Upgraded to v5.0.6: No route to host

Troubleshooting
1

Hello,

I am a university data center staff member and manage a cluster-deploy CryoSPARC instance.
The master runs on a VM, and workers are backed by a Slurm HPC cluster.
I just upgraded it from v4.7.1-cuda12 to v5.0.6 and ran Extensive Validation – EMPIAR-10025 – Testing Mode.
The head job J1 threw out an error “httpx.ConnectError: [Errno 113] No route to host“ while job J5 Curate Exposures is stuck in the Waiting state.

My understanding is J5 Curate Exposures runs on Master directly, and the head job J1, running on a Slurm compute node, was trying to programmatically manipulate J5. We double-checked Master VM firewall settings and confirmed ports 39000-39009 are open, and compute node can reach Master by instance domain name.

We have another old 4.7.1-cuda12 cluster-deploy instance (another VM with exact same setup), and Extensive Validation works ok there.

Any help would be appreciated.

Thanks

Drew

2

@drewli Please can you try whether the approach in Error Extensive Validation after upgrade to V5.0.2 - #9 by wtempel resolves this issue for you?

3

@wtempel Thanks for the info.

I just tried it, and it now throws out a different error “httpx.ConnectError: [Errno 111] Connection refused“

Both the head job and Curate Exposures job are on Master (VM)

4

For additional details about this error, please can you post the outputs of these command

project_id="P99" # replace with actual project ID
head_job_id="J1" # replace with actual job ID
curate_job_id="J5" # replace with actual job ID
cryosparcm job events $project_id $head_job_id
cryosparcm job events $project_id $curate_job_id
cryosparcm job log $project_id $curate_job_id
cryosparcm cli "api.jobs.find_one('$project_id', '$head_job_id')"
cryosparcm cli "api.jobs.find_one('$project_id', '$curate_job_id')"
5

Here are the logs (had to remove duplications to fit content length limit)

[ 19:56:23] [162 ] License is valid.
[ 19:56:23] [162 ] Running job on master node
[ 19:56:29] [152 ] Job P26-J1 started
[ 19:56:29] [152 ] Master running v5.0.6, worker running v5.0.6
[ 19:56:29] [154 ] Working in directory:
[ 19:56:29] [154 ] Running on lane None
[ 19:56:29] [154 ] Resources Allocated

Worker
CPU
GPU
RAM
SSD False
[ 19:56:29] [154 ] ──────────────────────────────────────────────────────────────
[ 19:56:29] [154 ] Importing job module for job type extensive_workflow_bench…
[ 19:56:29] [158 ] Job ready to run
[ 19:56:29] [158 ] ──────────────────────────────────────────────────────────────
[ 19:56:29] [158 ] Transparent hugepages are enabled. You may encounter stalls or performance problems with CryoSPARC jobs.
[ 19:56:29] [158 ] Downloading data from https://s3.wasabisys.com/cryosparc-test-data-dist/empiar_10025_subset_v1.tar…
(100% - Done!)
[ 20:00:45] [162 ] Downloaded and verified in 255.673s
[ 20:00:45] [162 ] Extracting test data to
…
[ 20:01:30] [163 ] Extracted in 44.988s
[ 20:01:30] [163 ] Removing temporary test data download at
<PATH>
[ 20:01:30] [163 ] Removed .tar in 0.318s.
[ 20:01:30] [163 ] Launching job: import_movies
Scheduling import_movies (import_movies) P26, J2
Job (import_movies) P26 J2 completed in 21.20s
[ 20:01:30] [163 ] Created job P26-J2, (import_movies, import_movies)
[ 20:01:30] [163 ] input group connects: {}
[ 20:02:18] [163 ] Launching job: patch_motion
Scheduling patch_motion_correction_multi (patch_motion_correction_multi) P26, J3
Job (patch_motion_correction_multi) P26 J3 completed in 205.34s
[ 20:02:18] [163 ] Created job P26-J3, (patch_motion, patch_motion_correction_multi)
[ 20:02:18] [163 ] input group connects: {‘movies’: [{‘input_job_name’: ‘import_movies’, ‘group_name’:
‘imported_movies’}]}
[ 20:06:29] [164 ] Launching job: patch_ctf_est
Scheduling patch_ctf_estimation_multi (patch_ctf_estimation_multi) P26, J4
Job (patch_ctf_estimation_multi) P26 J4 completed in 88.27s
[ 20:06:29] [164 ] Created job P26-J4, (patch_ctf_est, patch_ctf_estimation_multi)
[ 20:06:29] [164 ] input group connects: {‘exposures’: [{‘input_job_name’: ‘patch_motion’, ‘group_name’: ‘micrographs’}]}
[32] [164 ] Launching job: curate_exposures
Scheduling curate_exposures_v2 (curate_exposures_v2) P26, J5
Running post launch callback: interactive_exposure_curation
[32] [164 ] Created job P26-J5, (curate_exposures, curate_exposures_v2)
[32] [164 ] input group connects: {‘exposures’: [{‘input_job_name’: ‘patch_ctf_est’, ‘group_name’: ‘exposures’}]}
[55] [166 ] Traceback (most recent call last):
File
“
rts/default.py”, line 101, in map_httpcore_exceptions
yield
File
“
rts/default.py”, line 250, in handle_request
resp = self._pool.handle_request(req)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
“
/connection_pool.py”, line 256, in handle_request
raise exc from None
File
“
/connection_pool.py”, line 236, in handle_request
response = connection.handle_request(
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
“
/connection.py”, line 101, in handle_request
raise exc
File
“
/connection.py”, line 78, in handle_request
stream = self._connect(request)
^^^^^^^^^^^^^^^^^^^^^^
File
“
/connection.py”, line 124, in _connect
stream = self._network_backend.connect_tcp(**kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
“
ends/sync.py”, line 207, in connect_tcp
with map_exceptions(exc_map):
^^^^^^^^^^^^^^^^^^^^^^^
File
" line 158, in
exit
self.gen.throw(value)
File
“
ptions.py”, line 14, in map_exceptions
raise to_exc(exc) from exc
httpcore.ConnectError: [Errno 111] Connection refused

                           The above exception was the direct cause of the following exception:
                           
                           Traceback (most recent call last):
                             File "cli/run.py", line 236, in cli.run.register_thread_excepthook.init.run_with_except_hook
                             File

" line 1012, in

run
self._target(*self._args, **self._kwargs)
File
" line
303, in interactive_exposure_curation
fieldsres = jobs.interact(subjob, “get_fields_and_thresholds”, {})
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File " line
768, in interact
r = httpx.post(
^^^^^^^^^^^
File
"
, line 304, in post
return request(
^^^^^^^^
File
"
, line 109, in request
return client.request(
^^^^^^^^^^^^^^^
File
“
py”, line 825, in request
return self.send(request, auth=auth, follow_redirects=follow_redirects)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
“
py”, line 914, in send
response = self._send_handling_auth(
^^^^^^^^^^^^^^^^^^^^^^^^^
File
“
py”, line 942, in _send_handling_auth
response = self._send_handling_redirects(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
“
py”, line 979, in _send_handling_redirects
response = self._send_single_request(request)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
“
py”, line 1014, in _send_single_request
response = transport.handle_request(request)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
“
rts/default.py”, line 249, in handle_request
with map_httpcore_exceptions():
^^^^^^^^^^^^^^^^^^^^^^^^^
File
" line 158, in
exit
self.gen.throw(value)
File
“
rts/default.py”, line 118, in map_httpcore_exceptions
raise mapped_exc(message) from exc
httpx.ConnectError: [Errno 111] Connection refused
[35] [174 ] License is valid.
[35] [174 ] Running job on master node
[44] [152 ] Job P26-J5 started
[44] [152 ] Master running v5.0.6, worker running v5.0.6
[44] [154 ] Working in directory:
[44] [154 ] Running on lane None
[44] [154 ] Resources Allocated

Worker
CPU
GPU
RAM
SSD False
[44] [154 ] ──────────────────────────────────────────────────────────────
[44] [154 ] Importing job module for job type curate_exposures_v2…
[53] [355 ] Job ready to run
[53] [355 ] ──────────────────────────────────────────────────────────────
[53] [355 ] Transparent hugepages are enabled. You may encounter stalls or performance problems with CryoSPARC jobs.
[53] [356 ] Interactive job will run on port 40677
[53] [356 ] Loaded info for 20 micrographs
[53] [356 ] Loaded info for 0 particles
[54] [357 ] Calculating average intensity for each exposure…
[54] [357 ] Done in 0.00s
[54] [357 ] Loading CTF data…
[54] [357 ] Loading CTF stats data…
[54] [357 ] Loading rigid motion data…
[54] [357 ] Done in 0.06s
[54] [357 ] Average Intensity:
[54] [357 ] Min: -105.997 Max: -8.046
[54] [357 ] Average: -47.421 Median: -45.753
[54] [357 ] 0.5th percentile: -102.715 99.5th percentile: -9.265
[54] [FIGURE] Average Intensity

asset file=“J5_average_intensity.png” id=“6a2b15d6351a2b921ef3b52b”
asset file=“J5_average_intensity.pdf” id=“6a2b15d6351a2b921ef3b52d”

[54] [367 ] Average defocus (A):
[54] [367 ] Min: 12361.736 Max: 21641.865
[54] [367 ] Average: 16964.588 Median: 17146.977
[54] [367 ] 0.5th percentile: 12415.894 99.5th percentile: 21582.377
[54] [FIGURE] Average defocus (A)

asset file=“J5_average_defocus_a.png” id=“6a2b15d6351a2b921ef3b534”
asset file=“J5_average_defocus_a.pdf” id=“6a2b15d6351a2b921ef3b536”

[54] [370 ] Astigmatism (A):
[54] [370 ] Min: 99.530 Max: 262.176
[54] [370 ] Average: 186.081 Median: 191.294
[54] [370 ] 0.5th percentile: 100.757 99.5th percentile: 260.654
[54] [FIGURE] Astigmatism (A)

asset file=“J5_astigmatism_a.png” id=“6a2b15d6351a2b921ef3b53d”
asset file=“J5_astigmatism_a.pdf” id=“6a2b15d6351a2b921ef3b53f”

[54] [372 ] CTF fit resolution (A):
[54] [372 ] Min: 2.645 Max: 3.784
[54] [372 ] Average: 3.176 Median: 3.187
[54] [372 ] 0.5th percentile: 2.656 99.5th percentile: 3.754
[54] [FIGURE] CTF fit resolution (A)

asset file=“J5_ctf_fit_resolution_a.png” id=“6a2b15d6351a2b921ef3b546”
asset file=“J5_ctf_fit_resolution_a.pdf” id=“6a2b15d6351a2b921ef3b548”

[54] [374 ] Defocus Range:
[54] [374 ] Min: 183.555 Max: 672.586
[54] [374 ] Average: 400.096 Median: 404.824
[54] [374 ] 0.5th percentile: 187.054 99.5th percentile: 662.858
[54] [FIGURE] Defocus Range

asset file=“J5_defocus_range.png” id=“6a2b15d6351a2b921ef3b54f”
asset file=“J5_defocus_range.pdf” id=“6a2b15d6351a2b921ef3b551”

[54] [375 ] Defocus Tilt Angle (degrees):
[54] [375 ] Min: 0.471 Max: 4.361
[54] [375 ] Average: 2.495 Median: 2.772
[54] [375 ] 0.5th percentile: 0.491 99.5th percentile: 4.330
[54] [FIGURE] Defocus Tilt Angle (degrees)

asset file=“J5_defocus_tilt_angle_degrees.png” id=“6a2b15d6351a2b921ef3b558”
asset file=“J5_defocus_tilt_angle_degrees.pdf” id=“6a2b15d6351a2b921ef3b55a”

[54] [377 ] Relative Ice Thickness:
[54] [377 ] Min: 1.043 Max: 1.062
[54] [377 ] Average: 1.051 Median: 1.050
[54] [377 ] 0.5th percentile: 1.044 99.5th percentile: 1.061
[55] [FIGURE] Relative Ice Thickness

asset file=“J5_relative_ice_thickness.png” id=“6a2b15d6351a2b921ef3b561”
asset file=“J5_relative_ice_thickness.pdf” id=“6a2b15d6351a2b921ef3b563”

[55] [379 ] Total full-frame motion distance (pixels):
[55] [379 ] Min: 7.200 Max: 45.817
[55] [379 ] Average: 18.701 Median: 14.918
[55] [379 ] 0.5th percentile: 7.284 99.5th percentile: 45.713
[55] [FIGURE] Total full-frame motion distance (pixels)

asset file=“J5_total_full_frame_motion_distance_pixels.png” id=“6a2b15d7351a2b921ef3b56a”
asset file=“J5_total_full_frame_motion_distance_pixels.pdf” id=“6a2b15d7351a2b921ef3b56c”

[55] [380 ] Full-frame motion curvature:
[55] [380 ] Min: 3.226 Max: 9.171
[55] [380 ] Average: 5.189 Median: 4.338
[55] [380 ] 0.5th percentile: 3.243 99.5th percentile: 9.144
[55] [FIGURE] Full-frame motion curvature

asset file=“J5_full_frame_motion_curvature.png” id=“6a2b15d7351a2b921ef3b573”
asset file=“J5_full_frame_motion_curvature.pdf” id=“6a2b15d7351a2b921ef3b575”

[55] [382 ] Micrograph display will use shape (959, 927)
================= CRYOSPARC =================
Project P26 Job J5
Master Port 39000

MAIN PROCESS PID 3761896

14:08:42,805 core monitor INFO | MONITOR PROCESS PID 3762050
14:08:42,805 core monitor INFO | ========= monitor process now waiting for main process
14:08:42,805 core heartbeat INFO | ========= Updating heartbeat
================= CRYOSPARC =================
Project P26 Job J5
Master Port 39000

MAIN PROCESS PID 3761896
========= updating job startup information at 14:08:44.010043
========= now starting main process at 14:08:44.240959
14:08:44,755 core run INFO | Running job J5 of type curate_exposures_v2
14:08:44,755 core run INFO | Running job on hostname
14:08:44,755 core run INFO | Allocated Resources: lane=None lane_type=None hostname=‘’ target=None slots=ResourceSlots(CPU=, GPU=, RAM=) fixed=FixedResourceSlots(SSD=False) licenses_acquired=0
14:08:54,017 core heartbeat INFO | ========= Updating heartbeat
FutureWarning: Series.ravel is deprecated. The underlying array is already 1D, so ravel is not necessary. Use to_numpy() for conversion to a numpy array instead.
data = mics_df[field[“name”]].ravel()

Transparent hugepages setting: [always] madvise never

  • Serving Flask app ‘curate_exposures_v2’

  • Debug mode: off
    14:09:04,087 core heartbeat INFO | ========= Updating heartbeat
    …
    …
    14:10:54,179 core heartbeat INFO | ========= Updating heartbeat

    EXTERN got get_interactive_info 20:10:58.755360
    EXTERN done get_interactive_info 20:10:58.755415 0.00s
    EXTERN got get_available 20:10:58.883934
    EXTERN done get_available 20:10:58.883986 0.00s
    EXTERN got get_fields_and_thresholds 20:10:58.885679
    EXTERN done get_fields_and_thresholds 20:10:58.885695 0.00s
    EXTERN got get_individual_data_preview_thumbnail 20:10:58.999133
    EXTERN done get_individual_data_preview_thumbnail 20:10:59.006945 0.01s

    14:11:04,188 core heartbeat INFO | ========= Updating heartbeat
    …
    …
    2026-06-12 07:39:54,045 core heartbeat INFO | ========= Updating heartbeat
    {“id”: “6a2b12bc4b2e37b24c9a2841”, “updated_at”: " T20:09:39.897000Z", “created_at”: " T19:55:40.725000Z", “dumped_at”: " T20:09:10.640000Z", “last_dumped_version”: “v5.0.6”, “autodump”: false, “uid”: “J1”, “project_uid”: “P26”, “workspace_uids”: [“W1”], “spec”: {“type”: “extensive_workflow_bench”, “params”: {“dataset_selected”: “10025”, “dataset_data_dir”: “/bulk5/data/EMPIAR/10025/data/empiar_10025_subset”, “scheduling_mode”: “testing”, “run_advanced_jobs”: false, “workflow_extract_box_size”: 448, “workflow_extract_bin_size_small”: 256, “workflow_refine_symmetry”: “D7”, “workflow_refine_N”: 256, “workflow_abinit_num_init_iters”: 200, “workflow_abinit_num_final_iters”: 300, “workflow_multirefine_batch_size_per_class”: 1000, “workflow_refmotion_hyperopt_rmax”: 10.0, “workflow_refmotion_hyperopt_target_particles”: 12500, “workflow_refmotion_dose_target_particles”: 20000, “compute_use_ssd”: true, “compute_num_gpus”: 1, “resource_selection”: “usumae-gpu-grn::”, “send_data”: false, “random_seed”: 12345, “random_seed_default”: 12345}, “inputs”: {}, “outputs”: {}, “ui_tile_width”: 1, “ui_tile_height”: 1, “resource_spec”: {“cpu”: 1, “gpu”: 0, “ram”: 1, “ssd”: false}}, “job_dir”: “J1”, “job_dir_size”: 0, “job_dir_size_last_updated”: " T19:55:40.711000Z", “title”: “usumae-gpu-grn:: (1GPU) - EMPIAR-10025 - Testing Mode”, “description”: “”, “status”: “failed”, “created_by_user_id”: “679276c20b95c0a38433921b”, “queued_at”: " T19:56:21.525000Z", “started_at”: " T19:56:29.228000Z", “launched_at”: " T19:56:23.843000Z", “running_at”: " T19:56:29.749000Z", “failed_at”: " T :55.833000Z", “heartbeat_at”: " T :49.486000Z", “tokens_acquired_at”: " T19:56:23.833000Z", “last_scheduled_at”: " T19:56:22.202000Z", “last_accessed”: {“name”: “zhiyuli”, “accessed_at”: " T20:09:39.897000Z"}, “has_error”: true, “has_warning”: true, “version_created”: “v5.0.6”, “version”: “v5.0.6”, “priority”: 0, “deleted”: false, “deleting”: false, “parents”: , “children”: , “resources_allocated”: {“hostname”: “”, “slots”: {“CPU”: , “GPU”: , “RAM”: }, “fixed”: {“SSD”: false}, “licenses_acquired”: 0}, “queued_by_user_id”: “679276c20b95c0a38433921b”, “num_tokens”: 0, “job_sig”: “62”, “errors_run”: [{“message”: “Transparent hugepages are enabled. You may encounter stalls or performance problems with CryoSPARC jobs.”, “warning”: true}, {“message”: “Traceback (most recent call last):\n File " line 101, in map_httpcore_exceptions\n yield\n File " line 250, in handle_request\n resp = self._pool.handle_request(req)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File " line 256, in handle_request\n raise exc from None\n File " line 236, in handle_request\n response = connection.handle_request(\n ^^^^^^^^^^^^^^^^^^^^^^^^^^\n File " line 101, in handle_request\n raise exc\n File " line 78, in handle_request\n stream = self._connect(request)\n ^^^^^^^^^^^^^^^^^^^^^^\n File " line 124, in _connect\n stream = self._network_backend.connect_tcp(**kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File " line 207, in connect_tcp\n with map_exceptions(exc_map):\n ^^^^^^^^^^^^^^^^^^^^^^^\n File " line 158, in exit\n self.gen.throw(value)\n File " line 14, in map_exceptions\n raise to_exc(exc) from exc\nhttpcore.ConnectError: [Errno 111] Connection refused\n\nThe above exception was the direct cause of the following exception:\n\nTraceback (most recent call last):\n File “cli/run.py”, line 236, in cli.run.register_thread_excepthook.init.run_with_except_hook\n File " line 1012, in run\n self._target(*self._args, **self._kwargs)\n File " line 303, in interactive_exposure_curation\n fieldsres = jobs.interact(subjob, “get_fields_and_thresholds”, {})\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File " line 768, in interact\n r = httpx.post(\n ^^^^^^^^^^^\n File " line 304, in post\n return request(\n ^^^^^^^^\n File " line 109, in request\n return client.request(\n ^^^^^^^^^^^^^^^\n File " line 825, in request\n return self.send(request, auth=auth, follow_redirects=follow_redirects)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File " line 914, in send\n response = self._send_handling_auth(\n ^^^^^^^^^^^^^^^^^^^^^^^^^\n File " line 942, in _send_handling_auth\n response = self._send_handling_redirects(\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File " line 979, in _send_handling_redirects\n response = self._send_single_request(request)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File " line 1014, in _send_single_request\n response = transport.handle_request(request)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n File " line 249, in handle_request\n with map_httpcore_exceptions():\n ^^^^^^^^^^^^^^^^^^^^^^^^^\n File " line 158, in exit\n self.gen.throw(value)\n File " line 118, in map_httpcore_exceptions\n raise mapped_exc(message) from exc\nhttpx.ConnectError: [Errno 111] Connection refused\n”, “warning”: false}, {“message”: “[Errno 111] Connection refused”, “warning”: false}], “PID_monitor”: 3760905, “PID_main”: 3760752, “PID_workers”: , “cluster_job_monitor_retries”: 0, “cluster_job_custom_vars”: {}, “ui_tile_images”: , “is_experiment”: false, “enable_bench”: false, “bench”: {}, “bench_timings”: {}, “completed_count”: 0, “instance_information”: {“platform_node”: “”, “platform_release”: “5.14.0-611.49.1.el9_7.x86_64”, “platform_version”: “#1 SMP PREEMPT_DYNAMIC Thu Apr 23 13:13:41 UTC 2026”, “platform_architecture”: “x86_64”, “cpu_model”: “QEMU Virtual CPU version 2.5+”, “physical_cores”: 8, “max_cpu_freq”: 0.0, “total_memory”: “15.36GB”, “available_memory”: “11.55GB”, “used_memory”: “3.41GB”, “ofd_soft_limit”: 6000, “ofd_hard_limit”: 65535, “version”: “v5.0.6”}, “last_intermediate_data_cleared_amount”: 0, “intermediate_results_size_bytes”: 0, “is_final_result”: false, “is_ancestor_of_final_result”: false, “no_check_inputs_ready”: false, “progress”: , “tags”: , “starred_by”: , “uid_num”: 1, “project_uid_num”: 26, “status_num”: 40, “build_errors”: }
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