Issue building Relion4.0 on workstation

[eariascib]

Good morning,

I am trying to compile Relion4.0 on a dual GPU workstation and I am getting an error message when it tries to compile tomo_ctf_find.cpp.o

I would be very grateful if you could give me some assistance to solve this issue.

The workstation has the following configuration:

Environment:

• OS: Linux Mint 18.1. Linux kernel 4.4.0-53-generic
• MPI runtime: mpich-3.1.4
• RELION version Relion4.0
• Memory: 128 GB
• GPU: 2x GTX 1080Ti
  • CUDA 8.0

I have installed Relion3.1 in this machine before, but I am getting an error with this version. I have specifically entered as superuser:

git clone https://github.com/3dem/relion.git

cd relion

git checkout ver4.0

mkdir build

cd build/

cmake -DCUDA_ARCH=61 -DFORCE_OWN_FFTW=ON -DFORCE_OWN_FLTK=ON ..

make -j 6

Error message:

[ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//jaz/tomography/local_particle_refinement.cpp.o [ 19%] Building CXX object src/apps/CMakeFiles/relion_lib.dir//jaz/tomography/tomo_ctf_find.cpp.o /usr/local/relion_4.0_beta/src/jaz/tomography/local_particle_refinement.cpp: In member function ‘double LocalParticleRefinement::f(const std::vector&, void*) const’: /usr/local/relion_4.0_beta/src/jaz/tomography/local_particle_refinement.cpp:138:17: error: ‘isnan’ was not declared in this scope if (isnan(x[i])) return std::numeric_limits::max(); ^ /usr/local/relion_4.0_beta/src/jaz/tomography/local_particle_refinement.cpp:138:17: note: suggested alternative: In file included from /usr/local/relion_4.0_beta/src/funcs.h:50:0, from /usr/local/relion_4.0_beta/src/metadata_table.h:43, from /usr/local/relion_4.0_beta/src/jaz/tomography/particle_set.h:4, from /usr/local/relion_4.0_beta/src/jaz/tomography/local_particle_refinement.h:5, from /usr/local/relion_4.0_beta/src/jaz/tomography/local_particle_refinement.cpp:1: /usr/include/c++/5/cmath:641:5: note: ‘std::isnan’ isnan(_Tp x) ^ /usr/local/relion_4.0_beta/src/jaz/tomography/local_particle_refinement.cpp: In member function ‘void LocalParticleRefinement::grad(const std::vector&, std::vector&, void*) const’: /usr/local/relion_4.0_beta/src/jaz/tomography/local_particle_refinement.cpp:225:17: error: ‘isnan’ was not declared in this scope if (isnan(x[i])) return; ^ /usr/local/relion_4.0_beta/src/jaz/tomography/local_particle_refinement.cpp:225:17: note: suggested alternative: In file included from /usr/local/relion_4.0_beta/src/funcs.h:50:0, from /usr/local/relion_4.0_beta/src/metadata_table.h:43, from /usr/local/relion_4.0_beta/src/jaz/tomography/particle_set.h:4, from /usr/local/relion_4.0_beta/src/jaz/tomography/local_particle_refinement.h:5, from /usr/local/relion_4.0_beta/src/jaz/tomography/local_particle_refinement.cpp:1: /usr/include/c++/5/cmath:641:5: note: ‘std::isnan’ isnan(_Tp x) ^ /usr/local/relion_4.0_beta/src/jaz/tomography/local_particle_refinement.cpp: In member function ‘virtual double LocalParticleRefinement::gradAndValue(const std::vector&, std::vector&) const’: /usr/local/relion_4.0_beta/src/jaz/tomography/local_particle_refinement.cpp:401:17: error: ‘isnan’ was not declared in this scope if (isnan(x[i])) return std::numeric_limits::max(); ^ /usr/local/relion_4.0_beta/src/jaz/tomography/local_particle_refinement.cpp:401:17: note: suggested alternative: In file included from /usr/local/relion_4.0_beta/src/funcs.h:50:0, from /usr/local/relion_4.0_beta/src/metadata_table.h:43, from /usr/local/relion_4.0_beta/src/jaz/tomography/particle_set.h:4, from /usr/local/relion_4.0_beta/src/jaz/tomography/local_particle_refinement.h:5, from /usr/local/relion_4.0_beta/src/jaz/tomography/local_particle_refinement.cpp:1: /usr/include/c++/5/cmath:641:5: note: ‘std::isnan’ isnan(_Tp x) ^ src/apps/CMakeFiles/relion_lib.dir/build.make:2198: recipe for target 'src/apps/CMakeFiles/relion_lib.dir//jaz/tomography/local_particle_refinement.cpp.o' failed make[2]: [src/apps/CMakeFiles/relion_lib.dir/__/jaz/tomography/local_particle_refinement.cpp.o] Error 1 make[2]: Waiting for unfinished jobs.... CMakeFiles/Makefile2:4611: recipe for target 'src/apps/CMakeFiles/relion_lib.dir/all' failed make[1]: [src/apps/CMakeFiles/relion_lib.dir/all] Error 2 Makefile:127: recipe for target 'all' failed make: [all] Error 2

Thank you very much for your help. Kind regards, Ernesto.

[biochem-fan]

What if you replace all occurances of isnan with std::isnan in src/jaz/tomography/local_particle_refinement.cpp?

[lissumo]

(I think) you have to install a more recent version of gcc g++ (at least gcc-6)

[eariascib]

Thanks for the reply. I've installed gcc 7, 8 and 9 but I obtained a compilation error because the cuda version that we currently have (8.0) is not compatible with gcc versions higher than 5. I'll install a new version of the NVIDIA driver and CUDA and try again.

[biochem-fan]

@eariascib Did you try what I suggested last month?

[eariascib]

Yes, sorry. I think I replied to your email but I didn't post my response here. I did replace all occurrences of isnan with std::isnan in src/jaz/tomography/local_particle_refinement.cpp and the compilation went fine.