pymol-open-source
pymol-open-source copied to clipboard
Published
20 hours ago •
schrodinger
schrodinger
BUG `read_pdbstr` cause program to sleep forever
Describe the bug
Yesterday I found my calculation was not started after 11 hours.
I spend a whole day trace down the problem and found it is caused by cmd.read_pdbstr from a pymol2.PyMOL() session, which use to load PDB string into a pymol session in my Python script.
I then engineered a minimum reproduction of the bug in a simple script. I also found this bug does not exist in a specific pymol version I installed from a place I dont remember. (not the one in this repo) See reproduction below.
To Reproduce
Steps to reproduce the behavior:
- create a new conda environment
- run
conda install pymol-open-source -c conda-forge(This installed version=3.1.0 build=py39he07333a_0 on my machine) - run this script:
import multiprocessing
import pymol2
def grow_each_window(args):
print("start")
call_read_pdbstr()
print("pass")
def call_read_pdbstr():
pms = pymol2.PyMOL()
pms.start()
pdb_str = "ATOM 1 N ASP A 1 45.117 64.639 61.562 1.00 0.00"
pms.cmd.read_pdbstr(pdb_str, "obj1")
pms.stop()
call_read_pdbstr()
with multiprocessing.Pool(processes=4) as pool:
pool.map(grow_each_window, range(3))
- You will see the script stuck after printing start and never print out pass
Analysis
I made several experiment that removes the forever sleep
- comment out line 16 in the script, that is, not calling read_pdbstr() before the Pool. This will instantly print the "pass" out
- Use another environment in my machine.
lt also instantly print the "pass" out?!
In that environment, if I run
conda list pymol, I got:
# Name Version Build Channel
pymol 2.5.4 py39he7683a9_0 schrodinger
pymol-bundle 2.5.3 0 schrodinger
pymol-web-examples 2.4 1 schrodinger
For now I failed in all attempts reproducing this environment lol.
Analyzing the sleep process with pid shows that it is waiting for a lock
$ ps -o stat,wchan:40,pid,cmd -p 29735
STAT WCHAN PID CMD
S+ futex_wait_queue_me 29735 python reproduce_bug.py
Environment
- PyMOL Version: 3.1.0 build=py39he07333a_0
- PyMOL Source: conda pymol-open-source
- Operating System: Linux CentOS
- If you are using a conda environment, please supply your
conda list
click to see full list
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alsa-lib 1.2.13 hb9d3cd8_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
blosc 1.21.6 he440d0b_1 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.4 hb9d3cd8_0 conda-forge
ca-certificates 2025.1.31 hbcca054_0 conda-forge
cairo 1.18.2 h3394656_1 conda-forge
cyrus-sasl 2.1.27 h54b06d7_7 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
expat 2.6.4 h5888daf_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_3 conda-forge
fontconfig 2.15.0 h7e30c49_1 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
gettext 0.23.1 h5888daf_0 conda-forge
gettext-tools 0.23.1 h5888daf_0 conda-forge
glew 2.1.0 h9c3ff4c_2 conda-forge
glib 2.82.2 h07242d1_1 conda-forge
glib-tools 2.82.2 h4833e2c_1 conda-forge
glm 0.9.9.8 h00ab1b0_0 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
gst-plugins-base 1.24.7 h0a52356_0 conda-forge
gstreamer 1.24.7 hf3bb09a_0 conda-forge
harfbuzz 10.3.0 h76408a6_0 conda-forge
hdf4 4.2.15 h2a13503_7 conda-forge
hdf5 1.14.4 nompi_h2d575fe_105 conda-forge
icu 75.1 he02047a_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
ld_impl_linux-64 2.40 h12ee557_0
libaec 1.1.3 h59595ed_0 conda-forge
libasprintf 0.23.1 h8e693c7_0 conda-forge
libasprintf-devel 0.23.1 h8e693c7_0 conda-forge
libblas 3.9.0 31_h59b9bed_openblas conda-forge
libcap 2.71 h39aace5_0 conda-forge
libcblas 3.9.0 31_he106b2a_openblas conda-forge
libclang-cpp19.1 19.1.7 default_hb5137d0_1 conda-forge
libclang13 19.1.7 default_h9c6a7e4_1 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.12.1 h332b0f4_0 conda-forge
libdrm 2.4.124 hb9d3cd8_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libegl 1.7.0 ha4b6fd6_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.6.4 h5888daf_0 conda-forge
libffi 3.4.4 h6a678d5_1
libflac 1.4.3 h59595ed_0 conda-forge
libgcc 14.2.0 h77fa898_1 conda-forge
libgcc-ng 14.2.0 h69a702a_1 conda-forge
libgcrypt-lib 1.11.0 hb9d3cd8_2 conda-forge
libgettextpo 0.23.1 h5888daf_0 conda-forge
libgettextpo-devel 0.23.1 h5888daf_0 conda-forge
libgfortran 14.2.0 h69a702a_1 conda-forge
libgfortran5 14.2.0 hd5240d6_1 conda-forge
libgl 1.7.0 ha4b6fd6_2 conda-forge
libglib 2.82.2 h2ff4ddf_1 conda-forge
libglu 9.0.3 h03adeef_0 conda-forge
libglvnd 1.7.0 ha4b6fd6_2 conda-forge
libglx 1.7.0 ha4b6fd6_2 conda-forge
libgomp 14.2.0 h77fa898_1 conda-forge
libgpg-error 1.51 hbd13f7d_1 conda-forge
libiconv 1.18 h4ce23a2_1 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 31_h7ac8fdf_openblas conda-forge
libllvm19 19.1.7 ha7bfdaf_1 conda-forge
liblzma 5.6.4 hb9d3cd8_0 conda-forge
libnetcdf 4.9.2 nompi_h5ddbaa4_116 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libntlm 1.8 hb9d3cd8_0 conda-forge
libogg 1.3.5 h4ab18f5_0 conda-forge
libopenblas 0.3.29 pthreads_h94d23a6_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpciaccess 0.18 hd590300_0 conda-forge
libpng 1.6.47 h943b412_0 conda-forge
libpq 17.4 h27ae623_0 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsqlite 3.49.1 hee588c1_1 conda-forge
libssh2 1.11.1 hf672d98_0 conda-forge
libstdcxx 14.2.0 hc0a3c3a_1 conda-forge
libstdcxx-ng 14.2.0 h4852527_1 conda-forge
libsystemd0 257.3 h3dc2cb9_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.8.0 hc4a0caf_0 conda-forge
libxml2 2.13.6 h8d12d68_0 conda-forge
libzip 1.11.2 h6991a6a_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
lz4-c 1.10.0 h5888daf_1 conda-forge
mpg123 1.32.9 hc50e24c_0 conda-forge
mysql-common 9.0.1 h266115a_4 conda-forge
mysql-libs 9.0.1 he0572af_4 conda-forge
ncurses 6.4 h6a678d5_0
nspr 4.36 h5888daf_0 conda-forge
nss 3.108 h159eef7_0 conda-forge
numpy 2.0.2 py39h9cb892a_1 conda-forge
openldap 2.6.9 he970967_0 conda-forge
openssl 3.4.1 h7b32b05_0 conda-forge
packaging 24.2 pyhd8ed1ab_2 conda-forge
pcre2 10.44 hba22ea6_2 conda-forge
pip 25.0 py39h06a4308_0
pixman 0.44.2 h29eaf8c_0 conda-forge
ply 3.11 pyhd8ed1ab_3 conda-forge
pmw 2.0.1 py39hf3d152e_1008 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pulseaudio-client 17.0 hb77b528_0 conda-forge
pymol-open-source 3.1.0 py39he07333a_0 conda-forge
pyqt 5.15.9 py39h52134e7_5 conda-forge
pyqt5-sip 12.12.2 py39h3d6467e_5 conda-forge
python 3.9.18 h0755675_1_cpython conda-forge
python_abi 3.9 5_cp39 conda-forge
qt-main 5.15.15 hc3cb62f_2 conda-forge
readline 8.2 h5eee18b_0
setuptools 75.8.0 py39h06a4308_0
sip 6.7.12 py39h3d6467e_0 conda-forge
snappy 1.2.1 h8bd8927_1 conda-forge
sqlite 3.32.3 hcee41ef_1 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toml 0.10.2 pyhd8ed1ab_1 conda-forge
tomli 2.2.1 pyhd8ed1ab_1 conda-forge
tzdata 2025a h04d1e81_0
wheel 0.45.1 py39h06a4308_0
xcb-util 0.4.1 hb711507_2 conda-forge
xcb-util-image 0.4.0 hb711507_2 conda-forge
xcb-util-keysyms 0.4.1 hb711507_0 conda-forge
xcb-util-renderutil 0.3.10 hb711507_0 conda-forge
xcb-util-wm 0.4.2 hb711507_0 conda-forge
xkeyboard-config 2.43 hb9d3cd8_0 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.5 he73a12e_0 conda-forge
xorg-libx11 1.8.11 h4f16b4b_0 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdamage 1.1.6 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxfixes 6.0.1 hb9d3cd8_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxxf86vm 1.1.6 hb9d3cd8_0 conda-forge
xz 5.6.4 h5eee18b_1
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstd 1.5.7 hb8e6e7a_0 conda-forge
