Comments (19)
kyleabeauchamp
commented on September 17, 2024
Maybe a newer version of gcc and select them via update alternatives?
On Feb 22, 2014 4:44 AM, "Bharath Ramsundar" [email protected]
wrote:
The setup.py install script fails with the following error on my i686
ubuntu machine:bramsundar@bramsundar-HP-Pavilion-dv6-Notebook-PC:~/Devel/mixtape$ sudo
python setup.py installAttempting to autodetect OpenMP support...
Compiler supports OpenMP############################################################
The nvcc compiler could not be located in your $PATH. To
enable CUDA acceleration, either add it to your path, or set
$CUDAHOME
############################################################running install
Checking .pth file support in /usr/local/lib/python2.7/dist-packages/
/usr/bin/python -E -c pass
TEST PASSED: /usr/local/lib/python2.7/dist-packages/ appears to support
.pth files
running bdist_egg
running egg_info
writing requirements to mixtape.egg-info/requires.txt
writing mixtape.egg-info/PKG-INFO
writing top-level names to mixtape.egg-info/top_level.txt
writing dependency_links to mixtape.egg-info/dependency_links.txt
reading manifest file 'mixtape.egg-info/SOURCES.txt'
writing manifest file 'mixtape.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-i686/egg
running install_lib
running build_py
running build_ext
skipping 'src/reversibility.c' Cython extension (up-to-date)
skipping 'platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp' Cython extension
(up-to-date)
building 'mixtape._ghmm' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2
-Wall -Wstrict-prototypes -fPIC
-I/usr/local/lib/python2.7/dist-packages/numpy/core/include -
Iplatforms/cpu/kernels/include/ -Iplatforms/cpu/kernels/
-I/usr/include/python2.7 -c platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp
-o build/temp.linux- i686-2.7/platforms/cpu/wrappers/GaussianHMMCPUImpl.o
-fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is
valid for Ada/C/ObjC but not for C++ [enabled by default] In file included
from
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1760:0,
from
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:314:
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
warning: #warning "Using deprecated NumPy API, disable i
t by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
In file included from platforms/cpu/kernels/logsumexp.hpp:10:0,
from platforms/cpu/kernels/forward.hpp:8,
from platforms/cpu/kernels/do_estep.hpp:18,
from platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:321:
/usr/lib/gcc/i686-linux-gnu/4.6.1/include/emmintrin.h:32:3: error: #error
"SSE2 instruction set not enabled"
In file included from platforms/cpu/kernels/include/sse_mathfun.h:32:0,
from platforms/cpu/kernels/logsumexp.hpp:14,
from platforms/cpu/kernels/forward.hpp:8,
from platforms/cpu/kernels/do_estep.hpp:18,
from platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:321:
/usr/lib/gcc/i686-linux-gnu/4.6.1/include/xmmintrin.h:32:3: error: #error
"SSE instruction set not enabled"
In file included from platforms/cpu/kernels/logsumexp.hpp:14:0,
from platforms/cpu/kernels/forward.hpp:8,
from platforms/cpu/kernels/do_estep.hpp:18,
from platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:321:
platforms/cpu/kernels/include/sse_mathfun.h:45:9: error: '
_m128' does not name a type
platforms/cpu/kernels/include/sse_mathfun.h:51:9: error: '_m64' does not
name a type
platforms/cpu/kernels/include/sse_mathfun.h:93:3: error: '
_m128' does not name a type
platforms/cpu/kernels/include/sse_mathfun.h:94:3: error: '_m64' does not
name a type
platforms/cpu/kernels/include/sse_mathfun.h:112:1: error: 'v4sf' does not
name a type
platforms/cpu/kernels/include/sse_mathfun.h:214:1: error: 'v4sf' does not
name a type
platforms/cpu/kernels/include/sse_mathfun.h:332:1: error: 'v4sf' does not
name a type
platforms/cpu/kernels/include/sse_mathfun.h:449:1: error: 'v4sf' does not
name a type
platforms/cpu/kernels/include/sse_mathfun.h:568:16: error: variable or
field 'sincos_ps' declared void
platforms/cpu/kernels/include/sse_mathfun.h:568:16: error: 'v4sf' was not
declared in this scope
platforms/cpu/kernels/include/sse_mathfun.h:568:24: error: 'v4sf' was not
declared in this scope
platforms/cpu/kernels/include/sse_mathfun.h:568:30: error: 's' was not
declared in this scope
platforms/cpu/kernels/include/sse_mathfun.h:568:33: error: 'v4sf' was not
declared in this scope
platforms/cpu/kernels/include/sse_mathfun.h:568:39: error: 'c' was not
declared in this scope
In file included from platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:321:0:
platforms/cpu/kernels/do_estep.hpp:79:37: error: expected declaration
before end of line
error: command 'gcc' failed with exit status 1Reply to this email directly or view it on GitHubhttps://github.com//issues/35
.
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kyleabeauchamp
commented on September 17, 2024
**try
On Feb 22, 2014 10:09 AM, "Kyle Beauchamp" [email protected] wrote:
Maybe a newer version of gcc and select them via update alternatives?
On Feb 22, 2014 4:44 AM, "Bharath Ramsundar" [email protected]
wrote:The setup.py install script fails with the following error on my i686
ubuntu machine:bramsundar@bramsundar-HP-Pavilion-dv6-Notebook-PC:~/Devel/mixtape$ sudo
python setup.py installAttempting to autodetect OpenMP support...
Compiler supports OpenMP############################################################
The nvcc compiler could not be located in your $PATH. To
enable CUDA acceleration, either add it to your path, or set
$CUDAHOME
############################################################running install
Checking .pth file support in /usr/local/lib/python2.7/dist-packages/
/usr/bin/python -E -c pass
TEST PASSED: /usr/local/lib/python2.7/dist-packages/ appears to support
.pth files
running bdist_egg
running egg_info
writing requirements to mixtape.egg-info/requires.txt
writing mixtape.egg-info/PKG-INFO
writing top-level names to mixtape.egg-info/top_level.txt
writing dependency_links to mixtape.egg-info/dependency_links.txt
reading manifest file 'mixtape.egg-info/SOURCES.txt'
writing manifest file 'mixtape.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-i686/egg
running install_lib
running build_py
running build_ext
skipping 'src/reversibility.c' Cython extension (up-to-date)
skipping 'platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp' Cython extension
(up-to-date)
building 'mixtape._ghmm' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv
-O2 -Wall -Wstrict-prototypes -fPIC
-I/usr/local/lib/python2.7/dist-packages/numpy/core/include -
Iplatforms/cpu/kernels/include/ -Iplatforms/cpu/kernels/
-I/usr/include/python2.7 -c platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp
-o build/temp.linux- i686-2.7/platforms/cpu/wrappers/GaussianHMMCPUImpl.o
-fopenmp cc1plus: warning: command line option '-Wstrict-prototypes' is
valid for Ada/C/ObjC but not for C++ [enabled by default] In file included
from
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1760:0,
from
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:314:
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
warning: #warning "Using deprecated NumPy API, disable i
t by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
In file included from platforms/cpu/kernels/logsumexp.hpp:10:0,
from platforms/cpu/kernels/forward.hpp:8,
from platforms/cpu/kernels/do_estep.hpp:18,
from platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:321:
/usr/lib/gcc/i686-linux-gnu/4.6.1/include/emmintrin.h:32:3: error: #error
"SSE2 instruction set not enabled"
In file included from platforms/cpu/kernels/include/sse_mathfun.h:32:0,
from platforms/cpu/kernels/logsumexp.hpp:14,
from platforms/cpu/kernels/forward.hpp:8,
from platforms/cpu/kernels/do_estep.hpp:18,
from platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:321:
/usr/lib/gcc/i686-linux-gnu/4.6.1/include/xmmintrin.h:32:3: error: #error
"SSE instruction set not enabled"
In file included from platforms/cpu/kernels/logsumexp.hpp:14:0,
from platforms/cpu/kernels/forward.hpp:8,
from platforms/cpu/kernels/do_estep.hpp:18,
from platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:321:
platforms/cpu/kernels/include/sse_mathfun.h:45:9: error: '
_m128' does not name a type
platforms/cpu/kernels/include/sse_mathfun.h:51:9: error: '_m64' does not
name a type
platforms/cpu/kernels/include/sse_mathfun.h:93:3: error: '
_m128' does not name a type
platforms/cpu/kernels/include/sse_mathfun.h:94:3: error: '_m64' does not
name a type
platforms/cpu/kernels/include/sse_mathfun.h:112:1: error: 'v4sf' does not
name a type
platforms/cpu/kernels/include/sse_mathfun.h:214:1: error: 'v4sf' does not
name a type
platforms/cpu/kernels/include/sse_mathfun.h:332:1: error: 'v4sf' does not
name a type
platforms/cpu/kernels/include/sse_mathfun.h:449:1: error: 'v4sf' does not
name a type
platforms/cpu/kernels/include/sse_mathfun.h:568:16: error: variable or
field 'sincos_ps' declared void
platforms/cpu/kernels/include/sse_mathfun.h:568:16: error: 'v4sf' was not
declared in this scope
platforms/cpu/kernels/include/sse_mathfun.h:568:24: error: 'v4sf' was not
declared in this scope
platforms/cpu/kernels/include/sse_mathfun.h:568:30: error: 's' was not
declared in this scope
platforms/cpu/kernels/include/sse_mathfun.h:568:33: error: 'v4sf' was not
declared in this scope
platforms/cpu/kernels/include/sse_mathfun.h:568:39: error: 'c' was not
declared in this scope
In file included from platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:321:0:
platforms/cpu/kernels/do_estep.hpp:79:37: error: expected declaration
before end of line
error: command 'gcc' failed with exit status 1Reply to this email directly or view it on GitHubhttps://github.com//issues/35
.
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rmcgibbo
commented on September 17, 2024
@rbharath: can you paste the output of cat /proc/cpuinfo?
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rbharath
commented on September 17, 2024
I'll try updating to a newer version of gcc. Here's my pasted cat /proc/cpuinfo:
processor : 0
vendor_id : GenuineIntel
cpu family : 6
model : 37
model name : Intel(R) Core(TM) i5 CPU M 450 @ 2.40GHz
stepping : 5
cpu MHz : 1199.000
cache size : 3072 KB
physical id : 0
siblings : 4
core id : 0
cpu cores : 2
apicid : 0
initial apicid : 0
fdiv_bug : no
hlt_bug : no
f00f_bug : no
coma_bug : no
fpu : yes
fpu_exception : yes
cpuid level : 11
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx rdtscp lm constant_tsc arch_perfmon pebs bts xtopology nonstop_tsc aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm sse4_1 sse4_2 popcnt lahf_lm ida arat dts tpr_shadow vnmi flexpriority ept vpid
bogomips : 4788.49
clflush size : 64
cache_alignment : 64
address sizes : 36 bits physical, 48 bits virtual
power management:
processor : 1
vendor_id : GenuineIntel
cpu family : 6
model : 37
model name : Intel(R) Core(TM) i5 CPU M 450 @ 2.40GHz
stepping : 5
cpu MHz : 1199.000
cache size : 3072 KB
physical id : 0
siblings : 4
core id : 0
cpu cores : 2
apicid : 1
initial apicid : 1
fdiv_bug : no
hlt_bug : no
f00f_bug : no
coma_bug : no
fpu : yes
fpu_exception : yes
cpuid level : 11
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx rdtscp lm constant_tsc arch_perfmon pebs bts xtopology nonstop_tsc aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm sse4_1 sse4_2 popcnt lahf_lm ida arat dts tpr_shadow vnmi flexpriority ept vpid
bogomips : 4788.45
clflush size : 64
cache_alignment : 64
address sizes : 36 bits physical, 48 bits virtual
power management:
processor : 2
vendor_id : GenuineIntel
cpu family : 6
model : 37
model name : Intel(R) Core(TM) i5 CPU M 450 @ 2.40GHz
stepping : 5
cpu MHz : 1199.000
cache size : 3072 KB
physical id : 0
siblings : 4
core id : 2
cpu cores : 2
apicid : 4
initial apicid : 4
fdiv_bug : no
hlt_bug : no
f00f_bug : no
coma_bug : no
fpu : yes
fpu_exception : yes
cpuid level : 11
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx rdtscp lm constant_tsc arch_perfmon pebs bts xtopology nonstop_tsc aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm sse4_1 sse4_2 popcnt lahf_lm ida arat dts tpr_shadow vnmi flexpriority ept vpid
bogomips : 4788.46
clflush size : 64
cache_alignment : 64
address sizes : 36 bits physical, 48 bits virtual
power management:
processor : 3
vendor_id : GenuineIntel
cpu family : 6
model : 37
model name : Intel(R) Core(TM) i5 CPU M 450 @ 2.40GHz
stepping : 5
cpu MHz : 1199.000
cache size : 3072 KB
physical id : 0
siblings : 4
core id : 2
cpu cores : 2
apicid : 5
initial apicid : 5
fdiv_bug : no
hlt_bug : no
f00f_bug : no
coma_bug : no
fpu : yes
fpu_exception : yes
cpuid level : 11
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx rdtscp lm constant_tsc arch_perfmon pebs bts xtopology nonstop_tsc aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm sse4_1 sse4_2 popcnt lahf_lm ida arat dts tpr_shadow vnmi flexpriority ept vpid
bogomips : 4788.46
clflush size : 64
cache_alignment : 64
address sizes : 36 bits physical, 48 bits virtual
power management:
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rmcgibbo
commented on September 17, 2024
Okay. I was worried that your machine might not have SSE3 instructures, but it does.
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rmcgibbo
commented on September 17, 2024
It looks like you have gcc 4.6, so that shouldn't be the issue.
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rmcgibbo
commented on September 17, 2024
Try changing this line to
extra_compile_args = ['-msse3']
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rbharath
commented on September 17, 2024
Tried changing the line. Seems to get a little further, but build still fails:
The nvcc compiler could not be located in your $PATH. To
enable CUDA acceleration, either add it to your path, or set
$CUDAHOME
############################################################ �[0m
running install
Checking .pth file support in /usr/local/lib/python2.7/dist-packages/
/usr/bin/python -E -c pass
TEST PASSED: /usr/local/lib/python2.7/dist-packages/ appears to support .pth files
running bdist_egg
running egg_info
writing requirements to mixtape.egg-info/requires.txt
writing mixtape.egg-info/PKG-INFO
writing top-level names to mixtape.egg-info/top_level.txt
writing dependency_links to mixtape.egg-info/dependency_links.txt
reading manifest file 'mixtape.egg-info/SOURCES.txt'
writing manifest file 'mixtape.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-i686/egg
running install_lib
running build_py
running build_ext
skipping 'src/reversibility.c' Cython extension (up-to-date)
skipping 'platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp' Cython extension (up-to-date)
building 'mixtape._ghmm' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/local/lib/python2.7/dist-packages/numpy/core/include -Iplatforms/cpu/kernels/include/ -Iplatforms/cpu/kernels/ -I/usr/include/python2.7 -c platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp -o build/temp.linux-i686-2.7/platforms/cpu/wrappers/GaussianHMMCPUImpl.o -msse3 -fopenmp
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for Ada/C/ObjC but not for C++ [enabled by default]
In file included from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1760:0,
from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:314:
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp: In function ‘PyObject* __pyx_pf_7mixtape_5_ghmm_18GaussianHMMCPUImpl_2do_estep(__pyx_obj_7mixtape_5_ghmm_GaussianHMMCPUImpl*)’:
platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:3506:2218: error: no matching function for call to ‘do_estep(__pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, const float**, int&, __pyx_t_5numpy_int32_t*, int&, int&, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, float*)’
platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:3506:2218: note: candidate is:
platforms/cpu/kernels/do_estep.hpp:33:6: note: template<class REAL> void Mixtape::do_estep(const float*, const float*, const float*, const float*, const float*, const float**, int, const int*, int, int, float*, float*, float*, float*, float*)
platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:3687:2219: error: no matching function for call to ‘do_estep(__pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, const float**, int&, __pyx_t_5numpy_int32_t*, int&, int&, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, float*)’
platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:3687:2219: note: candidate is:
platforms/cpu/kernels/do_estep.hpp:33:6: note: template<class REAL> void Mixtape::do_estep(const float*, const float*, const float*, const float*, const float*, const float**, int, const int*, int, int, float*, float*, float*, float*, float*)
error: command 'gcc' failed with exit status 1
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rmcgibbo
commented on September 17, 2024
(I changed your comment to be in triple quotes to be readable)
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rmcgibbo
commented on September 17, 2024
What's the output of:
g++ -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/local/lib/python2.7/dist-packages/numpy/core/include -Iplatforms/cpu/kernels/include/ -Iplatforms/cpu/kernels/ -I/usr/include/python2.7 -c platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp -o build/temp.linux-i686-2.7/platforms/cpu/wrappers/GaussianHMMCPUImpl.o -msse3 -fopenmp
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rbharath
commented on September 17, 2024
Tried running it. Seems to be the same sort of error as earlier. It seems like __pyx_t_numpy_float_32_t* isn't being recognized as const float*:
bramsundar@bramsundar-HP-Pavilion-dv6-Notebook-PC:~/Devel/mixtape$ g++ -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/local/lib/python2.7/dist-packages/numpy/core/include -Iplatforms/cpu/kernels/include/ -Iplatforms/cpu/kernels/ -I/usr/include/python2.7 -c platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp -o build/temp.linux-i686-2.7/platforms/cpu/wrappers/GaussianHMMCPUImpl.o -msse3 -fopenmp
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for Ada/C/ObjC but not for C++ [enabled by default]
In file included from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1760:0,
from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4,
from platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:314:
/usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp: In function ‘PyObject* __pyx_pf_7mixtape_5_ghmm_18GaussianHMMCPUImpl_2do_estep(__pyx_obj_7mixtape_5_ghmm_GaussianHMMCPUImpl*)’:
platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:3506:2218: error: no matching function for call to ‘do_estep(__pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, const float**, int&, __pyx_t_5numpy_int32_t*, int&, int&, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, float*)’
platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:3506:2218: note: candidate is:
platforms/cpu/kernels/do_estep.hpp:33:6: note: template<class REAL> void Mixtape::do_estep(const float*, const float*, const float*, const float*, const float*, const float**, int, const int*, int, int, float*, float*, float*, float*, float*)
platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:3687:2219: error: no matching function for call to ‘do_estep(__pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, const float**, int&, __pyx_t_5numpy_int32_t*, int&, int&, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, __pyx_t_5numpy_float32_t*, float*)’
platforms/cpu/wrappers/GaussianHMMCPUImpl.cpp:3687:2219: note: candidate is:
platforms/cpu/kernels/do_estep.hpp:33:6: note: template<class REAL> void Mixtape::do_estep(const float*, const float*, const float*, const float*, const float*, const float**, int, const int*, int, int, float*, float*, float*, float*, float*)
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rmcgibbo
commented on September 17, 2024
Okay. We've got to do some digging to find what it's declare as.
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rmcgibbo
commented on September 17, 2024
Look in GaussianHMMCPUImpl.cpp, find the typedef for __pyx_t_5numpy_float32_t. In my copy, it's on line 668, which reads typedef npy_float32 __pyx_t_5numpy_float32_t;
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rmcgibbo
commented on September 17, 2024
Then, we look for npy_float32 in the numpy include directory, which on your machine is /usr/local/lib/python2.7/dist-packages/numpy/core/include.
So run
grep npy_float32 /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy*.h
On my machine, I get
$ grep npy_float32 /Users/rmcgibbo/miniconda/lib/python2.7/site-packages/numpy/core/include/numpy/*.h
/Users/rmcgibbo/miniconda/lib/python2.7/site-packages/numpy/core/include/numpy/noprefix.h:#define Float32 npy_float32
/Users/rmcgibbo/miniconda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_common.h: typedef double npy_float32;
/Users/rmcgibbo/miniconda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_common.h: typedef float npy_float32;
/Users/rmcgibbo/miniconda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_common.h: typedef npy_longdouble npy_float32;
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rmcgibbo
commented on September 17, 2024
Maybe the easiest way is actually, from python, make sure that
>>> print np.zeros(1, dtype=np.float32).itemsize
4
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rmcgibbo
commented on September 17, 2024
This [http://stackoverflow.com/questions/7168215/determine-sizeof-float-without-compilation] says that GCC doesn't have any platforms on which sizeof(float) != 4 though. I really don't know. Maybe we can just explicitly cast the __pyx_t_5numpy_float32_t* to float*? I don't know why this happens on one compiler but not another.
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rmcgibbo
commented on September 17, 2024
You would change https://github.com/rmcgibbo/mixtape/blob/master/platforms/cpu/wrappers/GaussianHMMCPUImpl.pyx#L130 to something like
do_estep_single(
<float*> &log_transmat[0,0], <float*> &log_transmat_T[0,0], <float*> &log_startprob[0], <float*> &means[0,0],
<float*> &vars[0,0]....
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rmcgibbo
commented on September 17, 2024
And also on line 137. Basically, you put the explicit cast <float*> or <float**>, etc, in before each argument.
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rbharath
commented on September 17, 2024
I made these changes and a few others. Seems to work on my box. I've made a pull request #43 for this.
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