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Amber-MD / pytraj

Python interface of cpptraj
https://amber-md.github.io/pytraj
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Speed of autoimage? #1507

Closed khoroshyy closed 4 years ago

khoroshyy commented 4 years ago

Hi. Hi, I was trying to apply autoimage to a this trajectory.. pytraj.Trajectory, 54500 frames: Size: 28.277379 (GB) <Topology: 23213 atoms, 3923 residues, 3035 mols, PBC with box type = ortho> But it tales ages , I am not even sure if it is working. Is there any way to check progress or speed it up? Thanks. Petro.

hainm commented 4 years ago

Can you try with with just few frames and measure the time?

traj2 = traj[:2]
tra2.autoimage()

speed it up?

Under the hood, it's cpptraj (C++) code so it's already super fast. :D I guess there's something wrong here.

Can you please also try with cpptraj itself? If that's still slow, cpptraj developer can have a look. :D https://github.com/Amber-MD/cpptraj

hainm commented 4 years ago

ah, you can try to see the progress here:

https://github.com/Amber-MD/pytraj#demo-interactive-data-exploration-with-jupyter-notebook-httpjupyterorg

khoroshyy commented 4 years ago

I have tried with 10 frames some time ago but it did not work also. I have not tried cpptraj yet. May be it has the same problem as nglview had, wrong cell data in trajectory. I will have to check.

khoroshyy commented 4 years ago

OK, now after I corrected the unit cell data in the trajectory, the command actually finishes running and does what it has to do quite fast. I do not understand why the it messes up alpha of the unit cell when loading it. is it problem of my file or of pytraj? Best. Petro.

hainm commented 4 years ago

is it problem of my file or of pytraj?

Can you please use 3rd party software (e.g: ncdump to doublecheck your unitcell data in traj). I dont think pytraj mutates your data if you don't explicitly tell it.

khoroshyy commented 4 years ago

Can you please use 3rd party software (e.g: ncdump to doublecheck your unitcell data in traj). I dont think pytraj mutates your data if you don't explicitly tell it.

If I run ncdump everything is there. For example : cell_spatial = "abc" ;

cell_angular = "alpha", "beta ", "gamma" ;

cell_lengths = 51.17, 61.27, 68.64 ;

cell_angles = 90, 90, 90 ; }

hainm commented 4 years ago

do you have any files (toy model) can be uploaded here so I can reproduce your issue? thanks.

khoroshyy commented 4 years ago

I will make some...

hainm commented 4 years ago

hi @khoroshyy: Are you still interested in this issue? If not, I can close this case. Cheers.

khoroshyy commented 4 years ago

Let me make an example trajectory and I will upload it.

On Tue, May 26, 2020, 7:53 AM Hai Nguyen notifications@github.com wrote:

hi @khoroshyy https://github.com/khoroshyy: Are you still interested in this issue? If not, I can close this case. Cheers.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Amber-MD/pytraj/issues/1507#issuecomment-633821236, or unsubscribe https://github.com/notifications/unsubscribe-auth/AANHQMCNM5A3DAACYAHY6HLRTNKMTANCNFSM4KKRWSIQ .

hainm commented 4 years ago

Since I have not heard from @khoroshyy yet, I go ahead closing this case. Thanks.