Configure SSD path when using standalone installation

Install, Configure and Update
1

We have added an SSD to our cryosparc machine.
During installation, we used --standalone option.

I tried to follow old post
How to update a worker’s configuration (ssd path) - Install, Configure and Update - CryoSPARC Discuss

But It appears we do have not worker node installed/configured.

When trying to run ./cryosparcw or ./cryosparcw connect.
We get:
ERROR: Is cryoSPARC installed? Run install.sh to complete installation. See https://guide.cryosparc.com for full instructions.

Our cryosparc instance has been running fine and working as expected.

cryosparcm cli “get_scheduler_targets()” returns

[{‘cache_path’: ‘/lscratch’, ‘cache_quota_mb’: None, ‘cache_reserve_mb’: 10000, ‘desc’: None, ‘gpus’: [{‘id’: 0, ‘mem’: 25447170048, ‘name’: ‘NVIDIA GeForce RTX 3090’}, {‘id’: 1, ‘mem’: 25447170048, ‘name’: ‘NVIDIA GeForce RTX 3090’}, {‘id’: 2, ‘mem’: 25447170048, ‘name’: ‘NVIDIA GeForce RTX 3090’}, {‘id’: 3, ‘mem’: 25447170048, ‘name’: ‘NVIDIA GeForce RTX 3090’}, {‘id’: 4, ‘mem’: 25447170048, ‘name’: ‘NVIDIA GeForce RTX 3090’}, {‘id’: 5, ‘mem’: 25447170048, ‘name’: ‘NVIDIA GeForce RTX 3090’}, {‘id’: 6, ‘mem’: 25447170048, ‘name’: ‘NVIDIA GeForce RTX 3090’}, {‘id’: 7, ‘mem’: 25447170048, ‘name’: ‘NVIDIA GeForce RTX 3090’}], ‘hostname’: ‘processingserver3’, ‘lane’: ‘default’, ‘monitor_port’: None, ‘name’: ‘processingserver3’, ‘resource_fixed’: {‘SSD’: True}, ‘resource_slots’: {‘CPU’: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127], ‘GPU’: [0, 1, 2, 3, 4, 5, 6, 7], ‘RAM’: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]}, ‘ssh_str’: ‘cryosparc@processingserver3’, ‘title’: ‘Worker node processingserver3’, ‘type’: ‘node’, ‘worker_bin_path’: ‘/net/primaryhot/zstorage/apps/cryosparc/cryosparc_worker/bin/cryosparcw’}]

Thanks a lot.

2

Welcome to the forum @jybjybjjyb .

Do you wish to configure this SSD for CryoSPARC particle caching? If so, what is the mountpoint to the relevant filesystem on that SSD?

Thanks for posting the get_scheduler_targets() output, which says that you do have a worker node installed, with scratch space under /lscratch.

This configuration may be outdated.
Please can you post the output of the commands

cryosparcm env | grep -v LICENSE
cat /net/primaryhot/zstorage/apps/cryosparc/cryosparc_worker/version
3

export “CRYOSPARC_MASTER_HOSTNAME=processingserver3”
export “CRYOSPARC_CLICK_WRAP=true”
export “CRYOSPARC_COMMAND_VIS_PORT=61003”
export “CRYOSPARC_CONDA_ENV=cryosparc_master_env”
export “CRYOSPARC_FORCE_USER=false”
export “CRYOSPARC_INSECURE=false”
export “CRYOSPARC_DEVELOP=false”
export “CRYOSPARC_DB_PATH=/net/warm/home/cryosparc/cryosparc_database”
export “CRYOSPARC_CLUSTER_JOB_MONITOR_MAX_RETRIES=1000000”
export “CRYOSPARC_DB_ENABLE_AUTH=true”
export “CRYOSPARC_HOSTNAME_CHECK=processingserver3”
export “CRYOSPARC_MONGO_PORT=61001”
export “CRYOSPARC_MONGO_FCV=3.6”
export “CRYOSPARC_MONGO_CACHE_GB=4”
export “CRYOSPARC_HEARTBEAT_SECONDS=60”
export “CRYOSPARC_ROOT_DIR=/net/warm/home/cryosparc/cryosparc_master”
export “CRYOSPARC_HTTP_APP_PORT=61000”
export “CRYOSPARC_COMMAND_CORE_PORT=61002”
export “CRYOSPARC_BASE_PORT=61000”
export “CRYOSPARC_DB_CONNECTION_TIMEOUT_MS=20000”
export “CRYOSPARC_PROJECT_DIR_PREFIX=CS-”
export “CRYOSPARC_PATH=/net/warm/home/cryosparc/cryosparc_master/deps/external/mongodb/bin:/net/warm/home/cryosparc/cryosparc_master/bin”
export “CRYOSPARC_LIVE_ENABLED=true”
export “CRYOSPARC_CLUSTER_JOB_MONITOR_INTERVAL=10”
export “CRYOSPARC_COMMAND_RTP_PORT=61005”
export “CRYOSPARC_SUPERVISOR_SOCK_FILE=/tmp/cryosparc-supervisor-418449108a892d39c2ca5330a210d835.sock”
export “CRYOSPARC_DB_ENABLE_AUTH_FLAG=–auth”
export “CRYOSPARC_HTTP_APP_LEGACY_PORT=61007”
export “CRYOSPARC_FORCE_HOSTNAME=false”
export “CRYOSPARC_HTTP_LIVEAPP_LEGACY_PORT=61006”
export “PATH=/net/warm/home/cryosparc/cryosparc_master/deps/external/mongodb/bin:/net/warm/home/cryosparc/cryosparc_master/bin:/net/warm/home/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/bin:/net/warm/home/cryosparc/cryosparc_master/deps/anaconda/condabin:/net/warm/home/cryosparc/cryosparc_master/bin:/net/warm/home/cryosparc/cryosparc_master/bin:/sbin:/bin:/usr/sbin:/usr/bin”
export “LD_LIBRARY_PATH=”
export “LD_PRELOAD=/net/warm/home/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/libpython3.8.so”
export “PYTHONPATH=/net/warm/home/cryosparc/cryosparc_master”
export “PYTHONNOUSERSITE=true”
export “CONDA_SHLVL=1”
export “CONDA_PROMPT_MODIFIER=(cryosparc_master_env)”
export “CONDA_EXE=/net/warm/home/cryosparc/cryosparc_master/deps/anaconda/bin/conda”
export “CONDA_PREFIX=/net/warm/home/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env”
export “CONDA_PYTHON_EXE=/net/warm/home/cryosparc/cryosparc_master/deps/anaconda/bin/python”
export “CONDA_DEFAULT_ENV=cryosparc_master_env”

We have managed a work around. We mounted out SSD as /lscratch so it works fine now.

But it would be good to know how to do this properly.

4

As you installed CryoSPARC with the --standalone option a command like

cryosparcw connect --worker processingserver3 --master processingserver3 \
    --port 61000 --ssdpath /lscratch

was likely executed “in the background” without you noticing.
cryosparcw connect (guide) must be run on the worker computer to register the worker in the CryoSPARC master’s database.
One appends the --update option to the command to update an existing worker registration (also modifying relevant paramaters like
--ssdpath /path/to/new/ssd).