# Pixi issues with AppImage Release

**URL:** <https://discuss.avogadro.cc/t/pixi-issues-with-appimage-release/7412>\
**Category:** Support\
**Created:** [April 13, 2026, 11:29pm UTC](https://discuss.avogadro.cc/t/pixi-issues-with-appimage-release/7412 "2026-04-13T23:29:41Z")\
**Posts on this page:** 14\
**Page:** 1

<div class="post-metadata">

**Author:** ![Helium5793](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/helium5793/32/3391_2.png) [@Helium5793](https://discuss.avogadro.cc/u/Helium5793)\
**Post date:** [April 13, 2026, 11:29pm UTC](https://discuss.avogadro.cc/t/pixi-issues-with-appimage-release/7412/1 "2026-04-13T23:29:41Z")

</div>

I just tried to write input to mopac for my structure and it said it need pixi and it wasn’t available. (linux appimage). As I just searched for Avogadro and pixi and came up with this discussion, I am wondering if pixi was actually set up in the appImage of Avogadro?

John

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<div class="post-metadata">

**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\
**Post date:** [April 14, 2026, 12:38am UTC](https://discuss.avogadro.cc/t/pixi-issues-with-appimage-release/7412/2 "2026-04-14T00:38:42Z")

</div>

> [@Helium5793](#):
>
> I am wondering if pixi was actually set up in the appImage of Avogadro?

It should be included in the AppImage, yes.

What was the _exact_ error / warning mesage?

---

<div class="post-metadata">

**Author:** ![Helium5793](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/helium5793/32/3391_2.png) [@Helium5793](https://discuss.avogadro.cc/u/Helium5793)\
**Post date:** [April 14, 2026, 11:59am UTC](https://discuss.avogadro.cc/t/pixi-issues-with-appimage-release/7412/3 "2026-04-14T11:59:30Z")

</div>

I loaded benzene as an example, but it also happened with several other molecules. I clicked on input –\>MOPAC and here is a screenshot:

Fedora 43 Linux, Appimage.

 ![mopac_input](https://discuss.avogadro.cc/uploads/default/original/2X/2/220fe2d3bbf8d0d359ac5f4bdb1ee60908d1cfc7.png)

---

<div class="post-metadata">

**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\
**Post date:** [April 14, 2026, 3:06pm UTC](https://discuss.avogadro.cc/t/pixi-issues-with-appimage-release/7412/4 "2026-04-14T15:06:21Z")

</div>

I’ll look into what’s happening with the AppImage, but the easiest workaround in the meantime is to install `pixi` yourself: [Installation - Pixi](https://pixi.prefix.dev/latest/installation/)

---

<div class="post-metadata">

**Author:** ![wlparker](https://discuss.avogadro.cc/letter_avatar_proxy/v4/letter/w/ecd19e/32.png) [@wlparker](https://discuss.avogadro.cc/u/wlparker)\
**Post date:** [April 20, 2026, 7:34pm UTC](https://discuss.avogadro.cc/t/pixi-issues-with-appimage-release/7412/5 "2026-04-20T19:34:44Z")

</div>

I am also having this issue with pixi when I try to generate a nwchem input file from an Appimage Linux installation. I installed pixi and still had no success

---

<div class="post-metadata">

**Author:** ![Helium5793](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/helium5793/32/3391_2.png) [@Helium5793](https://discuss.avogadro.cc/u/Helium5793)\
**Post date:** [May 5, 2026, 12:45pm UTC](https://discuss.avogadro.cc/t/pixi-issues-with-appimage-release/7412/6 "2026-05-05T12:45:11Z")

</div>

finally got around to this. I installed pixi on my fedora system. Here  
is a screenshot of the result. Again trying to save input for MOPAC.

Later today I will try the same in Windows.  
Before I installed pixi, I noted that most of the input choices require  
pixi.  
John

> **(attachments)**
>
> ![pixi_installed.png](https://discuss.avogadro.cc/uploads/default/original/2X/1/1dce057b783db01387a9d02e29f092bd05acdc0c.png)

---

<div class="post-metadata">

**Author:** ![Helium5793](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/helium5793/32/3391_2.png) [@Helium5793](https://discuss.avogadro.cc/u/Helium5793)\
**Post date:** [May 5, 2026, 4:16pm UTC](https://discuss.avogadro.cc/t/pixi-issues-with-appimage-release/7412/7 "2026-05-05T16:16:29Z")

</div>

I tried the same thing in windows 10 and it worked just fine.  
John

---

<div class="post-metadata">

**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\
**Post date:** [May 6, 2026, 8:13pm UTC](https://discuss.avogadro.cc/t/pixi-issues-with-appimage-release/7412/8 "2026-05-06T20:13:14Z")

</div>

Can you run the AppImage from the command line, e.g.

`AVO_PYTHON_SCRIPT_DEBUG=1 ./Avogadro.AppImage`

Here, I’m assuming that the AppImage is executable. It should self-extract and run, IIRC.

I’m curious to see why you’re getting that message.

---

<div class="post-metadata">

**Author:** ![Helium5793](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/helium5793/32/3391_2.png) [@Helium5793](https://discuss.avogadro.cc/u/Helium5793)\
**Post date:** [May 6, 2026, 9:33pm UTC](https://discuss.avogadro.cc/t/pixi-issues-with-appimage-release/7412/9 "2026-05-06T21:33:15Z")

</div>

Here is the terminal output from starting Avagodro

jduchek@HP-K:~$ AVO\_PYTHON\_SCRIPT\_DEBUG=1 ./Avogadro.AppImage  
bash: ./Avogadro.AppImage: No such file or directory  
jduchek@HP-K:~$ cd AppImages/  
jduchek@HP-K:~/AppImages$ AVO\_PYTHON\_SCRIPT\_DEBUG=1 ./Avogadro.AppImage  
bash: ./Avogadro.AppImage: No such file or directory  
jduchek@HP-K:~/AppImages$ ls  
4.9\_20210511\_Ultimaker\_Cura-4.9.1.AppImage  
arduino-ide\_2.2.1\_Linux\_64bit.AppImage  
arduino-ide\_2.3.6\_Linux\_64bit.AppImage  
Avogadro2-x86\_64.AppImage  
balenaEtcher-1.18.11-x64.AppImage  
CrealityPrint-V6.2.0.2827-x86\_64-Release.AppImage  
get\_icon.sh  
icons  
Lac861-x86\_64.AppImage  
MeshLab2020.07-linux.AppImage  
RePetier-host-docs.pdf  
Repetier-Host-x86\_64-2.2.2.AppImage  
ser\_player\_logo\_150x150.png  
SER\_Player-v1.7.3-x86\_64.AppImage  
squashfs-root  
Stellarium-24.2-qt5-x86\_64.AppImage  
UltiMaker-Cura-5.3.0-linux.AppImage  
UltiMaker-Cura-5.3.0-linux-modern.AppImage  
jduchek@HP-K:~/AppImages$ AVO\_PYTHON\_SCRIPT\_DEBUG=1 ./Avogadro2-x86\_64.AppImage  
Avogadroapp version: 2.0.0  
Avogadrolibs version: 2.0.0  
Qt version: 6.8.3  
qt.core.qobject.connect: QObject::connect(QObject, Unknown): invalid nullptr parameter  
SSL version: “OpenSSL 3.0.2 15 Mar 2022”  
Using locale: “en\_US”  
registering obmm plugins  
“/tmp/.mount\_Avogadwfk199/usr/bin/obabel” found: “/tmp/.mount\_Avogadwfk199/usr/bin/obabel: Open Babel 3.1.1 – Apr 1 2026 – 11:15:52”  
RPC server listening on: “/tmp/avogadro”  
current version is newer than latest release  
Open Babel formats ready: 142  
Setting default format to cjson.  
Executing “/home/jduchek/.pixi/bin/pixi” “run --as-is avogadro-generators mopac --debug --lang en\_US” \< “{“cjson”:{“atoms”:{“coords”:{“3d”:[-2.04281,2.69204,0.626229,-2.60254,3.93092,0.938338,-3.95446,4.02194,1.26942,-4.74661,2.87405,1.28865,-4.18686,1.63515,0.976653,-2.83499,1.54415,0.645353,-0.989543,2.62119,0.368203,-2.39893,0.57892,0.402116,-4.804,0.740778,0.991704,-5.79987,2.94501,1.5467,-1.98537,4.82526,0.923522,-4.39055,4.98721,1.51242]},“elements”:{“number”:[6,6,6,6,6,6,1,1,1,1,1,1]},“layer”:[0,0,0,0,0,0,0,0,0,0,0,0]},“bonds”:{“connections”:{“index”:[0,1,1,2,2,3,3,4,4,5,0,5,0,6,5,7,4,8,3,9,1,10,2,11]},“order”:[2,1,2,1,2,1,1,1,1,1,1,1]},“chemicalJson”:1,“layer”:{“enable”:{“Ball and Stick”:[true],“Cartoons”:[false],“Close Contacts”:[false],“Crystal Lattice”:[false],“Dipole Moment”:[false],“Force”:[false],“Labels”:[false],“Licorice”:[false],“Non-Covalent”:[false],“QTAIM”:[false],“Reference Axes”:[false],“Surfaces”:[false],“Van der Waals”:[false],“Wireframe”:[false]},“locked”:[false,false],“settings”:{“Ball and Stick”:[“true true 0.300000 0.100000 1.000000”]},“visible”:[true,true]},“properties”:{“fileName”:”/media/Science-4T/2026-Chemistry/CJSON/Johns\_Stuff/benzene.cjson",“modelView”:[[0.37197238206863403,-0.8686060309410095,-0.32732799649238586,4.938599586486816],[0.9045268893241882,0.4183780550956726,-0.08232038468122482,2.061976432800293],[0.208452045917511,-0.2654572129249573,0.9413101077079773,-12.811356544494629],[0,0,0,1]],“projection”:[[0.12265758216381073,0,0,0],[0,0.1666666716337204,0,0],[0,0,-0.051572613418102264,0],[0,0,0,1]],“totalCharge”:0,“totalSpinMultiplicity”:1}},“options”:{“COSMO”:true,“Calculation Type”:“Equilibrium Geometry”,“Charge”:0,“Filename Base”:“job”,“HF Type”:“RHF”,“Multiplicity”:1,“Other Solvent Dielectric”:“0.00”,“Processor Cores”:1,“Solvent”:“Water”,“Theory”:“PM7”,“Title”:“C6H6 | Equilibrium Geometry | PM7”}}"  
Working directory is “/home/jduchek/.local/share/OpenChemistry/Avogadro/plugins/avogenerators”  
“Error running script ‘/home/jduchek/.pixi/bin/pixi run --as-is avogadro-generators mopac --debug --lang en\_US’: Abnormal exit status 127 (Unknown error.: Unknown error)\n\nOutput:\navogadro-generators: command not found\n”  
Executing “/home/jduchek/.pixi/bin/pixi” “run --as-is avogadro-generators mopac --debug --lang en\_US” \< “{“cjson”:{“atoms”:{“coords”:{“3d”:[-2.04281,2.69204,0.626229,-2.60254,3.93092,0.938338,-3.95446,4.02194,1.26942,-4.74661,2.87405,1.28865,-4.18686,1.63515,0.976653,-2.83499,1.54415,0.645353,-0.989543,2.62119,0.368203,-2.39893,0.57892,0.402116,-4.804,0.740778,0.991704,-5.79987,2.94501,1.5467,-1.98537,4.82526,0.923522,-4.39055,4.98721,1.51242]},“elements”:{“number”:[6,6,6,6,6,6,1,1,1,1,1,1]},“layer”:[0,0,0,0,0,0,0,0,0,0,0,0]},“bonds”:{“connections”:{“index”:[0,1,1,2,2,3,3,4,4,5,0,5,0,6,5,7,4,8,3,9,1,10,2,11]},“order”:[2,1,2,1,2,1,1,1,1,1,1,1]},“chemicalJson”:1,“layer”:{“enable”:{“Ball and Stick”:[true],“Cartoons”:[false],“Close Contacts”:[false],“Crystal Lattice”:[false],“Dipole Moment”:[false],“Force”:[false],“Labels”:[false],“Licorice”:[false],“Non-Covalent”:[false],“QTAIM”:[false],“Reference Axes”:[false],“Surfaces”:[false],“Van der Waals”:[false],“Wireframe”:[false]},“locked”:[false,false],“settings”:{“Ball and Stick”:[“true true 0.300000 0.100000 1.000000”]},“visible”:[true,true]},“properties”:{“fileName”:”/media/Science-4T/2026-Chemistry/CJSON/Johns\_Stuff/benzene.cjson",“modelView”:[[0.37197238206863403,-0.8686060309410095,-0.32732799649238586,4.938599586486816],[0.9045268893241882,0.4183780550956726,-0.08232038468122482,2.061976432800293],[0.208452045917511,-0.2654572129249573,0.9413101077079773,-12.811356544494629],[0,0,0,1]],“projection”:[[0.12265758216381073,0,0,0],[0,0.1666666716337204,0,0],[0,0,-0.051572613418102264,0],[0,0,0,1]],“totalCharge”:0,“totalSpinMultiplicity”:1}},“options”:{“COSMO”:true,“Calculation Type”:“Equilibrium Geometry”,“Charge”:0,“Filename Base”:“job”,“HF Type”:“RHF”,“Multiplicity”:1,“Other Solvent Dielectric”:“0.00”,“Processor Cores”:1,“Solvent”:“Water”,“Theory”:“PM7”,“Title”:“C6H6 | Equilibrium Geometry | PM7”}}"  
Working directory is “/home/jduchek/.local/share/OpenChemistry/Avogadro/plugins/avogenerators”  
“Error running script ‘/home/jduchek/.pixi/bin/pixi run --as-is avogadro-generators mopac --debug --lang en\_US’: Abnormal exit status 127 (Unknown error.: Unknown error)\n\nOutput:\navogadro-generators: command not found\n”  
^C  
jduchek@HP-K:~/AppImages$

Once I loaded it I loaded benzene and asked to make MOPAC imput. Screen shot attached.

 ![Avagadro-inputMOPAC](https://discuss.avogadro.cc/uploads/default/original/2X/6/6e356869fb049a0d37e0e4cea932393ed6825864.png)

---

<div class="post-metadata">

**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\
**Post date:** [May 6, 2026, 11:20pm UTC](https://discuss.avogadro.cc/t/pixi-issues-with-appimage-release/7412/10 "2026-05-06T23:20:24Z")

</div>

> [@Helium5793](#):
>
> /home/jduchek/.local/share/OpenChemistry/Avogadro/plugins/avogenerators

Okay, first off, does this directory exist? (presumably)

If you go to the terminal, and type:

```bash
cd /home/jduchek/.local/share/OpenChemistry/Avogadro/plugins/avogenerators
ls -a

```

Hopefully, you’ll see a `.pixi` directory and a bunch of files

```auto
/home/jduchek/.pixi/bin/pixi run avogadro-generators mopac

```

In this case, I’ve removed the `--as-is` so it should attempt to fix the environment if it’s broken.

---

<div class="post-metadata">

**Author:** ![Helium5793](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/helium5793/32/3391_2.png) [@Helium5793](https://discuss.avogadro.cc/u/Helium5793)\
**Post date:** [May 7, 2026, 12:27pm UTC](https://discuss.avogadro.cc/t/pixi-issues-with-appimage-release/7412/11 "2026-05-07T12:27:14Z")

</div>

The directory exists. Inside the .pixi directory there are 2 files. .condapackageignore and .gitignore. I installed pixi according to the directions for linux at the site you gave me. I asked fedora where it was, and it says pixi is in the directory /home/jduchek/.pixi/bin/  
Curiously I ran 'cat pixi 'and got lots of gibberish, but the last paragraph was text:

GCC: (GNU) 9.4.0rustc version 1.90.0 (1159e78c4 2025-09-14)GCC: (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0.shstrtab.note.gnu.build-id.gnu.hash.dynsym.dynstr.rela.dyn.init.plt.plt.got.text.fini.rodata.eh\_frame\_hdr.gcc\_except\_table.eh\_frame.tdata.tbss.init\_array.fini\_array.data.rel.ro.dynamic.data.bss.comment

It looks like it thinks I am running Ubuntu?. I asked the pixi file for its size and it came back with 70840 so it isn’t empty, but may be in the wrong place?

---

<div class="post-metadata">

**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\
**Post date:** [May 7, 2026, 3:38pm UTC](https://discuss.avogadro.cc/t/pixi-issues-with-appimage-release/7412/12 "2026-05-07T15:38:27Z")

</div>

> [@Helium5793](#):
>
> The directory exists. Inside the .pixi directory there are 2 files. .condapackageignore and .gitignore.

Okay, so the generators didn’t get installed.

```bash
cd /home/jduchek/.local/share/OpenChemistry/Avogadro/plugins/avogenerators
pixi install

```

That should do it - I’ll see if I can add some more robust code to check installs.

> [@Helium5793](#):
>
> Curiously I ran 'cat pixi 'and got lots of gibberish

Yes, it’s a binary. I’m sure it was likely built on Ubuntu. There’s nothing particularly wrong with `pixi` itself - just that Avogadro expects certain things to happen and clearly those parts of the code need more error detection.

---

<div class="post-metadata">

**Author:** ![hisacro](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/hisacro/32/3195_2.png) [@hisacro](https://discuss.avogadro.cc/u/hisacro)\
**Post date:** [June 22, 2026, 1:50am UTC](https://discuss.avogadro.cc/t/pixi-issues-with-appimage-release/7412/14 "2026-06-22T01:50:06Z")

</div>

I’m on arch based machine as well and facing the same issue.

Avogadro appimage didn’t recognize pixie and I have install from the repository. I ran without `--as-is` on the `avogenerators`,

I get still get the error

> File ‘debug\_info’ poorly formed. Missing string ‘contents’ or ‘filePath’ \> members.

also when I run `/usr/bin/pixi run avogadro-generators mopac` it just stalls?

So, what fixed it for me is,

`$ cd ~/.local/share/OpenChemistry/Avogadro/plugins/avogenerators/.pixi`  
`$ /usr/bin/pixi run --as-is avogadro-generators orca --debug --lang en_US`

while it’s on one of the terminal, I opened avogadro on other, Now it seems to be fine

---

<div class="post-metadata">

**Author:** ![ghutchis](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/ghutchis/32/456_2.png) [@ghutchis](https://discuss.avogadro.cc/u/ghutchis)\
**Post date:** [August 15, 2026, 4:56pm UTC](https://discuss.avogadro.cc/t/pixi-issues-with-appimage-release/7412/15 "2026-08-15T16:56:50Z")

</div>

Thanks for all the help here. I finally had a chance to go through a bunch of these paths (e.g., finding `pixi` in the home directory, etc.)

I just merged this, which should solve a bunch of these issues for 2.1:

> <https://github.com/OpenChemistry/avogadrolibs/pull/2942>
>
> \- Ensure ${HOME}/.pixi/bin is checked for pixi
> \- Packages were never repaired b…/c the checksum didn't change
> \- scanDirectory() now checks for valid .pixi or venv and re-installs if needed
> \- Cleanup venv if switching to pixi install works cleanly
> 
> Developer Certificate of Origin
> Version 1.1
> 
> Copyright (C) 2004, 2006 The Linux Foundation and its contributors.
> 1 Letterman Drive
> Suite D4700
> San Francisco, CA, 94129
> 
> Everyone is permitted to copy and distribute verbatim copies of this
> license document, but changing it is not allowed.
> 
> 
> Developer's Certificate of Origin 1.1
> 
> By making a contribution to this project, I certify that:
> 
> (a) The contribution was created in whole or in part by me and I
> have the right to submit it under the open source license
> indicated in the file; or
> 
> (b) The contribution is based upon previous work that, to the best
> of my knowledge, is covered under an appropriate open source
> license and I have the right under that license to submit that
> work with modifications, whether created in whole or in part
> by me, under the same open source license (unless I am
> permitted to submit under a different license), as indicated
> in the file; or
> 
> (c) The contribution was provided directly to me by some other
> person who certified (a), (b) or (c) and I have not modified
> it.
> 
> (d) I understand and agree that this project and the contribution
> are public and that a record of the contribution (including all
> personal information I submit with it, including my sign-off) is
> maintained indefinitely and may be redistributed consistent with
> this project or the open source license(s) involved.
> 
> 
> 
> 
> \## Summary by CodeRabbit
> 
> \* \*\*New Features\*\*
> \* Improved package command discovery across Pixi environments and Python virtual environments.
> \* Added safer support for package setup commands and console scripts.
> \* Python package execution now uses the best available installed environment.
> 
> \* \*\*Bug Fixes\*\*
> \* Packages are reinstalled when their environment is missing or Pixi becomes available.
> \* Obsolete virtual environments are removed only after successful Pixi validation.
> \* Improved executable discovery, including Pixi installation locations.
> 
> \* \*\*Tests\*\*
> \* Added coverage for command discovery, environment migration, executable lookup, and platform-specific behavior.