# From bash to AiiDA

**URL:** <https://aiida.discourse.group/t/from-bash-to-aiida/752>\
**Category:** New to AiiDA\
**Created:** [July 15, 2026, 9:17am UTC](https://aiida.discourse.group/t/from-bash-to-aiida/752 "2026-07-15T09:17:36Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![hothello](https://yyz2.discourse-cdn.com/free1/user_avatar/aiida.discourse.group/hothello/32/430_2.png) [@hothello](https://aiida.discourse.group/u/hothello)\
**Post date:** [July 15, 2026, 9:17am UTC](https://aiida.discourse.group/t/from-bash-to-aiida/752/1 "2026-07-15T09:17:36Z")

</div>

Hello, I need a bit of help for getting started with AiiDA. I want to manage a simple workflow which is composed of three steps:

```bash
#!/bin/bash

basename="csh_s06_03"

# 1. custom python tool
python3 /home/aiida/cash/scripts/cash_create.py -n 3 3 2 -c 1.2 0.1 1 -w 0.005 -at -f ${basename}.lt -f1 /home/aiida/cash/lt/csh_header.lt -f2 /home/aiida/cash/lt/csh_simulation.lt

# 2. Render with Moltemplate
moltemplate.sh ${basename}.lt

# 3. Run the MD simulation with LAMMPS
mpirun -np 4 lmp__22Jul2 -in ${basename}.in -l ${basename}.log

```

I am using AiiDA version 2.8.0 in a docker container (`aiidateam/aiida-core-with-services:latest`) with persistent storage. I set up the following computers:

> **verdi computer list**
>
> ```auto
> (base) aiida@916a9ff68b01:~$ verdi computer show localhost
> --------------------------- ------------------------------------
> Label localhost
> PK 1
> UUID e66ac2f8-ad3c-407b-b94e-9e4837ae1e6d
> Description container computer
> Hostname localhost
> Transport type core.local
> Scheduler type core.direct
> Work directory /home/aiida/aiida_run/
> Shebang #!/bin/bash
> Mpirun command mpirun -np {tot_num_mpiprocs}
> Default #procs/machine 4
> Default memory (kB)/machine
> Prepend text
> Append text
> --------------------------- ------------------------------------
> (base) aiida@916a9ff68b01:~$ verdi computer show caska
> --------------------------- ------------------------------------
> Label caska
> PK 3
> UUID dfe74fac-7163-45f9-9c2a-ef763ab6db89
> Description Otello's laptop
> Hostname caska
> Transport type core.ssh
> Scheduler type core.direct
> Work directory /home/otello/material_solutions/science/aiida
> Shebang #!/bin/bash
> Mpirun command mpirun -np {tot_num_mpiprocs}
> Default #procs/machine 4
> Default memory (kB)/machine
> Prepend text
> Append text
> --------------------------- ------------------------------------
> 
> ```

and registered the following codes:

> **verdi code list**
>
> ```auto
> (base) aiida@916a9ff68b01:~$ verdi code show 1
> -------------------------- ------------------------------------
> PK 1
> UUID c07cb6af-789a-403e-b4d8-1a3a8a40c8fa
> Type core.code.installed
> Label lmp_22Jul25
> Description Local copy of LAMMPS
> Computer caska (caska), pk: 3
> Default `CalcJob` plugin aiida-lammps
> Escape using double quotes False
> Run with MPI
> Prepend script
> Append script
> Filepath executable /usr/local/bin/lmp_22Jul25_update4
> -------------------------- ------------------------------------
> (base) aiida@916a9ff68b01:~$ verdi code show 2
> -------------------------- ------------------------------------
> PK 2
> UUID 7e0d2e14-f7f2-47ac-9436-c454cc37f0db
> Type core.code.installed
> Label moltemplate
> Description Moltemplate on caska
> Computer caska (caska), pk: 3
> Default `CalcJob` plugin aiida-shell
> Escape using double quotes False
> Run with MPI
> Prepend script export PATH="$PATH:/home/otello/material_solutions/software/moltemplate/moltemplate:/home/otello/material_solutions/software/moltemplate/moltemplate/scripts"
> Append script
> Filepath executable /home/otello/material_solutions/software/moltemplate/moltemplate/scripts/moltemplate.sh
> -------------------------- ------------------------------------
> (base) aiida@916a9ff68b01:~$ verdi code show 3
> -------------------------- ------------------------------------
> PK 3
> UUID fd989c0a-c650-40d2-84db-f77ec2bbaf00
> Type core.code.portable
> Label cash_create
> Description tools to create C(A)SH structures with arbitrary composition
> Default `CalcJob` plugin core.shell
> Escape using double quotes False
> Run with MPI
> Prepend script
> Append script
> Filepath executable cash_create.py
> -------------------------- ------------------------------------
> 
> ```

Now, I started writing an AiiDA script based on `aiida-shell` implementing the first step, but it fails with the following error:

```auto
aiida.common.exceptions.NotExistent: No computer has been set for this calculation

```

Here is my script:

> **workflow01.py**
>
> ```python
> from aiida.orm import Float, Int, Str, SinglefileData, load_computer, load_code
> from aiida_shell import launch_shell_job
> from aiida import load_profile
> 
> load_profile()
> 
> code_cash_create = load_code('cash_create')
> 
> basename = 'csh_s06_03'
> 
> results, node = launch_shell_job(
> code_cash_create,
> arguments = (
> '-n {nx} {ny} {nz}'
> ' -c {ca_si_ratio} {al_si_ratio} {water_content}'
> ' -w {tolerance}'
> ' -at'
> ' -f {basename}.lt'
> ' -f1 {file_header}'
> ' -f2 {file_run}'
> ),
> nodes = {
> 'nx': Int(3),
> 'ny': Int(3),
> 'nz': Int(2),
> 'ca_si_ratio': Float(1.2),
> 'al_si_ratio': Float(0.1),
> 'water_content': Float(1),
> 'tolerance': Float(0.005),
> 'basename': Str(basename),
> 'file_header': SinglefileData(file='/home/aiida/cash/lt/csh_header.lt'),
> 'file_run': SinglefileData(file='/home/aiida/cash/lt/csh_equilibration.lt'),
> },
> outputs = [f'{basename}.lt'],
> metadata = {
> 'computer': load_computer('localhost'),
> 'options': {
> 'resources': {'num_machines': 1, 'num_mpiprocs_per_machine': 1},
> }
> }
> )
> 
> ```

To debug my profile setup, I run the following script:

> **test\_date.py**
>
> ```python
> from aiida.orm import load_computer
> from aiida_shell import launch_shell_job
> from aiida import load_profile
> 
> load_profile()
> results, node = launch_shell_job(
> 'date',
> metadata={'computer': load_computer('caska')}
> )
> print(results['stdout'].get_content())
> 
> ```

And it works, although with a massive overhead! I appreciate any comment on the main workflow.

Otello

---

<div class="post-metadata">

**Author:** ![t-reents](https://yyz2.discourse-cdn.com/free1/user_avatar/aiida.discourse.group/t-reents/32/82_2.png) [@t-reents](https://aiida.discourse.group/u/t-reents)\
**Post date:** [July 16, 2026, 5:34pm UTC](https://aiida.discourse.group/t/from-bash-to-aiida/752/2 "2026-07-16T17:34:15Z")

</div>

Hi @hothello

The issue is that you are using a `PortableCode`, which seems to have a bug in `aiida-shell`. I just opened a PR there ([Fix `prepare_shell_job_inputs` to be compatible with `PortableCode` by t-reents · Pull Request #119 · aiidateam/aiida-shell · GitHub](https://github.com/aiidateam/aiida-shell/pull/119)) and let you know once it’s fixed.

I could reproduce your error and the PR fixed it.

Best,  
Timo

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<div class="post-metadata">

**Author:** ![hothello](https://yyz2.discourse-cdn.com/free1/user_avatar/aiida.discourse.group/hothello/32/430_2.png) [@hothello](https://aiida.discourse.group/u/hothello)\
**Post date:** [July 17, 2026, 11:12am UTC](https://aiida.discourse.group/t/from-bash-to-aiida/752/3 "2026-07-17T11:12:06Z")

</div>

Hi Timo,

Thanks for confirming the bug. Meanwhile, I resorted to call the python script from a bash one. A silly workaround, but it allowed me to set up the workflow I wanted.

I guess another approach would have been to import functions in the file and define my own `@calcfunction` replacing the CLI to the script.

Best wishes,  
Otello

---

<div class="post-metadata">

**Author:** ![t-reents](https://yyz2.discourse-cdn.com/free1/user_avatar/aiida.discourse.group/t-reents/32/82_2.png) [@t-reents](https://aiida.discourse.group/u/t-reents)\
**Post date:** [August 13, 2026, 12:37pm UTC](https://aiida.discourse.group/t/from-bash-to-aiida/752/4 "2026-08-13T12:37:01Z")

</div>

Hi Otello,

just to let you know, the PR was just merged: [Fix `prepare_shell_job_inputs` to be compatible with `PortableCode` by t-reents · Pull Request #119 · aiidateam/aiida-shell · GitHub](https://github.com/aiidateam/aiida-shell/pull/119#pullrequestreview-4927010520)

Hence, if you checkout the main branch, you should even be able to use your original version.

Hope that helps and let us know in case you encounter further issues in the future!

Timo