CryoSPARC installation stuck at "command_core: started"

Install, Configure and Update
1

Dear CryoSPARC team,

I have troubles to get CryoSPARC running. I installed the software following the guide for a single workstation.
Unfortunately, the installation process was stuck over night at “command_core: started”.

The same issue persists, if I use cryosparcm restart.

cryosparcm status

CryoSPARC System master node installed at
/home/cemkguest/software/cryosparc/cryosparc_master
Current cryoSPARC version: v4.7.1

CryoSPARC process status:

app STOPPED Not started
app_api STOPPED Not started
app_api_dev STOPPED Not started
command_core RUNNING pid 11969, uptime 0:07:48
command_rtp STOPPED Not started
command_vis STOPPED Not started
database RUNNING pid 11865, uptime 0:07:52

An error ocurred while checking license status
Could not get license verification status. Are all CryoSPARC processes RUNNING?

A few helpful outputs for you:
curl https://get.cryosparc.com/checklicenseexists/$LICENSE_ID
{“success”: true}

cryosparcm log database | tail -n 30

2025-07-03T11:07:30.026+0200 I REPL [replexec-0] Starting replication fetcher thread
2025-07-03T11:07:30.026+0200 I REPL [replexec-0] Starting replication applier thread
2025-07-03T11:07:30.026+0200 I REPL [replexec-0] Starting replication reporter thread
2025-07-03T11:07:30.027+0200 I REPL [rsSync] transition to SECONDARY from RECOVERING
2025-07-03T11:07:30.027+0200 I REPL [rsSync] conducting a dry run election to see if we could be elected. current term: 7
2025-07-03T11:07:30.027+0200 I REPL [replexec-0] dry election run succeeded, running for election in term 8
2025-07-03T11:07:30.027+0200 I REPL [replexec-0] election succeeded, assuming primary role in term 8
2025-07-03T11:07:30.027+0200 I REPL [replexec-0] transition to PRIMARY from SECONDARY
2025-07-03T11:07:30.027+0200 I REPL [replexec-0] Resetting sync source to empty, which was :27017
2025-07-03T11:07:30.027+0200 I REPL [replexec-0] Entering primary catch-up mode.
2025-07-03T11:07:30.027+0200 I REPL [replexec-0] Exited primary catch-up mode.
2025-07-03T11:07:31.431+0200 I NETWORK [listener] connection accepted from 129.132.174.233:43816 #1 (1 connection now open)
2025-07-03T11:07:31.431+0200 I NETWORK [conn1] received client metadata from 129.132.174.233:43816 conn1: { driver: { name: “PyMongo”, version: “4.8.0” }, os: { type: “Linux”, name: “Linux”, architecture: “x86_64”, version: “6.8.0-47-generic” }, platform: “CPython 3.10.14.final.0” }
2025-07-03T11:07:31.432+0200 I NETWORK [conn1] end connection 129.132.174.233:43816 (0 connections now open)
2025-07-03T11:07:31.432+0200 I NETWORK [listener] connection accepted from 127.0.0.1:43120 #2 (1 connection now open)
2025-07-03T11:07:31.433+0200 I NETWORK [conn2] received client metadata from 127.0.0.1:43120 conn2: { driver: { name: “PyMongo”, version: “4.8.0” }, os: { type: “Linux”, name: “Linux”, architecture: “x86_64”, version: “6.8.0-47-generic” }, platform: “CPython 3.10.14.final.0” }
2025-07-03T11:07:32.027+0200 I REPL [rsSync] transition to primary complete; database writes are now permitted
2025-07-03T11:07:32.435+0200 I NETWORK [listener] connection accepted from 127.0.0.1:43132 #3 (2 connections now open)
2025-07-03T11:07:32.435+0200 I NETWORK [conn3] received client metadata from 127.0.0.1:43132 conn3: { driver: { name: “PyMongo”, version: “4.8.0” }, os: { type: “Linux”, name: “Linux”, architecture: “x86_64”, version: “6.8.0-47-generic” }, platform: “CPython 3.10.14.final.0” }
2025-07-03T11:07:32.438+0200 I ACCESS [conn3] Successfully authenticated as principal cryosparc_admin on admin from client 127.0.0.1:43132
2025-07-03T11:07:32.439+0200 I NETWORK [conn2] end connection 127.0.0.1:43120 (1 connection now open)
2025-07-03T11:07:32.439+0200 I NETWORK [conn3] end connection 127.0.0.1:43132 (0 connections now open)
2025-07-03T11:07:38.447+0200 I NETWORK [listener] connection accepted from 129.132.174.233:59968 #4 (1 connection now open)
2025-07-03T11:07:38.447+0200 I NETWORK [conn4] received client metadata from 129.132.174.233:59968 conn4: { driver: { name: “PyMongo”, version: “4.8.0” }, os: { type: “Linux”, name: “Linux”, architecture: “x86_64”, version: “6.8.0-47-generic” }, platform: “CPython 3.10.14.final.0” }
2025-07-03T11:07:38.448+0200 I NETWORK [conn4] end connection 129.132.174.233:59968 (0 connections now open)
2025-07-03T11:07:38.448+0200 I NETWORK [listener] connection accepted from 127.0.0.1:49346 #5 (1 connection now open)
2025-07-03T11:07:38.448+0200 I NETWORK [conn5] received client metadata from 127.0.0.1:49346 conn5: { driver: { name: “PyMongo”, version: “4.8.0” }, os: { type: “Linux”, name: “Linux”, architecture: “x86_64”, version: “6.8.0-47-generic” }, platform: “CPython 3.10.14.final.0” }
2025-07-03T11:07:38.448+0200 I NETWORK [listener] connection accepted from 127.0.0.1:49358 #6 (2 connections now open)
2025-07-03T11:07:38.448+0200 I NETWORK [conn6] received client metadata from 127.0.0.1:49358 conn6: { driver: { name: “PyMongo”, version: “4.8.0” }, os: { type: “Linux”, name: “Linux”, architecture: “x86_64”, version: “6.8.0-47-generic” }, platform: “CPython 3.10.14.final.0” }
2025-07-03T11:07:38.450+0200 I ACCESS [conn6] Successfully authenticated as principal cryosparc_user on admin from client 127.0.0.1:49358

2

Welcome to the forum @Tamino .
Various network-related configurations could contribute to this problem.
Please can you

  1. post the output of the command
    /home/cemkguest/software/cryosparc/cryosparc_master/bin/cryosparcm call env | grep -i proxy
  2. while command_core is RUNNING, collect and post the output of these commands in a fresh command shell
    eval $(/home/cemkguest/software/cryosparc/cryosparc_master/bin/cryosparcm env)
curl 127.0.0.1:$CRYOSPARC_COMMAND_CORE_PORT
curl -v ${CRYOSPARC_MASTER_HOSTNAME}:$CRYOSPARC_COMMAND_CORE_PORT
# record outputs, then
exit
3

(post deleted by author)

4

thank you @wtempel. Yes, it might very well be that our network configuration prevent correct running of cryosparc.

I gladly provide you with the output you requested. Please let me know if you need anything else!

cemkguest@phobos:~/software/cryosparc/cryosparc_master$ eval $(/home/cemkguest/software/cryosparc/cryosparc_master/bin/cryosparcm env)
curl 127.0.0.1:$CRYOSPARC_COMMAND_CORE_PORT
curl -v ${CRYOSPARC_MASTER_HOSTNAME}:$CRYOSPARC_COMMAND_CORE_PORT
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
<html><head>
<meta type="copyright" content="Copyright (C) 1996-2021 The Squid Software Foundation and contributors">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<title>ERROR: The requested URL could not be retrieved</title>
<style type="text/css"><!--
 /*
 * Copyright (C) 1996-2021 The Squid Software Foundation and contributors
 *
 * Squid software is distributed under GPLv2+ license and includes
 * contributions from numerous individuals and organizations.
 * Please see the COPYING and CONTRIBUTORS files for details.
 */

/*
 Stylesheet for Squid Error pages
 Adapted from design by Free CSS Templates
 http://www.freecsstemplates.org
 Released for free under a Creative Commons Attribution 2.5 License
*/

/* Page basics */
* {
	font-family: verdana, sans-serif;
}

html body {
	margin: 0;
	padding: 0;
	background: #efefef;
	font-size: 12px;
	color: #1e1e1e;
}

/* Page displayed title area */
#titles {
	margin-left: 15px;
	padding: 10px;
	padding-left: 100px;
	background: url('/squid-internal-static/icons/SN.png') no-repeat left;
}

/* initial title */
#titles h1 {
	color: #000000;
}
#titles h2 {
	color: #000000;
}

/* special event: FTP success page titles */
#titles ftpsuccess {
	background-color:#00ff00;
	width:100%;
}

/* Page displayed body content area */
#content {
	padding: 10px;
	background: #ffffff;
}

/* General text */
p {
}

/* error brief description */
#error p {
}

/* some data which may have caused the problem */
#data {
}

/* the error message received from the system or other software */
#sysmsg {
}

pre {
}

/* special event: FTP directory listing */
#dirmsg {
    font-family: courier, monospace;
    color: black;
    font-size: 10pt;
}
#dirlisting {
    margin-left: 2%;
    margin-right: 2%;
}
#dirlisting tr.entry td.icon,td.filename,td.size,td.date {
    border-bottom: groove;
}
#dirlisting td.size {
    width: 50px;
    text-align: right;
    padding-right: 5px;
}

/* horizontal lines */
hr {
	margin: 0;
}

/* page displayed footer area */
#footer {
	font-size: 9px;
	padding-left: 10px;
}


body
:lang(fa) { direction: rtl; font-size: 100%; font-family: Tahoma, Roya, sans-serif; float: right; }
:lang(he) { direction: rtl; }
 --></style>
</head><body id=ERR_ACCESS_DENIED>
<div id="titles">
<h1>ERROR</h1>
<h2>The requested URL could not be retrieved</h2>
</div>
<hr>

<div id="content">
<p>The following error was encountered while trying to retrieve the URL: <a href="http://127.0.0.1:40002/">http://127.0.0.1:40002/</a></p>

<blockquote id="error">
<p><b>Access Denied.</b></p>
</blockquote>

<p>Access control configuration prevents your request from being allowed at this time. Please contact your service provider if you feel this is incorrect.</p>

<p>Your cache administrator is <a href="mailto:root?subject=CacheErrorInfo%20-%20ERR_ACCESS_DENIED&amp;body=CacheHost%3A%20proxybd.ethz.ch%0D%0AErrPage%3A%20ERR_ACCESS_DENIED%0D%0AErr%3A%20%5Bnone%5D%0D%0ATimeStamp%3A%20Fri,%2004%20Jul%202025%2010%3A51%3A24%20GMT%0D%0A%0D%0AClientIP%3A%20129.132.174.233%0D%0A%0D%0AHTTP%20Request%3A%0D%0AGET%20%2F%20HTTP%2F1.1%0AUser-Agent%3A%20curl%2F8.5.0%0D%0AAccept%3A%20*%2F*%0D%0AProxy-Connection%3A%20Keep-Alive%0D%0AHost%3A%20127.0.0.1%3A40002%0D%0A%0D%0A%0D%0A">root</a>.</p>
<br>
</div>

<hr>
<div id="footer">
<p>Generated Fri, 04 Jul 2025 10:51:24 GMT by proxybd.ethz.ch (squid/4.15)</p>
<!-- ERR_ACCESS_DENIED -->
</div>
</body></html>
* Uses proxy env variable http_proxy == 'http://proxy.ethz.ch:3128/'
* Host proxy.ethz.ch:3128 was resolved.
* IPv6: (none)
* IPv4: 129.132.202.155
*   Trying 129.132.202.155:3128...
* Connected to proxy.ethz.ch (129.132.202.155) port 3128
> GET http://phobos:40002/ HTTP/1.1
> Host: phobos:40002
> User-Agent: curl/8.5.0
> Accept: */*
> Proxy-Connection: Keep-Alive
> 
< HTTP/1.1 503 Service Unavailable
< Server: squid/4.15
< Mime-Version: 1.0
< Date: Fri, 04 Jul 2025 10:51:24 GMT
< Content-Type: text/html;charset=utf-8
< Content-Length: 3703
< X-Squid-Error: ERR_DNS_FAIL 0
< Vary: Accept-Language
< Content-Language: en
< X-Cache: MISS from proxybd.ethz.ch
< X-Cache-Lookup: MISS from proxybd.ethz.ch:3128
< Via: 1.1 proxybd.ethz.ch (squid/4.15)
< Connection: close
< 
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
<html><head>
<meta type="copyright" content="Copyright (C) 1996-2021 The Squid Software Foundation and contributors">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<title>ERROR: The requested URL could not be retrieved</title>
<style type="text/css"><!-- 
 /*
 * Copyright (C) 1996-2021 The Squid Software Foundation and contributors
 *
 * Squid software is distributed under GPLv2+ license and includes
 * contributions from numerous individuals and organizations.
 * Please see the COPYING and CONTRIBUTORS files for details.
 */

/*
 Stylesheet for Squid Error pages
 Adapted from design by Free CSS Templates
 http://www.freecsstemplates.org
 Released for free under a Creative Commons Attribution 2.5 License
*/

/* Page basics */
* {
	font-family: verdana, sans-serif;
}

html body {
	margin: 0;
	padding: 0;
	background: #efefef;
	font-size: 12px;
	color: #1e1e1e;
}

/* Page displayed title area */
#titles {
	margin-left: 15px;
	padding: 10px;
	padding-left: 100px;
	background: url('/squid-internal-static/icons/SN.png') no-repeat left;
}

/* initial title */
#titles h1 {
	color: #000000;
}
#titles h2 {
	color: #000000;
}

/* special event: FTP success page titles */
#titles ftpsuccess {
	background-color:#00ff00;
	width:100%;
}

/* Page displayed body content area */
#content {
	padding: 10px;
	background: #ffffff;
}

/* General text */
p {
}

/* error brief description */
#error p {
}

/* some data which may have caused the problem */
#data {
}

/* the error message received from the system or other software */
#sysmsg {
}

pre {
}

/* special event: FTP directory listing */
#dirmsg {
    font-family: courier, monospace;
    color: black;
    font-size: 10pt;
}
#dirlisting {
    margin-left: 2%;
    margin-right: 2%;
}
#dirlisting tr.entry td.icon,td.filename,td.size,td.date {
    border-bottom: groove;
}
#dirlisting td.size {
    width: 50px;
    text-align: right;
    padding-right: 5px;
}

/* horizontal lines */
hr {
	margin: 0;
}

/* page displayed footer area */
#footer {
	font-size: 9px;
	padding-left: 10px;
}


body
:lang(fa) { direction: rtl; font-size: 100%; font-family: Tahoma, Roya, sans-serif; float: right; }
:lang(he) { direction: rtl; }
 --></style>
</head><body id=ERR_DNS_FAIL>
<div id="titles">
<h1>ERROR</h1>
<h2>The requested URL could not be retrieved</h2>
</div>
<hr>

<div id="content">
<p>The following error was encountered while trying to retrieve the URL: <a href="http://phobos:40002/">http://phobos:40002/</a></p>

<blockquote id="error">
<p><b>Unable to determine IP address from host name <q>phobos</q></b></p>
</blockquote>

<p>The DNS server returned:</p>
<blockquote id="data">
<pre>Name Error: The domain name does not exist.</pre>
</blockquote>

<p>This means that the cache was not able to resolve the hostname presented in the URL. Check if the address is correct.</p>

<p>Your cache administrator is <a href="mailto:root?subject=CacheErrorInfo%20-%20ERR_DNS_FAIL&amp;body=CacheHost%3A%20proxybd.ethz.ch%0D%0AErrPage%3A%20ERR_DNS_FAIL%0D%0AErr%3A%20%5Bnone%5D%0D%0ADNS%20ErrMsg%3A%20Name%20Error%3A%20The%20domain%20name%20does%20not%20exist.%0D%0ATimeStamp%3A%20Fri,%2004%20Jul%202025%2010%3A51%3A24%20GMT%0D%0A%0D%0AClientIP%3A%20129.132.174.233%0D%0A%0D%0AHTTP%20Request%3A%0D%0AGET%20%2F%20HTTP%2F1.1%0AUser-Agent%3A%20curl%2F8.5.0%0D%0AAccept%3A%20*%2F*%0D%0AProxy-Connection%3A%20Keep-Alive%0D%0AHost%3A%20phobos%3A40002%0D%0A%0D%0A%0D%0A">root</a>.</p>
<br>
</div>

<hr>
<div id="footer">
<p>Generated Fri, 04 Jul 2025 10:51:24 GMT by proxybd.ethz.ch (squid/4.15)</p>
<!-- ERR_DNS_FAIL -->
</div>
</body></html>
* Closing connection
5

Thanks @Tamino for posting the outputs, which suggest a number of possible approaches, depending on how you intend to configure and operate CryoSPARC. Please can you provide additional information:

  1. Do you intend to run CryoSPARC in single workstation, connected workers or cluster mode?
  2. What are the outputs of these commands on the CryoSPARC master node?
    hostname -f
host phobos
grep HOSTNAME /home/cemkguest/software/cryosparc/cryosparc_master/config.sh
/home/cemkguest/software/cryosparc/cryosparc_master/bin/cryosparcm call env | grep -i proxy
6

Dear @wtempel, thanks for the quick reply!

I am planning on using it only as a single workstation. It should only run on the local machine, with no additional workers or connected to the cluster (Only ssh connection to the machine for remote work)

Happily I provide you with the output of the commands:

cemkguest@phobos:~$ hostname -f
host phobos
grep HOSTNAME /home/cemkguest/software/cryosparc/cryosparc_master/config.sh
/home/cemkguest/software/cryosparc/cryosparc_master/bin/cryosparcm call env | grep -i proxy


phobos
phobos has address 129.132.174.233
phobos has IPv6 address fe80::d0b9:fd47:e64b:d9db
export CRYOSPARC_MASTER_HOSTNAME="phobos"
https_proxy=http://proxy.ethz.ch:3128/
http_proxy=http://proxy.ethz.ch:3128/
7

Thanks @Tamino. The topic Cryosparc not starting looks similar to your situation. Assuming that the --standalone installation was disrupted just after the installation of the cryosparc_master/ package, you may consider

  1. adding the line
    export NO_PROXY="${CRYOSPARC_MASTER_HOSTNAME},localhost,127.0.0.1"
    to the file
    /home/cemkguest/software/cryosparc/cryosparc_master/config.sh
    somewhere below the definition of CRYOSPARC_MASTER_HOSTNAME
  2. restarting CryoSPARC.
    The following steps would have been performed automatically in case of a smooth
    --standalone installation.
  3. creating the first user
  4. installing the cryosparc_worker/ package
  5. adding the line
    export NO_PROXY="phobos,localhost,127.0.0.1"
    to the file
    cryosparc_worker/config.sh
    (In case the master hostname changes from phobos in the future, phobos needs to be changed accordingly in the NO_PROXY definition.)
  6. connecting the worker component with a command like
    cryosparc_worker/bin/cryosparcw connect --master phobos --worker phobos --port 99999 --ssdpath /path/to/cache
    where the --port parameter needs to be changed from the nonsensical 99999 value to the CRYOSPARC_BASE_PORT value inside
    /home/cemkguest/software/cryosparc/cryosparc_master/config.sh
    and the --ssdpath parameter points to the actual path to be used for particle caching (or is replaced altogether with --nossd)