CNN for Cryo Tomogram annotation - libomp.dylib already initialized

[Jaime Llodra]

Dear Members of this group,

I am using EMAN2 for annotation of Cryo Electron tomograms using a convolutional neural network. I am at the training stipend get the following error message 

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

Any idea how to solve this problem?.

Maybe this is important but I am using EMAN2 on a Mac Pro OSX system. 

Thanks in advance for your help and support.

Have a good day

Jaime Llodra

[Steve Ludtke]

Hi Jaime,

need to know the complete output of e2version.py before we can offer suggestions. Note that while the deep-learning based tools should be usable on Macs, Tensorflow will be _very_ slow without an Nvidia GPU (Linux).

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

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[Jaime Llodra]

Hi Steve, 

thanks for your answer.

Here I am copying what's on the screen of the terminal showing the processes which led to the error message I reported.

NOT Writing notes, ppid=-2

Using CPU...

loading particles...

616 particles loaded, 616 in training set, 0 in validation set

(616, 20, 20)

Std of particles:  0.9426957

/Users/jl2235/System/Applications/bin/e2tomoseg_convnet.py:292: RuntimeWarning: invalid value encountered in true_divide

  label/=np.max(np.abs(label))

Setting up model...

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/.

Best,

Jaime

[Muyuan Chen]

I had this issue occasionally. It may happen when you run two similar jobs (neural networks or some other programs that uses openmp) at the same time. As suggested in the message, setting the environment variable should work. Simply run 

export KMP_DUPLICATE_LIB_OK=TRUE

In the terminal before running the Eman program. Despite the warnings, I haven’t noticed that it does any real damage anywhere yet. 

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/e6f1f3cc-0a14-4ad1-bef5-f29a2b04b4efn%40googlegroups.com.

[Steve Ludtke]

Hi Jaime,

did Muyuan's suggestion solve the issue?  Note that your answer, while still relevant, didn't actually answer the question I asked.

-----------------------------------------
Steven Ludtke, slud...@gmail.com 

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/e6f1f3cc-0a14-4ad1-bef5-f29a2b04b4efn%40googlegroups.com.

[Jaime Llodra]

Hi Steve,

here is the output of e2version.py

(base) TUAP227:EMAN2_test jl2235$ e2version.py

EMAN 2.99 ( GITHUB: 2021-07-15 12:34 - commit: bb6529a )

Your EMAN2 is running on: Mac OS 10.16 x86_64

Your Python version is: 3.7.9

(base) TUAP227:EMAN2_test jl2235$ 

I am waiting for the IT support team at my institution to work on Muyuan's suggestion

Promise I will read more carefully next time

Jaime

[Ludtke, Steven J.]

Hi Jaime,

I'm not quite sure what you are waiting for your IT team to do?  Muyuan's suggestion was to type:

export KMP_DUPLICATE_LIB_OK=TRUE

then run the program (in the same window). If you are using e2projectmanager, then you would type that command before running e2projectmanager.

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/279c921a-4b96-4b86-927c-ff6a81d5cc9bn%40googlegroups.com.

[Jaime Llodra]

Hi Steve,

Muyuan's suggestion worked.

I was able to run the training module without any problem.

Thanks a lot

Jaime