shogun @0.9.3 build failure

[tal.yarkoni@…]

I can't get shogun 0.9.3 to build; relevant (I think) part of log below; full log attached. I'm running 10.6.6 with MacPorts 1.9.2 and Xcode 3.2.6 on a new (early 2011) MacBook Pro. I've tried uninstalling, cleaning, and reinstalling the complete dependency tree and get the same error. Any suggestions would be much appreciated.

:info:build /opt/local/bin/g++-mp-4.4 -fPIC -pipe -O2 -m64 -g -Wall -Wno-unused-parameter -Wformat -Wformat-security -Wimplicit -Wparentheses -Wshadow -Wno-deprecated -O9 -fexpensive-optimizations -frerun-cse-after-loop -fcse-follow-jumps -finline-functions -fschedule-insns2 -fthread-jumps -fforce-addr -fstrength-reduce -funroll-loops -march=native -mtune=native -pthread -DSWIG_TYPE_TABLE=shogun -DDARWIN -DHAVE_POWL -DHAVE_SQRTL -DHAVE_ATLAS -DHAVE_LAPACK -DHAVE_LAPACK -DHAVE_LAPACK -DUSE_GLPK -DUSE_GZIP -DUSE_BZIP2 -DHAVE_LARGEFILE -DUSE_SHORTREAL_KERNELCACHE -DUSE_HMMPARALLELSTRUCTURES -DUSE_HMMPARALLEL -DUSE_BIGSTATES -DUSE_HMMCACHE -DUSE_REFERENCE_COUNTING -DGPL  -DSWIG_TYPE_TABLE=shogun -DDARWIN -DHAVE_POWL -DHAVE_SQRTL -DHAVE_ATLAS -DHAVE_LAPACK -DHAVE_LAPACK -DHAVE_LAPACK -DUSE_GLPK -DUSE_GZIP -DUSE_BZIP2 -DHAVE_LARGEFILE -DUSE_SHORTREAL_KERNELCACHE -DUSE_HMMPARALLELSTRUCTURES -DUSE_HMMPARALLEL -DUSE_BIGSTATES -DUSE_HMMCACHE -DUSE_REFERENCE_COUNTING -DGPL  -c -I. -I.. -I. -I..  -I/opt/local/include  -I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -I/opt/local/include  -I../libshogun -I.. -o classifier/KernelPerceptron.cpp.o classifier/KernelPerceptron.cpp
:info:build /opt/local/bin/g++-mp-4.4 -fPIC -pipe -O2 -m64 -g -Wall -Wno-unused-parameter -Wformat -Wformat-security -Wimplicit -Wparentheses -Wshadow -Wno-deprecated -O9 -fexpensive-optimizations -frerun-cse-after-loop -fcse-follow-jumps -finline-functions -fschedule-insns2 -fthread-jumps -fforce-addr -fstrength-reduce -funroll-loops -march=native -mtune=native -pthread -DSWIG_TYPE_TABLE=shogun -DDARWIN -DHAVE_POWL -DHAVE_SQRTL -DHAVE_ATLAS -DHAVE_LAPACK -DHAVE_LAPACK -DHAVE_LAPACK -DUSE_GLPK -DUSE_GZIP -DUSE_BZIP2 -DHAVE_LARGEFILE -DUSE_SHORTREAL_KERNELCACHE -DUSE_HMMPARALLELSTRUCTURES -DUSE_HMMPARALLEL -DUSE_BIGSTATES -DUSE_HMMCACHE -DUSE_REFERENCE_COUNTING -DGPL  -DSWIG_TYPE_TABLE=shogun -DDARWIN -DHAVE_POWL -DHAVE_SQRTL -DHAVE_ATLAS -DHAVE_LAPACK -DHAVE_LAPACK -DHAVE_LAPACK -DUSE_GLPK -DUSE_GZIP -DUSE_BZIP2 -DHAVE_LARGEFILE -DUSE_SHORTREAL_KERNELCACHE -DUSE_HMMPARALLELSTRUCTURES -DUSE_HMMPARALLEL -DUSE_BIGSTATES -DUSE_HMMCACHE -DUSE_REFERENCE_COUNTING -DGPL  -c -I. -I.. -I. -I..  -I/opt/local/include  -I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -I/opt/local/include  -I../libshogun -I.. -o classifier/KNN.cpp.o classifier/KNN.cpp
:info:build {standard input}:93:no such instruction: `vmovsd (%rdx,%rbx,8), %xmm0'
:info:build {standard input}:111:no such instruction: `vmovsd LC2(%rip), %xmm0'
...
goes on like this for a while...
...
:info:build {standard input}:4095:no such instruction: `vmovsd %xmm1, (%r8)'
:info:build {standard input}:4104:no such instruction: `vmovsd %xmm0, (%r9)'
:info:build make[1]: *** [classifier/KNN.cpp.o] Error 1
:info:build make: *** [all] Error 2
:info:build shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_shogun/work/shogun-0.9.3/src" && /usr/bin/make -j5 all " returned error 2
:error:build Target org.macports.build returned: shell command failed (see log for details)

[tal.yarkoni@…]

build log

[jmroot (Joshua Root)]

Please remember to cc the maintainer.

[tknapen@…]

I'm experiencing the same error on 10.7, with Xcode 4.2 and macports 2.0.3.

[tknapen@…]

Cc Me!

[tknapen@…]

Replying to tknapen@…:

I'm experiencing the same error on 10.7, with Xcode 4.2 and macports 2.0.3.

updating the portfile such that it downloads and configures version 1.1.0 of shogun doesn't matter - still the same error message.

[jmroot (Joshua Root)]

What variants are you building with? I can't reproduce with the default variants.

[ryandesign (Ryan Carsten Schmidt)]

Has duplicate #36909.

[ryandesign (Ryan Carsten Schmidt)]

Please check if this is still a problem with shogun 2.1.0.

[kthenriksson@…]

I don't use shogun and can't comment on whether this is still a problem, but if so, the issue is that gcc -march=native with a newish machine outputs new AVX instructions to the assember, such as vmovsd. However, the assembler is terribly old, and does not understand those instructions.

This is likely why jmr could not reproduce, because it is machine dependent. Ideally, the solution would be to install a newer assembler, but I don't believe it's possible. I can't find any way to install a newer version of the GNU assembler.

Instead, add the flag -mno-avx to CFLAGS and CXXFLAGS any time this error occurs. It is unfortunate that this is necessary, because those instructions can offer notable performance improvements.

[mf2k (Frank Schima)]

jameskyle has retired. See #44641.