/slurm
INSTALLED slurm/run1 from /nesi/nobackup/nesi99999/pletzera/cylc_patterns/cylc-src/slurm
$ cylc play slurm/run1

 ▪ ■ Cylc Workflow Engine 8.6.0
 ██ Copyright (C) 2008-2025 NIWA
▝▘ & British Crown (Met Office) & Contributors

INFO - Extracting job.sh to /home/pletzera/cylc-run/slurm/run1/.service/etc/job.sh
slurm/run1: login03.hpc.nesi.org.nz PID=1687313
login03~/nesi99999/cylc_patterns/cylc-src/slurm$ cylc cat-log slurm 
2025-11-03T10:32:56+13:00 INFO - Workflow: slurm/run1
2025-11-03T10:32:56+13:00 INFO - Scheduler: url=tcp://login03.hpc.nesi.org.nz:43094 pid=1687313
2025-11-03T10:32:56+13:00 INFO - Workflow publisher: url=tcp://login03.hpc.nesi.org.nz:43027
2025-11-03T10:32:56+13:00 INFO - Run: (re)start number=1, log rollover=1
2025-11-03T10:32:56+13:00 INFO - Cylc version: 8.6.0
2025-11-03T10:32:56+13:00 INFO - Run mode: live
2025-11-03T10:32:56+13:00 INFO - Initial point: 1
2025-11-03T10:32:56+13:00 INFO - Final point: 1
2025-11-03T10:32:56+13:00 INFO - Cold start from 1
2025-11-03T10:32:56+13:00 INFO - New flow: 1 (original flow from 1) 2025-11-03T10:32:56
2025-11-03T10:32:56+13:00 INFO - [1/a:waiting(runahead)] => waiting
2025-11-03T10:32:56+13:00 INFO - [1/a:waiting] => waiting(queued)
2025-11-03T10:32:56+13:00 INFO - [1/b:waiting(runahead)] => waiting
2025-11-03T10:32:56+13:00 INFO - [1/b:waiting] => waiting(queued)
2025-11-03T10:32:56+13:00 INFO - [1/a:waiting(queued)] => waiting
2025-11-03T10:32:56+13:00 INFO - [1/b:waiting(queued)] => waiting
2025-11-03T10:32:56+13:00 INFO - [1/a:waiting] => preparing
2025-11-03T10:32:56+13:00 INFO - [1/b:waiting] => preparing
2025-11-03T10:32:56+13:00 INFO - platform: mahuika-slurm - remote init (on login01)
2025-11-03T10:32:58+13:00 INFO - [1/b/01:preparing] submitted to localhost:background[1687565]
2025-11-03T10:32:58+13:00 INFO - [1/b/01:preparing] => submitted
2025-11-03T10:33:03+13:00 ERROR - platform: mahuika-slurm - initialisation did not complete
    COMMAND:
        ssh -oBatchMode=yes -oConnectTimeout=10 login01 env \
            CYLC_VERSION=8.6.0 bash --login -c 'exec "$0" "$@"' cylc \
            remote-init mahuika-slurm $HOME/cylc-run/slurm/run1
    RETURN CODE:
        0
    STDOUT:
        REMOTE INIT FAILED
        Unexpected key directory exists: /home/pletzera/cylc-run/slurm/run1/.service/client_public_keys Check global.cylc install target is configured correctly for this platform.
    STDERR:
        tput: No value for $TERM and no -T specified
        tput: No value for $TERM and no -T specified
        tput: No value for $TERM and no -T specified
        tput: No value for $TERM and no -T specified
        tput: No value for $TERM and no -T specified
2025-11-03T10:33:03+13:00 ERROR - [jobs-submit cmd] (init login01)
    [jobs-submit ret_code] 1
    [jobs-submit err] REMOTE INIT FAILED
2025-11-03T10:33:03+13:00 ERROR - [jobs-submit cmd] (remote init)
    [jobs-submit ret_code] 1
2025-11-03T10:33:03+13:00 ERROR - [1/a/01:preparing] submission failed
2025-11-03T10:33:03+13:00 INFO - [1/a/01:preparing] => submit-failed
2025-11-03T10:33:03+13:00 WARNING - [1/a/01:submit-failed] did not complete the required outputs:
    ⨯ ┆ succeeded
2025-11-03T10:33:04+13:00 INFO - [1/b/01:submitted] => running
2025-11-03T10:33:06+13:00 INFO - [1/b/01:running] => succeeded
2025-11-03T10:33:06+13:00 ERROR - Incomplete tasks:
    * 1/a did not complete the required outputs:
      ⨯ ┆ succeeded
2025-11-03T10:33:06+13:00 CRITICAL - Workflow stalled
2025-11-03T10:33:06+13:00 WARNING - PT1H stall timer starts NOW

```

---

<div class="post-metadata">

**Author:** ![dpmatthews](https://yyz2.discourse-cdn.com/free1/user_avatar/cylc.discourse.group/dpmatthews/32/26_2.png) [@dpmatthews](https://cylc.discourse.group/u/dpmatthews)\
**Post date:** [November 3, 2025, 8:38am UTC](https://cylc.discourse.group/t/configuring-cylc-on-reannz-nesi-platform/1259/6 "2025-11-03T08:38:40Z")

</div>

Your `mahuika-slurm` platform uses the same filesystem as the Cylc scheduler host so you need to set `install target = localhost`, i.e. change your `global.cylc` to be:

```auto
[platforms]
    [[mahuika-slurm]]
        hosts = login01,login02,login03
        job runner = slurm
        install target = localhost

```

See [Platform Configuration — Cylc 8.6.0 documentation](https://cylc.github.io/cylc-doc/stable/html/reference/config/writing-platform-configs.html#example-platform-configurations)

---

<div class="post-metadata">

**Author:** ![pletzer](https://yyz2.discourse-cdn.com/free1/user_avatar/cylc.discourse.group/pletzer/32/553_2.png) [@pletzer](https://cylc.discourse.group/u/pletzer)\
**Post date:** [November 5, 2025, 3:42am UTC](https://cylc.discourse.group/t/configuring-cylc-on-reannz-nesi-platform/1259/7 "2025-11-05T03:42:22Z")

</div>

Thanks Oliver. That worked!