Hi,
I get the error below while performing refinement on a set of particles. The other job types (like 2D classification, ab-initio, etc.,) have executed fine till this point. The error message is below:
Launched job nEbcgQ5qRTXnFHCMB
ERROR: No Heartbeat
This job was killed because a heartbeat was not received for 120 seconds.
The last 100 lines of the job standard output are printed below.
====== ENVIRONMENT ========
{‘NO_PROXY’: ‘localhost,127.0.0.0/8,psu.edu’, ‘http_proxy’: ‘http://proxy.aset.psu.edu:3128/’, ‘SHELL’: ‘/bin/bash’, ‘CRYOSPARC_BULK_DIR’: ‘/home/zuhaib/cryosparc/run/bulk’, ‘XDG_DATA_DIRS’: ‘/usr/share/gnome:/usr/local/share/:/usr/share/’, ‘SUPERVISOR_ENABLED’: ‘1’, ‘TEST_METADATA’: ‘{}’, ‘XDG_RUNTIME_DIR’: ‘/run/user/1000’, ‘PYTHONPATH’: ‘’, ‘CRYOSPARC_REGISTER_DONE’: ‘true’, ‘CRYOSPARC_METEOR_BINDIR’: ‘’, ‘DBUS_STARTER_BUS_TYPE’: ‘session’, ‘XDG_SESSION_ID’: ‘1’, ‘DBUS_SESSION_BUS_ADDRESS’: ‘unix:abstract=/tmp/dbus-fvX6HqLufp,guid=a9d99d96b238e1622a65f74a5b71f627’, ‘DESKTOP_SESSION’: ‘default’, ‘CRYOSPARC_RESULTS_MIGRATION_DONE’: ‘true’, ‘OMP_NUM_THREADS’: ‘1’, ‘CRYOSPARC_NODEJS_BINDIR’: ‘/home/zuhaib/cryosparc/nodejs/bin’, ‘XDG_MENU_PREFIX’: ‘gnome-’, ‘MAIL_URL’: ‘smtp://AKIAJADHF7LEXAXQPK5A:AiSF2bOjM26vMPV8TT2JMTbhNx5T+SDtEDQg8iHJToLY@email-smtp.us-east-1.amazonaws.com:465’, ‘ZEITGEIST_DATA_PATH’: ‘/home/zuhaib/.local/share/zeitgeist’, ‘MONGO_OPLOG_URL’: ‘mongodb://localhost:38001/local’, ‘BASH_FUNC_module%%’: ‘() { eval /opt/Modules/$MODULE_VERSION/bin/modulecmd bash $*\n}’, ‘DBUS_STARTER_ADDRESS’: ‘unix:abstract=/tmp/dbus-fvX6HqLufp,guid=a9d99d96b238e1622a65f74a5b71f627’, ‘CRYOSPARC_MASTER_HOSTNAME’: ‘051374’, ‘FTP_PROXY’: ‘http://proxy.aset.psu.edu:3128/’, ‘XDG_CURRENT_DESKTOP’: ‘GNOME’, ‘SUPERVISOR_GROUP_NAME’: ‘webapp’, ‘XDG_VTNR’: ‘7’, ‘CRYOSPARC_MONGODB_BINDIR’: ‘/home/zuhaib/cryosparc/mongodb/bin’, ‘PORT’: ‘38000’, ‘SUPERVISOR_SERVER_URL’: ‘unix:///tmp/supervisor-6830169599366923827.sock’, ‘XAUTHORITY’: ‘/var/run/gdm3/auth-for-zuhaib-LmluqN/database’, ‘SESSION_MANAGER’: ‘local/051374:@/tmp/.ICE-unix/1364,unix/051374:/tmp/.ICE-unix/1364’, ‘SHLVL’: ‘2’, ‘all_proxy’: ‘https://proxy.aset.psu.edu:3182’, ‘DISPLAY’: ‘:0’, ‘NODE_ENV’: ‘production’, ‘CRYOSPARC_DEVELOP’: ‘false’, ‘WINDOWID’: ‘27262982’, ‘GPG_AGENT_INFO’: ‘/run/user/1000/keyring/gpg:0:1’, ‘MODULESHOME’: ‘/opt/Modules/3.2.10’, ‘XDG_SESSION_DESKTOP’: ‘default’, ‘ROOT_URL’: ‘http://localhost:38000’, ‘CRYOSPARC_RAM_SLOTS’: ‘12’, ‘GDMSESSION’: ‘default’, ‘SUPERVISOR_PROCESS_NAME’: ‘webapp’, ‘CRYOSPARC_HTTP_PORT’: ‘38000’, ‘_’: ‘/home/zuhaib/cryosparc/anaconda2/bin/supervisord’, ‘MODULEPATH’: ‘/opt/Modules/versions:/opt/Modules/$MODULE_VERSION/modulefiles:/opt/Modules/modulefiles’, ‘LS_COLORS’: ‘rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:.tar=01;31:.tgz=01;31:.arc=01;31:.arj=01;31:.taz=01;31:.lha=01;31:.lz4=01;31:.lzh=01;31:.lzma=01;31:.tlz=01;31:.txz=01;31:.tzo=01;31:.t7z=01;31:.zip=01;31:.z=01;31:.Z=01;31:.dz=01;31:.gz=01;31:.lrz=01;31:.lz=01;31:.lzo=01;31:.xz=01;31:.bz2=01;31:.bz=01;31:.tbz=01;31:.tbz2=01;31:.tz=01;31:.deb=01;31:.rpm=01;31:.jar=01;31:.war=01;31:.ear=01;31:.sar=01;31:.rar=01;31:.alz=01;31:.ace=01;31:.zoo=01;31:.cpio=01;31:.7z=01;31:.rz=01;31:.cab=01;31:.jpg=01;35:.jpeg=01;35:.gif=01;35:.bmp=01;35:.pbm=01;35:.pgm=01;35:.ppm=01;35:.tga=01;35:.xbm=01;35:.xpm=01;35:.tif=01;35:.tiff=01;35:.png=01;35:.svg=01;35:.svgz=01;35:.mng=01;35:.pcx=01;35:.mov=01;35:.mpg=01;35:.mpeg=01;35:.m2v=01;35:.mkv=01;35:.webm=01;35:.ogm=01;35:.mp4=01;35:.m4v=01;35:.mp4v=01;35:.vob=01;35:.qt=01;35:.nuv=01;35:.wmv=01;35:.asf=01;35:.rm=01;35:.rmvb=01;35:.flc=01;35:.avi=01;35:.fli=01;35:.flv=01;35:.gl=01;35:.dl=01;35:.xcf=01;35:.xwd=01;35:.yuv=01;35:.cgm=01;35:.emf=01;35:.axv=01;35:.anx=01;35:.ogv=01;35:.ogx=01;35:.aac=00;36:.au=00;36:.flac=00;36:.m4a=00;36:.mid=00;36:.midi=00;36:.mka=00;36:.mp3=00;36:.mpc=00;36:.ogg=00;36:.ra=00;36:.wav=00;36:.axa=00;36:.oga=00;36:.spx=00;36:.xspf=00;36:’, ‘CRYOSPARC_CUDA_DEVS’: ‘0,1,2,3’, ‘HTTP_PROXY’: ‘http://proxy.aset.psu.edu:3128/’, ‘CRYOSPARC_LICENSE_ID’: ‘7fc3c6fb-372b-532e-b1b7-16e3a012fc82’, ‘CRYOSPARC_ROOT_DIR’: ‘/home/zuhaib/cryosparc’, ‘CRYOSPARC_UPLOAD_DIR’: ‘/home/zuhaib/cryosparc/run/bulk/uploads’, ‘CRYOSPARC_CACHE_CUSHION’: ‘10240.0’, ‘MODULE_VERSION’: ‘3.2.10’, ‘HOME’: ‘/home/zuhaib’, ‘LD_LIBRARY_PATH’: ‘/opt/cuda/8.0.61/lib64:’, ‘LANG’: ‘en_US.utf8’, ‘https_proxy’: ‘http://proxy.aset.psu.edu:3128/’, ‘GNOME_DESKTOP_SESSION_ID’: ‘this-is-deprecated’, ‘MKL_NUM_THREADS’: ‘1’, ‘CRYOSPARC_CODE_DIR’: ‘/home/zuhaib/cryosparc/cryosparc-compute’, ‘HTTP_FORWARDED_COUNT’: ‘1’, ‘ftp_proxy’: ‘http://proxy.aset.psu.edu:3128/’, ‘CRYOSPARC_ANACONDA_BINDIR’: ‘/home/zuhaib/cryosparc/anaconda2/bin’, ‘CRYOSPARC_INSECURE’: ‘false’, ‘CRYOSPARC_MONGO_PORT’: ‘38001’, ‘MONGO_URL’: ‘mongodb://localhost:38001/meteor’, ‘HTTPS_PROXY’: ‘http://proxy.aset.psu.edu:3128/’, ‘USER’: ‘zuhaib’, ‘USERNAME’: ‘zuhaib’, ‘GDM_LANG’: ‘en_US.utf8’, ‘NUMEXPR_NUM_THREADS’: ‘1’, ‘LOGNAME’: ‘zuhaib’, ‘XDG_SEAT’: ‘seat0’, ‘PATH’: ‘/home/zuhaib/cryosparc/mongodb/bin:/home/zuhaib/cryosparc/nodejs/bin:/home/zuhaib/cryosparc/anaconda2/bin:/opt/cuda/8.0.61/bin:/home/zuhaib/cryosparc/bin:/opt/focus/scripts/proc:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin’, ‘SSH_AGENT_PID’: ‘1401’, ‘TERM’: ‘xterm’, ‘no_proxy’: ‘localhost,127.0.0.0/8,psu.edu’, ‘WINDOWPATH’: ‘7’, ‘METEOR_SETTINGS’: ‘{“public”:{“webinstance”:false, “instancename”:“051374”, “instancetype”:“academicbeta”}}’, ‘CRYOSPARC_JOB_LOG_DIR’: ‘/home/zuhaib/cryosparc/run/sparcjobs’, ‘CRYOSPARC_SUPERVISOR_SOCK_FILE’: ‘/tmp/supervisor-6830169599366923827.sock’, ‘CRYOSPARC_INSTALL_TYPE’: ‘master’, ‘MODULE_VERSION_STACK’: ‘3.2.10’, ‘SSH_AUTH_SOCK’: ‘/run/user/1000/keyring/ssh’, ‘VTE_VERSION’: ‘3801’, ‘OLDPWD’: ‘/home/zuhaib/cryosparc’, ‘LOADEDMODULES’: ‘’, ‘APP_ID’: ‘1ipv1tp12xzfzhba088c’, ‘PWD’: ‘/home/zuhaib/cryosparc/cryosparc-webapp/bundle/programs/server’}
Traceback (most recent call last):
File “/home/zuhaib/cryosparc/cryosparc-compute/sparcjob.py”, line 23, in
import dataio
File “/home/zuhaib/cryosparc/cryosparc-compute/dataio/init.py”, line 8, in
from data import Dataset, SpoolingList, Prefetcher
File “/home/zuhaib/cryosparc/cryosparc-compute/dataio/data.py”, line 9, in
from util import dotdict
File “/home/zuhaib/cryosparc/cryosparc-compute/util/init.py”, line 10, in
from finitesum import FiniteRunningSum
File “/home/zuhaib/cryosparc/cryosparc-compute/util/finitesum.py”, line 8, in
import numpy as n
File “/home/zuhaib/.local/lib/python2.7/site-packages/numpy/init.py”, line 160, in
from . import random
File “/home/zuhaib/.local/lib/python2.7/site-packages/numpy/random/init.py”, line 99, in
from .mtrand import *
ImportError: /home/zuhaib/.local/lib/python2.7/site-packages/numpy/random/mtrand.so: undefined symbol: PyFPE_jbuf