AUR (en) - fsl

Git Clone URL:	https://aur.archlinux.org/fsl.git (read-only, click to copy)
Package Base:	fsl
Description:	A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data
Upstream URL:	http://www.fmrib.ox.ac.uk/fsl/
Licenses:	custom
Submitter:	fishburn
Maintainer:	tobac
Last Packager:	tobac
Votes:	12
Popularity:	0.000000
First Submitted:	2012-07-02 23:36 (UTC)
Last Updated:	2025-04-05 15:14 (UTC)

That's strange. Did you delete the sources before manually building it? My thinking is, maybe a dependency of fslsurface gets created later, i.e. too late, during the build process and by keeping the sources (and resulting files) in place you can make it build because that dependency still exists.

EDIT: I'm going to get my hands on an AMD machine, this weirdness has to stop (not that the CPU is necessarily the culprit, but it's a clue at least)

EDIT 2: It builds just fine on a recent Ryzen machine

javierbg commented on 2021-09-10 16:57 (UTC)

Reinstalling CUDA did not solve this. I tried running './build fslsurface' in the "src/fsl" directory and, surprisingly, it completed successfully. I have actually been able to build everything by copying the commands from the PKGBUILD file (NJOBS=6), but running makepkg is unsuccessful.

It is running on a laptop with an AMD Ryzen 5 4500U laptop (HP Probook x360 435 G7).

tobac commented on 2021-09-10 10:58 (UTC) (edited on 2021-09-10 11:01 (UTC) by tobac)

So it's the same error? Does reinstalling CUDA solve this? Could you try to cd into "/home/javier/Descargas/fsl/src/fsl" and run './build fslsurface'? And what CPU do you run this on?

The thing is, I was never able to reproduce this. On all machines tested (five in total, some virtual, some bare-metal), the build process runs just fine with or without CUDA.

javierbg commented on 2021-09-10 08:56 (UTC)

I'm trying to reinstall (last time CUDA was needed and I removed it), but I get the following error while building fslsurface:

Making project src/fslsurface

Building dependency file depend.mk
/bin/rm -f /tmp/fslgrot *.o *.a *.exe core depend.mk
/bin/rm -f /tmp/fslgrot fslsurfacemaths 
Building dependency file depend.mk
g++  -Wall -ansi -pedantic -Wno-long-long -std=c++11     -m64 -g -O3 -fexpensive-optimizations -m64 -I/usr/include/boost -I/home/javier/Descargas/fsl/src/fsl/extras/include/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD -I/home/javier/Descargas/fsl/src/fsl/extras/include/ -I/usr/include -I. -I/home/javier/Descargas/fsl/src/fsl/include -I/home/javier/Descargas/fsl/src/fsl/include  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS   -c -o fslsurfacefns.o fslsurfacefns.cc
g++  -Wall -ansi -pedantic -Wno-long-long -std=c++11     -m64 -g -O3 -fexpensive-optimizations -m64 -I/usr/include/boost -I/home/javier/Descargas/fsl/src/fsl/extras/include/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD -I/home/javier/Descargas/fsl/src/fsl/extras/include/ -I/usr/include -I. -I/home/javier/Descargas/fsl/src/fsl/include -I/home/javier/Descargas/fsl/src/fsl/include  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS   -c -o fslsurfaceio.o fslsurfaceio.cc
g++  -Wall -ansi -pedantic -Wno-long-long -std=c++11     -m64 -g -O3 -fexpensive-optimizations -m64 -I/usr/include/boost -I/home/javier/Descargas/fsl/src/fsl/extras/include/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD -I/home/javier/Descargas/fsl/src/fsl/extras/include/ -I/usr/include -I. -I/home/javier/Descargas/fsl/src/fsl/include -I/home/javier/Descargas/fsl/src/fsl/include  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS   -c -o fslsurface.o fslsurface.cc
g++  -Wall -ansi -pedantic -Wno-long-long -std=c++11     -m64 -g -O3 -fexpensive-optimizations -m64 -I/usr/include/boost -I/home/javier/Descargas/fsl/src/fsl/extras/include/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD -I/home/javier/Descargas/fsl/src/fsl/extras/include/ -I/usr/include -I. -I/home/javier/Descargas/fsl/src/fsl/include -I/home/javier/Descargas/fsl/src/fsl/include  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS   -c -o fslsurface_first.o fslsurface_first.cc
g++  -Wall -ansi -pedantic -Wno-long-long -std=c++11     -m64 -g -O3 -fexpensive-optimizations -m64 -I/usr/include/boost -I/home/javier/Descargas/fsl/src/fsl/extras/include/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD -I/home/javier/Descargas/fsl/src/fsl/extras/include/ -I/usr/include -I. -I/home/javier/Descargas/fsl/src/fsl/include -I/home/javier/Descargas/fsl/src/fsl/include  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS   -c -o fslsurface_dataconv.o fslsurface_dataconv.cpp
g++  -Wall -ansi -pedantic -Wno-long-long -std=c++11     -m64 -g -O3 -fexpensive-optimizations -m64 -I/usr/include/boost -I/home/javier/Descargas/fsl/src/fsl/extras/include/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD -I/home/javier/Descargas/fsl/src/fsl/extras/include/ -I/usr/include -I. -I/home/javier/Descargas/fsl/src/fsl/include -I/home/javier/Descargas/fsl/src/fsl/include  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS   -c -o fslsurfacemaths.o fslsurfacemaths.cpp
fslsurfacefns.cc: In instantiation of 'void fslsurface_name::conn2dist(fslsurface_name::fslSurface<T, T2>&, const T2&, std::__cxx11::list<std::pair<T2, T2> >&, std::vector<std::__cxx11::list<std::pair<T2, T> > >&) [with T = float; T2 = unsigned int]':
fslsurfacefns.cc:702:40:   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:945:171:   required from here
fslsurfacefns.cc:510:16: warning: variable 'notFoundDup' set but not used [-Wunused-but-set-variable]
510 |           bool notFoundDup=true;
    |                ^~~~~~~~~~~
In file included from /usr/include/string.h:519,
                from /usr/include/c++/11.1.0/cstring:42,
                from /home/javier/Descargas/fsl/src/fsl/extras/include/armawrap/armawrap/armadillo:24,
                from /home/javier/Descargas/fsl/src/fsl/extras/include/armawrap/armawrap/armawrap.hpp:13,
                from /home/javier/Descargas/fsl/src/fsl/extras/include/armawrap/armawrap/newmat.h:8,
                from /home/javier/Descargas/fsl/src/fsl/extras/include/armawrap/armawrap/newmatap.h:4,
                from /home/javier/Descargas/fsl/src/fsl/include/newimage/newimage.h:80,
                from /home/javier/Descargas/fsl/src/fsl/include/newimage/newimageall.h:72,
                from /home/javier/Descargas/fsl/src/fsl/include/shapeModel/shapeModel.h:73,
                from ./fslsurface_first.h:71,
                from fslsurface_first.cc:64:
In function 'char* strncpy(char*, const char*, size_t)',
    inlined from 'void NEWIMAGE::volume<T>::setAuxFile(std::string) [with T = short int]' at /home/javier/Descargas/fsl/src/fsl/include/newimage/newimage.h:361:53,
    inlined from 'void NEWIMAGE::copybasicproperties(const NEWIMAGE::volume<T>&, NEWIMAGE::volume<U>&) [with S = short int; D = short int]' at /home/javier/Descargas/fsl/src/fsl/include/newimage/newimage.h:952:20:
/usr/include/bits/string_fortified.h:95:34: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 24 equals destination size [-Wstringop-truncation]
95 |   return __builtin___strncpy_chk (__dest, __src, __len,
    |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
96 |                                   __glibc_objsize (__dest));
    |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~
ar -r libfslsurface.a  fslsurfacefns.o fslsurfaceio.o fslsurface.o
ar: creating libfslsurface.a
g++  -Wall -ansi -pedantic -Wno-long-long -std=c++11     -m64 -g -O3 -fexpensive-optimizations -m64 -I/usr/include/boost -I/home/javier/Descargas/fsl/src/fsl/extras/include/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD -I/home/javier/Descargas/fsl/src/fsl/extras/include/ -I/usr/include -I. -I/home/javier/Descargas/fsl/src/fsl/include -I/home/javier/Descargas/fsl/src/fsl/include  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -Wl,-rpath,'$ORIGIN/../lib' -L/usr/lib -llapack -lopenblas  -L/home/javier/Descargas/fsl/src/fsl/extras/lib -L/usr/lib -L. -L/home/javier/Descargas/fsl/src/fsl/lib -L/home/javier/Descargas/fsl/src/fsl/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o fslsurfacemaths fslsurfacemaths.o fslsurfaceio.o fslsurfacefns.o fslsurface_first.o fslsurface.o -lgiftiio -lexpat -lfirst_lib -lmeshclass -lshapeModel -lfslvtkio -lmeshclass -lnewimage -lmiscmaths -lNewNifti -lznz -lutils -lcprob -lz
/usr/bin/ld: fslsurfacemaths.o: in function `main':
/home/javier/Descargas/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:691: undefined reference to `NEWIMAGE::volume<short> fslsurface_name::fillMesh<float, unsigned int>(fslsurface_name::fslSurface<float, unsigned int> const&, NEWIMAGE::volume<short> const&, int const&)'
/usr/bin/ld: /home/javier/Descargas/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:326: undefined reference to `fslsurface_name::getFSLtoNIFTIxfm(NEWIMAGE::volume<float> const&)'
/usr/bin/ld: /home/javier/Descargas/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:351: undefined reference to `fslsurface_name::meshRegLeastSq(fslsurface_name::fslSurface<float, unsigned int> const&, fslsurface_name::fslSurface<float, unsigned int> const&, unsigned int const&)'
/usr/bin/ld: /home/javier/Descargas/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:643: undefined reference to `fslsurface_name::vertexMVglm(fslsurface_name::fslSurface<float, unsigned int>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
/usr/bin/ld: /home/javier/Descargas/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:634: undefined reference to `fslsurface_name::FtoP(std::vector<float, std::allocator<float> > const&, int const&, int const&)'
/usr/bin/ld: /home/javier/Descargas/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:621: undefined reference to `fslsurface_name::reconAllSurfacesAndSave(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/usr/bin/ld: /home/javier/Descargas/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:605: undefined reference to `fslsurface_name::reconSurface_from_bvars(fslsurface_name::fslSurface<float, unsigned int>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
collect2: error: ld returned 1 exit status
make: *** [Makefile:32: fslsurfacemaths] Error 1
ar -r libfslsurface_backcompat.a fslsurface_first.o fslsurface_dataconv.o
ar: creating libfslsurface_backcompat.a
make: Target 'all' not remade because of errors.

========================= 
ERROR::Could not make fslsurface successfully





!!ERROR in BUILD!!
Could not make the following projects successfully:
    fslsurface

tobac commented on 2021-09-10 00:41 (UTC)

Just released 6.0.5-5 which supports current GCC versions. Also, enabling CUDA is now possible by setting an environment variable, for example by running "CUDA=1 makepkg" or "CUDA=1 paru -S fsl" or whatever command you're using. This is arguably neater and more intuitive. Setting "CUDA" to 1 in the PKGBUILD is still possible. I'm sorry if you have to laboriously rebuild now, but being able to remove gcc9 from your system is hopefully justification and incentive enough.

tobac commented on 2021-09-07 18:40 (UTC)

All right. Set CUDA=1 in the PKGBUILD to enable CUDA support and remember to install cuda-9.1 first.

tobac commented on 2021-09-05 18:35 (UTC)

That's exactly what I'm planning on doing :)

keiichiiownsu12 commented on 2021-09-05 18:25 (UTC)

Re CUDA:

Looks like fsl only supports up to version 10.1. eddy_cuda only supports version 9.1. You could add 9.1 as an optional-dependency.

tobac commented on 2021-09-05 16:28 (UTC) (edited on 2021-09-05 16:31 (UTC) by tobac)

Just pushed FSL 6.0.5. I had to include another couple of weird workarounds, but was able to streamline the build process somewhat. Compiling is now done in parallel, where the number of parallel jobs defaults to the number of CPUs as determined by nproc(1). Feel free to change the NJOBS variable to an appropriate number in the PKGBUILD file. GPU-based compilation and CUDA support is disabled for now -- couldn't get it to work, which might have something to do with the CUDA version shipped with Arch. I'm trying a few things, but didn't want to hold back with the update until then. Ideally we'll have a "enable CUDA" switch in the future for those who want/need it without having to pull an enormous package even if you don't. Enjoy.

keiichiiownsu12 commented on 2021-06-28 23:32 (UTC)

Adding to the conversation on build issues: I recently tried to build the fsl package, with CUDA installed. Build failed for fdt and ptx2...again.

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Package Details: fsl 6.0.7.17-1

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tobac commented on 2021-09-10 17:04 (UTC) (edited on 2021-09-11 05:46 (UTC) by tobac)