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virtualcell / vcell

Virtual Cell Framework
http://vcell.org/
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M1 Mac Build Failure - update build instructions #422

Open ahalev opened 1 year ago

ahalev commented 1 year ago

I'm attempting to set up the command line interface to VCell on an M1 Mac (arch64) using the instructions here and am running into issues installing dependencies; I am having test errors in running the dependency install.

Specifically, I am unable to load the libraries vcell/vcell-core/../nativelibs/mac64/libcombinej.jnilib and vcell/vcell-core/../nativelibs/mac64/libjhdf5.jnilib.

Any suggestions would be appreciated. Full error logs are below. Thank you!

[ERROR] Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.004 s <<< FAILURE! - in cbit.vcell.resource.NativeLibTest
[ERROR] loadEm(cbit.vcell.resource.NativeLibTest)  Time elapsed: 0.004 s  <<< ERROR!
java.lang.UnsatisfiedLinkError: Can't load library: /Users/ahalev/Dropbox/Avishai/gradSchool/year5/vcell/vcell-core/../nativelibs/mac64/libcombinej.jnilib
        at cbit.vcell.resource.NativeLibTest.loadEm(NativeLibTest.java:16)
[ERROR] Tests run: 2, Failures: 0, Errors: 2, Skipped: 0, Time elapsed: 0 s <<< FAILURE! - in cbit.vcell.simdata.DataSetControllerImplTest
[ERROR] testGetDataIdentifiers(cbit.vcell.simdata.DataSetControllerImplTest)  Time elapsed: 0 s  <<< ERROR!
java.lang.UnsatisfiedLinkError: Can't load library: /Users/ahalev/Dropbox/Avishai/gradSchool/year5/vcell/vcell-core/../nativelibs/mac64/libjhdf5.jnilib
        at cbit.vcell.simdata.DataSetControllerImplTest.setUp(DataSetControllerImplTest.java:35)

[ERROR] testDoDataOperation(cbit.vcell.simdata.DataSetControllerImplTest)  Time elapsed: 0 s  <<< ERROR!
java.lang.UnsatisfiedLinkError: Can't load library: /Users/ahalev/Dropbox/Avishai/gradSchool/year5/vcell/vcell-core/../nativelibs/mac64/libjhdf5.jnilib
        at cbit.vcell.simdata.DataSetControllerImplTest.setUp(DataSetControllerImplTest.java:35)
jcschaff commented 10 months ago

must be verified on M1/M2 box.

jcschaff commented 10 months ago

build verified on Macos Ventura 13.4 using updated instructions in README.md referenced in README_BioSim.md

CodeByDrescher commented 2 months ago

The issues described here are actually still present; CLI still uses the old HDF library, which does NOT support ARM arch. With JHDF now updated to use attributes, we should be able to actually fix this issue.