Having trouble with V3.0 update

Install, Configure and Update
1

Hello,

I tried to update my system this morning, and now I can’t get back onto cryosparc. This is the script that it gave me after the update:

Updating to version v3.0.0.
=============================
CryoSPARC is running.
Stopping cryosparc 
channel 2: open failed: connect failed: Connection refused
channel 2: open failed: connect failed: Connection refused
command_proxy: stopped
command_vis: stopped
webapp: stopped
command_core: stopped
database: stopped
Shut down
  Downloading master update...
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  3  769M    3 26.3M    0     0  9235k      0  0:01:25  0:00:02  0:01:23 11.9Mchannel 2: open failed: connect failed: Connection refused
 40  769M   40  310M    0     0  19.5M      0  0:00:39  0:00:15  0:00:24 27.8Mchannel 2: open failed: connect failed: Connection refused
100  769M  100  769M    0     0  26.9M      0  0:00:28  0:00:28 --:--:-- 34.4M
  Downloading worker update...
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2903M  100 2903M    0     0  29.0M      0  0:01:39  0:01:39 --:--:-- 40.2M
  Done.

 Update will now be applied to the master installation, 
 followed by worker installations on other nodes.

  Deleting old files...
  Extracting...
  Done.
  Updating dependencies...
Could not find conda environment: cryosparc_master_env
You can list all discoverable environments with `conda info --envs`.

Warning: Could not activate conda environment; this indicates that a cryoSPARC installation is either incomplete or in progress
===================================================
Warning: cryoSPARC v2 dependencies and cryosparc2_worker.tar.gz detected.
Performing full v3 worker update in 10 seconds (to cancel, press Ctrl + C)
...
 
===================================================
Installing latest master dependencies.
===================================================
 
  Checking dependencies... 
  Dependencies for python have changed - reinstalling...
  ------------------------------------------------------------------------
Collecting package metadata (current_repodata.json): done                                                                                                                                                                                      
Solving environment: donepy37_0.tar.bz2:  97%|âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ    | 33/35 [00:01<00:01,  1.59it/s]
Extracting : python-3.7.7-hcff3b4d_5.conda:  91%|âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ             | 31/35 [00:01<00:03,  1.12it/s]
## Package Plan ##ks-1.7.1-py37_0.conda:  69%|âââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââââ                                                  | 23/35 [00:01<00:10,  1.12it/s]
Extracting : ncurses-6.2-he6710b0_1.conda:  17%|ââââââââââââââââââââââââââââ                                                                                                                                    | 5/35 [00:01<00:26,  1.12it/s]
  environment location: /home/cryosparc_user/software/cryosparc/cryosparc2_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.
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
  Dependencies for mongodb have changed - reinstalling...
  ------------------------------------------------------------------------
  mongodb 3.4.10 installation successful.
  ------------------------------------------------------------------------
  Completed.
  Completed dependency check. 
/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/etc/profile.d/conda.sh: eval: line 59: syntax error near unexpected token `site.USER_BASE'
/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/etc/profile.d/conda.sh: eval: line 59: `export PATH='/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/condabin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/external/mongodb/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/external/mongodb/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin: -c 'import site; print(site.USER_BASE)')/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/usr/local/IMOD/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/cryosparc_user/.local/bin:/home/cryosparc_user/bin''
 
Successfully updated master to version v3.0.0.
===================================================
 
/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/etc/profile.d/conda.sh: eval: line 59: syntax error near unexpected token `site.USER_BASE'
/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/etc/profile.d/conda.sh: eval: line 59: `export PATH='/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/condabin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/external/mongodb/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/external/mongodb/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin: -c 'import site; print(site.USER_BASE)')/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/usr/local/IMOD/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/cryosparc_user/.local/bin:/home/cryosparc_user/bin''
Starting cryoSPARC System master process..
/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin/cryosparcm: line 615: supervisorctl: command not found
CryoSPARC is already running.
If you would like to restart, use cryosparcm restart
/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/etc/profile.d/conda.sh: eval: line 59: syntax error near unexpected token `site.USER_BASE'
/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/etc/profile.d/conda.sh: eval: line 59: `export PATH='/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/condabin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/external/mongodb/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/external/mongodb/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin: -c 'import site; print(site.USER_BASE)')/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/usr/local/IMOD/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/cryosparc_user/.local/bin:/home/cryosparc_user/bin''
/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin/cryosparcm: line 133: supervisorctl: command not found
CryoSPARC is running.
Stopping cryosparc 
/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin/cryosparcm: line 737: supervisorctl: command not found
[cryosparc_user@c107925 ~]$ channel 2: open failed: connect failed: Connection refused
channel 3: open failed: connect failed: Connection refused
channel 2: open failed: connect failed: Connection refused
channel 3: open failed: connect failed: Connection refused
channel 2: open failed: connect failed: Connection refused
channel 3: open failed: connect failed: Connection refused
channel 2: open failed: connect failed: Connection refused
channel 2: open failed: connect failed: Connection refused
channel 3: open failed: connect failed: Connection refused
channel 2: open failed: connect failed: Connection refused
channel 2: open failed: connect failed: Connection refused
channel 3: open failed: connect failed: Connection refused

I then tried to restart cryosparc, and this is what I got:

[cryosparc_user@c107925 ~]$ cryosparcm restart
/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/etc/profile.d/conda.sh: eval: line 59: syntax error near unexpected token `site.USER_BASE'
/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/etc/profile.d/conda.sh: eval: line 59: `export PATH='/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/condabin: -c 'import site; print(site.USER_BASE)')/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/usr/local/IMOD/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/cryosparc_user/.local/bin:/home/cryosparc_user/bin''
/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/etc/profile.d/conda.sh: eval: line 59: syntax error near unexpected token `site.USER_BASE'
/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/etc/profile.d/conda.sh: eval: line 59: `export PATH='/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/external/mongodb/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/condabin: -c 'import site; print(site.USER_BASE)')/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/usr/local/IMOD/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/cryosparc_user/.local/bin:/home/cryosparc_user/bin''
/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin/cryosparcm: line 133: supervisorctl: command not found
CryoSPARC is running.
Stopping cryosparc 
/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin/cryosparcm: line 737: supervisorctl: command not found

I can’t ssh to the computer now, and I’m not really sure what to do. Any advice or help would be greatly appreciated!

  • Meranda
2

Hi @merandamasse,

Thanks for reporting. We are investigating. In the meantime can you tell us:

  • OS and version
  • default shell that you use in the cryosparc_user account
  • can you send the ~/.bashrc file from cryosparc_user

Are you unable to SSH into the machine entirely? Can you SSH as another user besides cryosparc_user? We’re not sure how the installation failure would have caused any problem with SSH.

3

Hi Ali,

I’m on a Linux computer running CentOS7.
Bash is the default shell I’m using for the cryosparc_user account.

For the ~/.bashrc file, do you mean I should run that command? Sorry I’m a little new to Linux.

As for the SSH, I misspoke. I can SSH to my computer under cryosparc_user, what I can’t do is ssh to the localhost to get onto cryosparc if that makes sense.

Thanks!
Meranda

4

To get the .bashrc file, you can run run this command:

cat ~/.bashrc

And send me the the full result.

When you do that, could you also the the same thing for the ~/.profile file?

cat ~/.profile
5

Here is the bashrc:

[cryosparc_user@c107925 ~]$ cat ~/.bashrc
# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

# Uncomment the following line if you don't like systemctl's auto-paging feature:
# export SYSTEMD_PAGER=

# User specific aliases and functions
# Added by cryoSPARC:
export PATH="/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin":$PATH
export PATH=" -c 'import site; print(site.USER_BASE)')/bin:$PATH"

and then here is the profile:

[cryosparc_user@c107925 ~]$ cat ~/.profile
cat: /home/cryosparc_user/.profile: No such file or directory
6

Okay, it looks like there’s an error in that last line of you ~/.bashrc file that’s preventing cryoSPARC from starting. If you remove the last line, cryoSPARC should be able to start.

You can edit that file to remove that last time with this command:

sed -i '$ d' ~/.bashrc

Output ~/.bashrc with cat ~/.bashrc and make sure there is no line that says export PATH=" -c 'import site; print(site.USER_BASE)')/bin:$PATH". If not, run the same sed command again.

Then try to start cryoSPARC with cryosparcm start.

Let me know if you run into any trouble with this.

7

Thank you!
So I did all of that but it appears it still isn’t working:

[cryosparc_user@c107925 ~]$ cat ~/.bashrc
# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

# Uncomment the following line if you don't like systemctl's auto-paging feature:
# export SYSTEMD_PAGER=

# User specific aliases and functions
# Added by cryoSPARC:
[cryosparc_user@c107925 ~]$ cryosparcm start
/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/etc/profile.d/conda.sh: eval: line 59: syntax error near unexpected token `site.USER_BASE'
/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/etc/profile.d/conda.sh: eval: line 59: `export PATH='/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/envs/cryosparc_master_env/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/deps/anaconda/condabin: -c 'import site; print(site.USER_BASE)')/bin:/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin:/usr/local/relion-3/bin:/usr/local/mpich-3.2.1/bin:/usr/local/cuda/bin:/usr/local/IMOD/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/motioncorr_v2.1/bin:/usr/local/Gctf_v1.06/bin:/usr/local/Gctf_v0.50/bin:/usr/local/ResMap:/usr/local/summovie_1.0.2/bin:/usr/local/unblur_1.0.2/bin:/usr/local/EMAN_2.21/bin:/home/cryosparc_user/.local/bin:/home/cryosparc_user/bin''
Starting cryoSPARC System master process..
Fatal Python error: _PyMainInterpreterConfig_Read: memory allocation failed
ValueError: character U+6900632d is not in range [U+0000; U+10ffff]

Current thread 0x00007fb6ccb13740 (most recent call first):
[cryosparc_user@c107925 ~]$ channel 2: open failed: connect failed: Connection refused
channel 3: open failed: connect failed: Connection refused
channel 2: open failed: connect failed: Connection refused
channel 2: open failed: connect failed: Connection refused
channel 3: open failed: connect failed: Connection refused
channel 2: open failed: connect failed: Connection refused
channel 3: open failed: connect failed: Connection refused
channel 2: open failed: connect failed: Connection refused
channel 3: open failed: connect failed: Connection refused
channel 2: open failed: connect failed: Connection refused
channel 3: open failed: connect failed: Connection refused
channel 2: open failed: connect failed: Connection refused
channel 3: open failed: connect failed: Connection refused
channel 2: open failed: connect failed: Connection refused
channel 2: open failed: connect failed: Connection refused
channel 3: open failed: connect failed: Connection refused
channel 2: open failed: connect failed: Connection refused
8

Oops, my bad, forgot to mention that you have to log-out and re-log in via SSH to get the change to register. Does doing that fix it?

9

No worries. So I did do that and now it’s not recognizing cryosparcm commands.

[cryosparc_user@c107925 ~]$ cryosparcm start
bash: cryosparcm: command not found...
[cryosparc_user@c107925 ~]$
10

It looks like the sed command removed one too many lines. Try this:

echo 'export PATH="/home/cryosparc_user/software/cryosparc/cryosparc2_master/bin":$PATH' >> ~/.bashrc
source ~/.bashrc

Then try again (no need to log in and out)

11

Ahh YES! It looks like it’s working! Thank you SO much. I really appreciate it because this is still very new to me. Thanks again!!

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12

No problem, glad you got it working!

2 Likes
13

I think I’ve had a ~similar problem, at least related to file naming. I noticed some code was added to cryosparcm to catch the downloaded tar files preserving the old filename, but not sure the same was added to the corresponding code in cryosparcw. I deleted all the tar files and forced a re-update… which seems to have worked thus far.

Also thinking of just changing the root dir names and removing the 2 to make things clean… gonna grep the entire tree just to double check this isn’t hardcoded anywhere.

14

@yoshiokc both cryosparcm and cryosparcw should be able to correctly upgrade from 2 to 3, do you have the output of the cryosparcm update and/or cryosparcw update commands you ran?

If you’re doing a manual update with cryosparcm update --override, note that for v2 → v3 the updater downloads the v3 worker tarball as cryosparc2_worker.tar.gz. You should keep the same filename when you copy this file over to the cryosparc2_worker directory. Does this apply to you?

If you’re changing the root directory name from cryosparc2_* to cryosparc_*, you should be able to so like this:

  1. Rename the cryosparc2_master and cryosparc2_worker folders to cryosparc_master and cryosparc_worker respectively
  2. Force-reinstall dependencies on master:
    cd cryosparc_master
bin/cryosparcm forcedeps
  3. Log into a machine with GPU set up if you haven’t already
  4. Reinstall dependencies
    cd cryosparc_worker
bin/cryosparcw forcedeps
  5. Update your .bashrc or other shell profile files to ensure the PATH is correctly set to the cryosparc_master/bin and/or cryosparc_worker/bin
15

(That last part is optional, cryoSPARC v3 will still work if the directories were initially installed at cryosparc2_master and cryosparc2_worker)

16

thanks, I mostly followed that advice but then got a CUDA error when trying to build against CUDA 11.1. Trying again with 11.0, or 11.2? When I tried to force just a pycuda rebuild, I think the newcuda flag refers to the older pycuda tarball.

17

note, I had already tried this before I saw your replies, but forgetting the forceps command, I just opted to delete the full worker directory and re-extract the tarball: but I noticed an odd thing, the tarball has a cryosparc_worker directory and a single file: cryosparc2_worker/version. Is that for code to check for legacy installs?

PS, using CUDA 11.0 instead of 11.1 seems to have worked

18

We’ve verified the cryoSPARC v3 does with with CUDA 11.1, do you have output you got when you tried to rebuild pycuda?

Yes cryosparc2_worker/version is not necessary for new installs, only for updating from 2 to 3. You may safely remove this this file and folder.

19

pycuda built fine when I gave it the 11.1 directory, the runtime complained of: " Failed to import the CUDA driver interface, with an error message indicating that the version of your CUDA header does not match the version of your CUDA driver"

but pretty sure the installed driver should be good through 11.2, so maybe there is just something broken about the 11.1 install

20

nvmind, I must be high. The last CUDA update I installed was 11.1, and the driver on this system is recent, but not most recent- I’ll update it and it will probably work.

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