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
It should be included in the AppImage, yes.
What was the exact error / warning mesage?
I’ll look into what’s happening with the AppImage, but the easiest workaround in the meantime is to install pixi yourself: Installation - Pixi
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
I tried the same thing in windows 10 and it worked just fine.
John
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.
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.
Okay, first off, does this directory exist? (presumably)
If you go to the terminal, and type:
cd /home/jduchek/.local/share/OpenChemistry/Avogadro/plugins/avogenerators
ls -a
Hopefully, you’ll see a .pixi directory and a bunch of files
/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.
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?
Okay, so the generators didn’t get installed.
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.
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.