Training... OMP: Error #15: Initializing libiomp5.dylib, but found libomp.dylib already initialized.

[Gábor Oroszlán]

HI All,

I am totally new to eman2, so apologies if I have dark spots. In neural network interactive particle picking when I hit Train, I receive the following lines, and a window with "python quit unexpectedly":

Training...
OMP: Error #15: Initializing libiomp5.dylib, but found libomp.dylib already initialized.
OMP: Hint This means that multiple copies of the OpenMP runtime have been linked into the program. That is dangerous, since it can degrade performance or cause incorrect results. The best thing to do is to ensure that only a single OpenMP runtime is linked into the process, e.g. by avoiding static linking of the OpenMP runtime in any library. As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results. For more information, please see http://www.intel.com/software/products/support/.

Could you help me with this issue?

Thanks very much,

Gabor

[MuyuanChen]

Are you sure you are not running multiple instances of the program? Or instances of other EMAN neural network related programs?

Also what is the version of EMAN you are running? I have vague memory of running into this sort of error in the past but haven’t seen it for a while, so I was assuming that someone solved this at a lower level… Anyway, last time I had this problem, using the “undocumented workaround” and set the environment variable before running the program seems to solve the issue. 

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[Gábor Oroszlán]

Thank you for getting back to me. I am not sure about anything, I am hardly familiar with EMAN2 and the whole environment, I was doing a tutorial with my own data set. How can I check if multiple instances are running or not? I am using Eman2 2.91. Could you detail the solution you suggested, or give a link for a description?  I could not find any similar topic in previous chats.

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[MuyuanChen]

To test, I would just look at the task manager and kill all EMAN related programs, then re-start the particle picking process and see if the error is triggered again. 

I was talking about the solution mentioned in the error message: 

 As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results.

Just run “export KMP_DUPLICATE_LIB_OK=TRUE” before running the program in the command line.

Muyuan

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[Gábor Oroszlán]

Thank you. It must be a stupid one again but how can I kill all eman related programs? And I should run the suggested command before initiating eman2 or before running e2projectmanager? 

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[Muyuan Chen]

Depending on your system. In some linux distribution you can simply find some task manager GUI, in which you can search EMAN then kill all related programs. This can probably be done easily top, although it would be easier to google the exact command. You can always just restart your machine that should clean up everything.

Before executing the particle boxing program. Although running it earlier shouldn't hurt either.

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[Gábor Oroszlán]

The export command helped, thanks very much!

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