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No Native Library when Running using CLI #344

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duhai-alshukaili opened this issue Jan 3, 2024 · 5 comments
Open

No Native Library when Running using CLI #344

duhai-alshukaili opened this issue Jan 3, 2024 · 5 comments

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@duhai-alshukaili
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When I try to run the shell script I get the following error:

Running PSL Inference.
790 [main] INFO org.linqs.psl.runtime.Runtime - PSL Runtime Version 3.0.1-SNAPSHOT-b33adfd
1992 [main] ERROR com.zaxxer.hikari.pool.HikariPool - HikariPool-1 - Exception during pool initializat
ion.
java.sql.SQLException: Error opening connection
at org.sqlite.SQLiteConnection.open(SQLiteConnection.java:258) ~[psl-cli-3.0.1-SNAPSHOT.jar:?]
at org.sqlite.SQLiteConnection.(SQLiteConnection.java:61) ~[psl-cli-3.0.1-SNAPSHOT.jar:?]
at org.sqlite.jdbc3.JDBC3Connection.(JDBC3Connection.java:23) ~[psl-cli-3.0.1-SNAPSHOT.ja
r:?]
at org.sqlite.jdbc4.JDBC4Connection.(JDBC4Connection.java:19) ~[psl-cli-3.0.1-SNAPSHOT.ja
r:?]
at org.sqlite.JDBC.createConnection(JDBC.java:104) ~[psl-cli-3.0.1-SNAPSHOT.jar:?]
at org.sqlite.JDBC.connect(JDBC.java:77) ~[psl-cli-3.0.1-SNAPSHOT.jar:?]
at com.zaxxer.hikari.util.DriverDataSource.getConnection(DriverDataSource.java:121) ~[psl-cli-3
.0.1-SNAPSHOT.jar:?]
at com.zaxxer.hikari.pool.PoolBase.newConnection(PoolBase.java:364) ~[psl-cli-3.0.1-SNAPSHOT.ja
r:?]
at com.zaxxer.hikari.pool.PoolBase.newPoolEntry(PoolBase.java:206) ~[psl-cli-3.0.1-SNAPSHOT.jar
:?]
at com.zaxxer.hikari.pool.HikariPool.createPoolEntry(HikariPool.java:476) ~[psl-cli-3.0.1-SNAPS
HOT.jar:?]
at com.zaxxer.hikari.pool.HikariPool.checkFailFast(HikariPool.java:561) ~[psl-cli-3.0.1-SNAPSHO
T.jar:?]
at com.zaxxer.hikari.pool.HikariPool.(HikariPool.java:115) ~[psl-cli-3.0.1-SNAPSHOT.jar:?
]
at com.zaxxer.hikari.HikariDataSource.(HikariDataSource.java:81) ~[psl-cli-3.0.1-SNAPSHOT
.jar:?]
at org.linqs.psl.database.rdbms.driver.DatabaseDriver.(DatabaseDriver.java:59) ~[psl-cli-
3.0.1-SNAPSHOT.jar:?]
at org.linqs.psl.database.rdbms.driver.SQLiteDriver.(SQLiteDriver.java:53) ~[psl-cli-3.0.
1-SNAPSHOT.jar:?]
at org.linqs.psl.database.rdbms.driver.SQLiteDriver.(SQLiteDriver.java:43) ~[psl-cli-3.0.
1-SNAPSHOT.jar:?]
at org.linqs.psl.runtime.Runtime.initDataStore(Runtime.java:246) ~[psl-cli-3.0.1-SNAPSHOT.jar:?
]
at org.linqs.psl.runtime.Runtime.runInferenceInternal(Runtime.java:403) ~[psl-cli-3.0.1-SNAPSHO
T.jar:?]
at org.linqs.psl.runtime.Runtime.runInference(Runtime.java:364) ~[psl-cli-3.0.1-SNAPSHOT.jar:?]
at org.linqs.psl.runtime.Runtime.runInternal(Runtime.java:172) ~[psl-cli-3.0.1-SNAPSHOT.jar:?]
at org.linqs.psl.runtime.Runtime.run(Runtime.java:122) ~[psl-cli-3.0.1-SNAPSHOT.jar:?]
at org.linqs.psl.runtime.Runtime.run(Runtime.java:99) ~[psl-cli-3.0.1-SNAPSHOT.jar:?]
at org.linqs.psl.cli.Launcher.run(Launcher.java:126) ~[psl-cli-3.0.1-SNAPSHOT.jar:?]
at org.linqs.psl.cli.Launcher.main(Launcher.java:142) ~[psl-cli-3.0.1-SNAPSHOT.jar:?]
at org.linqs.psl.cli.Launcher.main(Launcher.java:130) ~[psl-cli-3.0.1-SNAPSHOT.jar:?]
Caused by: java.lang.Exception: No native library found for os.name=Windows .....

I am using Windows with JDK 1.8.0 (Amazon Corrto) and Maven 3.9.6.
@eriq-augustine
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eriq-augustine commented Jan 3, 2024 •
edited
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Hello.

What are you trying to run exactly, a PSL example?
If so, which one?

Are you building your own version (I see you are using a development version)?

What happens when you use a release version (2.4.0)?
(If using PSL examples, you can git checkout 2.4.0.)

@duhai-alshukaili
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duhai-alshukaili commented Jan 4, 2024 •
edited
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Hello Eriq,

I am trying to run the PSL examples. I tried three with the same results: simple-acquaintances, smokers, and friendship.

I am not building my version. I just followed the steps in the Getting Started with PSL:

git clone https://github.com/linqs/psl-examples.git
cd psl-examples/simple-acquaintances/cli

./run.sh

I tried with version 2.4.0. Still the same error.

Running PSL Inference.
825  [main] INFO  org.linqs.psl.runtime.Runtime  - PSL Runtime Version 2.4.0-aad67da
2032 [main] ERROR com.zaxxer.hikari.pool.HikariPool  - HikariPool-1 - Exception during pool initialization.
java.sql.SQLException: Error opening connection
        at org.sqlite.SQLiteConnection.open(SQLiteConnection.java:258) ~[psl-cli-2.4.0.jar:?]
        at org.sqlite.SQLiteConnection.<init>(SQLiteConnection.java:61) ~[psl-cli-2.4.0.jar:?]
        at org.sqlite.jdbc3.JDBC3Connection.<init>(JDBC3Connection.java:23) ~[psl-cli-2.4.0.jar:?]
        at org.sqlite.jdbc4.JDBC4Connection.<init>(JDBC4Connection.java:19) ~[psl-cli-2.4.0.jar:?]
        at org.sqlite.JDBC.createConnection(JDBC.java:104) ~[psl-cli-2.4.0.jar:?]
        at org.sqlite.JDBC.connect(JDBC.java:77) ~[psl-cli-2.4.0.jar:?]
        at com.zaxxer.hikari.util.DriverDataSource.getConnection(DriverDataSource.java:121) ~[psl-cli-2.4.0.jar:?]
        at com.zaxxer.hikari.pool.PoolBase.newConnection(PoolBase.java:364) ~[psl-cli-2.4.0.jar:?]
        at com.zaxxer.hikari.pool.PoolBase.newPoolEntry(PoolBase.java:206) ~[psl-cli-2.4.0.jar:?]
        at com.zaxxer.hikari.pool.HikariPool.createPoolEntry(HikariPool.java:476) ~[psl-cli-2.4.0.jar:?]
        at com.zaxxer.hikari.pool.HikariPool.checkFailFast(HikariPool.java:561) ~[psl-cli-2.4.0.jar:?]
        at com.zaxxer.hikari.pool.HikariPool.<init>(HikariPool.java:115) ~[psl-cli-2.4.0.jar:?]
        at com.zaxxer.hikari.HikariDataSource.<init>(HikariDataSource.java:81) ~[psl-cli-2.4.0.jar:?]
        at org.linqs.psl.database.rdbms.driver.DatabaseDriver.<init>(DatabaseDriver.java:59) ~[psl-cli-2.4.0.jar:?]
        at org.linqs.psl.database.rdbms.driver.SQLiteDriver.<init>(SQLiteDriver.java:53) ~[psl-cli-2.4.0.jar:?]
        at org.linqs.psl.database.rdbms.driver.SQLiteDriver.<init>(SQLiteDriver.java:43) ~[psl-cli-2.4.0.jar:?]
        at org.linqs.psl.runtime.Runtime.initDataStore(Runtime.java:247) ~[psl-cli-2.4.0.jar:?]
        at org.linqs.psl.runtime.Runtime.runInferenceInternal(Runtime.java:404) ~[psl-cli-2.4.0.jar:?]
        at org.linqs.psl.runtime.Runtime.runInference(Runtime.java:365) ~[psl-cli-2.4.0.jar:?]
        at org.linqs.psl.runtime.Runtime.runInternal(Runtime.java:172) ~[psl-cli-2.4.0.jar:?]
        at org.linqs.psl.runtime.Runtime.run(Runtime.java:122) ~[psl-cli-2.4.0.jar:?]
        at org.linqs.psl.runtime.Runtime.run(Runtime.java:99) ~[psl-cli-2.4.0.jar:?]
        at org.linqs.psl.cli.Launcher.run(Launcher.java:126) ~[psl-cli-2.4.0.jar:?]
        at org.linqs.psl.cli.Launcher.main(Launcher.java:142) ~[psl-cli-2.4.0.jar:?]
        at org.linqs.psl.cli.Launcher.main(Launcher.java:130) ~[psl-cli-2.4.0.jar:?]
Caused by: java.lang.Exception: No native library found for os.name=Windows, os.arch=x86_64, paths=[C:\Program Files\Java\jdk1.8.0_202\bin;C:\Windows\Sun\Java\bin;C:\Windows\system32;C:\Windows;C:\Users\t104\bin;C:\Program Files\Git\mingw64\bin;C:\Program Files\Git\usr\local\bin;C:\Program Files\Git\usr\bin;C:\Program Files\Git\usr\bin;C:\Program Files\Git\mingw64\bin;C:\Program Files\Git\usr\bin;C:\Users\t104\bin;C:\Program Files\Java\jdk1.8.0_202\bin;C:\Program Files\Python\Python311\Scripts;C:\Program Files\Python\Python311;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0;C:\Windows\System32\OpenSSH;C:\Program Files\dotnet;C:\Program Files\Git\cmd;C:\Program Files\sqlite-win-x64-3440200;C:\Program Files\apache-maven-3.9.6\bin;C:\Program Files (x86)\Common Files\Oracle\Java\javapath;C:\Users\t104\AppData\Local\Microsoft\WindowsApps;C:\Users\t104\AppData\Local\Programs\Microsoft VS Code\bin;C:\texlive\2017\bin\win32;C:\Program Files\Git\usr\bin\vendor_perl;C:\Program Files\Git\usr\bin\core_perl;.]
        at org.sqlite.SQLiteJDBCLoader.loadSQLiteNativeLibrary(SQLiteJDBCLoader.java:375) ~[psl-cli-2.4.0.jar:?]
        at org.sqlite.SQLiteJDBCLoader.initialize(SQLiteJDBCLoader.java:68) ~[psl-cli-2.4.0.jar:?]
        at org.sqlite.core.NativeDB.load(NativeDB.java:62) ~[psl-cli-2.4.0.jar:?]
        at org.sqlite.SQLiteConnection.open(SQLiteConnection.java:255) ~[psl-cli-2.4.0.jar:?]
        ... 24 more
Unexpected exception!
com.zaxxer.hikari.pool.HikariPool$PoolInitializationException: Failed to initialize pool: Error opening connection
        at com.zaxxer.hikari.pool.HikariPool.throwPoolInitializationException(HikariPool.java:596)
        at com.zaxxer.hikari.pool.HikariPool.checkFailFast(HikariPool.java:582)
        at com.zaxxer.hikari.pool.HikariPool.<init>(HikariPool.java:115)
        at com.zaxxer.hikari.HikariDataSource.<init>(HikariDataSource.java:81)
        at org.linqs.psl.database.rdbms.driver.DatabaseDriver.<init>(DatabaseDriver.java:59)
        at org.linqs.psl.database.rdbms.driver.SQLiteDriver.<init>(SQLiteDriver.java:53)
        at org.linqs.psl.database.rdbms.driver.SQLiteDriver.<init>(SQLiteDriver.java:43)
        at org.linqs.psl.runtime.Runtime.initDataStore(Runtime.java:247)
        at org.linqs.psl.runtime.Runtime.runInferenceInternal(Runtime.java:404)
        at org.linqs.psl.runtime.Runtime.runInference(Runtime.java:365)
        at org.linqs.psl.runtime.Runtime.runInternal(Runtime.java:172)
        at org.linqs.psl.runtime.Runtime.run(Runtime.java:122)
        at org.linqs.psl.runtime.Runtime.run(Runtime.java:99)
        at org.linqs.psl.cli.Launcher.run(Launcher.java:126)
        at org.linqs.psl.cli.Launcher.main(Launcher.java:142)
        at org.linqs.psl.cli.Launcher.main(Launcher.java:130)
Caused by: java.sql.SQLException: Error opening connection
        at org.sqlite.SQLiteConnection.open(SQLiteConnection.java:258)
        at org.sqlite.SQLiteConnection.<init>(SQLiteConnection.java:61)
        at org.sqlite.jdbc3.JDBC3Connection.<init>(JDBC3Connection.java:23)
        at org.sqlite.jdbc4.JDBC4Connection.<init>(JDBC4Connection.java:19)
        at org.sqlite.JDBC.createConnection(JDBC.java:104)
        at org.sqlite.JDBC.connect(JDBC.java:77)
        at com.zaxxer.hikari.util.DriverDataSource.getConnection(DriverDataSource.java:121)
        at com.zaxxer.hikari.pool.PoolBase.newConnection(PoolBase.java:364)
        at com.zaxxer.hikari.pool.PoolBase.newPoolEntry(PoolBase.java:206)
        at com.zaxxer.hikari.pool.HikariPool.createPoolEntry(HikariPool.java:476)
        at com.zaxxer.hikari.pool.HikariPool.checkFailFast(HikariPool.java:561)
        ... 14 more
Caused by: java.lang.Exception: No native library found for os.name=Windows, os.arch=x86_64, paths=[C:\Program Files\Java\jdk1.8.0_202\bin;C:\Windows\Sun\Java\bin;C:\Windows\system32;C:\Windows;C:\Users\t104\bin;C:\Program Files\Git\mingw64\bin;C:\Program Files\Git\usr\local\bin;C:\Program Files\Git\usr\bin;C:\Program Files\Git\usr\bin;C:\Program Files\Git\mingw64\bin;C:\Program Files\Git\usr\bin;C:\Users\t104\bin;C:\Program Files\Java\jdk1.8.0_202\bin;C:\Program Files\Python\Python311\Scripts;C:\Program Files\Python\Python311;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0;C:\Windows\System32\OpenSSH;C:\Program Files\dotnet;C:\Program Files\Git\cmd;C:\Program Files\sqlite-win-x64-3440200;C:\Program Files\apache-maven-3.9.6\bin;C:\Program Files (x86)\Common Files\Oracle\Java\javapath;C:\Users\t104\AppData\Local\Microsoft\WindowsApps;C:\Users\t104\AppData\Local\Programs\Microsoft VS Code\bin;C:\texlive\2017\bin\win32;C:\Program Files\Git\usr\bin\vendor_perl;C:\Program Files\Git\usr\bin\core_perl;.]
        at org.sqlite.SQLiteJDBCLoader.loadSQLiteNativeLibrary(SQLiteJDBCLoader.java:375)
        at org.sqlite.SQLiteJDBCLoader.initialize(SQLiteJDBCLoader.java:68)
        at org.sqlite.core.NativeDB.load(NativeDB.java:62)
        at org.sqlite.SQLiteConnection.open(SQLiteConnection.java:255)
        ... 24 more
ERROR: Failed to run infernce.

I am suspecting that there might be an issue with SQLite driver. However, I could not pin point what exactly it is.

@eriq-augustine
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Humm....

It does look like some issue between Windows and SQLite.
I don't have a Windows machine, so can't say anything for sure, but here are my thoughts in the order I think you should try things.

Are you using WSL?

I could not find anything that looked exactly like your issue in the driver's bug tracker, but this issue (xerial/sqlite-jdbc#791 ) indicates that it may be a configuration issue with the machine.
Is SQLite3 installed on your machine (I thought it was pretty standard for most Windows machines).

After that, you can try downloading a new version of the driver and putting that in your classpath so it loads before the other driver bundled with the PSL jar:
https://github.com/xerial/sqlite-jdbc

If those don't work and you are not using WSL, then we could try it in WSL.

@duhai-alshukaili
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It seems like it is a Windows "thing". I just ran it in a Debian Linux. Both 3.0.1-SNAPSHOT and 2.4.0 work. I noticed, though, that I am getting a warning about the LAPACK library.

@eriq-augustine
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Interesting, thanks for checking.

The LAPACK warning (if it is the one I think it is) is just saying that no native LAPACK implementation is installed on the machine, so it will fall back to a native Java implementation.
You can generally ignore this unless you need high performance, then you can just install it through the normal means on your system (on Debian, probably apt install liblapack3).

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@eriq-augustine @duhai-alshukaili