Wow, quick work. I'll absolutely try tomorrow's build. Thanks a ton, Eric. Re Bug Reports: will do henceforth, assumed it's me not the game this time. Kind regards to developers, Artem On Fri, Jun 7, 2024 at 2:10 PM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Artie, There were a couple of elusive and pernicious bugs in the ChimeraX C++ code that could cause crashes when Python ran garbage collection. We fixed one a couple of months ago (so the fix isn't in the 1.7.1 release you are using) and fixed the other one *today*, so it will only be in the release candidate and daily builds starting tomorrow. So I recommend getting tomorrow's 1.8 release candidate and seeing if that works better for you. As an aside, it is generally better to report bugs using the Help→Report A Bug menu item, since that's includes extensive information about your system and ChimeraX's version and configuration, and since most bugs aren't of general interest to all users -- though this particular one may be somewhat of an exception.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 7, 2024, at 12:42 PM, Artie Kushner via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi, I hope the summer is starting off really well for you.
tldr: I leave ChimeraX running movie/image generating commands from a python script in a tmux session and it segfaults on multiple machines.
I was wondering if someone has encountered this before or can lend advice as to why this happens. I'd like to produce some movies (or at least pictures) in bulk (around 2000 individual molecules). I preprocess each one (load locally or open, add some representation, and either start recording a movie or "save XXXX.png"). After about 8-10 successful movies or images are produced I get a ChimeraX segfault and the process dies.
This is quite perplexing to me because - I tried it on multiple machines: Ubuntu 22.04, installed from the .deb <https://www.cgl.ucsf.edu/chimerax/download.html> and Arch, installed from aur distribution. - both with `--offscreen` and `--nogui` flags and without them ( in fact, following up some threads in the mailing list it seems like it's not possible to produce movies with --nogui, just pngs) - there seems to be *no* excessive memory or page cache issues, although i haven't profiled it. Only one core is occupied when rendering both mp4/png's.
Below I'm attaching a crash log from one of the machines (Ubuntu 22.04) and the description of my setup, which is a little awkward, but I don't think it's the cause since it produces some samples successfully before crashing. I hope i'm wrong.
Best regards and any tips are really appreciated! I was really looking forward to having some crisp images.
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I start the process by calling a python script at the command line: ` chimerax --script "/home/student/dev/riboxyz/chimerax/ribrepr.py" --nogui --offscreen` when i tried generated images. This was after I gave up on getting the movies, which i did by just opening a ChimeraX gui on our workstation and calling a "loop.py" after a load the commands from "ribrepr.py" file from the gui command line. I do both in a tmux session.
```loop.py import os from chimerax.core.commands import run from concurrent.futures import ThreadPoolExecutor
*DEST_DIR* = "/home/rtviii/dev/riboxyz/chimerax/movies"
# This expands to ~1800 PDB ids: rcsb_id:= {4UG0, 7K00 and so on} for rcsb_id in os.listdir('/home/rtviii/dev/RIBETL_DATA'): movie_dir = os.path.join(DEST_DIR, "{}.mp4".format(rcsb_id)) print("Attempting to write ", movie_dir) if "{}.mp4".format(rcsb_id) in os.listdir(DEST_DIR): print("Skipping {}. Exists".format(rcsb_id)) continue else: run(session,"ribmovie {}".format(rcsb_id)) # <---- ribmovie command corresponds to the `*produce_and_save_movie*` in ribrepr.py below ```
The contents of the `ribrepr.py` are just to register a command for custom visualization of a given molecule + loop over molecules for image generation.
``` ribrepr.py import enum import json import os import sys from chimerax.core.commands import register, CmdDesc from chimerax.atomic import ResiduesArg, Chains, ChainArg, StructureArg from chimerax.atomic import Structure, AtomicStructure, Chain from chimerax.core.commands import run, runscript from chimerax.core.commands import CmdDesc, register, StringArg
# https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/t...
# just a data folder, it exists. *RIBETL_DATA* = os.environ.get("RIBETL_DATA", "/home/rtviii/dev/RIBETL_DATA")
class *PolymerClass*(str, enum.Enum): tRNA = "tRNA" bS1m = "bS1m" # ... another ~200 enum members, redacted for brevity
CHIMERAX_COLORS = [ ["tan", "#d2b48c"], ["sienna", "#a0522d"], #... more colors redacted for brevity ]
# helper function to map colors def *get_polymer_color*(polymer_class:str): polyix = list(map(lambda x: x.value, (PolymerClass))) class_index = polyix.index(polymer_class) % len(polyix)
if polymer_class == None: return "gray" return CHIMERAX_COLORS[(class_index % len(CHIMERAX_COLORS))][1]
def *ribosome_representation*(session, structure: AtomicStructure): for _ in list(PolymerClass): print(_.name)
from chimerax.core.commands import run from chimerax.core.colors import hex_color from chimerax.atomic import Residue, Atom, Chain
# i get the PDB ID from the StructureArg rcsb_id = str(structure.name).upper().split('.')[0] # <-- the structure gets opened with the basename ex "(5AFI.cif)" run(session, "set bgColor white") run(session, "sym #1 assembly 1") # take only one assembly if multiple are available run(session, "hide #2")
with open(os.path.join(RIBETL_DATA, rcsb_id, "{}.json".format(rcsb_id)), "r") as f: profile = json.load(f) # load my annotations, just a json file
#--------------------------------------------[ This whole bit just colors by chain annotation basically] polymers = {} polymer_chains = [ *profile["proteins"], *profile["rnas"], *profile["other_polymers"], ] [ polymers.update(x) for x in [{chain["auth_asym_id"]: chain} for chain in polymer_chains] ]
c: Chain for c in structure.chains: aaid = c.chain_id polyclass = None if len(polymers[aaid]["nomenclature"]) < 1: continue else: polyclass = polymers[aaid]["nomenclature"][0] if polymers[aaid]["entity_poly_polymer_type"] == "RNA": run(session, "surf /{}".format(aaid)) run(session, "transp /{} 100".format(aaid)) run(session, "color /{} gray".format(aaid)) else: run(session, "show /{} cartoon".format(aaid, get_polymer_color(polyclass))) run(session, "color /{} {}".format(aaid, get_polymer_color(polyclass))) #--------------------------------------------[ This whole bit just colors by chain annotation basically] run(session, "graphics silhouettes true width 1") run(session, "light soft")
# # ! Didn't work out for now. This is how i tried to make movies. (Loop over every structure (loop.py above) and call this command). Chimerax segfaults when looped on this. # def *produce_and_save_movie*(session, target:str): # print("GOT TARGET", target) # RCSB_ID = target # run(session, "open /home/rtviii/dev/RIBETL_DATA/{}/{}.cif".format(RCSB_ID, RCSB_ID)) # run(session, "sym #1 assembly 1") # take only one assembly if multiple are available # run(session, "ribrep #2") # run(session, "movie record") # run(session, "turn y 2 180") # run(session, "wait 180") # run(session, "movie encode /home/rtviii/dev/riboxyz/chimerax/movies/{}.mp4".format(RCSB_ID)) # run(session, "close all")
# # ! This is just to not download the mmcif files i have locally. def *register_ribetl_command*(logger): def ribetl(session, rcsb_id:str): rcsb_id = rcsb_id.upper() run(session, "open /home/rtviii/dev/RIBETL_DATA/{}/{}.cif".format(rcsb_id, rcsb_id)) desc = CmdDesc( required= [("rcsb_id", StringArg)], ) register("ribetl", desc, ribetl, logger=logger)
# # ! Register the above repr sequence as a command. def *register_ribrepr_command*(logger): from chimerax.core.commands import CmdDesc, register from chimerax.atomic import AtomicStructureArg, Chain, Residue, Atom
desc = CmdDesc( required = [("structure", AtomicStructureArg)], required_arguments = ["structure"], synopsis = "representation ", ) register("ribrep", desc, ribosome_representation, logger=logger)
*register_ribrepr_command*(session.logger) *register_ribetl_command*(session.logger)
# This loop expands into a list of ~1800 PDB : 5AFI, 4UG0 and so on. for rcsb_id in os.listdir(RIBETL_DATA): run(session,"open {}".format(rcsb_id)) run(session,"ribrep #1") run(session,"save /home/student/dev/riboxyz/chimerax/{}.png width 800 height 800 transparentBackgroun d true".format(rcsb_id)) run(session,"close all") ```
Let me know if i can elucidate this situation further with hardware specs or whatnot. I'm quite at loss as to how to proceed with this.
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