error PYP Can't write to

[FlorianBeckOle]

Hi,

I tried to run pyp on a gpfs exported filesystem and I get the error below:
(The filesystem is not read only I tested with
touch /fs/pool/pool-fbeck/misc/testPYP/T20S/.pyp_history
and it workde wihout error.)

pyp -data_mode spr -scope_voltage 300 -scope_pixel 0.66 -data_path='./nextpyp_spr_tutorial/14*.tif' -gain_reference='./nextpyp_spr_tutorial/14*.tif' -gain_flipv -detect_rad 80 -detect_method all -detect_dist 40 -slurm_tasks 7 -slurm_memory 70 -slurm_merge_tasks 7 -slurm_merge_memory 70
Launching pyp ...
Reading configuration file at: /fs/pool/pool-bmapps/hpcl8/app/soft/PYP/0.7.1/config.toml
2025-08-07 13:55:48 [INFO] /opt/pyp/bin/run/pyp:3992 | Job 585738843_1 running nextPYP v0.7.1 on hpcl9301 using 1 task(s) ?
2025-08-07 13:55:48 [ERROR] /opt/pyp/bin/run/pyp:4059 | Can't write to /fs/pool/pool-fbeck/misc/testPYP/T20S/.pyp_history
2025-08-07 13:55:48 [INFO] /opt/pyp/bin/run/pyp:3602 | Filesystem Size Used Avail Use% Mounted on
2025-08-07 13:55:48 [INFO] /opt/pyp/bin/run/pyp:3602 | gpfs-me5024-03-10 390T 293T 98T 76% /fs/pool/pool-briggs-scratch/PYP
Traceback (most recent call last):
File "/opt/pyp/bin/run/pyp", line 4053, in
with open(".pyp_history", "a") as f:

[abartesaghi]

This issue may stem from Apptainer not automatically binding filesystem paths, making them inaccessible to nextPYP. To resolve this, try adding /fs/pool/pool-fbeck/misc to the list of binds in your config.toml configuration file. This will make all folders under that path available to nextPYP.

I assume you are running the pyp command from the folder /fs/pool/pool-fbeck/misc/testPYP/T20S? If that is the case, that path should be automatically added to the binds (unless your singularity/apptainer installation is configured not to do so, in which case the suggestion above should fix the problem).

Looking at your command, I noticed that the parameter -gain_reference is not pointing to the location of the gain reference, but to the data itself. You may want to use something like -gain_reference='/fs/pool/pool-fbeck/misc/testPYP/T20S/nextpyp_spr_tutorial/Gain.mrc' instead.

Also, you need to use absolute paths when specifying the -data_path option, for example, -data_path='/fs/pool/pool-fbeck/misc/testPYP/T20S/nextpyp_spr_tutorial/14*.tif'

[FlorianBeckOle]

thanks the bind did the trick.

Florian