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On my work computer on Windows 10, ./sirius --help (or any other way to start SIRIUS, such as the GUI) takes several minutes (>6 min, see log below).
On my (much less powerful) home computer on Windows 10, the same takes 15 seconds.
I suspect that this has something to do with the Cortex XDR system https://www.paloaltonetworks.com/cortex/cortex-xdr protecting our computers; but I can't say for sure. Cortex uses some CPU but there is no useful info there. Now I don't know how much that is a SIRIUS problem but it's certainly a problem.
By the way, the user gets asked for firewall permissions; are those necessary or can one safely say no to all? If necessary, that means every user needs admin rights?
$ ./sirius --help
Jul 03, 2024 10:11:05 AM org.apache.commons.beanutils.FluentPropertyBeanIntrospector introspect
INFO: Error when creating PropertyDescriptor for public final void org.apache.commons.configuration2.AbstractConfiguration.setProperty(java.lang.String,java.lang.Object)! Ignoring this property.
Jul 03, 2024 10:11:09 AM de.unijena.bioinf.ms.frontend.core.ApplicationCore <clinit>
INFO: Sirius Workspace Successfull initialized at: C:\Users\stravsmi\.sirius-6.0
Jul 03, 2024 10:11:09 AM de.unijena.bioinf.ms.frontend.core.ApplicationCore <clinit>
INFO: You run SIRIUS 6.0.0 on windows 10_amd64
Jul 03, 2024 10:11:09 AM de.unijena.bioinf.ms.frontend.core.ApplicationCore <clinit>
INFO: You run SIRIUS in 'SERVICE' mode.
Jul 03, 2024 10:11:10 AM de.unijena.bioinf.ms.frontend.core.ApplicationCore <clinit>
INFO: Sirius was compiled with the following ILP solvers: GLPK-v1.7.0 (included), Gurobi-v9.1.1, CPLEX-v12.7.1, COIN-OR-v2.10.8.2
Jul 03, 2024 10:11:10 AM de.unijena.bioinf.ms.frontend.core.ApplicationCore <clinit>
INFO: Treebuilder priorities loaded from 'sirius.properties' are: [CLP, GUROBI, CPLEX]
Jul 03, 2024 10:11:10 AM de.unijena.bioinf.ms.frontend.core.ApplicationCore <clinit>
INFO: CPU check done. 4 cores that handle 8 threads were found.
Jul 03, 2024 10:11:14 AM de.unijena.bioinf.ChemistryBase.jobs.SiriusJobs getGlobalJobManager
INFO: Job manager successful initialized with 6 CPU thread(s) and 2 IO thread(s).
Jul 03, 2024 10:11:14 AM de.unijena.bioinf.rest.ProxyManager decorateWithPoolSettings
INFO: Starting http Client with MaxPerRoute=3 / maxTotal=5 (CPU-Threads=6).
Jul 03, 2024 10:11:36 AM de.unijena.bioinf.ms.frontend.core.ApplicationCore <clinit>
INFO: Web API initialized.
Jul 03, 2024 10:11:36 AM de.unijena.bioinf.ms.middleware.SiriusMiddlewareApplication main
INFO: Starting Application Core
Jul 03, 2024 10:11:42 AM de.unijena.bioinf.ms.frontend.Run parseArgs
INFO: Running with following arguments: [--help]
Jul 03, 2024 10:13:40 AM org.springframework.boot.StartupInfoLogger logStarting
INFO: Starting SiriusMiddlewareApplication v6.0.0 using Java 21.0.3 with PID 5024 (C:\Software\sirius-6.0.0-win64-release\sirius\app\sirius_rest_service-6.0.0-boot.jar started by stravsmi in C:\Software\sirius-6.0.0-win64-release\sirius)
Jul 03, 2024 10:13:40 AM org.springframework.boot.SpringApplication logStartupProfileInfo
INFO: No active profile set, falling back to 1 default profile: "default"
Jul 03, 2024 10:16:27 AM org.springframework.boot.web.embedded.jetty.JettyServletWebServerFactory getWebServer
INFO: Server initialized with port: 0
Jul 03, 2024 10:16:27 AM org.eclipse.jetty.server.Server doStart
INFO: jetty-12.0.6; built: 2024-01-30T02:43:24.387Z; git: 78ab6e6ba163f89cdd97f2ae0283fbb5e371cfaf; jvm 21.0.3+9-LTS
Jul 03, 2024 10:16:28 AM org.eclipse.jetty.ee10.servlet.ServletContextHandler$ServletContextApi log
INFO: Initializing Spring embedded WebApplicationContext
Jul 03, 2024 10:16:28 AM org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext prepareWebApplicationContext
INFO: Root WebApplicationContext: initialization completed in 153877 ms
Jul 03, 2024 10:16:36 AM org.eclipse.jetty.session.DefaultSessionIdManager doStart
INFO: Session workerName=node0
Jul 03, 2024 10:16:36 AM org.eclipse.jetty.server.handler.ContextHandler doStart
INFO: Started osbwej.JettyEmbeddedWebAppContext@294ab038{application,/,b=[file:/C:/Users/stravsmi/AppData/Local/Temp/jetty-docbase.0.17798025399828615248/, URLResource@E1A12F79(jar:nested:///C:/Software/sirius-6.0.0-win64-release/sirius/app/sirius_rest_service-6.0.0-boot.jar/!BOOT-INF/lib/swagger-ui-5.10.3.jar!/META-INF/resources/)],a=AVAILABLE,h=oeje10s.SessionHandler@55849272{STARTED}}
Jul 03, 2024 10:16:36 AM org.eclipse.jetty.ee10.servlet.ServletContextHandler doStart
INFO: Started osbwej.JettyEmbeddedWebAppContext@294ab038{application,/,b=[file:/C:/Users/stravsmi/AppData/Local/Temp/jetty-docbase.0.17798025399828615248/, URLResource@E1A12F79(jar:nested:///C:/Software/sirius-6.0.0-win64-release/sirius/app/sirius_rest_service-6.0.0-boot.jar/!BOOT-INF/lib/swagger-ui-5.10.3.jar!/META-INF/resources/)],a=AVAILABLE,h=oeje10s.SessionHandler@55849272{STARTED}}
Jul 03, 2024 10:16:36 AM org.eclipse.jetty.server.Server doStart
INFO: Started oejs.Server@27bc2650{STARTING}[12.0.6,sto=0] @339713ms
Jul 03, 2024 10:16:37 AM de.unijena.bioinf.ms.middleware.service.databases.ChemDbServiceImpl <init>
INFO: Scanning for custom databases...
Jul 03, 2024 10:16:39 AM de.unijena.bioinf.ms.middleware.service.databases.ChemDbServiceImpl <init>
INFO: ...found:
Jul 03, 2024 10:16:52 AM org.springframework.boot.actuate.endpoint.web.EndpointLinksResolver <init>
INFO: Exposing 1 endpoint(s) beneath base path '/actuator'
Jul 03, 2024 10:16:56 AM org.springframework.boot.autoconfigure.web.servlet.WelcomePageHandlerMapping <init>
INFO: Adding welcome page: ServletContext resource [/index.html]
Jul 03, 2024 10:17:46 AM org.eclipse.jetty.ee10.servlet.ServletContextHandler$ServletContextApi log
INFO: Initializing Spring DispatcherServlet 'dispatcherServlet'
Jul 03, 2024 10:17:46 AM org.springframework.web.servlet.FrameworkServlet initServletBean
INFO: Initializing Servlet 'dispatcherServlet'
Jul 03, 2024 10:17:46 AM org.springframework.web.servlet.FrameworkServlet initServletBean
INFO: Completed initialization in 2 ms
Jul 03, 2024 10:17:47 AM org.eclipse.jetty.server.AbstractConnector doStart
INFO: Started ServerConnector@6296c184{HTTP/1.1, (http/1.1)}{0.0.0.0:63894}
Jul 03, 2024 10:17:47 AM org.springframework.boot.web.embedded.jetty.JettyWebServer start
INFO: Jetty started on port 63894 (http/1.1) with context path '/'
SIRIUS Service is running on port: 63894
SIRIUS Service started successfully!
Jul 03, 2024 10:17:47 AM org.springframework.boot.StartupInfoLogger logStarted
INFO: Started SiriusMiddlewareApplication in 354.944 seconds (process running for 410.499)
Usage: sirius [-hV] [--noCite] [--recompute] [--buffer=<initialInstanceBuffer>]
[--cores=<numOfCores>] [--log=<logLevel>] [--maxmz=<maxMz>]
[--workspace=<workspace>] [[-o=<outputProjectLocation>]
[--update-fingerprint-version]] [[[--allow-ms1-only]
-i=<inputPath>[,<inputPath>...] [-i=<inputPath>[,
<inputPath>...]]... [--ignore-formula]] [-z=<parentMz>
[-1=<ms1File>[,<ms1File>...]] [--adduct=<ionType>] -2=<ms2File>[,
<ms2File>...] [-f=<formula>]]...] [COMMAND]
-h, --help Show this help message and exit.
-V, --version Print version information and exit.
--log, --loglevel=<logLevel>
Set logging level of the Jobs SIRIUS will execute.
Valid values: SEVERE, WARNING, INFO, FINER, ALL
Default: WARNING
--cores, --threads, --processors=<numOfCores>
Number of simultaneous worker thread to be used for
compute intense workload. If not specified SIRIUS
chooses a reasonable number based you CPU specs.
--buffer, --instance-buffer=<initialInstanceBuffer>
Number of instances that will be loaded into the
Memory. A larger buffer ensures that there are
enough instances available to use all cores
efficiently during computation. A smaller buffer
saves Memory. To load all instances immediately
set it to -1. Default (numeric value 0): 3 x
--cores. Note that for <DATASET_TOOLS> the
compound buffer may have no effect because this
tools may have to load compounds simultaneously
into the memory.
Default: 0
--workspace=<workspace>
Specify sirius workspace location. This is the
directory for storing Property files, logs,
databases and caches. This is NOT for the
project-space that stores the results! Default is
$USER_HOME/.sirius-<MINOR_VERSION>
--recompute Recompute results of ALL tools where results are
already present. Per default already present
results will be preserved and the instance will
be skipped for the corresponding Task/Tool
--maxmz=<maxMz> Only considers compounds with a precursor m/z lower
or equal [--maxmz]. All other compounds in the
input will be skipped.
Default: Infinity
--noCite, --noCitations, --no-citations
Do not write summary files to the project-space
Specify OUTPUT Project-Space:
-o, -p, --output, --project=<outputProjectLocation>
Specify the project-space to write into. If no
[--input] is specified it is also used as input.
For compression use the File ending .zip or .
sirius.
--update-fingerprint-version
Updates Fingerprint versions of the input project
to the one used by this SIRIUS version.
WARNING: All Fingerprint related results (CSI:
FingerID, CANOPUS) will be lost!
Specify multi-compound inputs (.ms, .mgf, .mzML/.mzXml, .sirius):
-i, --input=<inputPath>[,<inputPath>...]
Specify the input in multi-compound input formats:
Preprocessed mass spectra in .ms or .mgf file
format or LC/MS runs in .mzML/.mzXml format but
also any other file type e.g. to provide input
for STANDALONE tools.
--ignore-formula ignore given molecular formula if present in .ms or
.mgf input files.
--allow-ms1-only Allow MS1 only data to be imported.
Specify generic inputs (CSV) on per compound level:
-1, --ms1=<ms1File>[,<ms1File>...]
MS1 spectra files
-2, --ms2=<ms2File>[,<ms2File>...]
MS2 spectra files
-z, --mz, --precursor, --parentmass=<parentMz>
The mass of the parent ion for the specified ms2
spectra
--adduct, --ionization=<ionType>
Specify the adduct for this compound
Default: [M+?]+
-f, --formula=<formula> Specify the neutralized formula of this compound.
This will be used for tree computation. If given
no mass decomposition will be performed.
Commands:
config
<CONFIGURATION> Override all
possible default configurations
of this toolbox from the command
line.
custom-db, DB <STANDALONE> Generate a custom
searchable structure/spectral
database. Import multiple files
with compounds into this DB.
similarity <STANDALONE> Computes the
similarity between all compounds
in the dataset and outputs a
matrix of similarities.
decomp, mass-decomposition <STANDALONE> Small tool to
decompose masses with given
deviation, ionization, chemical
alphabet and chemical filter.
mgf-export, MGF <STANDALONE> Exports the spectra of
a given input as mgf.
fingerprinter, FP <STANDALONE> Compute SIRIUS
compatible fingerprints from
PubChem standardized SMILES in
tsv format.
service, rest, REST <STANDALONE> Starts SIRIUS as a
background (REST) service that
can be requested via a REST-API.
login <STANDALONE> Allows a user to login
for SIRIUS Webservices (e.g. CSI:
FingerID or CANOPUS) and securely
store a personal access token.
settings <STANDALONE> Configure persistent
(technical) settings of SIRIUS (e.
g. ProxySettings or ILP Solver).
install-autocompletion <INSTALL> generates and installs an
Autocompletion-Script with all
subcommands. Default installation
is for the current user.
summaries, write-summaries, W <STANDALONE, POSTPROCESSING> Write
Summary files from a given
project-space into the given
project-space or a custom
location.
lcms-align, A <PREPROCESSING> Align and merge
compounds of multiple LCMS Runs.
Use this tool if you want to
import from mzML/mzXml.
formulas, trees, formula, sirius <COMPOUND TOOL> Identify molecular
formula for each compound
individually using fragmentation
trees and isotope patterns.
structures, structure-db-search, structure
<COMPOUND TOOL> Search in molecular
structure db for each compound
Individually using CSI:FingerID
structure database search.
fingerprints, fingerprint <COMPOUND TOOL> Predict molecular
fingerprint from MS/MS and
fragmentation trees for each
compound individually using CSI:
FingerID fingerprint prediction.
zodiac, rerank-formulas <DATASET TOOL> Identify Molecular
formulas of all compounds in a
dataset together using ZODIAC.
classes, canopus, compound-classes <COMPOUND TOOL> Predict compound
categories for each compound
individually based on its
predicted molecular fingerprint
(CSI:FingerID) using CANOPUS.
spectra-search, library-search <COMPOUND TOOL> Computes the
similarity between all
compounds/features in the
project-space (queries) one vs
all spectra in the selected
databases.
denovo-structures, msnovelist <COMPOUND TOOL> Predict MsNovelist
compound candidates and compare
them against molecular
fingerprint using CSI:FingerID
scoring method.
Destroy Project Provider Service...
Destroy Project Provider Service DONE
Destroy Compute Service...
Destroy Compute Service DONE
The text was updated successfully, but these errors were encountered:
Hey Michele,
I do not know much about this. So just a few guesses.
SIRIUS 6 release before 6.0.4 where not signed properly. Since 6.0.4 we provide signe msi installers again which might convince the security tools to be less protective. But the msi installer also needs admin rights.
On my work computer on Windows 10,
./sirius --help
(or any other way to start SIRIUS, such as the GUI) takes several minutes (>6 min, see log below).On my (much less powerful) home computer on Windows 10, the same takes 15 seconds.
I suspect that this has something to do with the Cortex XDR system https://www.paloaltonetworks.com/cortex/cortex-xdr protecting our computers; but I can't say for sure. Cortex uses some CPU but there is no useful info there. Now I don't know how much that is a SIRIUS problem but it's certainly a problem.
By the way, the user gets asked for firewall permissions; are those necessary or can one safely say no to all? If necessary, that means every user needs admin rights?
The text was updated successfully, but these errors were encountered: