Neuron mechanism fails with MacOS .dylib files[Bug]

[neuroml]

Neuron mechanism fails with MacOS .dylib files[Bug]

[sanjayankur31]

Thanks @christian-oreilly , I've opened PR #86 to fix this.

[christian-oreilly]

Note that I can run pynml.run_lems_with_jneuroml_neuron(...) which generates the .mod before crashing. Then I can run nrnivmodl and

import shutil
shutil.copy("x86_64/libnrnmech.dylib", "x86_64/libnrnmech.so")

and then call again pynml.run_lems_with_jneuroml_neuron(...) and it works fine. So, looks to me like you would just need to add the "dylib" extension in the files checked around

org.neuroml.export/src/main/java/org/neuroml/export/neuron/ProcessManager.java

Lines 178 to 220 in ce18e86

	/* *.la */
	String filename1 = directoryToExecuteIn + System.getProperty("file.separator") + myArch + System.getProperty("file.separator") + "libnrnmech.la";
	filesToBeCreated.add(new File(filename1));
	E.info("Name of file to be created: " + filename1);
	// In case, e.g. a 32 bit JDK is used on a 64 bit system
	String filename2 = directoryToExecuteIn + System.getProperty("file.separator") + backupArchDir + System.getProperty("file.separator") + "libnrnmech.la";
	/* Only add if it does not already exist: prevent duplication */
	if (!filename1.equals(filename2)){
	filesToBeCreated.add(new File(filename2));
	E.info("Name of file to be created: " + filename2);
	}
	/* *.so */
	filename1 = directoryToExecuteIn + System.getProperty("file.separator") + myArch + System.getProperty("file.separator") + "libnrnmech.so";
	filesToBeCreated.add(new File(filename1));
	E.info("Name of file to be created: " + filename1);
	// In case, e.g. a 32 bit JDK is used on a 64 bit system
	filename2 = directoryToExecuteIn + System.getProperty("file.separator") + backupArchDir + System.getProperty("file.separator") + "libnrnmech.so";
	/* Only add if it does not already exist: prevent duplication */
	if (!filename1.equals(filename2)){
	filesToBeCreated.add(new File(filename2));
	E.info("Name of file to be created: " + filename2);
	}
	/**
	* @todo Needs checking on Mac/powerpc/i686
	*/
	if (Utils.isMacBasedPlatform())
	{
	String filename = directoryToExecuteIn + System.getProperty("file.separator") + Utils.getArchSpecificDir() + System.getProperty("file.separator") + "libnrnmech.la";
	E.info("Name of file to be created: " + filename);
	filesToBeCreated.add(new File(filename));
	filename = directoryToExecuteIn + System.getProperty("file.separator") + "umac" + System.getProperty("file.separator") + "libnrnmech.la";
	E.info("Name of file to be created: " + filename);
	filesToBeCreated.add(new File(filename));
	}
	commandToExecute = neuronHome.getCanonicalPath() + System.getProperty("file.separator") + "bin" + System.getProperty("file.separator") + "nrnivmodl";
	E.info("commandToExecute: " + commandToExecute);

[christian-oreilly]

Sorry, I hit the button by mistake.

[pgleeson]

@christian-oreilly Please try with the latest version of pyNeuroML: https://pypi.org/project/pyNeuroML/#history to see if this issue is fixed for you.