Tenserflow issue with OpenMP

[michoug]

Hi, I'm on a mac and when I ran the command

qiime songbird multinomial --i-table redsea.biom.qza --m-metadata-file data/redsea/redsea_metadata.txt --p-formula "Depth+Temperature+Salinity+Oxygen+Fluorescence+Nitrate" --o-differentials differentials.qza --o-regression-stats regression-stats.qza --o-regression-biplot regression-biplot.qza --verbose

I got this error

OMP: Error #15: Initializing libiomp5.dylib, but found libiomp5.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/.
Abort trap: 6

that I solved using this link where the answer is installing this package

conda install nomkl

It could maybe be useful to add it to the dependencies?

[mortonjt]

That's actually very useful. Thanks!

On Thu, Mar 14, 2019, 3:55 AM michoug [email protected] wrote:

Hi, I'm on a mac and when I ran the command

qiime songbird multinomial --i-table redsea.biom.qza --m-metadata-file data/redsea/redsea_metadata.txt --p-formula "Depth+Temperature+Salinity+Oxygen+Fluorescence+Nitrate" --o-differentials differentials.qza --o-regression-stats regression-stats.qza --o-regression-biplot regression-biplot.qza --verbose

I got this error

OMP: Error #15: Initializing libiomp5.dylib, but found libiomp5.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/. Abort trap: 6

that I solved using this link https://github.com/dmlc/xgboost/issues/1715#issuecomment-439584629 where the answer is installing this package

conda install nomkl

It could maybe be useful to add it to the dependencies?

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