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BUG read_pdbstr cause program to sleep forever #436

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shaoqx opened this issue Feb 22, 2025 · 1 comment
Open

BUG read_pdbstr cause program to sleep forever #436

shaoqx opened this issue Feb 22, 2025 · 1 comment

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@shaoqx
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shaoqx commented Feb 22, 2025 •
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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:

  1. create a new conda environment
  2. run conda install pymol-open-source -c conda-forge (This installed version=3.1.0 build=py39he07333a_0 on my machine)
  3. 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))
  1. You will see the script stuck after printing start and never print out pass

Analysis

I made several experiment that removes the forever sleep

  1. comment out line 16 in the script, that is, not calling read_pdbstr() before the Pool.
    This will instantly print the "pass" out
  2. 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
@shaoqx
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shaoqx commented Feb 22, 2025

I found if I set the start method of multiprocessing to "spawn" install of the default "fork" the problem is gone. However, fork is in principle more efficient and likely there is a bug related to pymol2.PyMol()

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