Installation Freeze

KunFang93 · August 14, 2024, 1:37pm

Dear CryoSPARC team,

Thanks for providing this wonderful tool. I tried to install but it stuck in command_core: started. My installation command is ./install.sh --standalone --license [redacted] --worker_path /home/jk4882/data/CryoSPARC_data --ssdpath /mnt/data/ --initial_email [redacted] --initial_username jkang --initial_firstname Junqing --initial_lastname Kang
And below is my screen output

************ CRYOSPARC SYSTEM: STANDALONE INSTALLER **************

  Input initial user password:
  Input initial user password (again):

 Installation Settings:
   License ID              : [redacted]
   Root Directory          : /mnt/data/cryosparc_master
   Master Hostname         : icrc4lcga001
   Database Directory      : /mnt/data/cryosparc_database
   Base HTTP Port Number   : 39000
   Developer Install       : false
   Operating System        : Linux
   Insecure Install        : false
   Standalone Install      : true
   Worker Root Directory   : /home/jk4882/data/CryoSPARC_data
   Initial User Email      : [redacted]
   Initial User Name       : jkang
   Initial First Name      : Junqing
   Initial Last Name       : Kang
   SSD                     : true
   SSD Path                : /mnt/data/
   Version                 : v4.5.3

******************************************************************

The CryoSPARC System master installation will host a database,
web application, and command layer for CryoSPARC, but will not
perform processing jobs.

Please read and confirm the above settings. The CryoSPARC database
will be stored at the database directory which is relative to the
root directory, unless provided as an absolute path.
You can change the database directory now by passing the --dbpath
parameter to this installer, or later via the command line.

Are the above settings correct?
1) Yes
2) No
#? 1
Continuing.

******************************************************************

 Setting up hard-coded config.sh environment variables

******************************************************************

 Installing all dependencies.

Warning: conda environment not found; this indicates that a cryoSPARC installation is either incomplete or in progress
  Checking dependencies...
  Dependencies for python have changed - reinstalling...
  ------------------------------------------------------------------------
  Installing anaconda python...
  ------------------------------------------------------------------------
PREFIX=/mnt/data/cryosparc_master/deps/anaconda
Unpacking payload ...
Extracting _libgcc_mutex-0.1-conda_forge.tar.bz2
Extracting ca-certificates-2024.2.2-hbcca054_0.conda
Extracting ld_impl_linux-64-2.40-h41732ed_0.conda
Extracting libstdcxx-ng-13.2.0-h7e041cc_5.conda
Extracting pybind11-abi-4-hd8ed1ab_3.tar.bz2
Extracting python_abi-3.10-4_cp310.conda
Extracting tzdata-2024a-h0c530f3_0.conda
Extracting libgomp-13.2.0-h807b86a_5.conda
Extracting _openmp_mutex-4.5-2_gnu.tar.bz2
Extracting libgcc-ng-13.2.0-h807b86a_5.conda
Extracting bzip2-1.0.8-hd590300_5.conda
Extracting c-ares-1.27.0-hd590300_0.conda
Extracting fmt-10.2.1-h00ab1b0_0.conda
Extracting icu-73.2-h59595ed_0.conda
Extracting keyutils-1.6.1-h166bdaf_0.tar.bz2
Extracting libev-4.33-hd590300_2.conda
Extracting libffi-3.4.2-h7f98852_5.tar.bz2
Extracting libiconv-1.17-hd590300_2.conda
Extracting libnsl-2.0.1-hd590300_0.conda
Extracting libuuid-2.38.1-h0b41bf4_0.conda
Extracting libxcrypt-4.4.36-hd590300_1.conda
Extracting libzlib-1.2.13-hd590300_5.conda
Extracting lz4-c-1.9.4-hcb278e6_0.conda
Extracting lzo-2.10-h516909a_1000.tar.bz2
Extracting ncurses-6.4.20240210-h59595ed_0.conda
Extracting openssl-3.2.1-hd590300_1.conda
Extracting reproc-14.2.4.post0-hd590300_1.conda
Extracting xz-5.2.6-h166bdaf_0.tar.bz2
Extracting yaml-cpp-0.8.0-h59595ed_0.conda
Extracting libedit-3.1.20191231-he28a2e2_2.tar.bz2
Extracting libnghttp2-1.58.0-h47da74e_1.conda
Extracting libsolv-0.7.28-hfc55251_0.conda
Extracting libsqlite-3.45.2-h2797004_0.conda
Extracting libssh2-1.11.0-h0841786_0.conda
Extracting libxml2-2.12.6-h232c23b_0.conda
Extracting readline-8.2-h8228510_1.conda
Extracting reproc-cpp-14.2.4.post0-h59595ed_1.conda
Extracting tk-8.6.13-noxft_h4845f30_101.conda
Extracting zstd-1.5.5-hfc55251_0.conda
Extracting krb5-1.21.2-h659d440_0.conda
Extracting libarchive-3.7.2-h2aa1ff5_1.conda
Extracting python-3.10.14-hd12c33a_0_cpython.conda
Extracting libcurl-8.6.0-hca28451_0.conda
Extracting menuinst-2.0.2-py310hff52083_0.conda
Extracting archspec-0.2.3-pyhd8ed1ab_0.conda
Extracting boltons-23.1.1-pyhd8ed1ab_0.conda
Extracting brotli-python-1.1.0-py310hc6cd4ac_1.conda
Extracting certifi-2024.2.2-pyhd8ed1ab_0.conda
Extracting charset-normalizer-3.3.2-pyhd8ed1ab_0.conda
Extracting colorama-0.4.6-pyhd8ed1ab_0.tar.bz2
Extracting distro-1.9.0-pyhd8ed1ab_0.conda
Extracting idna-3.6-pyhd8ed1ab_0.conda
Extracting jsonpointer-2.4-py310hff52083_3.conda
Extracting libmamba-1.5.7-had39da4_0.conda
Extracting packaging-24.0-pyhd8ed1ab_0.conda
Extracting platformdirs-4.2.0-pyhd8ed1ab_0.conda
Extracting pluggy-1.4.0-pyhd8ed1ab_0.conda
Extracting pycosat-0.6.6-py310h2372a71_0.conda
Extracting pycparser-2.21-pyhd8ed1ab_0.tar.bz2
Extracting pysocks-1.7.1-pyha2e5f31_6.tar.bz2
Extracting ruamel.yaml.clib-0.2.8-py310h2372a71_0.conda
Extracting setuptools-69.2.0-pyhd8ed1ab_0.conda
Extracting truststore-0.8.0-pyhd8ed1ab_0.conda
Extracting wheel-0.43.0-pyhd8ed1ab_0.conda
Extracting cffi-1.16.0-py310h2fee648_0.conda
Extracting jsonpatch-1.33-pyhd8ed1ab_0.conda
Extracting libmambapy-1.5.7-py310h39ff949_0.conda
Extracting pip-24.0-pyhd8ed1ab_0.conda
Extracting ruamel.yaml-0.18.6-py310h2372a71_0.conda
Extracting tqdm-4.66.2-pyhd8ed1ab_0.conda
Extracting urllib3-2.2.1-pyhd8ed1ab_0.conda
Extracting requests-2.31.0-pyhd8ed1ab_0.conda
Extracting zstandard-0.22.0-py310h1275a96_0.conda
Extracting conda-package-streaming-0.9.0-pyhd8ed1ab_0.conda
Extracting conda-package-handling-2.2.0-pyh38be061_0.conda
Extracting conda-24.1.2-py310hff52083_0.conda
Extracting conda-libmamba-solver-24.1.0-pyhd8ed1ab_0.conda
Extracting mamba-1.5.7-py310h51d5547_0.conda

Installing base environment...


                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

Transaction

  Prefix: /mnt/data/cryosparc_master/deps/anaconda

  Updating specs:

   - conda-forge/linux-64::_libgcc_mutex==0.1=conda_forge[md5=d7c89558ba9fa0495403155b64376d81]
   - conda-forge/linux-64::ca-certificates==2024.2.2=hbcca054_0[md5=2f4327a1cbe7f022401b236e915a5fef]
   - conda-forge/linux-64::ld_impl_linux-64==2.40=h41732ed_0[md5=7aca3059a1729aa76c597603f10b0dd3]
   - conda-forge/linux-64::libstdcxx-ng==13.2.0=h7e041cc_5[md5=f6f6600d18a4047b54f803cf708b868a]
   - conda-forge/noarch::pybind11-abi==4=hd8ed1ab_3[md5=878f923dd6acc8aeb47a75da6c4098be]
   - conda-forge/linux-64::python_abi==3.10=4_cp310[md5=26322ec5d7712c3ded99dd656142b8ce]
   - conda-forge/noarch::tzdata==2024a=h0c530f3_0[md5=161081fc7cec0bfda0d86d7cb595f8d8]
   - conda-forge/linux-64::libgomp==13.2.0=h807b86a_5[md5=d211c42b9ce49aee3734fdc828731689]
   - conda-forge/linux-64::_openmp_mutex==4.5=2_gnu[md5=73aaf86a425cc6e73fcf236a5a46396d]
   - conda-forge/linux-64::libgcc-ng==13.2.0=h807b86a_5[md5=d4ff227c46917d3b4565302a2bbb276b]
   - conda-forge/linux-64::bzip2==1.0.8=hd590300_5[md5=69b8b6202a07720f448be700e300ccf4]
   - conda-forge/linux-64::c-ares==1.27.0=hd590300_0[md5=f6afff0e9ee08d2f1b897881a4f38cdb]
   - conda-forge/linux-64::fmt==10.2.1=h00ab1b0_0[md5=35ef8bc24bd34074ebae3c943d551728]
   - conda-forge/linux-64::icu==73.2=h59595ed_0[md5=cc47e1facc155f91abd89b11e48e72ff]
   - conda-forge/linux-64::keyutils==1.6.1=h166bdaf_0[md5=30186d27e2c9fa62b45fb1476b7200e3]
   - conda-forge/linux-64::libev==4.33=hd590300_2[md5=172bf1cd1ff8629f2b1179945ed45055]
   - conda-forge/linux-64::libffi==3.4.2=h7f98852_5[md5=d645c6d2ac96843a2bfaccd2d62b3ac3]
   - conda-forge/linux-64::libiconv==1.17=hd590300_2[md5=d66573916ffcf376178462f1b61c941e]
   - conda-forge/linux-64::libnsl==2.0.1=hd590300_0[md5=30fd6e37fe21f86f4bd26d6ee73eeec7]
   - conda-forge/linux-64::libuuid==2.38.1=h0b41bf4_0[md5=40b61aab5c7ba9ff276c41cfffe6b80b]
   - conda-forge/linux-64::libxcrypt==4.4.36=hd590300_1[md5=5aa797f8787fe7a17d1b0821485b5adc]
   - conda-forge/linux-64::libzlib==1.2.13=hd590300_5[md5=f36c115f1ee199da648e0597ec2047ad]
   - conda-forge/linux-64::lz4-c==1.9.4=hcb278e6_0[md5=318b08df404f9c9be5712aaa5a6f0bb0]
   - conda-forge/linux-64::lzo==2.10=h516909a_1000[md5=bb14fcb13341b81d5eb386423b9d2bac]
   - conda-forge/linux-64::ncurses==6.4.20240210=h59595ed_0[md5=97da8860a0da5413c7c98a3b3838a645]
   - conda-forge/linux-64::openssl==3.2.1=hd590300_1[md5=9d731343cff6ee2e5a25c4a091bf8e2a]
   - conda-forge/linux-64::reproc==14.2.4.post0=hd590300_1[md5=82ca53502dfd5a64a80dee76dae14685]
   - conda-forge/linux-64::xz==5.2.6=h166bdaf_0[md5=2161070d867d1b1204ea749c8eec4ef0]
   - conda-forge/linux-64::yaml-cpp==0.8.0=h59595ed_0[md5=965eaacd7c18eb8361fd12bb9e7a57d7]
   - conda-forge/linux-64::libedit==3.1.20191231=he28a2e2_2[md5=4d331e44109e3f0e19b4cb8f9b82f3e1]
   - conda-forge/linux-64::libnghttp2==1.58.0=h47da74e_1[md5=700ac6ea6d53d5510591c4344d5c989a]
   - conda-forge/linux-64::libsolv==0.7.28=hfc55251_0[md5=66d4f5d8256542d9ebfa341d690c5e03]
   - conda-forge/linux-64::libsqlite==3.45.2=h2797004_0[md5=866983a220e27a80cb75e85cb30466a1]
   - conda-forge/linux-64::libssh2==1.11.0=h0841786_0[md5=1f5a58e686b13bcfde88b93f547d23fe]
   - conda-forge/linux-64::libxml2==2.12.6=h232c23b_0[md5=d86653ff5ccb88bf7f13833fdd8789e0]
   - conda-forge/linux-64::readline==8.2=h8228510_1[md5=47d31b792659ce70f470b5c82fdfb7a4]
   - conda-forge/linux-64::reproc-cpp==14.2.4.post0=h59595ed_1[md5=715e1d720ec1a03715bebd237972fca5]
   - conda-forge/linux-64::tk==8.6.13=noxft_h4845f30_101[md5=d453b98d9c83e71da0741bb0ff4d76bc]
   - conda-forge/linux-64::zstd==1.5.5=hfc55251_0[md5=04b88013080254850d6c01ed54810589]
   - conda-forge/linux-64::krb5==1.21.2=h659d440_0[md5=cd95826dbd331ed1be26bdf401432844]
   - conda-forge/linux-64::libarchive==3.7.2=h2aa1ff5_1[md5=3bf887827d1968275978361a6e405e4f]
   - conda-forge/linux-64::python==3.10.14=hd12c33a_0_cpython[md5=2b4ba962994e8bd4be9ff5b64b75aff2]
   - conda-forge/linux-64::libcurl==8.6.0=hca28451_0[md5=704739398d858872cb91610f49f0ef29]
   - conda-forge/linux-64::menuinst==2.0.2=py310hff52083_0[md5=4837faab0d3e665df57fef662148c6a3]
   - conda-forge/noarch::archspec==0.2.3=pyhd8ed1ab_0[md5=192278292e20704f663b9c766909d67b]
   - conda-forge/noarch::boltons==23.1.1=pyhd8ed1ab_0[md5=56febe65315cc388a5d20adf2b39a74d]
   - conda-forge/linux-64::brotli-python==1.1.0=py310hc6cd4ac_1[md5=1f95722c94f00b69af69a066c7433714]
   - conda-forge/noarch::certifi==2024.2.2=pyhd8ed1ab_0[md5=0876280e409658fc6f9e75d035960333]
   - conda-forge/noarch::charset-normalizer==3.3.2=pyhd8ed1ab_0[md5=7f4a9e3fcff3f6356ae99244a014da6a]
   - conda-forge/noarch::colorama==0.4.6=pyhd8ed1ab_0[md5=3faab06a954c2a04039983f2c4a50d99]
   - conda-forge/noarch::distro==1.9.0=pyhd8ed1ab_0[md5=bbdb409974cd6cb30071b1d978302726]
   - conda-forge/noarch::idna==3.6=pyhd8ed1ab_0[md5=1a76f09108576397c41c0b0c5bd84134]
   - conda-forge/linux-64::jsonpointer==2.4=py310hff52083_3[md5=08ec1463dbc5c806a32fc431874032ca]
   - conda-forge/linux-64::libmamba==1.5.7=had39da4_0[md5=9fff450354fbcd1510ef178730732241]
   - conda-forge/noarch::packaging==24.0=pyhd8ed1ab_0[md5=248f521b64ce055e7feae3105e7abeb8]
   - conda-forge/noarch::platformdirs==4.2.0=pyhd8ed1ab_0[md5=a0bc3eec34b0fab84be6b2da94e98e20]
   - conda-forge/noarch::pluggy==1.4.0=pyhd8ed1ab_0[md5=139e9feb65187e916162917bb2484976]
   - conda-forge/linux-64::pycosat==0.6.6=py310h2372a71_0[md5=0adaac9a86d59adae2bc86b3cdef2df1]
   - conda-forge/noarch::pycparser==2.21=pyhd8ed1ab_0[md5=076becd9e05608f8dc72757d5f3a91ff]
   - conda-forge/noarch::pysocks==1.7.1=pyha2e5f31_6[md5=2a7de29fb590ca14b5243c4c812c8025]
   - conda-forge/linux-64::ruamel.yaml.clib==0.2.8=py310h2372a71_0[md5=dcf6d2535586c77b31425ed835610c54]
   - conda-forge/noarch::setuptools==69.2.0=pyhd8ed1ab_0[md5=da214ecd521a720a9d521c68047682dc]
   - conda-forge/noarch::truststore==0.8.0=pyhd8ed1ab_0[md5=08316d001eca8854392cf2837828ea11]
   - conda-forge/noarch::wheel==0.43.0=pyhd8ed1ab_0[md5=6e43a94e0ee67523b5e781f0faba5c45]
   - conda-forge/linux-64::cffi==1.16.0=py310h2fee648_0[md5=45846a970e71ac98fd327da5d40a0a2c]
   - conda-forge/noarch::jsonpatch==1.33=pyhd8ed1ab_0[md5=bfdb7c5c6ad1077c82a69a8642c87aff]
   - conda-forge/linux-64::libmambapy==1.5.7=py310h39ff949_0[md5=58d84efb37d517c64f4e48f75fd6180d]
   - conda-forge/noarch::pip==24.0=pyhd8ed1ab_0[md5=f586ac1e56c8638b64f9c8122a7b8a67]
   - conda-forge/linux-64::ruamel.yaml==0.18.6=py310h2372a71_0[md5=50b7d9b39099cdbabf65bf27df73a793]
   - conda-forge/noarch::tqdm==4.66.2=pyhd8ed1ab_0[md5=2b8dfb969f984497f3f98409a9545776]
   - conda-forge/noarch::urllib3==2.2.1=pyhd8ed1ab_0[md5=08807a87fa7af10754d46f63b368e016]
   - conda-forge/noarch::requests==2.31.0=pyhd8ed1ab_0[md5=a30144e4156cdbb236f99ebb49828f8b]
   - conda-forge/linux-64::zstandard==0.22.0=py310h1275a96_0[md5=54698ba13cd3494547b289cd86a2176a]
   - conda-forge/noarch::conda-package-streaming==0.9.0=pyhd8ed1ab_0[md5=38253361efb303deead3eab39ae9269b]
   - conda-forge/noarch::conda-package-handling==2.2.0=pyh38be061_0[md5=8a3ae7f6318376aa08ea753367bb7dd6]
   - conda-forge/linux-64::conda==24.1.2=py310hff52083_0[md5=d7a8a166cf89ed19a7d3ee41b71a5d6f]
   - conda-forge/noarch::conda-libmamba-solver==24.1.0=pyhd8ed1ab_0[md5=304dc78ad6e52e0fd663df1d484c1531]
   - conda-forge/linux-64::mamba==1.5.7=py310h51d5547_0[md5=5977cafef2904d1588d0c23b94846f2c]


  Package                         Version  Build               Channel           Size
───────────────────────────────────────────────────────────────────────────────────────
  Install:
───────────────────────────────────────────────────────────────────────────────────────

  + _libgcc_mutex                     0.1  conda_forge         conda-forge     Cached
  + _openmp_mutex                     4.5  2_gnu               conda-forge     Cached
  + archspec                        0.2.3  pyhd8ed1ab_0        conda-forge     Cached
  + boltons                        23.1.1  pyhd8ed1ab_0        conda-forge     Cached
  + brotli-python                   1.1.0  py310hc6cd4ac_1     conda-forge     Cached
  + bzip2                           1.0.8  hd590300_5          conda-forge     Cached
  + c-ares                         1.27.0  hd590300_0          conda-forge     Cached
  + ca-certificates              2024.2.2  hbcca054_0          conda-forge     Cached
  + certifi                      2024.2.2  pyhd8ed1ab_0        conda-forge     Cached
  + cffi                           1.16.0  py310h2fee648_0     conda-forge     Cached
  + charset-normalizer              3.3.2  pyhd8ed1ab_0        conda-forge     Cached
  + colorama                        0.4.6  pyhd8ed1ab_0        conda-forge     Cached
  + conda                          24.1.2  py310hff52083_0     conda-forge     Cached
  + conda-libmamba-solver          24.1.0  pyhd8ed1ab_0        conda-forge     Cached
  + conda-package-handling          2.2.0  pyh38be061_0        conda-forge     Cached
  + conda-package-streaming         0.9.0  pyhd8ed1ab_0        conda-forge     Cached
  + distro                          1.9.0  pyhd8ed1ab_0        conda-forge     Cached
  + fmt                            10.2.1  h00ab1b0_0          conda-forge     Cached
  + icu                              73.2  h59595ed_0          conda-forge     Cached
  + idna                              3.6  pyhd8ed1ab_0        conda-forge     Cached
  + jsonpatch                        1.33  pyhd8ed1ab_0        conda-forge     Cached
  + jsonpointer                       2.4  py310hff52083_3     conda-forge     Cached
  + keyutils                        1.6.1  h166bdaf_0          conda-forge     Cached
  + krb5                           1.21.2  h659d440_0          conda-forge     Cached
  + ld_impl_linux-64                 2.40  h41732ed_0          conda-forge     Cached
  + libarchive                      3.7.2  h2aa1ff5_1          conda-forge     Cached
  + libcurl                         8.6.0  hca28451_0          conda-forge     Cached
  + libedit                  3.1.20191231  he28a2e2_2          conda-forge     Cached
  + libev                            4.33  hd590300_2          conda-forge     Cached
  + libffi                          3.4.2  h7f98852_5          conda-forge     Cached
  + libgcc-ng                      13.2.0  h807b86a_5          conda-forge     Cached
  + libgomp                        13.2.0  h807b86a_5          conda-forge     Cached
  + libiconv                         1.17  hd590300_2          conda-forge     Cached
  + libmamba                        1.5.7  had39da4_0          conda-forge     Cached
  + libmambapy                      1.5.7  py310h39ff949_0     conda-forge     Cached
  + libnghttp2                     1.58.0  h47da74e_1          conda-forge     Cached
  + libnsl                          2.0.1  hd590300_0          conda-forge     Cached
  + libsolv                        0.7.28  hfc55251_0          conda-forge     Cached
  + libsqlite                      3.45.2  h2797004_0          conda-forge     Cached
  + libssh2                        1.11.0  h0841786_0          conda-forge     Cached
  + libstdcxx-ng                   13.2.0  h7e041cc_5          conda-forge     Cached
  + libuuid                        2.38.1  h0b41bf4_0          conda-forge     Cached
  + libxcrypt                      4.4.36  hd590300_1          conda-forge     Cached
  + libxml2                        2.12.6  h232c23b_0          conda-forge     Cached
  + libzlib                        1.2.13  hd590300_5          conda-forge     Cached
  + lz4-c                           1.9.4  hcb278e6_0          conda-forge     Cached
  + lzo                              2.10  h516909a_1000       conda-forge     Cached
  + mamba                           1.5.7  py310h51d5547_0     conda-forge     Cached
  + menuinst                        2.0.2  py310hff52083_0     conda-forge     Cached
  + ncurses                  6.4.20240210  h59595ed_0          conda-forge     Cached
  + openssl                         3.2.1  hd590300_1          conda-forge     Cached
  + packaging                        24.0  pyhd8ed1ab_0        conda-forge     Cached
  + pip                              24.0  pyhd8ed1ab_0        conda-forge     Cached
  + platformdirs                    4.2.0  pyhd8ed1ab_0        conda-forge     Cached
  + pluggy                          1.4.0  pyhd8ed1ab_0        conda-forge     Cached
  + pybind11-abi                        4  hd8ed1ab_3          conda-forge     Cached
  + pycosat                         0.6.6  py310h2372a71_0     conda-forge     Cached
  + pycparser                        2.21  pyhd8ed1ab_0        conda-forge     Cached
  + pysocks                         1.7.1  pyha2e5f31_6        conda-forge     Cached
  + python                        3.10.14  hd12c33a_0_cpython  conda-forge     Cached
  + python_abi                       3.10  4_cp310             conda-forge     Cached
  + readline                          8.2  h8228510_1          conda-forge     Cached
  + reproc                   14.2.4.post0  hd590300_1          conda-forge     Cached
  + reproc-cpp               14.2.4.post0  h59595ed_1          conda-forge     Cached
  + requests                       2.31.0  pyhd8ed1ab_0        conda-forge     Cached
  + ruamel.yaml                    0.18.6  py310h2372a71_0     conda-forge     Cached
  + ruamel.yaml.clib                0.2.8  py310h2372a71_0     conda-forge     Cached
  + setuptools                     69.2.0  pyhd8ed1ab_0        conda-forge     Cached
  + tk                             8.6.13  noxft_h4845f30_101  conda-forge     Cached
  + tqdm                           4.66.2  pyhd8ed1ab_0        conda-forge     Cached
  + truststore                      0.8.0  pyhd8ed1ab_0        conda-forge     Cached
  + tzdata                          2024a  h0c530f3_0          conda-forge     Cached
  + urllib3                         2.2.1  pyhd8ed1ab_0        conda-forge     Cached
  + wheel                          0.43.0  pyhd8ed1ab_0        conda-forge     Cached
  + xz                              5.2.6  h166bdaf_0          conda-forge     Cached
  + yaml-cpp                        0.8.0  h59595ed_0          conda-forge     Cached
  + zstandard                      0.22.0  py310h1275a96_0     conda-forge     Cached
  + zstd                            1.5.5  hfc55251_0          conda-forge     Cached

  Summary:

  Install: 78 packages

  Total download: 0 B

───────────────────────────────────────────────────────────────────────────────────────



Transaction starting
Linking _libgcc_mutex-0.1-conda_forge
Linking ca-certificates-2024.2.2-hbcca054_0
Linking ld_impl_linux-64-2.40-h41732ed_0
Linking libstdcxx-ng-13.2.0-h7e041cc_5
Linking pybind11-abi-4-hd8ed1ab_3
Linking python_abi-3.10-4_cp310
Linking tzdata-2024a-h0c530f3_0
Linking libgomp-13.2.0-h807b86a_5
Linking _openmp_mutex-4.5-2_gnu
Linking libgcc-ng-13.2.0-h807b86a_5
Linking bzip2-1.0.8-hd590300_5
Linking c-ares-1.27.0-hd590300_0
Linking fmt-10.2.1-h00ab1b0_0
Linking icu-73.2-h59595ed_0
Linking keyutils-1.6.1-h166bdaf_0
Linking libev-4.33-hd590300_2
Linking libffi-3.4.2-h7f98852_5
Linking libiconv-1.17-hd590300_2
Linking libnsl-2.0.1-hd590300_0
Linking libuuid-2.38.1-h0b41bf4_0
Linking libxcrypt-4.4.36-hd590300_1
Linking libzlib-1.2.13-hd590300_5
Linking lz4-c-1.9.4-hcb278e6_0
Linking lzo-2.10-h516909a_1000
Linking ncurses-6.4.20240210-h59595ed_0
Linking openssl-3.2.1-hd590300_1
Linking reproc-14.2.4.post0-hd590300_1
Linking xz-5.2.6-h166bdaf_0
Linking yaml-cpp-0.8.0-h59595ed_0
Linking libedit-3.1.20191231-he28a2e2_2
Linking libnghttp2-1.58.0-h47da74e_1
Linking libsolv-0.7.28-hfc55251_0
Linking libsqlite-3.45.2-h2797004_0
Linking libssh2-1.11.0-h0841786_0
Linking libxml2-2.12.6-h232c23b_0
Linking readline-8.2-h8228510_1
Linking reproc-cpp-14.2.4.post0-h59595ed_1
Linking tk-8.6.13-noxft_h4845f30_101
Linking zstd-1.5.5-hfc55251_0
Linking krb5-1.21.2-h659d440_0
Linking libarchive-3.7.2-h2aa1ff5_1
Linking python-3.10.14-hd12c33a_0_cpython
Linking libcurl-8.6.0-hca28451_0
Linking menuinst-2.0.2-py310hff52083_0
Linking archspec-0.2.3-pyhd8ed1ab_0
Linking boltons-23.1.1-pyhd8ed1ab_0
Linking brotli-python-1.1.0-py310hc6cd4ac_1
Linking certifi-2024.2.2-pyhd8ed1ab_0
Linking charset-normalizer-3.3.2-pyhd8ed1ab_0
Linking colorama-0.4.6-pyhd8ed1ab_0
Linking distro-1.9.0-pyhd8ed1ab_0
Linking idna-3.6-pyhd8ed1ab_0
Linking jsonpointer-2.4-py310hff52083_3
Linking libmamba-1.5.7-had39da4_0
Linking packaging-24.0-pyhd8ed1ab_0
Linking platformdirs-4.2.0-pyhd8ed1ab_0
Linking pluggy-1.4.0-pyhd8ed1ab_0
Linking pycosat-0.6.6-py310h2372a71_0
Linking pycparser-2.21-pyhd8ed1ab_0
Linking pysocks-1.7.1-pyha2e5f31_6
Linking ruamel.yaml.clib-0.2.8-py310h2372a71_0
Linking setuptools-69.2.0-pyhd8ed1ab_0
Linking truststore-0.8.0-pyhd8ed1ab_0
Linking wheel-0.43.0-pyhd8ed1ab_0
Linking cffi-1.16.0-py310h2fee648_0
Linking jsonpatch-1.33-pyhd8ed1ab_0
Linking libmambapy-1.5.7-py310h39ff949_0
Linking pip-24.0-pyhd8ed1ab_0
Linking ruamel.yaml-0.18.6-py310h2372a71_0
Linking tqdm-4.66.2-pyhd8ed1ab_0
Linking urllib3-2.2.1-pyhd8ed1ab_0
Linking requests-2.31.0-pyhd8ed1ab_0
Linking zstandard-0.22.0-py310h1275a96_0
Linking conda-package-streaming-0.9.0-pyhd8ed1ab_0
Linking conda-package-handling-2.2.0-pyh38be061_0
Linking conda-24.1.2-py310hff52083_0
Linking conda-libmamba-solver-24.1.0-pyhd8ed1ab_0
Linking mamba-1.5.7-py310h51d5547_0
Transaction finished
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
  Dependencies for mongodb have changed - reinstalling...
  ------------------------------------------------------------------------
  mongodb 3.6.23 installation successful.
  ------------------------------------------------------------------------
  Completed.
  Completed dependency check.

************ CRYOSPARC MASTER INSTALLATION COMPLETE **************

 CryoSPARC System master has now been installed.
 Add bin directory to your ~/.bashrc ?
1) Yes
2) No
#? 1
 cryosparc bin directory already in PATH, skipped.

************ CRYOSPARC SYSTEM: STANDALONE INSTALLER **************

  The installer will now download, install and connect the worker
  package on this machine. The worker package will allow CryoSPARC
  to run compute jobs.

******************************************************************

 Starting CryoSPARC...

Starting CryoSPARC System master process...
CryoSPARC is not already running.
configuring database...
    creating cryosparc_admin
    cryosparc_admin created
    creating cryosparc_user
    cryosparc_user created
    configuration complete
database: started
database OK
command_core: started

The process stuck here and running for about 30h. I wondered if you could shed some light on how to deal with it?

Thanks again!

Best,
Kun

wtempel · August 14, 2024, 2:23pm

Welcome to the forum @KunFang93 .
Please ensure your posts do not disclose confidential information, such as the CryoSPARC license ID.

If your terminal still shows

database OK
command_core: started

please can you open another terminal on the icrc4lcga001 computer, run the following commands and post their outputs:

ps -eo user,pid,ppid,command | grep -e cryosparc_ -e mongo
tail -n 5 /mnt/data/cryosparc_master/run/database.log
tail -n 5 /mnt/data/cryosparc_master/run/command_core.log
grep "^127" /etc/hosts
curl 127.0.0.1:39001
curl icrc4lcga001:39001
sudo ss -anp | grep :3900[0-9] | sed 's/\s\+/ /g'

KunFang93 · August 15, 2024, 3:36am

Sorry for the late reply. I ctrl+C break the process and cannot get back to command_core: started. So I deleted all folders and restart it again. Now I stuck in the same place. Here is the outputs for all the commands.

(base) jk4882@icrc4lcga001:~/data/cryosparc_master$ ps -eo user,pid,ppid,command | grep -e cryosparc_ -e mongo
jk4882      7416    7039 bash /mnt/data/cryosparc_master/bin/cryosparcm start
jk4882      7446       1 python /mnt/data/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/supervisord -c /mnt/data/cryosparc_master/supervisord.conf
jk4882      7625    7446 mongod --auth --dbpath /mnt/data/cryosparc_database --port 39001 --oplogSize 64 --replSet meteor --wiredTigerCacheSizeGB 4 --bind_ip_all
jk4882      7729    7446 python /mnt/data/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn -n command_core -b 0.0.0.0:39002 cryosparc_command.command_core:start() -c /mnt/data/cryosparc_master/gunicorn.conf.py
jk4882      7730    7729 python /mnt/data/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin/gunicorn -n command_core -b 0.0.0.0:39002 cryosparc_command.command_core:start() -c /mnt/data/cryosparc_master/gunicorn.conf.py
jk4882      8133    6889 grep --color=auto -e cryosparc_ -e mongo
(base) jk4882@icrc4lcga001:~/data/cryosparc_master$ tail -n 5 /mnt/data/cryosparc_master/run/database.log
2024-08-15T03:33:48.350+0000 I NETWORK  [listener] connection accepted from 127.0.0.1:48568 #5 (1 connection now open)
2024-08-15T03:33:48.351+0000 I NETWORK  [conn5] received client metadata from 127.0.0.1:48568 conn5: { driver: { name: "PyMongo", version: "4.6.2" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "6.8.0-40-generic" }, platform: "CPython 3.10.13.final.0" }
2024-08-15T03:33:48.352+0000 I NETWORK  [listener] connection accepted from 127.0.0.1:48578 #6 (2 connections now open)
2024-08-15T03:33:48.352+0000 I NETWORK  [conn6] received client metadata from 127.0.0.1:48578 conn6: { driver: { name: "PyMongo", version: "4.6.2" }, os: { type: "Linux", name: "Linux", architecture: "x86_64", version: "6.8.0-40-generic" }, platform: "CPython 3.10.13.final.0" }
2024-08-15T03:33:48.358+0000 I ACCESS   [conn6] Successfully authenticated as principal cryosparc_user on admin from client 127.0.0.1:48578
(base) jk4882@icrc4lcga001:~/data/cryosparc_master$ tail -n 5 /mnt/data/cryosparc_master/run/command_core.log
2024-08-15 03:33:43 info                 INFO     | Using worker: threads
2024-08-15 03:33:43 info                 INFO     | Booting worker with pid: 7730
2024-08-15 03:33:43,341 start                INFO     |  === STARTED ===
2024-08-15 03:33:43,342 background_worker    INFO     |  === STARTED ===
2024-08-15 03:33:43,342 run                  INFO     | === STARTED TASKS WORKER ===
(base) jk4882@icrc4lcga001:~/data/cryosparc_master$ grep "^127" /etc/hosts
127.0.0.1 localhost
127.0.1.1 icrc4lcga001
(base) jk4882@icrc4lcga001:~/data/cryosparc_master$ curl 127.0.0.1:39001
It looks like you are trying to access MongoDB over HTTP on the native driver port.
(base) jk4882@icrc4lcga001:~/data/cryosparc_master$ curl icrc4lcga001:39001
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<HTML><HEAD><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
<TITLE>ERROR: The requested URL could not be retrieved</TITLE>
<STYLE>

body {
   display: block;
   font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif;
   text-rendering: optimizelegibility;
   text-align: center;
}

#sign {
   color: #5A5A5A;
   font-weight: 600;
   margin: 60px 0 20px 0;
}

#headline {
   color: #5A5A5A;
   font-size: 48px;
   font-weight: 200;
   min-height: 48px;
   letter-spacing: -1px;
   line-height: 48px;
   margin: 0 0 10px 0;
}

#byline {
   color: #999999;
   font-size: 20px;
   font-weight: 300;
   min-height: 25px;
   line-height: 25px;
   margin: 0 0 30px 0;
}

#details {
   color: #5A5A5A;
   font-size: 16px;
   height: 24px;
   line-height: 24px;
   margin: 20px 0 0 0;
}
    .icon,
    .icon::before,
    .icon::after
    {
        position: relative;
        padding: 0;
        margin: 0;
    }

    .icon {
        font-size: 88px;
        color: transparent;
    }
    .icon.warning {
        display: inline-block;

        top: 0.225em;
        width: 1.15em;
        height: 1.15em;
        overflow: hidden;
        border: none;
        background-color: transparent;
        border-radius: 0.625em;
    }

    .icon.warning::before {
        content: "";
        display: block;
        top: -0.08em;
        left: 0.0em;
        position: absolute;
        border: transparent 0.6em solid;
        border-bottom-color: #5a5a5a;
        border-bottom-width: 1em;
        border-top-width: 0;
        box-shadow: #999 0 1px 1px;
    }

    .icon.warning::after {
        display: block;
        position: absolute;
        top: 0.3em;
        left: 0;
        width: 100%;
        padding: 0 1px;
        text-align: center;
        Xfont-family: "Garamond";
        font-family: "Arial";
        content: "!";
        font-size: 0.65em;
        font-weight: bold;
        color: #FFFFFF;
    }
</STYLE>
</HEAD><BODY>
<div id="error-container" class="container">
    <div style="align: center; padding-bottom: 10px;">
       <span id="sign" class="icon warning"></span>
       <h1 id="headline">The requested URL could not be retrieved.</h1>
       <p id="byline">Unable to determine IP address from host name for <I>icrc4lcga001</I></p>
     </div>
</div>
</BODY>
</HTML>
(base) jk4882@icrc4lcga001:~/data/cryosparc_master$ sudo ss -anp | grep :3900[0-9] | sed 's/\s\+/ /g'
[sudo] password for jk4882:
Sorry, try again.
[sudo] password for jk4882:
tcp LISTEN 0 128 0.0.0.0:39001 0.0.0.0:* users:(("mongod",pid=7625,fd=10))
tcp LISTEN 0 2048 0.0.0.0:39002 0.0.0.0:* users:(("python",pid=7730,fd=6),("python",pid=7729,fd=6))
tcp ESTAB 0 0 127.0.0.1:48568 127.0.0.1:39001 users:(("python",pid=7730,fd=12))
tcp ESTAB 0 0 127.0.0.1:48578 127.0.0.1:39001 users:(("python",pid=7730,fd=13))
tcp ESTAB 0 0 127.0.0.1:39001 127.0.0.1:48568 users:(("mongod",pid=7625,fd=40))
tcp ESTAB 0 0 127.0.0.1:39001 127.0.0.1:48578 users:(("mongod",pid=7625,fd=42))
tcp TIME-WAIT 0 0 127.0.0.1:53528 127.0.0.1:39001
(base) jk4882@icrc4lcga001:~/data/cryosparc_master$

Thank you so much for your time and help!

Best,
Kun

wtempel · August 15, 2024, 1:25pm

Thanks. Please can you also post the output of the command

cryosparcm call env | grep -i proxy

KunFang93 · August 15, 2024, 4:32pm

Thanks for your prompt response! I try cryosparcm but it isn’t in env. So I call it under bin folder

(base) jk4882@icrc4lcga001:~/data/cryosparc_master$ ./bin/cryosparcm call env |grep -i proxy
no_proxy=localhost,::1,127.0.0.1,.columbia.edu
ftp_proxy=http://XXX@bpc3.cumc.columbia.edu:8080
https_proxy=http://bcp3.cumc.columbia.edu:8080
telnet_proxy=http://XXX@bpc3.cumc.columbia.edu:8080
http_proxy=http://bcp3.cumc.columbia.edu:8080

Thanks for your time again!

Best,
Kun

wtempel · August 15, 2024, 9:59pm

You may want to try adding icrc4lcga001 to that no_proxy list for the purposes of CryoSPARC:

completely stop CryoSPARC

add the line

export no_proxy=localhost,::1,127.0.0.1,${CRYOSPARC_MASTER_HOSTNAME},.columbia.edu

somewhere below the

export CRYOSPARC_MASTER_HOSTNAME=

definition inside `/mnt/data/cryosparc_master/config.sh

run the command
/mnt/data/cryosparc_master/bin/cryosparcm start

Does this work?

KunFang93 · August 15, 2024, 10:35pm

It works! Thank you sooo much!!

Best,
Kun