List index out of range

Install, Configure and Update
1

Getting list index out of range when trying to run any jobs. I didnt encounter errors on install. cryosparmstatus

CryoSPARC System master node installed at
/home/roger/cryosparc_master
Current cryoSPARC version: v3.1.0

cryosparcm process status:

app RUNNING pid 3095, uptime 0:10:54
app_dev STOPPED Not started
command_core RUNNING pid 3013, uptime 0:11:03
command_rtp RUNNING pid 3038, uptime 0:11:00
command_vis RUNNING pid 3034, uptime 0:11:01
database RUNNING pid 2938, uptime 0:11:05
liveapp RUNNING pid 3115, uptime 0:10:52
liveapp_dev STOPPED Not started
watchdog_dev STOPPED Not started
webapp RUNNING pid 3071, uptime 0:10:55
webapp_dev STOPPED Not started

global config variables:

export CRYOSPARC_LICENSE_ID=“xxxxxxxxxxxxxxx”
export CRYOSPARC_MASTER_HOSTNAME=“localhost”
export CRYOSPARC_DB_PATH="/home/roger/cryosparc_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=false
export CRYOSPARC_CLICK_WRAP=true

2

error log

ERROR: ld.so: object '/home/roger/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/[libpython3.7m.so](http://libpython3.7m.so)' from LD_PRELOAD cannot be preloaded (failed to map segment from shared object): ignored.
ERROR: ld.so: object '/home/roger/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/libtiff.so' from LD_PRELOAD cannot be preloaded (failed to map segment from shared object): ignored.
ERROR: ld.so: object '/home/roger/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/[libpython3.7m.so](http://libpython3.7m.so)' from LD_PRELOAD cannot be preloaded (failed to map segment from shared object): ignored.
ERROR: ld.so: object '/home/roger/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/libtiff.so' from LD_PRELOAD cannot be preloaded (failed to map segment from shared object): ignored.
ERROR: ld.so: object '/home/roger/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/[libpython3.7m.so](http://libpython3.7m.so)' from LD_PRELOAD cannot be preloaded (failed to map segment from shared object): ignored.
ERROR: ld.so: object '/home/roger/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/libtiff.so' from LD_PRELOAD cannot be preloaded (failed to map segment from shared object): ignored.
ERROR: ld.so: object '/home/roger/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/[libpython3.7m.so](http://libpython3.7m.so)' from LD_PRELOAD cannot be preloaded (failed to map segment from shared object): ignored.
ERROR: ld.so: object '/home/roger/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/libtiff.so' from LD_PRELOAD cannot be preloaded (failed to map segment from shared object): ignored.
ERROR: ld.so: object '/home/roger/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/[libpython3.7m.so](http://libpython3.7m.so)' from LD_PRELOAD cannot be preloaded (failed to map segment from shared object): ignored.
ERROR: ld.so: object '/home/roger/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/libtiff.so' from LD_PRELOAD cannot be preloaded (failed to map segment from shared object): ignored.
ERROR: ld.so: object '/home/roger/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/[libpython3.7m.so](http://libpython3.7m.so)' from LD_PRELOAD cannot be preloaded (failed to map segment from shared object): ignored.
ERROR: ld.so: object '/home/roger/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/libtiff.so' from LD_PRELOAD cannot be preloaded (failed to map segment from shared object): ignored.
ERROR: ld.so: object '/home/roger/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/[libpython3.7m.so](http://libpython3.7m.so)' from LD_PRELOAD cannot be preloaded (failed to map segment from shared object): ignored.
ERROR: ld.so: object '/home/roger/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/libtiff.so' from LD_PRELOAD cannot be preloaded (failed to map segment from shared object): ignored.
ERROR: ld.so: object '/home/roger/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/[libpython3.7m.so](http://libpython3.7m.so)' from LD_PRELOAD cannot be preloaded (failed to map segment from shared object): ignored.
ERROR: ld.so: object '/home/roger/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/libtiff.so' from LD_PRELOAD cannot be preloaded (failed to map segment from shared object): ignored.>

This was installed on a single standalone workstation on OpenSuse15.2 Leap, which I know isn’t supported, but any help would be appreciated :slight_smile: Thank you!

3

i tried forcing dependencies reinstall

Checking dependencies... 
  Forcing dependencies to be reinstalled...
  ------------------------------------------------------------------------
  Installing anaconda python...
  ------------------------------------------------------------------------
PREFIX=/home/roger/cryosparc_master/deps/anaconda
Unpacking payload ...
Collecting package metadata (current_repodata.json): done                               
Solving environment: done

## Package Plan ##

  environment location: /home/roger/cryosparc_master/deps/anaconda

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - ca-certificates==2020.1.1=0
    - certifi==2020.4.5.1=py37_0
    - cffi==1.14.0=py37he30daa8_1
    - chardet==3.0.4=py37_1003
    - conda-package-handling==1.6.1=py37h7b6447c_0
    - conda==4.8.3=py37_0
    - cryptography==2.9.2=py37h1ba5d50_0
    - idna==2.9=py_1
    - ld_impl_linux-64==2.33.1=h53a641e_7
    - libedit==3.1.20181209=hc058e9b_0
    - libffi==3.3=he6710b0_1
    - libgcc-ng==9.1.0=hdf63c60_0
    - libstdcxx-ng==9.1.0=hdf63c60_0
    - ncurses==6.2=he6710b0_1
    - openssl==1.1.1g=h7b6447c_0
    - pip==20.0.2=py37_3
    - pycosat==0.6.3=py37h7b6447c_0
    - pycparser==2.20=py_0
    - pyopenssl==19.1.0=py37_0
    - pysocks==1.7.1=py37_0
    - python==3.7.7=hcff3b4d_5
    - readline==8.0=h7b6447c_0
    - requests==2.23.0=py37_0
    - ruamel_yaml==0.15.87=py37h7b6447c_0
    - setuptools==46.4.0=py37_0
    - six==1.14.0=py37_0
    - sqlite==3.31.1=h62c20be_1
    - tk==8.6.8=hbc83047_0
    - tqdm==4.46.0=py_0
    - urllib3==1.25.8=py37_0
    - wheel==0.34.2=py37_0
    - xz==5.2.5=h7b6447c_0
    - yaml==0.1.7=had09818_2
    - zlib==1.2.11=h7b6447c_3


The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  ca-certificates    pkgs/main/linux-64::ca-certificates-2020.1.1-0
  certifi            pkgs/main/linux-64::certifi-2020.4.5.1-py37_0
  cffi               pkgs/main/linux-64::cffi-1.14.0-py37he30daa8_1
  chardet            pkgs/main/linux-64::chardet-3.0.4-py37_1003
  conda              pkgs/main/linux-64::conda-4.8.3-py37_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.1-py37h7b6447c_0
  cryptography       pkgs/main/linux-64::cryptography-2.9.2-py37h1ba5d50_0
  idna               pkgs/main/noarch::idna-2.9-py_1
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.33.1-h53a641e_7
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_1
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.2-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1g-h7b6447c_0
  pip                pkgs/main/linux-64::pip-20.0.2-py37_3
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py37h7b6447c_0
  pycparser          pkgs/main/noarch::pycparser-2.20-py_0
  pyopenssl          pkgs/main/linux-64::pyopenssl-19.1.0-py37_0
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py37_0
  python             pkgs/main/linux-64::python-3.7.7-hcff3b4d_5
  readline           pkgs/main/linux-64::readline-8.0-h7b6447c_0
  requests           pkgs/main/linux-64::requests-2.23.0-py37_0
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.87-py37h7b6447c_0
  setuptools         pkgs/main/linux-64::setuptools-46.4.0-py37_0
  six                pkgs/main/linux-64::six-1.14.0-py37_0
  sqlite             pkgs/main/linux-64::sqlite-3.31.1-h62c20be_1
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  tqdm               pkgs/main/noarch::tqdm-4.46.0-py_0
  urllib3            pkgs/main/linux-64::urllib3-1.25.8-py37_0
  wheel              pkgs/main/linux-64::wheel-0.34.2-py37_0
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  yaml               pkgs/main/linux-64::yaml-0.1.7-had09818_2
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3


Preparing transaction: done
Executing transaction: done
installation finished.
  ------------------------------------------------------------------------
    Done.
    anaconda python installation successful.
  ------------------------------------------------------------------------
  Extracting all conda packages...
  ------------------------------------------------------------------------
..........................................................................
  ------------------------------------------------------------------------
    Done.
    conda packages installation successful.
  ------------------------------------------------------------------------
  Main dependency installation completed. Continuing...
  ------------------------------------------------------------------------
  Completed.
  Currently checking hash for mongodb
  Forcing reinstall for dependency mongodb...
  ------------------------------------------------------------------------
  mongodb 3.4.10 installation successful.
  ------------------------------------------------------------------------
  Completed.
  Completed dependency check. 
roger@install:~> crysosparcm restart
If 'crysosparcm' is not a typo you can use command-not-found to lookup the package that contains it, like this:
    cnf crysosparcm
roger@install:~> cryosparcm restart 
CryoSPARC is running.
Stopping cryoSPARC 
app: stopped
command_core: stopped
command_rtp: stopped
command_vis: stopped
liveapp: stopped
webapp: stopped
database: stopped
Shut down
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: started
command_core: started
command_core connection succeeded

command_vis: started
command_rtp: started
command_rtp connection succeeded

webapp: started
app: started
liveapp: started
-----------------------------------------------------

CryoSPARC master started. 
 From this machine, access cryoSPARC at
    http://localhost:39000
 and access cryoSPARC Live at
    http://localhost:39006
 please note the legacy cryoSPARC Live application is running at
    http://localhost:39007

 From other machines on the network, access cryoSPARC at
    http://localhost:39000
 and access cryoSPARC Live at
    http://localhost:39006


Startup can take several minutes. Point your browser to the address
and refresh until you see the cryoSPARC web interface.
4

Doh, I didn’t realize the worker also needed to be downloaded and installed. Works fine on OpenSuse and Ubuntu.

2 Likes