OpenBLAS undefined symbols
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Kirill Katsnelson
Aug 17, 2015, 3:24:34 PM8/17/15
to kaldi-developers
Not likely a kaldi problem; looks like I am having a wrong dependency
somewhere. I am getting a few undefined symbols when compiling against
OpenBLAS. I thought these were defined in libgfortran, but it is
certainly referenced in the command line. Has anyone seen that?
kkm@yupana:~/work/travis-temp/src[master *]$ make
. . . . .
g++ -msse -msse2 -Wall -I.. -pthread -DKALDI_DOUBLEPRECISION=0
-DHAVE_POSIX_MEMALIGN -Wno-sign-compare -Wno-unused-local-typedefs
-Winit-self -DHAVE_EXECINFO_H=1 -rdynamic -DHAVE_CXXABI_H
-DHAVE_OPENBLAS -I /usr/include -I
/home/kkm/work/travis-temp/tools/openfst/include -Wno-sign-compare -g
-rdynamic -Wl,-rpath=/home/kkm/work/travis-temp/tools/openfst/lib
align-equal.cc ../lm/kaldi-lm.a ../decoder/kaldi-decoder.a
../lat/kaldi-lat.a ../hmm/kaldi-hmm.a ../transform/kaldi-transform.a
../gmm/kaldi-gmm.a ../tree/kaldi-tree.a ../matrix/kaldi-matrix.a
../util/kaldi-util.a ../base/kaldi-base.a ../thread/kaldi-thread.a
-L/home/kkm/work/travis-temp/tools/openfst/lib -lfst -L/usr/lib
-lopenblas -lgfortran -Wl,-rpath=/usr/lib -lm -lpthread -ldl -o align-equal
../matrix/kaldi-matrix.a(kaldi-matrix.o): In function
`kaldi::clapack_Xgetrf2(int*, int*, float*, int*, int*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:395:
undefined reference to `sgetrf_'
../matrix/kaldi-matrix.a(kaldi-matrix.o): In function
`kaldi::clapack_Xgetrf2(int*, int*, double*, int*, int*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:400:
undefined reference to `dgetrf_'
../matrix/kaldi-matrix.a(kaldi-matrix.o): In function
`kaldi::clapack_Xgetri2(int*, float*, int*, int*, float*, int*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:407:
undefined reference to `sgetri_'
../matrix/kaldi-matrix.a(kaldi-matrix.o): In function
`kaldi::clapack_Xgetri2(int*, double*, int*, int*, double*, int*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:412:
undefined reference to `dgetri_'
../matrix/kaldi-matrix.a(kaldi-matrix.o): In function
`kaldi::clapack_Xgesvd(char*, char*, int*, int*, float*, int*, float*,
float*, int*, float*, int*, float*, int*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:423:
undefined reference to `sgesvd_'
../matrix/kaldi-matrix.a(kaldi-matrix.o): In function
`kaldi::clapack_Xgesvd(char*, char*, int*, int*, double*, int*, double*,
double*, int*, double*, int*, double*, int*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:433:
undefined reference to `dgesvd_'
../matrix/kaldi-matrix.a(sp-matrix.o): In function
`kaldi::clapack_Xsptri(int*, float*, int*, float*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:438:
undefined reference to `ssptri_'
../matrix/kaldi-matrix.a(sp-matrix.o): In function
`kaldi::clapack_Xsptri(int*, double*, int*, double*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:442:
undefined reference to `dsptri_'
../matrix/kaldi-matrix.a(sp-matrix.o): In function
`kaldi::clapack_Xsptrf(int*, float*, int*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:447:
undefined reference to `ssptrf_'
../matrix/kaldi-matrix.a(sp-matrix.o): In function
`kaldi::clapack_Xsptrf(int*, double*, int*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:451:
undefined reference to `dsptrf_'
../matrix/kaldi-matrix.a(tp-matrix.o): In function
`kaldi::clapack_Xtptri(int*, float*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:386:
undefined reference to `stptri_'
../matrix/kaldi-matrix.a(tp-matrix.o): In function
`kaldi::clapack_Xtptri(int*, double*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:389:
undefined reference to `dtptri_'
. . . . .
kkm@yupana:~/work/travis-temp/src[master *]$ find /usr -name 'libgfortran*'
/usr/lib/x86_64-linux-gnu/libgfortran.so.3
/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
/usr/lib/gcc/x86_64-linux-gnu/4.9/libgfortran.spec
/usr/lib/gcc/x86_64-linux-gnu/4.9/libgfortran.so
/usr/lib/gcc/x86_64-linux-gnu/4.9/libgfortran.a
/usr/lib/gcc/x86_64-linux-gnu/4.9/libgfortranbegin.a
/usr/share/doc/libgfortran-4.9-dev
/usr/share/doc/libgfortran3
somewhere. I am getting a few undefined symbols when compiling against
OpenBLAS. I thought these were defined in libgfortran, but it is
certainly referenced in the command line. Has anyone seen that?
kkm@yupana:~/work/travis-temp/src[master *]$ make
. . . . .
g++ -msse -msse2 -Wall -I.. -pthread -DKALDI_DOUBLEPRECISION=0
-DHAVE_POSIX_MEMALIGN -Wno-sign-compare -Wno-unused-local-typedefs
-Winit-self -DHAVE_EXECINFO_H=1 -rdynamic -DHAVE_CXXABI_H
-DHAVE_OPENBLAS -I /usr/include -I
/home/kkm/work/travis-temp/tools/openfst/include -Wno-sign-compare -g
-rdynamic -Wl,-rpath=/home/kkm/work/travis-temp/tools/openfst/lib
align-equal.cc ../lm/kaldi-lm.a ../decoder/kaldi-decoder.a
../lat/kaldi-lat.a ../hmm/kaldi-hmm.a ../transform/kaldi-transform.a
../gmm/kaldi-gmm.a ../tree/kaldi-tree.a ../matrix/kaldi-matrix.a
../util/kaldi-util.a ../base/kaldi-base.a ../thread/kaldi-thread.a
-L/home/kkm/work/travis-temp/tools/openfst/lib -lfst -L/usr/lib
-lopenblas -lgfortran -Wl,-rpath=/usr/lib -lm -lpthread -ldl -o align-equal
../matrix/kaldi-matrix.a(kaldi-matrix.o): In function
`kaldi::clapack_Xgetrf2(int*, int*, float*, int*, int*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:395:
undefined reference to `sgetrf_'
../matrix/kaldi-matrix.a(kaldi-matrix.o): In function
`kaldi::clapack_Xgetrf2(int*, int*, double*, int*, int*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:400:
undefined reference to `dgetrf_'
../matrix/kaldi-matrix.a(kaldi-matrix.o): In function
`kaldi::clapack_Xgetri2(int*, float*, int*, int*, float*, int*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:407:
undefined reference to `sgetri_'
../matrix/kaldi-matrix.a(kaldi-matrix.o): In function
`kaldi::clapack_Xgetri2(int*, double*, int*, int*, double*, int*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:412:
undefined reference to `dgetri_'
../matrix/kaldi-matrix.a(kaldi-matrix.o): In function
`kaldi::clapack_Xgesvd(char*, char*, int*, int*, float*, int*, float*,
float*, int*, float*, int*, float*, int*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:423:
undefined reference to `sgesvd_'
../matrix/kaldi-matrix.a(kaldi-matrix.o): In function
`kaldi::clapack_Xgesvd(char*, char*, int*, int*, double*, int*, double*,
double*, int*, double*, int*, double*, int*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:433:
undefined reference to `dgesvd_'
../matrix/kaldi-matrix.a(sp-matrix.o): In function
`kaldi::clapack_Xsptri(int*, float*, int*, float*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:438:
undefined reference to `ssptri_'
../matrix/kaldi-matrix.a(sp-matrix.o): In function
`kaldi::clapack_Xsptri(int*, double*, int*, double*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:442:
undefined reference to `dsptri_'
../matrix/kaldi-matrix.a(sp-matrix.o): In function
`kaldi::clapack_Xsptrf(int*, float*, int*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:447:
undefined reference to `ssptrf_'
../matrix/kaldi-matrix.a(sp-matrix.o): In function
`kaldi::clapack_Xsptrf(int*, double*, int*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:451:
undefined reference to `dsptrf_'
../matrix/kaldi-matrix.a(tp-matrix.o): In function
`kaldi::clapack_Xtptri(int*, float*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:386:
undefined reference to `stptri_'
../matrix/kaldi-matrix.a(tp-matrix.o): In function
`kaldi::clapack_Xtptri(int*, double*, int*)':
/home/kkm/work/travis-temp/src/matrix/../matrix/cblas-wrappers.h:389:
undefined reference to `dtptri_'
. . . . .
kkm@yupana:~/work/travis-temp/src[master *]$ find /usr -name 'libgfortran*'
/usr/lib/x86_64-linux-gnu/libgfortran.so.3
/usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
/usr/lib/gcc/x86_64-linux-gnu/4.9/libgfortran.spec
/usr/lib/gcc/x86_64-linux-gnu/4.9/libgfortran.so
/usr/lib/gcc/x86_64-linux-gnu/4.9/libgfortran.a
/usr/lib/gcc/x86_64-linux-gnu/4.9/libgfortranbegin.a
/usr/share/doc/libgfortran-4.9-dev
/usr/share/doc/libgfortran3
Daniel Povey
Aug 17, 2015, 3:47:54 PM8/17/15
to kaldi-developers
These are from LAPACK rather than BLAS per se, but a web search reveals that they seem to be implemented in OpenBLAS, and they must have been working before. Grep in the OpenBLAS libraries, maybe they have split up the OpenBLAS library into BLAS and LAPACK portions.
Dan
Dan
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Daniel Povey
Aug 17, 2015, 4:03:50 PM8/17/15
to kaldi-developers
BTW, doing "make clean" and "make" in the matrix/ directory is a good practice if you change things like the BLAS library- just to make sure it's not an error due to that.
Dan
Kirill Katsnelson
Aug 17, 2015, 5:41:40 PM8/17/15
to kaldi-de...@googlegroups.com
I am using Ubuntu packages, since prepackaged libraries will make CI
turnaround shorter. I do not know how the packages are made.
But thanks anyway, -llapack solved it. Does it make sense to add this to
the linker flags in the Kaldi Makefile, or should we consider it just a
packaging quirk and leave Makefile alone?
-kkm
> <mailto:kaldi-developers%2Bunsu...@googlegroups.com>.
> <mailto:kaldi-de...@googlegroups.com>.
> <https://groups.google.com/d/msgid/kaldi-developers/CAEWAuySCZ495PyfE%3Dkb4okf9Hd_M19aUNOtMTe1zCAaktMS05w%40mail.gmail.com?utm_medium=email&utm_source=footer>.
turnaround shorter. I do not know how the packages are made.
But thanks anyway, -llapack solved it. Does it make sense to add this to
the linker flags in the Kaldi Makefile, or should we consider it just a
packaging quirk and leave Makefile alone?
-kkm
> <mailto:kaldi-de...@googlegroups.com>.
> Visit this group at http://groups.google.com/group/kaldi-developers.
> To view this discussion on the web visit
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>
>
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> For more options, visit https://groups.google.com/d/optout.
>
>
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Daniel Povey
Aug 17, 2015, 5:50:17 PM8/17/15
to kaldi-developers
If you install OpenBLAS the normal way, from source, it just produces a single library. So adding that flag might produce linking errors on a normal Kaldi install.
Dan
Dan
--
ls -l OpenBLAS/lib*
-rw-r--r-- 1 dpovey fax 0 Aug 4 14:06 OpenBLAS/lib.grd
lrwxrwxrwx 1 dpovey fax 34 Aug 4 14:06 OpenBLAS/libopenblas.a -> libopenblas_sandybridgep-r0.2.14.a
lrwxrwxrwx 1 dpovey fax 35 Aug 4 14:07 OpenBLAS/libopenblas.so -> libopenblas_sandybridgep-r0.2.14.so
lrwxrwxrwx 1 dpovey fax 35 Aug 4 14:07 OpenBLAS/libopenblas.so.0 -> libopenblas_sandybridgep-r0.2.14.so
-rw-r--r-- 1 dpovey fax 54231058 Aug 4 14:06 OpenBLAS/libopenblas_sandybridgep-r0.2.14.a
-rwxr-xr-x 1 dpovey fax 25541935 Aug 4 14:07 OpenBLAS/libopenblas_sandybridgep-r0.2.14.so
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