topic Hi Kirk, in Intel® oneAPI Math Kernel Library

Cannot compile theano tests with icpc and mkl libraries

Kirk_W_ — Thu, 15 Sep 2016 23:14:06 GMT

Hi everyone,

I've been trying to compile theano tests using icpc and linking against mkl-libraries. I've used the following link line and compiler settings.

link line:

-L${MKLROOT}/lib -lmkl_intel_ilp64 -lmkl_core -lmkl_intel_thread -lpthread -lm -ldl

compiler options:

-DMKL_ILP64 -qopenmp -I${MKLROOT}/include

I've been getting the following errors. If anyone can help me because this error is driving me crazy. I've tried many things such as changing flags or even changing the compiler. I've also used g++-6 but still couldn't run the tests. Everything has failed so far.

Problem occurred during compilation with the command line below:
icpc -dynamiclib -g -O3 -fno-math-errno -Wno-unused-label -Wno-unused-variable -Wno-write-strings -Wl,-rpath,/opt/intel/mkl/lib -DMKL_ILP64 -I/opt/intel/mkl/include -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -m64 -fPIC -undefined dynamic_lookup -I/Users/jm/anaconda2/lib/python2.7/site-packages/numpy/core/include -I/Users/jm/anaconda2/include/python2.7 -I/Users/jm/anaconda2/lib/python2.7/site-packages/theano/gof -L/opt/intel/mkl/lib -L/Users/jm/anaconda2/lib -fvisibility=hidden -o /Users/jm/.theano/compiledir_Darwin-15.6.0-x86_64-i386-64bit-i386-2.7.12-64/tmpiCtphp/8f7c39861f82e0c5784c93e52bab9c26.so /Users/jm/.theano/compiledir_Darwin-15.6.0-x86_64-i386-64bit-i386-2.7.12-64/tmpiCtphp/mod.cpp -lmkl_intel_ilp64 -lmkl_core -lmkl_tbb_thread -ltbb -lstdc++ -lpthread -lm -ldl

Hi Kirk,

Ying_H_Intel — Sun, 18 Sep 2016 06:21:49 GMT

Hi Kirk,

You mentioned the can't compile theano test, not configure theano itself, right? . What is exact error message? does the file /Users/jm/.theano/compiledir_Darwin-15.6.0-x86_64-i386-64bit-i386-2.7.12-64/tmpiCtphp/mod.cpp include any BLAS or LAPACK (or other MKL function)?

Could you please tell us the hardware and OS you are using? In most of cases ( for example, the mod.cpp will depend on the MKL library ) , you can try the MKL link advisor from https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/ to find required MKL library.

Best Regards,

Ying

FYI, configure theano to using BLAS library in http://deeplearning.net/software/theano/install.html

Hi Ying,

Kirk_W_ — Sun, 18 Sep 2016 16:46:05 GMT

Hi Ying,

thanks for your answer. Just to clarify some things. My goal is to use icpc and mkl-intel library version 11.3 which I have installed to compile theano code. The problem is that it doesn't work.

I have already used the MKL link advisor. That's were I got the settings from in the first place.

My os is OS X 10.11 and the hardware cpu: intel-i5 and ram: 8Gb.

I think the problem lies in the linking process. I think that the settings for the MKL link advisor are not correct.

The way that I test it is by running the theano tests which fail. Then I simply try a minimal dot product example which also fails to compile.

If anyone could replicate this issue I would be grateful. I would really like to know how to properly link icpc and intel-mkl libraries against theano so that I can compile code properly?

Thanks!

Hi Kirk,

Ying_H_Intel — Mon, 19 Sep 2016 08:53:38 GMT

Hi Kirk,

Thanks for the details. Could you please tell the step to reproduce the problem?

For example,

Install theano http://deeplearning.net/software/theano/install.html#osx

Then what operation are you doing?

and What is exact error message when you try a minimal dot product example which also fails to compile.

Best Regards,
Ying

Hi Ying,

Kirk_W_ — Mon, 19 Sep 2016 12:09:13 GMT

Hi Ying,

thank you for you reply. The exact steps to reproduce my environment are the following:

1. Install anaconda https://www.continuum.io/downloads for python 2.7.x

2. brew install graphviz "if you don't already have it in you system"

3. Install theano developer version, through "pip install --no-deps git+git://github.com/Theano/Theano.git" recommended by developers, said to be solving some issues

Alternatively you could do: "pip install Theano"

"pip install --upgrade --no-deps Theano"

4. conda install pydot-ng or pip install pydot

5. pip install graphviz (this is different from command 2. Simply an interface of python to command 2)

6. Configuration: need to tell theano what compiler, libraries and flags to use. "Create a .theanorc file in you home directory"

7. Put the following inside .theanorc in order to use icpc and intel-mkl

[global]

cxx = icpc

openmp = True --> you have to install this first via brew install openmp --without-multilib

[gcc]

cxxflags = -DMKL_ILP64 -qopenmp -I${MKLROOT}/include

[blas]

ldflags = -L${MKLROOT}/lib -lmkl_intel_ilp64 -lmkl_core -lmkl_intel_thread -lpthread -lm -ldl

8. To test if everything works correctly first I run the tests and then the minimal dot product example. To run the tests execute the following in a terminal. " python -c "import theano; theano.test()" ". Notice the inside double quotes are important! This results into errors and failure for me. Tests don't build clean

9. Another test that I do is the following simple minimal dot product.

import theano

import theano.tensor as tt

import numpy as np

x, w = tt.matrices('x', 'w')

f = theano.function([x, w], tt.dot(x, w), allow_input_downcast=True)

f(np.random.randn(5, 6), np.random.randn(6, 4))

Below is the error that I get from the minimal example above:

In [1]: import theano

In [2]: import theano.tensor as tt

In [3]: import numpy as np

In [4]: x, w = tt.matrices('x', 'w')

In [5]: f = theano.function([x,w], tt.dot(x,w), allow_input_downcast=True)

WARNING (theano.gof.cmodule): OPTIMIZATION WARNING: Theano was not able to find the g++ parameters that tune the compilation to your specific CPU. This can slow down the execution of Theano functions. Please submit the following lines to Theano's mailing list so that we can fix this problem:

['# 1 "-"\n', 'icpc version 16.0.3 (gcc version 4.9.0 compatibility)\n', '/usr/local/bin/icpc-16.0-base/bin/intel64/mcpcom --target_efi2 -_g -mP3OPT_inline_alloca -D__ICC=1600 -D__INTEL_COMPILER=1600 -D__INTEL_COMPILER_UPDATE=3 -D__BLOCKS__ -D__SIZE_WIDTH__=64 -D__PTRDIFF_TYPE__=long "-D__SIZE_TYPE__=unsigned long" -D__WCHAR_TYPE__=int -D__WINT_TYPE__=int "-D__INTMAX_TYPE__=long int" "-D__UINTMAX_TYPE__=long unsigned int" -D__LONG_MAX__=9223372036854775807L -D__QMSPP_ -D__OPTIMIZE__ -D__NO_MATH_INLINES -D__NO_STRING_INLINES -D__GNUC_GNU_INLINE__ -D__GNUC__=4 -D__GNUC_MINOR__=9 -D__GNUC_PATCHLEVEL__=0 -D__clang__=1 -D__clang_patchlevel__=0 -D__clang_minor__=3 -D__clang_major__=7 -D__clang_version__=7.3.0 -D__APPLE_CC__=5226 -D__ENVIRONMENT_MAC_OS_X_VERSION_MIN_REQUIRED__=1116 -D__LITTLE_ENDIAN__ -D__DYNAMIC__ "-D__private_extern__=__attribute__((visibility("hidden")))" -D__LP64__ -D_LP64 -D__GXX_ABI_VERSION=1002 -D__USER_LABEL_PREFIX__=_ -D__REGISTER_PREFIX__= -D__INTEL_RTTI__ -D__x86_64 -D__x86_64__ -D__amd64 -D__amd64__ "-_Acpu(x86_64)" "-_Amachine(x86_64)" -D__INTEL_COMPILER_BUILD_DATE=20160415 -D__PIC__ -D__APPLE__ -D__MACH__ -D__pentium4 -D__pentium4__ -D__tune_pentium4__ -D__SSE2__ -D__SSE2_MATH__ -D__SSE3__ -D__SSSE3__ -D__SSE4_1__ -D__SSE4_2__ -D__SSE__ -D__SSE_MATH__ -D__MMX__ -D__AVX__ -D__AVX_I__ -D__AVX2__ -D__FMA__ -_k -_8 -_l --has_new_stdarg_support -_D -_a -_b -E --gnu_version=40900 -_W5 --gcc-extern-inline --clang_version=30700 --multibyte_chars --blocks --clang_lib_extensions -D_LIBCPP_HAS_NO_VARIADICS -D_LIBCPP_HAS_NO_RVALUE_REFERENCES -mGLOB_diag_suppress_sys --array_section --simd --simd_func --clang_extensions -mP1OPT_print_version=FALSE -mGLOB_em64t=TRUE -mP1OPT_version=16.0-intel64 -mGLOB_diag_use_message_catalog=FALSE -\n', '#include "..." search starts here:\n', '#include <...> search starts here:\n', ' /usr/local/bin/icpc-16.0-base/compiler/include/intel64\n', ' /usr/local/bin/icpc-16.0-base/compiler/include\n', ' /System/Library/Frameworks\n', ' /Library/Frameworks\n', ' /Library/Developer/CommandLineTools/usr/bin/../lib/clang/7.3.0/include\n', ' /usr/local/include\n', ' /usr/include/\n', ' /usr/include\n', 'End of search list.\n']

In [6]: f(np.random.randn(4,5), np.random.randn(5,6))

Segmentation fault: 11

Thanks!

And if I try to link gcc6

Kirk_W_ — Mon, 19 Sep 2016 12:30:05 GMT

And if I try to link gcc6 against intel-mkl libraries and run the above minimal example, I get the following errors:

f = theano.function([x,w], tt.dot(x,w), allow_input_downcast=True)

Problem occurred during compilation with the command line below:

g++-6c -dynamiclib -g -O3 -fno-math-errno -Wno-unused-label -Wno-unused-variable -Wno-write-strings -Wl,--no-as-needed -Wl,-rpath,/opt/intel/mkl/lib -DMKL_ILP64 -m64 -I/opt/intel/mkl/include -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -m64 -fPIC -undefined dynamic_lookup -I/Users/jm/anaconda2/lib/python2.7/site-packages/numpy/core/include -I/Users/jm/anaconda2/include/python2.7 -I/Users/jm/anaconda2/lib/python2.7/site-packages/theano/gof -L/opt/intel/mkl/lib -L/Users/jm/anaconda2/lib -fvisibility=hidden -o /Users/jm/.theano/compiledir_Darwin-15.6.0-x86_64-i386-64bit-i386-2.7.12-64/tmpHSLq3t/20e25ec3332be5b692d497e191c73eba.so /Users/jm/.theano/compiledir_Darwin-15.6.0-x86_64-i386-64bit-i386-2.7.12-64/tmpHSLq3t/mod.cpp -lmkl_intel_ilp64 -lmkl_core -lmkl_intel_thread -liomp5 -lpthread -lm -ldl

ERROR (theano.gof.cmodule): [Errno 2] No such file or directory

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

OSError Traceback (most recent call last)

<ipython-input-9-69d89bc7defb> in <module>()

----> 1 f = theano.function([x,w], tt.dot(x,w), allow_input_downcast=True)

/Users/jm/anaconda2/lib/python2.7/site-packages/theano/compile/function.pyc in function(inputs, outputs, mode, updates, givens, no_default_updates, accept_inplace, name, rebuild_strict, allow_input_downcast, profile, on_unused_input)

324 on_unused_input=on_unused_input,

325 profile=profile,

--> 326 output_keys=output_keys)

327 # We need to add the flag check_aliased inputs if we have any mutable or

328 # borrowed used defined inputs

/Users/jm/anaconda2/lib/python2.7/site-packages/theano/compile/pfunc.pyc in pfunc(params, outputs, mode, updates, givens, no_default_updates, accept_inplace, name, rebuild_strict, allow_input_downcast, profile, on_unused_input, output_keys)

482 accept_inplace=accept_inplace, name=name,

483 profile=profile, on_unused_input=on_unused_input,

--> 484 output_keys=output_keys)

485

486

/Users/jm/anaconda2/lib/python2.7/site-packages/theano/compile/function_module.pyc in orig_function(inputs, outputs, mode, accept_inplace, name, profile, on_unused_input, output_keys)

1787 on_unused_input=on_unused_input,

1788 output_keys=output_keys).create(

-> 1789 defaults)

1790

1791 t2 = time.time()

/Users/jm/anaconda2/lib/python2.7/site-packages/theano/compile/function_module.pyc in create(self, input_storage, trustme, storage_map)

1651 theano.config.traceback.limit = theano.config.traceback.compile_limit

1652 _fn, _i, _o = self.linker.make_thunk(

-> 1653 input_storage=input_storage_lists, storage_map=storage_map)

1654 finally:

1655 theano.config.traceback.limit = limit_orig

/Users/jm/anaconda2/lib/python2.7/site-packages/theano/gof/link.pyc in make_thunk(self, input_storage, output_storage, storage_map)

697 return self.make_all(input_storage=input_storage,

698 output_storage=output_storage,

--> 699 storage_map=storage_map)[:3]

700

701 def make_all(self, input_storage, output_storage):

/Users/jm/anaconda2/lib/python2.7/site-packages/theano/gof/vm.pyc in make_all(self, profiler, input_storage, output_storage, storage_map)

1049 storage_map,

1050 compute_map,

-> 1051 no_recycling))

1052 if not hasattr(thunks[-1], 'lazy'):

1053 # We don't want all ops maker to think about lazy Ops.

/Users/jm/anaconda2/lib/python2.7/site-packages/theano/gof/op.pyc in make_thunk(self, node, storage_map, compute_map, no_recycling)

973 try:

974 return self.make_c_thunk(node, storage_map, compute_map,

--> 975 no_recycling)

976 except (NotImplementedError, utils.MethodNotDefined):

977 logger.debug('Falling back on perform')

/Users/jm/anaconda2/lib/python2.7/site-packages/theano/gof/op.pyc in make_c_thunk(self, node, storage_map, compute_map, no_recycling)

873 logger.debug('Trying CLinker.make_thunk')

874 outputs = cl.make_thunk(input_storage=node_input_storage,

--> 875 output_storage=node_output_storage)

876 fill_storage, node_input_filters, node_output_filters = outputs

877

/Users/jm/anaconda2/lib/python2.7/site-packages/theano/gof/cc.pyc in make_thunk(self, input_storage, output_storage, storage_map, keep_lock)

1188 cthunk, in_storage, out_storage, error_storage = self.__compile__(

1189 input_storage, output_storage, storage_map,

-> 1190 keep_lock=keep_lock)

1191

1192 res = _CThunk(cthunk, init_tasks, tasks, error_storage)

/Users/jm/anaconda2/lib/python2.7/site-packages/theano/gof/cc.pyc in __compile__(self, input_storage, output_storage, storage_map, keep_lock)

1129 output_storage,

1130 storage_map,

-> 1131 keep_lock=keep_lock)

1132 return (thunk,

1133 [link.Container(input, storage) for input, storage in

/Users/jm/anaconda2/lib/python2.7/site-packages/theano/gof/cc.pyc in cthunk_factory(self, error_storage, in_storage, out_storage, storage_map, keep_lock)

1584 else:

1585 module = get_module_cache().module_from_key(

-> 1586 key=key, lnk=self, keep_lock=keep_lock)

1587

1588 vars = self.inputs + self.outputs + self.orphans

/Users/jm/anaconda2/lib/python2.7/site-packages/theano/gof/cmodule.pyc in module_from_key(self, key, lnk, keep_lock)

1143 try:

1144 location = dlimport_workdir(self.dirname)

-> 1145 module = lnk.compile_cmodule(location)

1146 name = module.__file__

1147 assert name.startswith(location)

/Users/jm/anaconda2/lib/python2.7/site-packages/theano/gof/cc.pyc in compile_cmodule(self, location)

1490 lib_dirs=self.lib_dirs(),

1491 libs=libs,

-> 1492 preargs=preargs)

1493 except Exception as e:

1494 e.args += (str(self.fgraph),)

/Users/jm/anaconda2/lib/python2.7/site-packages/theano/gof/cmodule.pyc in compile_str(module_name, src_code, location, include_dirs, lib_dirs, libs, preargs, py_module, hide_symbols)

2277

2278 try:

-> 2279 p_out = output_subprocess_Popen(cmd)

2280 compile_stderr = decode(p_out[1])

2281 except Exception:

/Users/jm/anaconda2/lib/python2.7/site-packages/theano/misc/windows.pyc in output_subprocess_Popen(command, **params)

80 params['stdout'] = subprocess.PIPE

81 params['stderr'] = subprocess.PIPE

---> 82 p = subprocess_Popen(command, **params)

83 # we need to use communicate to make sure we don't deadlock around

84 # the stdour/stderr pipe.

/Users/jm/anaconda2/lib/python2.7/site-packages/theano/misc/windows.pyc in subprocess_Popen(command, **params)

42 try:

---> 43 proc = subprocess.Popen(command, startupinfo=startupinfo, **params)

44 finally:

45 if stdin is not None:

/Users/jm/anaconda2/lib/python2.7/subprocess.pyc in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags)

709 p2cread, p2cwrite,

710 c2pread, c2pwrite,

--> 711 errread, errwrite)

712 except Exception:

713 # Preserve original exception in case os.close raises.

/Users/jm/anaconda2/lib/python2.7/subprocess.pyc in _execute_child(self, args, executable, preexec_fn, close_fds, cwd, env, universal_newlines, startupinfo, creationflags, shell, to_close, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite)

1341 raise

1342 child_exception = pickle.loads(data)

-> 1343 raise child_exception

1344

1345

OSError: [Errno 2] No such file or directory

Hi Kirk,

Ying_H_Intel — Tue, 20 Sep 2016 04:14:51 GMT

Hi Kirk,

thank for the step by step. I try almost same

1. Install anaconda https://www.continuum.io/downloads for python 2.7.x (command line)

i haven't try homebrew and conda

3. Install theano

: "pip install Theano"

"pip install --upgrade --no-deps Theano"

4. pip install pydot

5. pip install graphviz

6. Configuration: need to tell theano what compiler, libraries and flags to use. "Create a .theanorc file in you home directory"

7. Put the following inside .theanorc in order to use icpc and intel-mkl

[global]

cxx = icpc

openmp = True --> you have to install this first via brew install openmp --without-multilib

[gcc]

cxxflags = -DMKL_ILP64 -qopenmp -I${MKLROOT}/include

[blas]

ldflags = -L-L/opt/intel/compilers_and_libraries_2016.3.170/mac/mkl/lib/-lmkl_intel_ilp64 -lmkl_core -lmkl_intel_thread -lpthread -lm -ldl

-> I can't use the $MKLROOT. although i have source /opt/intel/compilers_and_libraries_2016.3.170/mac/mkl/bin/mklvars.sh intel64

>python test.py

I got segmentation error too.

But it is not problem to run with

[global]
cxx = icpc
openmp = True ( as icpc support OpenMP, i don't install openMP from other places)

[gcc]
cxxflags = -DMKL_LP64 -qopenmp -I${MKLROOT}/include

[blas]
ldflags = -L/opt/intel/compilers_and_libraries_2016.3.170/mac/mkl/lib -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lpthread -lm -ldl

Last login: Wed Sep 21 00:25:59 2016
macmini01:~ yhu5$ icpc -v
icpc version 17.0.0 (gcc version 4.9.0 compatibility)
macmini01:~ yhu5$ source /opt/intel/compilers_and_libraries_2017.0.
compilers_and_libraries_2017.0.092/ compilers_and_libraries_2017.0.102/
macmini01:~ yhu5$ source /opt/intel/compilers_and_libraries_2016.3.170/
.version licensing/ mac/
macmini01:~ yhu5$ source /opt/intel/compilers_and_libraries_2016.3.170/mac/
bin/ documentation/ man/ pkg_bin/
compiler/ link_install.sh mkl/
macmini01:~ yhu5$ source /opt/intel/compilers_and_libraries_2016.3.170/mac/mkl/b in/mklvars.sh intel64
macmini01:~ yhu5$ python test.py ( i add me= f(np.random.randn(4,5), np.random.randn(5,6)), print me
WARNING (theano.gof.cmodule): OPTIMIZATION WARNING: your Theano flag `cxx` seems not to be the g++ compiler. So we disable the compiler optimization specific to g++ that tell to compile for a specific CPU. At worst, this could cause slow do wn.
You can add those parameters to the compiler yourself via the Theano fl ag `gcc.cxxflags`.
[[ 1.27863428 1.28816199 2.83958232 -0.35235211]
[ 2.46670051 2.72214105 2.85460089 -0.99719573]
[-3.06628748 0.67908877 1.68852227 -3.37025947]
[-1.6107379 -1.37031813 -1.47781715 -2.912304 ]
[-4.03258646 -0.75107235 -2.93471964 -2.51097149]]
macmini01:~ yhu5$

So what i can suggest

1. try -DMKL_LP64 -lmkl_intel_lp64 ....

2 may be try latest MKL 2017 , which can be get from https://software.intel.com/en-us/intel-mkl/ => get This Library for free

(although i'm in icpc in 2017 and MKL using 2016)

3. I can reproduce the error with gcc. , seems not direct MKL related. ERROR (theano.gof.cmodule): [Errno 2] No such file or directory. it should be wrong file or directory.

Best Regards,

Ying

Hi Ying,

Kirk_W_ — Tue, 20 Sep 2016 11:56:14 GMT

Hi Ying,

thanks for the reply. Did you manage to run the tests without problems with icpc+intel-mkl?

One question though, how can you update the intel-mkl to a newer version? I mean do I have to uninstall what I have already installed in my system and then re-install the new version?

Thanks!

Hi Kirk,

Ying_H_Intel — Thu, 22 Sep 2016 03:18:00 GMT

Hi Kirk,

I did further investigation. The problem of segmentation error should be the ILP64, where theano use "int" type as matrix size input, which is 32bit by default. the ILP64 means int 64bit. So the correct MKL library should be

[global]
cxx = icpc
openmp = True ( as icpc support OpenMP, i don't install openMP from other places)

[gcc]
cxxflags = -I${MKLROOT}/include

[blas]
ldflags = -L/opt/intel/compilers_and_libraries_2016.3.170/mac/mkl/lib -lmkl_intel_ilp64 -lmkl_core -lmkl_intel_thread -lpthread -lm -ldl

Last login: Wed Sep 21 00:25:59 2016

You may try it and let me know if it work for you.

Yes, the "-lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread" should work with both clang /gcc too. They can run without problem.

You can upgrade to Intel MKL by any way. Usually, you don't need uninstall the old version. Different version should be install to different folder. and the /opt/intel/mkl will link the latest version.

Best Regards,

Ying

Kirk_W_ — Fri, 23 Sep 2016 13:06:57 GMT

Hi Yiing,

thank you so much for your support. So, I've tried your settings and run the theano tests but I get a Segmentation fault:11

Here is the output from that segmentation fault:

Theano version 0.9.0dev2.dev-8e4dff3581eefcc4cd6dcfa06b99f44338c5ffec
theano is installed in /Users/jm/anaconda2/lib/python2.7/site-packages/theano
NumPy version 1.11.1
NumPy relaxed strides checking option: False
NumPy is installed in /Users/jm/anaconda2/lib/python2.7/site-packages/numpy
Python version 2.7.12 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:43:17) [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)]
nose version 1.3.7
/Users/jm/anaconda2/lib/python2.7/site-packages/theano/misc/pycuda_init.py:35: UserWarning: PyCUDA import failed in theano.misc.pycuda_init
warnings.warn("PyCUDA import failed in theano.misc.pycuda_init")
/Users/jm/anaconda2/lib/python2.7/site-packages/theano/sandbox/gpuarray/__init__.py:10: UserWarning: theano.sandbox.gpuarray has been moved to theano.gpuarray. Please update your code and pickles. If the warning persists, clear theano's cache ('$theano/bin/theano-cache clear').
warnings.warn(message)
.WARNING (theano.gof.cmodule): OPTIMIZATION WARNING: Theano was not able to find the g++ parameters that tune the compilation to your specific CPU. This can slow down the execution of Theano functions. Please submit the following lines to Theano's mailing list so that we can fix this problem:
['# 1 "-"\n', 'icpc version 16.0.3 (gcc version 4.9.0 compatibility)\n', '/usr/local/bin/icpc-16.0-base/bin/intel64/mcpcom --target_efi2 -_g -mP3OPT_inline_alloca -D__ICC=1600 -D__INTEL_COMPILER=1600 -D__INTEL_COMPILER_UPDATE=3 -D__BLOCKS__ -D__SIZE_WIDTH__=64 -D__PTRDIFF_TYPE__=long "-D__SIZE_TYPE__=unsigned long" -D__WCHAR_TYPE__=int -D__WINT_TYPE__=int "-D__INTMAX_TYPE__=long int" "-D__UINTMAX_TYPE__=long unsigned int" -D__LONG_MAX__=9223372036854775807L -D__QMSPP_ -D__OPTIMIZE__ -D__NO_MATH_INLINES -D__NO_STRING_INLINES -D__GNUC_GNU_INLINE__ -D__GNUC__=4 -D__GNUC_MINOR__=9 -D__GNUC_PATCHLEVEL__=0 -D__clang__=1 -D__clang_patchlevel__=0 -D__clang_minor__=3 -D__clang_major__=7 -D__clang_version__=7.3.0 -D__APPLE_CC__=5226 -D__ENVIRONMENT_MAC_OS_X_VERSION_MIN_REQUIRED__=1116 -D__LITTLE_ENDIAN__ -D__DYNAMIC__ "-D__private_extern__=__attribute__((visibility("hidden")))" -D__LP64__ -D_LP64 -D__GXX_ABI_VERSION=1002 -D__USER_LABEL_PREFIX__=_ -D__REGISTER_PREFIX__= -D__INTEL_RTTI__ -D__x86_64 -D__x86_64__ -D__amd64 -D__amd64__ "-_Acpu(x86_64)" "-_Amachine(x86_64)" -D__INTEL_COMPILER_BUILD_DATE=20160415 -D__PIC__ -D__APPLE__ -D__MACH__ -D__pentium4 -D__pentium4__ -D__tune_pentium4__ -D__SSE2__ -D__SSE2_MATH__ -D__SSE3__ -D__SSSE3__ -D__SSE4_1__ -D__SSE4_2__ -D__SSE__ -D__SSE_MATH__ -D__MMX__ -D__AVX__ -D__AVX_I__ -D__AVX2__ -D__FMA__ -_k -_8 -_l --has_new_stdarg_support -_D -_a -_b -E --gnu_version=40900 -_W5 --gcc-extern-inline --clang_version=30700 --multibyte_chars --blocks --clang_lib_extensions -D_LIBCPP_HAS_NO_VARIADICS -D_LIBCPP_HAS_NO_RVALUE_REFERENCES -mGLOB_diag_suppress_sys --array_section --simd --simd_func --clang_extensions -mP1OPT_print_version=FALSE -mGLOB_em64t=TRUE -mP1OPT_version=16.0-intel64 -mGLOB_diag_use_message_catalog=FALSE -\n', '#include "..." search starts here:\n', '#include <...> search starts here:\n', ' /usr/local/opt/openblas/include\n', ' /opt/intel/compilers_and_libraries_2016.3.170/mac/compiler/include\n', ' /usr/local/bin/icpc-16.0-base/compiler/include/intel64\n', ' /usr/local/bin/icpc-16.0-base/compiler/include\n', ' /System/Library/Frameworks\n', ' /Library/Frameworks\n', ' /Library/Developer/CommandLineTools/usr/bin/../lib/clang/7.3.0/include\n', ' /usr/local/include\n', ' /usr/include/\n', ' /usr/include\n', 'End of search list.\n']
.....Segmentation fault: 11

Best Regards,

K.W.

Hi K.W,

Ying_H_Intel — Mon, 26 Sep 2016 03:02:18 GMT

Hi K.W,

Thanks for letting me know. From the output, last segmenttation fault , it seems no MKL library information, right?

How about just run the small test.py with pin install theano (no the developer version) ?

import theano

import theano.tensor as tt

import numpy as np

x, w = tt.matrices('x', 'w')

f = theano.function([x, w], tt.dot(x, w), allow_input_downcast=True,mode='DebugMode')

me = f(np.random.randn(5, 6), np.random.randn(6, 4))
print me

Best Regards,
Ying

P.S as i mentioned, i can run the test fine with the below step:

1. Install anaconda https://www.continuum.io/downloads for python 2.7.x (command line) (i haven't try homebrew and conda )

3. Install theano

"pip install Theano"

"pip install --upgrade --no-deps Theano"

4. pip install pydot

5. pip install graphviz

6. Configuration: need to tell theano what compiler, libraries and flags to use. "Create a .theanorc file in you home directory"

7. Put the following inside .theanorc in order to use icpc and intel-mkl

[global]
cxx = icpc
openmp = True ( as icpc support OpenMP, i don't install openMP from other places)

[gcc]
cxxflags = -I${MKLROOT}/include

[blas]
ldflags = -L/opt/intel/compilers_and_libraries_2016.3.170/mac/mkl/lib -lmkl_intel_lp64 -lmkl_core -lmkl_intel_thread -lpthread -lm -ldl

Hi Ying,

Kirk_W_ — Mon, 03 Oct 2016 10:00:41 GMT

Hi Ying,

apologies for my late reply. I tried but still get a segmentation fault.

I think I'm still gonna have to do some more debugging.

But the bottom line is that I still cannot make it work.