Update from 4.2 to 4.5.1 failed

JMB · May 29, 2024, 4:25pm

Hi there,
I just updated from 4.2 to 4.5.1 and after restart my jobs are stalled during lunching.

I ran “cryosparcm test install” and everytning looks fine
but running “cryosparcm test workers P30” does not look good.
I addition I include the “job.log” of P30 J97.

How shall I proceede?

Running installation tests…
✓ Running as cryoSPARC owner
✓ Running on master node
✓ CryoSPARC is running
✓ Connected to command_core at http://msr:61002
✓ CRYOSPARC_LICENSE_ID environment variable is set
✓ License has correct format
✓ Insecure mode is disabled
✓ License server set to “https://get.cryosparc.com”
✓ Connection to license server succeeded
✓ License server returned success status code 200
✓ License server returned valid JSON response
✓ License exists and is valid
✓ CryoSPARC is running v4.5.1
✓ Running the latest version of CryoSPARC
Could not get latest patch (status code 404)
✓ Patch update not required
✓ Admin user has been created
✓ GPU worker connected.

but running “cryosparcm test workers P30” does not look good.
2) ***********************************************
Running worker tests…
2024-05-29 18:03:32,630 log CRITICAL | Worker test results
2024-05-29 18:03:32,630 log CRITICAL | msr
2024-05-29 18:03:32,630 log CRITICAL | ✕ LAUNCH
2024-05-29 18:03:32,630 log CRITICAL | Error:
2024-05-29 18:03:32,630 log CRITICAL | See P30 J97 for more information
2024-05-29 18:03:32,630 log CRITICAL | SSD
2024-05-29 18:03:32,630 log CRITICAL | Did not run: Launch test failed
2024-05-29 18:03:32,630 log CRITICAL | GPU
2024-05-29 18:03:32,631 log CRITICAL | Did not run: Launch test failed

I addition I include the “job.log” of P30 J97
3) ***********************************************
================= CRYOSPARCW ======= 2024-05-29 18:01:31.462829 =========
Project P30 Job J97
Master msr Port 61002

========= monitor process now starting main process at 2024-05-29 18:01:31.462869
MAINPROCESS PID 69217
Traceback (most recent call last):
File “/home/cryosparc/cryosparc_worker/cryosparc_tools/cryosparc/command.py”, line 104, in func
with make_json_request(self, “/api”, data=data) as request:
File “/home/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/contextlib.py”, line 113, in enter
return next(self.gen)
File “/home/cryosparc/cryosparc_worker/cryosparc_tools/cryosparc/command.py”, line 191, in make_request
raise CommandClient.Error(client, error_reason, url=url)
cryosparc_tools.cryosparc.command.Error: *** CommandClient: (http://msr:61002/api) HTTP Error 400 Bad Request; please check cryosparcm log command_core for additional information.
Response from server: b’\n \n Bad Request\n \n \n

Bad Request

\n Invalid Method 'Invalid HTTP method: 'post''\n \n\n’

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File “”, line 1, in
File “cryosparc_master/cryosparc_compute/run.py”, line 173, in cryosparc_compute.run.run
File “/home/cryosparc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 126, in connect
cli = client.CommandClient(master_hostname, int(master_command_core_port), service=“command_core”)
File “/home/cryosparc/cryosparc_worker/cryosparc_compute/client.py”, line 36, in init
super().init(service, host, port, url, timeout, headers, cls=NumpyEncoder)
File “/home/cryosparc/cryosparc_worker/cryosparc_tools/cryosparc/command.py”, line 91, in init
self._reload() # attempt connection immediately to gather methods
File “/home/cryosparc/cryosparc_worker/cryosparc_tools/cryosparc/command.py”, line 118, in _reload
system = self._get_callable(“system.describe”)()
File “/home/cryosparc/cryosparc_worker/cryosparc_tools/cryosparc/command.py”, line 107, in func
raise CommandClient.Error(
cryosparc_tools.cryosparc.command.Error: *** CommandClient: (http://msr:61002) Did not receive a JSON response from method “system.describe” with params ()
*** CommandClient: (http://msr:61002/api) HTTP Error 400 Bad Request; please check cryosparcm log command_core for additional information.
Response from server: b’\n \n Bad Request\n \n \n

Bad Request

\n Invalid Method 'Invalid HTTP method: 'post''\n \n\n’
*** CommandClient: (http://msr:61002/api) HTTP Error 400 Bad Request; please check cryosparcm log command_core for additional information.
Response from server: b’\n \n Bad Request\n \n \n

Bad Request

\n Invalid Method 'Invalid HTTP method: 'post''\n \n\n’
Process Process-1:
Traceback (most recent call last):
File “/home/cryosparc/cryosparc_worker/cryosparc_tools/cryosparc/command.py”, line 104, in func
with make_json_request(self, “/api”, data=data) as request:
File “/home/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/contextlib.py”, line 113, in enter
return next(self.gen)
File “/home/cryosparc/cryosparc_worker/cryosparc_tools/cryosparc/command.py”, line 191, in make_request
raise CommandClient.Error(client, error_reason, url=url)
cryosparc_tools.cryosparc.command.CommandClient.Error: *** CommandClient: (http://msr:61002/api) HTTP Error 400 Bad Request; please check cryosparcm log command_core for additional information.
Response from server: b’\n \n Bad Request\n \n \n

Bad Request

\n Invalid Method 'Invalid HTTP method: 'post''\n \n\n’

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File “/home/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/multiprocessing/process.py”, line 315, in _bootstrap
self.run()
File “/home/cryosparc/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.8/multiprocessing/process.py”, line 108, in run
self._target(*self._args, **self._kwargs)
File “cryosparc_master/cryosparc_compute/run.py”, line 32, in cryosparc_compute.run.main
File “/home/cryosparc/cryosparc_worker/cryosparc_compute/jobs/runcommon.py”, line 126, in connect
cli = client.CommandClient(master_hostname, int(master_command_core_port), service=“command_core”)
File “/home/cryosparc/cryosparc_worker/cryosparc_compute/client.py”, line 36, in init
super().init(service, host, port, url, timeout, headers, cls=NumpyEncoder)
File “/home/cryosparc/cryosparc_worker/cryosparc_tools/cryosparc/command.py”, line 91, in init
self._reload() # attempt connection immediately to gather methods
File “/home/cryosparc/cryosparc_worker/cryosparc_tools/cryosparc/command.py”, line 118, in _reload
system = self._get_callable(“system.describe”)()
File “/home/cryosparc/cryosparc_worker/cryosparc_tools/cryosparc/command.py”, line 107, in func
raise CommandClient.Error(
cryosparc_tools.cryosparc.command.CommandClient.Error: *** CommandClient: (http://msr:61002) Did not receive a JSON response from method “system.describe” with params ()

wtempel · May 29, 2024, 6:45pm

Please can you post the outputs of these commands

On the master

hostname -f 
host $(hostname -f)
cryosparcm cli "get_scheduler_targets()"

On one of the CryoSPARC worker computers (the master, in case of a “Single Workstation” instance)
```
host msr
curl msr:61002
cat /home/cryosparc/cryosparc_worker/version
```

JMB · May 29, 2024, 8:06pm

Dear wtempel,

concerning “cat /home/cryosparc/cryosparc_worker/version” it looks that the worker was not updated, right?

hostname -f
msr

host $(hostname -f)
Host msr not found: 2(SERVFAIL)

cryosparcm cli “get_scheduler_targets()”
[{‘cache_path’: ‘/scr/cryosparc’, ‘cache_quota_mb’: None, ‘cache_reserve_mb’: 10000, ‘desc’: None, ‘gpus’: [{‘id’: 0, ‘mem’: 11539054592, ‘name’: ‘NVIDIA GeForce RTX 2080 Ti’}, {‘id’: 1, ‘mem’: 11539054592, ‘name’: ‘NVIDIA GeForce RTX 2080 Ti’}, {‘id’: 2, ‘mem’: 11539054592, ‘name’: ‘NVIDIA GeForce RTX 2080 Ti’}, {‘id’: 3, ‘mem’: 11539054592, ‘name’: ‘NVIDIA GeForce RTX 2080 Ti’}, {‘id’: 4, ‘mem’: 11539054592, ‘name’: ‘NVIDIA GeForce RTX 2080 Ti’}, {‘id’: 5, ‘mem’: 11539054592, ‘name’: ‘NVIDIA GeForce RTX 2080 Ti’}, {‘id’: 6, ‘mem’: 11539054592, ‘name’: ‘NVIDIA GeForce RTX 2080 Ti’}, {‘id’: 7, ‘mem’: 11539054592, ‘name’: ‘NVIDIA GeForce RTX 2080 Ti’}], ‘hostname’: ‘msr’, ‘lane’: ‘default’, ‘monitor_port’: None, ‘name’: ‘msr’, ‘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, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255], ‘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]}, ‘ssh_str’: ‘cryosparc@msr’, ‘title’: ‘Worker node msr’, ‘type’: ‘node’, ‘worker_bin_path’: ‘/home/cryosparc/cryosparc_worker/bin/cryosparcw’}]

host msr
Host msr not found: 2(SERVFAIL)

curl msr:61002
Hello World from cryosparc command core.

cat /home/cryosparc/cryosparc_worker/version
v4.2.1

wtempel · May 29, 2024, 9:12pm

Correct. But I am surprised the update failed under these circumstances. You can try the following in a fresh shell under the cryosparc account:

eval $( /home/cryosparc/cryosparc_worker/bin/cryosparcw env)
cd /home/cryosparc/cryosparc_worker/
curl -L https://get.cryosparc.com/download/worker-v4.5.1/$CRYOSPARC_LICENSE_ID -o cryosparc_worker.tar.gz
./bin/cryosparcw update

I you see
Successfully updated. after running these commands, you can

exit the shell (to avoid inadvertently running commands inside the loaded CryoSPARC environment)
try the worker test again

JMB · May 29, 2024, 9:51pm

as suggested by “cryosparcm test workers P30” to run
“nvidia-smi -pm 1” as root

A second
“cryosparcm test workers P30” prints the following
Running worker tests…
2024-05-29 23:44:43,952 log CRITICAL | Worker test results
2024-05-29 23:44:43,952 log CRITICAL | msr
2024-05-29 23:44:43,952 log CRITICAL | ✓ LAUNCH
2024-05-29 23:44:43,952 log CRITICAL | ✓ SSD
2024-05-29 23:44:43,952 log CRITICAL | ✓ GPU
2024-05-29 23:44:43,958 log CRITICAL | NVIDIA GeForce RTX 2080 Ti @ 00000000:87:00.0: GPU Software Power Cap is Active

wtempel · June 3, 2024, 6:50pm

is a warning, not an error. For details, see nvidia-smi documentation:

nvidia-smi --help-query-gpu | grep -A 1  sw_power_cap

JMB · June 4, 2024, 3:05pm

OK - thanks for the help.
Once the worker was uptated as suggested cSPA is running fine again

Update from 4.2 to 4.5.1 failed

I addition I include the “job.log” of P30 J97 3) *********************************************** ================= CRYOSPARCW ======= 2024-05-29 18:01:31.462829 ========= Project P30 Job J97 Master msr Port 61002

Bad Request

Bad Request

Bad Request

Bad Request

I addition I include the “job.log” of P30 J97
3) ***********************************************
================= CRYOSPARCW ======= 2024-05-29 18:01:31.462829 =========
Project P30 Job J97
Master msr Port 61002