Using multiple instances (BEAST 2.5.1)

[carlo pacioni]

I used to be able to run multiple instances of BEAST from command line, however with BEAST 2.5.0 and 2.5.1 I receive a message saying that the library of some package is already in use by another application. I have only tried this on W7.  I notice that this only happens when the analysis uses the same BEAST packages. Does anyone know a work around (the error message - pasted below - seems to suggest that I should install additional libraries needed for jblas, but it seems strange to me). Any suggestions?

Thakns,

carlo

-- org.jblas ERROR Could not create the temp file: java.io.FileNotFoundException: C:\Users\CP\AppData\Local\Temp\libgcc_s_sjlj-1.dll (The process cannot access the file because it is being used by another process).

-- org.jblas ERROR Could not create the temp file: java.io.FileNotFoundException: C:\Users\CP\AppData\Local\Temp\libgfortran-3.dll (The process cannot access the file because it is being used by another process).

-- org.jblas ERROR Couldn't load copied link file: java.lang.UnsatisfiedLinkError: C:\Users\CP\AppData\Local\Temp\jblas346047130813548182jblas.dll: Can't find dependent libraries.

On Windows, you need some additional support libraries.

For example, you can install the two packages in cygwin:

   mingw64-x86_64-gcc-core   mingw64-x86_64-gfortran

and add the directory <cygwin-home>\usr\x86_64-w64-mingw32\sys-root\mingw\bin to your path.

For more information, see http://github.com/mikiobraun/jblas/wiki/Missing-Libraries

Exception in thread "main" java.lang.UnsatisfiedLinkError: org.jblas.NativeBlas.dgemm(CCIIID[DII[DIID[DII)V

at org.jblas.NativeBlas.dgemm(Native Method)

at org.jblas.SimpleBlas.gemm(SimpleBlas.java:251)

at org.jblas.DoubleMatrix.mmuli(DoubleMatrix.java:1697)

at org.jblas.DoubleMatrix.mmul(DoubleMatrix.java:3054)

at org.jblas.MatrixFunctions.expm(MatrixFunctions.java:430)

at multitypetree.operators.UniformizationRetypeOperator.getBranchTypeProb(Unknown Source)

at multitypetree.operators.NodeShiftRetype.nonRootProposal(Unknown Source)

at multitypetree.operators.NodeShiftRetype.proposal(Unknown Source)

at beast.core.Operator.proposal(Unknown Source)

at beast.core.MCMC.propagateState(Unknown Source)

at beast.core.MCMC.doLoop(Unknown Source)

at beast.core.MCMC.run(Unknown Source)

at beast.app.BeastMCMC.run(Unknown Source)

at beast.app.beastapp.BeastMain.<init>(Unknown Source)

at beast.app.beastapp.BeastMain.main(Unknown Source)

[Remco Bouckaert]

Hi Carlo,

What version of java are you using? If you have java 8, does the problem persist when you start BEAST using the jar file like so:

java -Dbeast.load.jars=true -jar /path/to/BEAST/lib/beast.jar xyz.xml

?

Cheers,

Remco

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[carlo pacioni]

Hi Remco,

I have installed java 1.8.0.171-b11. On a second machine with java 1.8.0.181-b13 the same error occurs.

I usually copy beast.exe and the whole lib folder where I have the input file and start beast as you suggest. 

Cheers,

carlo

[Remco Bouckaert]

Hi Carlo,

I tried to replicate the problem on a Windows 10 computer, but had not trouble running two BEAST runs at the same time with the BEASTLabs, Model Selection and Nested sampling packages installed, so this is perhaps a problem caused by the jblas library used by one of the packages. Have you noticed this problem when using a package that does not load jblas?

The link in the error message suggests installing extra libraries — these libraries are to support jblas, a library for linear algebra, which uses optimised non-java code from these extra libraries. Can you try to install these libraries and set the path for them and see if the problem persists?

Cheers,

Remco

[Carlo Pacioni]

Hi Remco 

yes you're right again I can run two instances with EBSP model or two instances with BDSKY model but I can't run two instances where the model is BDMM. however I can run one BDMM model  and one other instances with any of the other models so I think the problem might be with multi type tree or the BDMM. I will try to install the libraries and see whether they solve the problem I'll let you know.

Cheers 

Carlo 

[Carlo Pacioni]

Hi again,

tried to install the libraries, but it doesn't seems to fix the problem. I have to admit that the installation process of the gcc and gfortran libraries and what directories need to go in the path is not exactly straightforward, so I may have missed something there. 

I have CC'ed Tim in case he has any additional suggestions.

Cheers,

carlo

[Qiqi Yang]

Hi Carlo,

I've also encountered the problem and exactly been through same processes as you of installing gcc & gfortran libraries, but it didn't work. Did you find out how to run multiple MTT instances at last? would love to know any updates from you!

Cheers,

Qiqi

在 2018年9月26日星期三 UTC+8下午1:37:20，carlo pacioni写道：