Hey,
I tried to compile fsl from source to optimize it for our "super"computer. Most of it did work fine, except that it didnt work for
fslsurface and (probably depend) film/ptx2. I followed the guide from the wiki and only changed one compiler option in
systemvars.mk:
ARCHFLAGS = -march=corei7-avx
I've added the fslsurface part of build.log below.
Do you have any ideas?
Thanks,
Matthias
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Making project src/fslsurface
/bin/rm -f /tmp/fslgrot *.o *.a *.exe core depend.mk
/bin/rm -f /tmp/fslgrot fslsurfacemaths
/home/matthias/fslbuild/fsl/config/common/rules.mk:320: depend.mk: Datei oder Verzeichnis nicht gefunden
Building dependency file depend.mk
c++ -Wall -ansi -pedantic -Wno-long-long -march=corei7-avx -O3 -fexpensive-optimizations -march=corei7-avx -I/home/matthias/fslbuild/fsl/extras/include/newmat -I/home/matthias/fslbuild/fsl/extras/include/libprob -I/home/matthias/fslbuild/fsl/extras/include -I/home/matthias/fslbuild/fsl/include/niftiio -I. -I/home/matthias/fslbuild/fsl/include -I/home/matthias/fslbuild/fsl/include -c -o fslsurfacefns.o fslsurfacefns.cc
fslsurfacefns.cc: In instantiation of ‘void fslsurface_name::conn2dist(fslsurface_name::fslSurface<T, T2>&, const T2&, std::list<std::pair<T2, T2> >&, std::vector<std::list<std::pair<T2, T> > >&) [with T = float; T2 = unsigned int]’:
fslsurfacefns.cc:704:17: required from ‘void fslsurface_name::sc_smooth_gaussian_geodesic(fslsurface_name::fslSurface<T, T2>&, const unsigned int&, const T&, const T&, bool) [with T = float; T2 = unsigned int]’
fslsurfacefns.cc:947:173: required from here
fslsurfacefns.cc:510:22: warning: variable ‘notFoundDup’ set but not used [-Wunused-but-set-variable]
In file included from ./fslsurfacefns.h:70:0,
from fslsurfacefns.cc:64:
./fslsurface_structs.h: In instantiation of ‘double fslsurface_name::vec3<T>::norm() [with T = float]’:
fslsurfacefns.cc:1960:36: required from ‘void fslsurface_name::writeTimeSeries(const fslsurface_name::fslSurface<T, T2>&, NEWIMAGE::volume4D<S1>&, const string&) [with T = float; T2 = unsigned int; std::string = std::basic_string<char>]’
fslsurfacefns.cc:1978:185: required from here
./fslsurface_structs.h:141:44: error: ‘sqrt’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
In file included from /home/matthias/fslbuild/fsl/include/miscmaths/miscmaths.h:77:0,
from /home/matthias/fslbuild/fsl/include/newimage/newimage.h:81,
from /home/matthias/fslbuild/fsl/include/newimage/newimageall.h:72,
from ./fslsurfacefns.h:72,
from fslsurfacefns.cc:64:
/usr/include/c++/4.7/cmath:485:3: note: ‘float std::sqrt(float)’ declared here, later in the translation unit
In file included from ./fslsurfacefns.h:70:0,
from fslsurfacefns.cc:64:
./fslsurface_structs.h: In instantiation of ‘void fslsurface_name::vec3<T>::normalize() [with T = float]’:
fslsurfacefns.cc:522:25: required from ‘void fslsurface_name::conn2dist(fslsurface_name::fslSurface<T, T2>&, const T2&, std::list<std::pair<T2, T2> >&, std::vector<std::list<std::pair<T2, T> > >&) [with T = float; T2 = unsigned int]’
fslsurfacefns.cc:704:17: required from ‘void fslsurface_name::sc_smooth_gaussian_geodesic(fslsurface_name::fslSurface<T, T2>&, const unsigned int&, const T&, const T&, bool) [with T = float; T2 = unsigned int]’
fslsurfacefns.cc:947:173: required from here
./fslsurface_structs.h:134:9: error: ‘sqrt’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
In file included from /home/matthias/fslbuild/fsl/include/miscmaths/miscmaths.h:77:0,
from /home/matthias/fslbuild/fsl/include/newimage/newimage.h:81,
from /home/matthias/fslbuild/fsl/include/newimage/newimageall.h:72,
from ./fslsurfacefns.h:72,
from fslsurfacefns.cc:64:
/usr/include/c++/4.7/cmath:485:3: note: ‘float std::sqrt(float)’ declared here, later in the translation unit
make: *** [fslsurfacefns.o] Fehler 1
c++ -Wall -ansi -pedantic -Wno-long-long -march=corei7-avx -O3 -fexpensive-optimizations -march=corei7-avx -I/home/matthias/fslbuild/fsl/extras/include/newmat -I/home/matthias/fslbuild/fsl/extras/include/libprob -I/home/matthias/fslbuild/fsl/extras/include -I/home/matthias/fslbuild/fsl/include/niftiio -I. -I/home/matthias/fslbuild/fsl/include -I/home/matthias/fslbuild/fsl/include -c -o fslsurfaceio.o fslsurfaceio.cc
c++ -Wall -ansi -pedantic -Wno-long-long -march=corei7-avx -O3 -fexpensive-optimizations -march=corei7-avx -I/home/matthias/fslbuild/fsl/extras/include/newmat -I/home/matthias/fslbuild/fsl/extras/include/libprob -I/home/matthias/fslbuild/fsl/extras/include -I/home/matthias/fslbuild/fsl/include/niftiio -I. -I/home/matthias/fslbuild/fsl/include -I/home/matthias/fslbuild/fsl/include -c -o fslsurface.o fslsurface.cc
c++ -Wall -ansi -pedantic -Wno-long-long -march=corei7-avx -O3 -fexpensive-optimizations -march=corei7-avx -I/home/matthias/fslbuild/fsl/extras/include/newmat -I/home/matthias/fslbuild/fsl/extras/include/libprob -I/home/matthias/fslbuild/fsl/extras/include -I/home/matthias/fslbuild/fsl/include/niftiio -I. -I/home/matthias/fslbuild/fsl/include -I/home/matthias/fslbuild/fsl/include -c -o fslsurface_first.o fslsurface_first.cc
c++ -Wall -ansi -pedantic -Wno-long-long -march=corei7-avx -O3 -fexpensive-optimizations -march=corei7-avx -I/home/matthias/fslbuild/fsl/extras/include/newmat -I/home/matthias/fslbuild/fsl/extras/include/libprob -I/home/matthias/fslbuild/fsl/extras/include -I/home/matthias/fslbuild/fsl/include/niftiio -I. -I/home/matthias/fslbuild/fsl/include -I/home/matthias/fslbuild/fsl/include -c -o fslsurface_dataconv.o fslsurface_dataconv.cpp
c++ -Wall -ansi -pedantic -Wno-long-long -march=corei7-avx -O3 -fexpensive-optimizations -march=corei7-avx -I/home/matthias/fslbuild/fsl/extras/include/newmat -I/home/matthias/fslbuild/fsl/extras/include/libprob -I/home/matthias/fslbuild/fsl/extras/include -I/home/matthias/fslbuild/fsl/include/niftiio -I. -I/home/matthias/fslbuild/fsl/include -I/home/matthias/fslbuild/fsl/include -c -o fslsurfacemaths.o fslsurfacemaths.cpp
make: Das Target »all« wurde wegen Fehlern nicht aktualisiert.
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ERROR::Could not make fslsurface successfully
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