Micromamba crash issue during installation

orangeboomerang · November 26, 2024, 10:09am

Hi, we are trying to install the latest cryosparc on our cluster but running into issues. Please see below. We are installing as usual, any advice would be appreciated.

######################################################################

DURING INSTALLATION WE GET THIS ERROR

To activate this environment, use:

micromamba activate /(path)/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda

Or to execute a single command in this environment, use:

micromamba run -p /(path)/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda mycommand

installation finished.

------------------------------------------------------------------------

Done.

anaconda python installation successful.

------------------------------------------------------------------------

Extracting all conda packages...

------------------------------------------------------------------------

.................................................................................................Traceback (most recent call last):

File "/(path)/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda/bin/conda", line 12, in <module>

from conda.cli import main

ModuleNotFoundError: No module named 'conda'

[check_install_deps.sh](https://check_install_deps.sh/): 66: ERROR: installing python failed.

############################################################################

WHEN WE TRY TO START CRYOSPARC

Starting CryoSPARC System master process...

CryoSPARC is not already running.

Traceback (most recent call last):

File "/(path)/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda/bin/conda", line 12, in <module>

from conda.cli import main

ModuleNotFoundError: No module named 'conda'

Warning: Could not activate conda environment; this indicates that a cryoSPARC installation is either incomplete or in progress

configuring database...

Traceback (most recent call last):

File "<string>", line 1, in <module>

File "/(path)/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/cryosparc_compute/database_management.py", line 35, in configure_mongo

mongod = subprocess.Popen(command, stdout=output, stderr=output)

File "/(path)/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/subprocess.py", line 971, in *init*

self._execute_child(args, executable, preexec_fn, close_fds,

File "/(path)/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/subprocess.py", line 1863, in _execute_child

raise child_exception_type(errno_num, err_msg, err_filename)

FileNotFoundError: [Errno 2] No such file or directory: 'mongod'

[2024-11-22T11:45:18+01:00] Error configuring database. Most recent database log lines:

(/(path)/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT5700

thanks in advance

Jesse

wtempel · November 26, 2024, 3:08pm

@orangeboomerang Please can you post the actual command you entered into the terminal before eventually seeing this error?

orangeboomerang · November 26, 2024, 3:26pm

hi,

it is our IT dept installing. Here is what they told me they used as a command:

./install.sh --license ${LICENSE_ID} \
--worker_path ${root_dir}/cryosparc_worker \
--ssdpath ${name_ssd_path} \
--port ${PORTN}

wtempel · November 26, 2024, 4:47pm

Is this path prefix literal, or has it been altered for anonymization?

This command corresponds to a single workstation (combined master & worker) CryoSPARC instance, where installation automatically performs multiple steps:

cryosparc_master/install.sh
cryosparc_worker/install.sh
cryosparc_worker/bin/cryosparcw connect

If I interpret information from the first post, where comments seem to be interleaved with actual screen output, correctly, the first of the above steps has failed. The IT dept may want to test running the first step, aka Master Node Only installation and collect

output of the command env before running the installation command

output of the commands

./install.sh --license ${LICENSE_ID} --port ${PORTN}

for troubleshooting.

selefant2 · November 27, 2024, 8:44am

Hi

we are running the first step

cryosparc_master/install.sh

Those are the instructions we run

module load micromamba/20241106
eval "$(micromamba shell hook --shell bash)"

./install.sh    --license ${LICENSE_ID} \
                --worker_path ${root_dir}/cryosparc_worker \
                --ssdpath ${name_ssd_path} \
                --port ${PORTN}

######################################################################

DURING INSTALLATION WE GET THIS ERROR

To activate this environment, use:

micromamba activate /(path)/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda

Or to execute a single command in this environment, use:

micromamba run -p /(path)/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda mycommand

installation finished.

Done.

anaconda python installation successful.

Extracting all conda packages…

…Traceback (most recent call last):

File “/(path)/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda/bin/conda”, line 12, in

from conda.cli import main

ModuleNotFoundError: No module named ‘conda’

check_install_deps.sh: 66: ERROR: installing python failed.

############################################################################

WHEN WE TRY TO START CRYOSPARC

Starting CryoSPARC System master process…

CryoSPARC is not already running.

Traceback (most recent call last):

File “/(path)/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda/bin/conda”, line 12, in

from conda.cli import main

ModuleNotFoundError: No module named ‘conda’

Warning: Could not activate conda environment; this indicates that a cryoSPARC installation is either incomplete or in progress

configuring database…

Traceback (most recent call last):

File “”, line 1, in

File “/(path)/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/cryosparc_compute/database_management.py”, line 35, in configure_mongo

mongod = subprocess.Popen(command, stdout=output, stderr=output)

File “/(path)/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/subprocess.py”, line 971, in init

self._execute_child(args, executable, preexec_fn, close_fds,

File “/(path)/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.10/subprocess.py”, line 1863, in _execute_child

raise child_exception_type(errno_num, err_msg, err_filename)

FileNotFoundError: [Errno 2] No such file or directory: ‘mongod’

[2024-11-22T11:45:18+01:00] Error configuring database. Most recent database log lines:

(/(path)/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT5700

wtempel · November 27, 2024, 4:26pm

These commands should not typically be needed before running
cryosparc_master/install.sh
I do not know their effect on the subsequent ./install.sh command.

Also, I missed earlier that

may be invalid or incomplete. Is the installation of a “single workstation” (combined master and worker, details) intended? If so, additional parameters are needed. If not,
--ssdpath and --worker_path should not be used.

If you continue to experience problems during installation, please try in a clean environment (no modules or conda environments loaded) inside a freshly unpacked cryosparc_master/ directory and post the outputs:

env | grep -v LICENSE_ID
PORTN=99999 # replace with actual port
LICENSE_ID="xxxxx" # replace with actual license ID 
./install.sh --license ${LICENSE_ID} --port ${PORTN}

and post the outputs. For this test, you may additionally use the
--dbpath parameter, but omit the --worker_path and --ssdpath parameters.
Please post the outputs:

concealing the license ID
clearly distinguishing between
- commands entered
- comments added by you
- actual screen outputs
indicating alterations to actual screen outputs

(formatting guide)

selefant1 · November 29, 2024, 10:39am

As you suggested I tried with a clean environment,
this is what I get, it does not find conda …
that’s why in the previous installation I loaded micromamba

Transaction finished

To activate this environment, use:

micromamba activate /nfs/scistore23/schurgrp/cryoschurgrp/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda

Or to execute a single command in this environment, use:

micromamba run -p /nfs/scistore23/schurgrp/cryoschurgrp/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda mycommand

installation finished.

Done.
anaconda python installation successful.

Extracting all conda packages…

…Traceback (most recent call last):
File “/nfs/scistore23/schurgrp/cryoschurgrp/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda/bin/conda”, line 12, in
from conda.cli import main
ModuleNotFoundError: No module named ‘conda’
check_install_deps.sh: 66: ERROR: installing python failed.

WARNING
We need to starting cryosparc manually
cryosparcm start

wtempel · November 29, 2024, 3:37pm

@selefant1 Please can you post the output of this command

run on the CryoSPARC master host, under the Linux account that “owns” the CryoSPARC installation.

selefant1 · November 30, 2024, 10:58am

Dear Wtempel,

Thank you very much for your help and for trying to get CryoSPARC up and running.

Could you please let us know what specific information you would need from the output of the command:

$ env | grep -v LICENSE_ID

For security reasons, we’d prefer not to share the entire setup. We apologize for any inconvenience this may cause and appreciate your understanding.

Best regards,

wtempel · December 2, 2024, 7:26pm

Understood!
How about
env | grep PATH
?

selefant1 · December 3, 2024, 2:43pm

MANPATH=/mnt/nfs/clustersw/Debian/bookworm/lmod/8.6.12/share/man:
MODULEPATH_ROOT=/mnt/nfs/clustersw/Debian/bookworm/modulefiles
PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
MODULEPATH=/mnt/nfs/clustersw/Debian/bookworm/modulefiles/Linux:/mnt/nfs/clustersw/Debian/bookworm/modulefiles/Core:/mnt/nfs/clustersw/Debian/bookworm/lmod/8.6.12/modulefiles/Core

wtempel · December 6, 2024, 7:37pm

@selefant1 You may want to try the following

Navigate to the directory where you wish to install CryoSPARC
Remove the cryosparc_master/ directory from a previous failed installation, if it exists.
Extract cryosparc_master.tar.gz

Then run

conda deactivate # just in case
PORTN=99999 # replace with actual port
LICENSE_ID="xxxxx" # replace with actual license ID 
env -i ./install.sh --license ${LICENSE_ID} --port ${PORTN} 2>&1 | tee install_master.out

If this does not work:

Remove the cryosparc_master/ directory from the failed installation.
Again extract cryosparc_master.tar.gz.

From the lower half of the file

cryosparc_master/deps_bundle_hashes/python/install_python.sh

remove the lines

source ${CRYOSPARC_ROOT_DIR}/deps/anaconda/etc/profile.d/conda.sh
conda config --file "$conda_config_file" --set auto_update_conda False
conda config --file "$conda_config_file" --set pip_interop_enabled True
conda config --file "$conda_config_file" --set channel_priority flexible

Run the commands

conda deactivate # just in case
PORTN=99999 # replace with actual port
LICENSE_ID="xxxxx" # replace with actual license ID 
env -i ./install.sh --license ${LICENSE_ID} --port ${PORTN} 2>&1 | tee install_master2.out

Any luck?
The purpose of the tee commands is to preserve the outputs for analysis in case neither approach works.

selefant1 · December 9, 2024, 9:33am

Hi!

I just tried and both methods failed

Those are the error messages

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-24.3.0-py310hff52083_0
Linking conda-libmamba-solver-24.1.0-pyhd8ed1ab_0
Linking mamba-1.5.8-py310h51d5547_0

Transaction finished

To activate this environment, use:

micromamba activate /nfs/scistore23/schurgrp/cryoschurgrp/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda

Or to execute a single command in this environment, use:

micromamba run -p /nfs/scistore23/schurgrp/cryoschurgrp/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda mycommand

installation finished.

Done.
anaconda python installation successful.

Extracting all conda packages…

…Traceback (most recent call last):
File “/nfs/scistore23/schurgrp/cryoschurgrp/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda/bin/conda”, line 12, in
from conda.cli import main
ModuleNotFoundError: No module named ‘conda’
check_install_deps.sh: 66: ERROR: installing python failed.

selefant1 · December 9, 2024, 9:34am

The other output

Linking conda-24.3.0-py310hff52083_0
Linking conda-libmamba-solver-24.1.0-pyhd8ed1ab_0
Linking mamba-1.5.8-py310h51d5547_0

Transaction finished

To activate this environment, use:

micromamba activate /nfs/scistore23/schurgrp/cryoschurgrp/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda

Or to execute a single command in this environment, use:

micromamba run -p /nfs/scistore23/schurgrp/cryoschurgrp/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda mycommand

installation finished.

Done.
anaconda python installation successful.

Extracting all conda packages…

…Traceback (most recent call last):
File “/nfs/scistore23/schurgrp/cryoschurgrp/cryosparc_v4.6.2_gpu136Master_gpu136Worker_PORT57000_LIC_38df2812/cryosparc_master/deps/anaconda/bin/conda”, line 12, in
from conda.cli import main
ModuleNotFoundError: No module named ‘conda’
check_install_deps.sh: 66: ERROR: installing python failed.

wtempel · December 9, 2024, 4:39pm

@selefant1 Thanks for trying that. Please hold on to the install_master*.out files, we may want to look at them. What are the outputs of these commands on the computer where you attempted the installation:

uname -a
cat /etc/*release
cat /proc/1/sched | head -n 1

orangeboomerang · December 13, 2024, 11:51am

hi,
@selefant1 is apparently unable to post his reply, it’s not clear why.

He asked me to post the output below:


uname -a

Linux gpu62 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux

cryoschurgrp@gpu62:~$ cat /etc/*release

PRETTY_NAME="Debian GNU/Linux 12 (bookworm)"

NAME="Debian GNU/Linux"

VERSION_ID="12"

VERSION="12 (bookworm)"

VERSION_CODENAME=bookworm

ID=debian

HOME_URL="https://www.debian.org/"

SUPPORT_URL="https://www.debian.org/support"

BUG_REPORT_URL="https://bugs.debian.org/"

cryoschurgrp@gpu62:~$ cat /proc/1/sched | head -n 1

systemd (1, #threads: 1

wtempel · December 13, 2024, 7:50pm

Thanks @orangeboomerang . Please can you also compress and send us the install_master*.out mentioned in Micromamba crash issue during installation - #12 by wtempel.

selefant2 · January 9, 2025, 12:36pm

Dear wtempel,

I just downloaded the latest version of CryoSPARC, but the error still occurs, and we’re unable to complete the installation.

Please, below you can find the the full output of the process.

Currently Loaded Modules:

cuda/12.0.0

************ CRYOSPARC SYSTEM: MASTER INSTALLER **************

 Installation Settings:
   License ID              : XXXX
   Root Directory          : XXXX
   Master Hostname         : XXXX
   Database Directory      : XXXX
   Base HTTP Port Number   : XXXX
   Developer Install       : false
   Operating System        : Linux
   Insecure Install        : false
   Standalone Install      : false
   Version                 : v4.6.2

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

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=XXXX
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-1.28.1-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_2.conda
Extracting libsqlite-3.45.2-h2797004_0.conda
Extracting libssh2-1.11.0-h0841786_0.conda
Extracting libxml2-2.12.6-h232c23b_1.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-8.7.1-hca28451_0.conda
Extracting menuinst-2.0.2-py310hff52083_0.conda
Extracting archspec-0.2.3-pyhd8ed1ab_0.conda
Extracting boltons-24.0.0-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-1.5.8-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-2.22-pyhd8ed1ab_0.conda
Extracting pysocks-1.7.1-pyha2e5f31_6.tar.bz2
Extracting ruamel.yaml.clib-0.2.8-py310h2372a71_0.conda
Extracting setuptools-69.5.1-pyhd8ed1ab_0.conda
Extracting truststore-0.8.0-pyhd8ed1ab_0.conda
Extracting wheel-0.43.0-pyhd8ed1ab_1.conda
Extracting cffi-1.16.0-py310h2fee648_0.conda
Extracting jsonpatch-1.33-pyhd8ed1ab_0.conda
Extracting libmambapy-1.5.8-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-24.3.0-py310hff52083_0.conda
Extracting conda-libmamba-solver-24.1.0-pyhd8ed1ab_0.conda
Extracting mamba-1.5.8-py310h51d5547_0.conda

Installing base environment...

Transaction

  Prefix: XXXX

  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==1.28.1=hd590300_0[md5=dcde58ff9a1f30b0037a2315d1846d1f]
   - 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_2[md5=535bafe1ed0a5bdd3f4c125ca05d378c]
   - 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_1[md5=6853448e9ca1cfd5f15382afd2a6d123]
   - 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==8.7.1=hca28451_0[md5=755c7f876815003337d2c61ff5d047e5]
   - 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==24.0.0=pyhd8ed1ab_0[md5=61de176bd62041f9cd5bd4fcd09eb0ff]
   - 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==1.5.8=had39da4_0[md5=def669885dc103d8acb7ac2ac35e0b2f]
   - 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==2.22=pyhd8ed1ab_0[md5=844d9eb3b43095b031874477f7d70088]
   - 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==69.5.1=pyhd8ed1ab_0[md5=7462280d81f639363e6e63c81276bd9e]
   - conda-forge/noarch::truststore==0.8.0=pyhd8ed1ab_0[md5=08316d001eca8854392cf2837828ea11]
   - conda-forge/noarch::wheel==0.43.0=pyhd8ed1ab_1[md5=0b5293a157c2b5cd513dd1b03d8d3aae]
   - 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==1.5.8=py310h39ff949_0[md5=37f8aa15b73c4691eeec15caf45aab25]
   - 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==24.3.0=py310hff52083_0[md5=4187d17c4b75d8f7757820e835c507c9]
   - conda-forge/noarch::conda-libmamba-solver==24.1.0=pyhd8ed1ab_0[md5=304dc78ad6e52e0fd663df1d484c1531]
   - conda-forge/linux-64::mamba==1.5.8=py310h51d5547_0[md5=3b335eaa4894cbb5379a75f83a4d6b40]


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

  + _libgcc_mutex                     0.1  conda_forge         conda-forge         
  + ca-certificates              2024.2.2  hbcca054_0          conda-forge         
  + ld_impl_linux-64                 2.40  h41732ed_0          conda-forge         
  + libstdcxx-ng                   13.2.0  h7e041cc_5          conda-forge         
  + pybind11-abi                        4  hd8ed1ab_3          conda-forge         
  + python_abi                       3.10  4_cp310             conda-forge         
  + tzdata                          2024a  h0c530f3_0          conda-forge         
  + libgomp                        13.2.0  h807b86a_5          conda-forge         
  + _openmp_mutex                     4.5  2_gnu               conda-forge         
  + libgcc-ng                      13.2.0  h807b86a_5          conda-forge         
  + bzip2                           1.0.8  hd590300_5          conda-forge         
  + c-ares                         1.28.1  hd590300_0          conda-forge         
  + fmt                            10.2.1  h00ab1b0_0          conda-forge         
  + icu                              73.2  h59595ed_0          conda-forge         
  + keyutils                        1.6.1  h166bdaf_0          conda-forge         
  + libev                            4.33  hd590300_2          conda-forge         
  + libffi                          3.4.2  h7f98852_5          conda-forge         
  + libiconv                         1.17  hd590300_2          conda-forge         
  + libnsl                          2.0.1  hd590300_0          conda-forge         
  + libuuid                        2.38.1  h0b41bf4_0          conda-forge         
  + libxcrypt                      4.4.36  hd590300_1          conda-forge         
  + libzlib                        1.2.13  hd590300_5          conda-forge         
  + lz4-c                           1.9.4  hcb278e6_0          conda-forge         
  + lzo                              2.10  h516909a_1000       conda-forge         
  + ncurses                  6.4.20240210  h59595ed_0          conda-forge         
  + openssl                         3.2.1  hd590300_1          conda-forge         
  + reproc                   14.2.4.post0  hd590300_1          conda-forge         
  + xz                              5.2.6  h166bdaf_0          conda-forge         
  + yaml-cpp                        0.8.0  h59595ed_0          conda-forge         
  + libedit                  3.1.20191231  he28a2e2_2          conda-forge         
  + libnghttp2                     1.58.0  h47da74e_1          conda-forge         
  + libsolv                        0.7.28  hfc55251_2          conda-forge         
  + libsqlite                      3.45.2  h2797004_0          conda-forge         
  + libssh2                        1.11.0  h0841786_0          conda-forge         
  + libxml2                        2.12.6  h232c23b_1          conda-forge         
  + readline                          8.2  h8228510_1          conda-forge         
  + reproc-cpp               14.2.4.post0  h59595ed_1          conda-forge         
  + tk                             8.6.13  noxft_h4845f30_101  conda-forge         
  + zstd                            1.5.5  hfc55251_0          conda-forge         
  + krb5                           1.21.2  h659d440_0          conda-forge         
  + libarchive                      3.7.2  h2aa1ff5_1          conda-forge         
  + python                        3.10.14  hd12c33a_0_cpython  conda-forge         
  + libcurl                         8.7.1  hca28451_0          conda-forge         
  + menuinst                        2.0.2  py310hff52083_0     conda-forge         
  + archspec                        0.2.3  pyhd8ed1ab_0        conda-forge         
  + boltons                        24.0.0  pyhd8ed1ab_0        conda-forge         
  + brotli-python                   1.1.0  py310hc6cd4ac_1     conda-forge         
  + certifi                      2024.2.2  pyhd8ed1ab_0        conda-forge         
  + charset-normalizer              3.3.2  pyhd8ed1ab_0        conda-forge         
  + colorama                        0.4.6  pyhd8ed1ab_0        conda-forge         
  + distro                          1.9.0  pyhd8ed1ab_0        conda-forge         
  + idna                              3.6  pyhd8ed1ab_0        conda-forge         
  + jsonpointer                       2.4  py310hff52083_3     conda-forge         
  + libmamba                        1.5.8  had39da4_0          conda-forge         
  + packaging                        24.0  pyhd8ed1ab_0        conda-forge         
  + platformdirs                    4.2.0  pyhd8ed1ab_0        conda-forge         
  + pluggy                          1.4.0  pyhd8ed1ab_0        conda-forge         
  + pycosat                         0.6.6  py310h2372a71_0     conda-forge         
  + pycparser                        2.22  pyhd8ed1ab_0        conda-forge         
  + pysocks                         1.7.1  pyha2e5f31_6        conda-forge         
  + ruamel.yaml.clib                0.2.8  py310h2372a71_0     conda-forge         
  + setuptools                     69.5.1  pyhd8ed1ab_0        conda-forge         
  + truststore                      0.8.0  pyhd8ed1ab_0        conda-forge         
  + wheel                          0.43.0  pyhd8ed1ab_1        conda-forge         
  + cffi                           1.16.0  py310h2fee648_0     conda-forge         
  + jsonpatch                        1.33  pyhd8ed1ab_0        conda-forge         
  + libmambapy                      1.5.8  py310h39ff949_0     conda-forge         
  + pip                              24.0  pyhd8ed1ab_0        conda-forge         
  + ruamel.yaml                    0.18.6  py310h2372a71_0     conda-forge         
  + tqdm                           4.66.2  pyhd8ed1ab_0        conda-forge         
  + urllib3                         2.2.1  pyhd8ed1ab_0        conda-forge         
  + requests                       2.31.0  pyhd8ed1ab_0        conda-forge         
  + zstandard                      0.22.0  py310h1275a96_0     conda-forge         
  + conda-package-streaming         0.9.0  pyhd8ed1ab_0        conda-forge         
  + conda-package-handling          2.2.0  pyh38be061_0        conda-forge         
  + conda                          24.3.0  py310hff52083_0     conda-forge         
  + conda-libmamba-solver          24.1.0  pyhd8ed1ab_0        conda-forge         
  + mamba                           1.5.8  py310h51d5547_0     conda-forge         

  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-1.28.1-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_2
Linking libsqlite-3.45.2-h2797004_0
Linking libssh2-1.11.0-h0841786_0
Linking libxml2-2.12.6-h232c23b_1
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-8.7.1-hca28451_0
Linking menuinst-2.0.2-py310hff52083_0
Linking archspec-0.2.3-pyhd8ed1ab_0
Linking boltons-24.0.0-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-1.5.8-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-2.22-pyhd8ed1ab_0
Linking pysocks-1.7.1-pyha2e5f31_6
Linking ruamel.yaml.clib-0.2.8-py310h2372a71_0
Linking setuptools-69.5.1-pyhd8ed1ab_0
Linking truststore-0.8.0-pyhd8ed1ab_0
Linking wheel-0.43.0-pyhd8ed1ab_1
Linking cffi-1.16.0-py310h2fee648_0
Linking jsonpatch-1.33-pyhd8ed1ab_0
Linking libmambapy-1.5.8-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-24.3.0-py310hff52083_0
Linking conda-libmamba-solver-24.1.0-pyhd8ed1ab_0
Linking mamba-1.5.8-py310h51d5547_0

Transaction finished

To activate this environment, use:

    micromamba activate XXXX

Or to execute a single command in this environment, use:

    micromamba run -p XXXX mycommand

installation finished.
  ------------------------------------------------------------------------
    Done.
    anaconda python installation successful.
  ------------------------------------------------------------------------
  Extracting all conda packages...
  ------------------------------------------------------------------------
.................................................................................................Traceback (most recent call last):
  File "XXXX", line 12, in <module>
    from conda.cli import main
ModuleNotFoundError: No module named 'conda'
check_install_deps.sh: 66: ERROR: installing python failed.

WARNING
We need to starting cryosparc manually
cryosparcm start

selefant2 · January 9, 2025, 12:41pm

Dear wtempel,

for your information, maybe it can help, I run the following instructions for the installation

env -i ./install.sh --license ${LICENSE_ID} --port ${PORTN} 2>&1 | tee install_master2.out

(by the way I did not find and file install_master2.out, I had to do copy/paste)

wtempel · January 9, 2025, 6:56pm

Thanks @selefant2. Please can you post the outputs of these commands

echo $SHELL
cd /path/to/cryosparc_master
grep "$(df . | tail -n 1 | awk '{print $NF}') " /proc/mounts