CorrMM is the original CPU OP

Xuwen_T_Intel · ‎06-12-2017

Hi,

I helped someone else to post his problem here about the use of Intel distribution for Python. He used anaconda2 to install Intel distribution for python and encountered a problem when he tried to execute his code. The error messages are listed below and his problem is in CorrMM. Please provide your precious suggestions for solving this problem. His code used Theano and he installed the latest Intel distribution for python.

Thanks.

Traceback (most recent call last):

File "./deepMedicRun", line 141, in <module>

deepMedicTest.deepMedicTestMain(absPathToTestConf, absPathToCnnModelGivenInCmdLine)

File "/home/intel_ai/deepmedic/deepmedic/frontEndModules/deepMedicTest.py", line 302, in deepMedicTestMain

cnn3dInstance.compileTestAndVisualisationFunction(*testSessionParameters.getTupleForCompilationOfTestFunc())

File "/home/intel_ai/deepmedic/deepmedic/cnn3d.py", line 626, in compileTestAndVisualisationFunction

givens=givensSet

File "/root/.local/lib/python2.7/site-packages/Theano-0.9.0.dev2-py2.7.egg/theano/compile/function.py", line 326, in function

output_keys=output_keys)

File "/root/.local/lib/python2.7/site-packages/Theano-0.9.0.dev2-py2.7.egg/theano/compile/pfunc.py", line 484, in pfunc

output_keys=output_keys)

File "/root/.local/lib/python2.7/site-packages/Theano-0.9.0.dev2-py2.7.egg/theano/compile/function_module.py", line 1786, in orig_function

defaults)

File "/root/.local/lib/python2.7/site-packages/Theano-0.9.0.dev2-py2.7.egg/theano/compile/function_module.py", line 1650, in create

input_storage=input_storage_lists, storage_map=storage_map)

File "/root/.local/lib/python2.7/site-packages/Theano-0.9.0.dev2-py2.7.egg/theano/gof/link.py", line 699, in make_thunk

storage_map=storage_map)[:3]

File "/root/.local/lib/python2.7/site-packages/Theano-0.9.0.dev2-py2.7.egg/theano/gof/vm.py", line 1051, in make_all

no_recycling))

File "/root/.local/lib/python2.7/site-packages/Theano-0.9.0.dev2-py2.7.egg/theano/gof/op.py", line 932, in make_thunk

no_recycling)

File "/root/.local/lib/python2.7/site-packages/Theano-0.9.0.dev2-py2.7.egg/theano/gof/op.py", line 833, in make_c_thunk

output_storage=node_output_storage)

File "/root/.local/lib/python2.7/site-packages/Theano-0.9.0.dev2-py2.7.egg/theano/gof/cc.py", line 1190, in make_thunk

keep_lock=keep_lock)

File "/root/.local/lib/python2.7/site-packages/Theano-0.9.0.dev2-py2.7.egg/theano/gof/cc.py", line 1131, in __compile__

keep_lock=keep_lock)

File "/root/.local/lib/python2.7/site-packages/Theano-0.9.0.dev2-py2.7.egg/theano/gof/cc.py", line 1589, in cthunk_factory

key=key, lnk=self, keep_lock=keep_lock)

File "/root/.local/lib/python2.7/site-packages/Theano-0.9.0.dev2-py2.7.egg/theano/gof/cmodule.py", line 1145, in module_from_key

module = lnk.compile_cmodule(location)

File "/root/.local/lib/python2.7/site-packages/Theano-0.9.0.dev2-py2.7.egg/theano/gof/cc.py", line 1492, in compile_cmodule

preargs=preargs)

File "/root/.local/lib/python2.7/site-packages/Theano-0.9.0.dev2-py2.7.egg/theano/gof/cmodule.py", line 2313, in compile_str

(status, compile_stderr.replace('\n', '. ')))

Exception: ('The following error happened while compiling the node', CorrMM{valid, (1, 1), (1, 1)}(Reshape{4}.0, Subtensor{::, ::, ::int64, ::int64}.0), '\n', 'Compilation failed (return status=1):

/bin/ld: cannot find -lmkl_rt. collect2: error: ld returned 1 exit status. ', '[CorrMM{valid, (1, 1), (1, 1)}(<TensorType(float32, 4D)>, <TensorType(float32, 4D)>)]')

Xuwen_T_Intel · ‎06-13-2017

I checked the Theano website and found that CorrMM was carried out on the GPU in Theano 0.8. Has this API been supported by MKL in Intel Python distribution update 3 already?

Peng_Z_Intel · ‎06-13-2017

CorrMM is the original CPU OP and the Theano doesn't find the mkl_rt.so in the library path from your log.

Please add the path of mkl_rt.so into LIBRARY_PATH.

Thanks,

Todd_T_Intel · ‎06-13-2017

In case it is not clear, libmkl_rt.so is found in <python_env_root>/lib in the Intel Distribution for Python.

If this does not resolve the problem, it is very helpful to post the output of "conda info" and "conda list", which tells a great deal about the environment.

-Todd

Xuwen_T_Intel · ‎06-13-2017

Hi, Peng and Todd

Thanks for the suggestions. We will post the output of "conda list" and "conda info" at a later time.

Anyway we ever used the "locate libmkl_rt.so" and found several libmkl_rt.so files in different directories.

find: `/run/user/1000/gvfs': Permission denied
/home/intel_ai/anaconda2/pkgs/mkl-2017.0.3-intel_6/lib/libmkl_rt.so
/home/intel_ai/anaconda2/pkgs/mkl-2017.0.1-0/lib/libmkl_rt.so
/home/intel_ai/anaconda2/envs/idp2/lib/libmkl_rt.so
/home/intel_ai/anaconda2/lib/libmkl_rt.so
/opt/intel/compilers_and_libraries_2017.2.174/Linux

Xuwen_T_Intel · ‎06-13-2017

Hi, Todd

The output of "conda info" and "conda list" is list below.

[intel_ai@localhost deepmedic]$ conda info

Current conda install:

platform : linux-64

conda version : 4.3.21

conda is private : False

conda-env version : 4.3.21

conda-build version : not installed

python version : 2.7.13.final.0

requests version : 2.14.2

root environment : /home/intel_ai/anaconda2 (writable)

default environment : /home/intel_ai/anaconda2

envs directories : /home/intel_ai/anaconda2/envs

/home/intel_ai/.conda/envs

package cache : /home/intel_ai/anaconda2/pkgs

/home/intel_ai/.conda/pkgs

channel URLs : https://conda.anaconda.org/intel/linux-64

https://conda.anaconda.org/intel/noarch

https://conda.anaconda.org/conda-forge/linux-64

https://conda.anaconda.org/conda-forge/noarch

https://repo.continuum.io/pkgs/free/linux-64

https://repo.continuum.io/pkgs/free/noarch

https://repo.continuum.io/pkgs/r/linux-64

https://repo.continuum.io/pkgs/r/noarch

https://repo.continuum.io/pkgs/pro/linux-64

https://repo.continuum.io/pkgs/pro/noarch

config file : /home/intel_ai/.condarc

netrc file : None

offline mode : False

user-agent : conda/4.3.21 requests/2.14.2 CPython/2.7.13 Linux/3.10.0-327.36.3.el7.xppsl_1.5.0.4036.x86_64 CentOS Linux/7.3.1611 glibc/2.17

UID:GID : 1000:1000

------------------------------------------------------------

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cython 0.25.2 py27_0

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dask 0.14.3 py27_1

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lazy-object-proxy 1.2.2 py27_0

libffi 3.2.1 1

libgcc 4.8.5 2

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libprotobuf 3.2.0 0 anaconda

libsodium 1.0.10 0

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mkl 2017.0.1 0

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mock 2.0.0 py27_0 anaconda

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pycrypto 2.6.1 py27_6

pycurl 7.43.0 py27_2

pydicom 0.9.9 <pip>

pydicom 0.9.9 py27_0 conda-forge

pyflakes 1.5.0 py27_0

pygments 2.2.0 py27_0

pylint 1.6.4 py27_1

pyodbc 4.0.16 py27_0

pyopenssl 17.0.0 py27_0

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pyqt 5.6.0 py27_2

pytables 3.3.0 np112py27_0

pytest 3.0.7 py27_0

python 2.7.13 0

python-dateutil 2.6.0 py27_0

pytorch 0.1.12 py27_2cu80 [cuda80] soumith

pytz 2017.2 py27_0

pywavelets 0.5.2 np112py27_0

pyyaml 3.12 py27_0

pyzmq 16.0.2 py27_0

qt 5.6.2 4

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qtconsole 4.3.0 py27_0

qtpy 1.2.1 py27_0

readline 6.2 2

requests 2.14.2 py27_0

rope 0.9.4 py27_1

ruamel_yaml 0.11.14 py27_1

scandir 1.5 py27_0

scikit-image 0.13.0 np112py27_0

scikit-learn 0.18.1 np112py27_1

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a problem of using Intel distribution for python