# Can we add uqstat to vk83 payu conda?
**URL:** https://forum.access-hive.org.au/t/can-we-add-uqstat-to-vk83-payu-conda/5156
**Category:** Technical
**Tags:** help
**Created:** [2 September 2025 01:33 UTC](https://forum.access-hive.org.au/t/can-we-add-uqstat-to-vk83-payu-conda/5156 "2025-09-02T01:33:34Z")
**Posts on this page:** 13
**Page:** 1
### Author:  [@adele-morrison](https://forum.access-hive.org.au/u/adele-morrison)
#### Post date: [2 September 2025 01:33 UTC](https://forum.access-hive.org.au/t/can-we-add-uqstat-to-vk83-payu-conda/5156/1 "2025-09-02T01:33:34Z")
I am having trouble doing both:
```auto
module use /g/data/vk83/modules
module load payu
```
and
```auto
module use /g/data/xp65/public/modules
module load nci-scripts
```
at the same time, so I can `payu run` and `uqstat` in the same terminal.
@Aidan suggests perhaps the best solution to this is to add nci-scripts to the payu conda environment.
---
### Author:  [@Aidan](https://forum.access-hive.org.au/u/Aidan)
#### Post date: [2 September 2025 04:48 UTC](https://forum.access-hive.org.au/t/can-we-add-uqstat-to-vk83-payu-conda/5156/2 "2025-09-02T04:48:23Z")
---
### Author:  [@Aidan](https://forum.access-hive.org.au/u/Aidan)
#### Post date: [2 September 2025 04:55 UTC](https://forum.access-hive.org.au/t/can-we-add-uqstat-to-vk83-payu-conda/5156/3 "2025-09-02T04:55:26Z")
@adele-morrison can you paste in the text of the error you got when you tried to do this?
I loaded both and had no issue running either `nqstat` or `payu`
```plaintext
$ module use /g/data/vk83/modules
$ module load payu
Loading payu/1.1.7
Loading requirement: singularity
$ module use /g/data/xp65/public/modules
$ module load nci-scripts
$ payu -h
usage: payu [-h] [--version]
{archive,branch,build,checkout,clone,collate,ghsetup,init,list,profile,push,run,setup,sweep,sync} ...
positional arguments:
{archive,branch,build,checkout,clone,collate,ghsetup,init,list,profile,push,run,setup,sweep,sync}
options:
-h, --help show this help message and exit
--version show program's version number and exit
$ nqstat
Job ID S Proj User Queue Job Name Used Request CPUs CPU%
----------------------------------------------------------------------------------
148497993 R xx99 xx9999 normalbw sys-dashboard- 05:10:03 08:00:00 1 1
148499836 R xx99 xx9999 normalbw jupyter-lab 04:50:29 08:00:00 8 0
```
---
### Author:  [@Aidan](https://forum.access-hive.org.au/u/Aidan)
#### Post date: [2 September 2025 06:48 UTC](https://forum.access-hive.org.au/t/can-we-add-uqstat-to-vk83-payu-conda/5156/4 "2025-09-02T06:48:23Z")
Doh! I typed `nqstat` instead of `uqstat`.
So now I do get an error. Is it the same as yours @adele-morrison?
```txt
$ module use /g/data/vk83/modules
$ module load payu
Loading payu/1.1.7
Loading requirement: singularity
$ module use /g/data/xp65/public/modules
$ module load nci-scripts
$ payu -h
usage: payu [-h] [--version]
{archive,branch,build,checkout,clone,collate,ghsetup,init,list,profile,push,run,setup,sweep,sync} ...
positional arguments:
{archive,branch,build,checkout,clone,collate,ghsetup,init,list,profile,push,run,setup,sweep,sync}
options:
-h, --help show this help message and exit
--version show program's version number and exit
$ uqstat
/g/data/xp65/public/apps/med_conda_scripts/analysis3.d/bin/python: line 121: /g/data/vk83/apps/base_conda/envs/analysis3-25.07/bin/python: No such file or directory
$
```
---
### Author:  [@adele-morrison](https://forum.access-hive.org.au/u/adele-morrison)
#### Post date: [2 September 2025 09:57 UTC](https://forum.access-hive.org.au/t/can-we-add-uqstat-to-vk83-payu-conda/5156/5 "2025-09-02T09:57:03Z")
Yep, same error. payu seems to work fine, but uqstat does not work.
---
### Author:  [@Aidan](https://forum.access-hive.org.au/u/Aidan)
#### Post date: [3 September 2025 07:14 UTC](https://forum.access-hive.org.au/t/can-we-add-uqstat-to-vk83-payu-conda/5156/6 "2025-09-03T07:14:54Z")
The short answer is that they’re both using `conda` python environments that are not playing well together.
This is a solved problem for the version of `payu` in `payu/dev`, and we’ll shortly be releasing a new version of `payu` that will also not have this problem
```auto
$ module use /g/data/xp65/public/modules
$ module load nci-scripts
$ uqstat -h
usage: uqstat [-h] [--historical] [--format {table,csv,json}] [--project PROJECT] [--comment]
Print more detailed information from qstat
Returns the following columns for each job:
project: NCI project the job was submitted under
job_name: Name of the job
queue: Queue the job was submitted to
state: Current state - 'Q' in queue, 'R' running, 'H' held, 'E' finished
ncpus: Number of cpus requested
walltime: Walltime the job has run for so far
su: SU cost of the job so far
mem_pct: Percent of the memory request used
cpu_pct: Percent of time CPUs have been active
qtime: Time the job spent in the queue before starting
If 'mem_pct' is below 80% make sure you're not requesting too much memory (4GB
per CPU or less is fine)
If 'cpu_pct' is below 80% and you're requesting more than one CPU make sure
your job is making proper use of parallelisation
options:
-h, --help show this help message and exit
--historical, -x Show historical info
--format {table,csv,json}, -f {table,csv,json}
Output format
--project PROJECT, -P PROJECT
Show all jobs in a project
--comment, -c Show PBS queue comment
$ module use /g/data/vk83/prerelease/modules/
$ module load payu
Loading payu/dev-20250828T223708Z-0fd643d
Loading requirement: singularity
$ uqstat -h
usage: uqstat [-h] [--historical] [--format {table,csv,json}] [--project PROJECT] [--comment]
Print more detailed information from qstat
Returns the following columns for each job:
project: NCI project the job was submitted under
job_name: Name of the job
queue: Queue the job was submitted to
state: Current state - 'Q' in queue, 'R' running, 'H' held, 'E' finished
ncpus: Number of cpus requested
walltime: Walltime the job has run for so far
su: SU cost of the job so far
mem_pct: Percent of the memory request used
cpu_pct: Percent of time CPUs have been active
qtime: Time the job spent in the queue before starting
If 'mem_pct' is below 80% make sure you're not requesting too much memory (4GB
per CPU or less is fine)
If 'cpu_pct' is below 80% and you're requesting more than one CPU make sure
your job is making proper use of parallelisation
options:
-h, --help show this help message and exit
--historical, -x Show historical info
--format {table,csv,json}, -f {table,csv,json}
Output format
--project PROJECT, -P PROJECT
Show all jobs in a project
--comment, -c Show PBS queue comment
$ payu -h
usage: payu [-h] [--version]
{archive,branch,build,checkout,clone,collate,ghsetup,init,list,profile,push,run,setup,sweep,sync} ...
positional arguments:
{archive,branch,build,checkout,clone,collate,ghsetup,init,list,profile,push,run,setup,sweep,sync}
options:
-h, --help show this help message and exit
--version show program's version number and exit
$
```
I will update this topic when there is a new released version of `payu` that works as well, but you should be fine to use `payu/dev` in the mean time if you’re feeling adventurous.
---
### Author:  [@atteggiani](https://forum.access-hive.org.au/u/atteggiani)
#### Post date: [3 September 2025 08:31 UTC](https://forum.access-hive.org.au/t/can-we-add-uqstat-to-vk83-payu-conda/5156/7 "2025-09-03T08:31:02Z")
Just a bit more context on this.
The issue is not (or at least not only) related to the `payu` ennvironment.
I get a similar error without any module loaded (I enabled debug logs with `CMS_CONDA_DEBUG_SCRIPTS=1`):
```sh
$ module purge
$ module use /g/data/xp65/public/modules
$ module load nci-scripts
$ CMS_CONDA_DEBUG_SCRIPTS=1 uqstat -h
wrapper_bin = /g/data/xp65/public/apps/med_conda_scripts/analysis3-25.08.d/bin
conf_file = /g/data/xp65/public/apps/med_conda_scripts/analysis3-25.08.d/bin/launcher_conf.sh
PROG_ARGS = /g/data/xp65/public/apps/nci_scripts/uqstat
cmd_to_run = /g/data/xp65/public/apps/med_conda_scripts/analysis3.d/bin/python /g/data/xp65/public/apps/nci_scripts/uqstat
CONTAINER_OVERLAY_PATH after override check =
SINGULARITYENV_PREPEND_PATH= /g/data/xp65/public/apps/nci_scripts/:/home/565/dm5220/.local/bin:/g/data3/tm70/dm5220/projects/bin:/scratch/tm70/dm5220/micromamba/condabin:/opt/pbs/default/bin:/opt/nci/bin:/opt/bin:/opt/Modules/v4.3.0/bin:/opt/pbs/default/bin
overlay_args= --overlay=
binding args= /etc,/half-root,/local,/ram,/run,/system,/usr,/var/lib/sss,/var/run/munge,/sys/fs/cgroup,/iointensive
Singularity invocation: /opt/singularity/bin/singularity -s exec --bind /etc,/half-root,/local,/ram,/run,/system,/usr,/var/lib/sss,/var/run/munge,/sys/fs/cgroup,/iointensive --overlay= /g/data/xp65/public/apps/med_conda/etc/base.sif /g/data/xp65/public/apps/med_conda_scripts/analysis3.d/bin/python /g/data/xp65/public/apps/nci_scripts/uqstat
wrapper_bin = /g/data/xp65/public/apps/med_conda_scripts/analysis3-25.08.d/bin
conf_file = /g/data/xp65/public/apps/med_conda_scripts/analysis3-25.08.d/bin/launcher_conf.sh
PROG_ARGS = /g/data/xp65/public/apps/nci_scripts/uqstat
cmd_to_run = /g/data/xp65/public/apps/med_conda_scripts/analysis3.d/bin/python /g/data/xp65/public/apps/nci_scripts/uqstat
CONTAINER_OVERLAY_PATH after override check =
Short circuit detected, running: exec -a /g/data/xp65/public/apps/med_conda_scripts/analysis3.d/bin/python /home/565/dm5220/miniconda3/bin/conda/envs/analysis3-25.08/bin/python /g/data/xp65/public/apps/nci_scripts/uqstat
/g/data/xp65/public/apps/med_conda_scripts/analysis3.d/bin/python: line 121: /home/565/dm5220/miniconda3/bin/conda/envs/analysis3-25.08/bin/python: Not a directory
/g/data/xp65/public/apps/med_conda_scripts/analysis3.d/bin/python: line 121: exec: /home/565/dm5220/miniconda3/bin/conda/envs/analysis3-25.08/bin/python: cannot execute: Not a directory
```
The error is related to [this issue](https://github.com/ACCESS-NRI/ACCESS-Analysis-Conda/issues/260).
The `/g/data/xp65/public/apps/med_conda_scripts/analysis3.d/bin/python` script at line 121 has:
```py
121 exec -a "${0}" "${cmd_to_run[@]}"
```
which, from lines 109 and 119:
```py
109 export CONDA_BASE="${CONDA_BASE_ENV_PATH}/envs/${myenv}"
```
```py
119 cmd_to_run[0]="${CONDA_BASE}/bin/${cmd_to_run[0]##*/}"
```
can be expanded as:
```py
121(expanded) exec -a "${0}" "${CONDA_BASE_ENV_PATH}/envs/${myenv}/bin/${cmd_to_run[0]##*/}" ${cmd_to_run[@]:1}
```
From the output errors, it can be seen that `CONDA_BASE_ENV_PATH` gets evaluated to my custom `conda` directory (`/home/565/dm5220/miniconda3/bin/conda`) in my case, and to the `payu` conda directory (`/g/data/vk83/apps/base_conda`) when the `payu` module is loaded.
This should not happen and, instead, `CONDA_BASE_ENV_PATH` should always be evaluated to the `conda/analysis3` conda env directory `/g/data/xp65/public/apps/med_conda/` (or whatever the directory with the current `conda/analysis` environment within the singularity container is)
@rbeucher
---
### Author:  [@rbeucher](https://forum.access-hive.org.au/u/rbeucher)
#### Post date: [3 September 2025 09:32 UTC](https://forum.access-hive.org.au/t/can-we-add-uqstat-to-vk83-payu-conda/5156/8 "2025-09-03T09:32:45Z")
I am starting to wonder if it would be simpler to put it in the container…
---
### Author:  [@Aidan](https://forum.access-hive.org.au/u/Aidan)
#### Post date: [3 September 2025 23:43 UTC](https://forum.access-hive.org.au/t/can-we-add-uqstat-to-vk83-payu-conda/5156/9 "2025-09-03T23:43:33Z")
---
### Author:  [@Aidan](https://forum.access-hive.org.au/u/Aidan)
#### Post date: [3 September 2025 23:45 UTC](https://forum.access-hive.org.au/t/can-we-add-uqstat-to-vk83-payu-conda/5156/10 "2025-09-03T23:45:00Z")
@atteggiani has pointed out this is a broader problem. He is tracking that, so he will update the topic when there are relevant changes available.
---
### Author:  [@atteggiani](https://forum.access-hive.org.au/u/atteggiani)
#### Post date: [20 October 2025 00:52 UTC](https://forum.access-hive.org.au/t/can-we-add-uqstat-to-vk83-payu-conda/5156/11 "2025-10-20T00:52:22Z")
This problem should be fixed now.
Could you please confirm @adele-morrison?
---
### Author:  [@adele-morrison](https://forum.access-hive.org.au/u/adele-morrison)
#### Post date: [20 October 2025 03:58 UTC](https://forum.access-hive.org.au/t/can-we-add-uqstat-to-vk83-payu-conda/5156/12 "2025-10-20T03:58:41Z")
Yes I can confirm there are no more errors, we can now use payu and uqstat simultaneously! Thanks @atteggiani !
---
### Author:  [@atteggiani](https://forum.access-hive.org.au/u/atteggiani)
#### Post date: [20 October 2025 05:03 UTC](https://forum.access-hive.org.au/t/can-we-add-uqstat-to-vk83-payu-conda/5156/13 "2025-10-20T05:03:04Z")