Can't Compile NVBIO

[Stanley Fujimoto]

I am trying to compile NVBIO using nvcc 6.5 and gcc 4.4.7 but I receive this error:

 

[ 40%] Building CXX object nvbio/CMakeFiles/nvbio.dir/basic/atomics.cpp.o
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp: In function ‘void nvbio::host_release_fence()’:
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:53: error: ‘__ATOMIC_RELEASE’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:53: error: ‘__atomic_thread_fence’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp: In function ‘void nvbio::host_acquire_fence()’:
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:61: error: ‘__ATOMIC_ACQUIRE’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:61: error: ‘__atomic_thread_fence’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp: In function ‘nvbio::int32 nvbio::host_atomic_add(nvbio::int32*, nvbio::int32)’:
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:68: error: ‘__ATOMIC_RELAXED’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:68: error: ‘__atomic_fetch_add’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp: In function ‘nvbio::uint32 nvbio::host_atomic_add(nvbio::uint32*, nvbio::uint32)’:
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:81: error: ‘__ATOMIC_RELAXED’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:81: error: ‘__atomic_fetch_add’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp: In function ‘nvbio::int64 nvbio::host_atomic_add(nvbio::int64*, nvbio::int64)’:
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:94: error: ‘__ATOMIC_RELAXED’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:94: error: ‘__atomic_fetch_add’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp: In function ‘nvbio::uint64 nvbio::host_atomic_add(nvbio::uint64*, nvbio::uint64)’:
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:107: error: ‘__ATOMIC_RELAXED’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:107: error: ‘__atomic_fetch_add’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp: In function ‘nvbio::int32 nvbio::host_atomic_sub(nvbio::int32*, nvbio::int32)’:
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:120: error: ‘__ATOMIC_RELAXED’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:120: error: ‘__atomic_fetch_sub’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp: In function ‘nvbio::uint32 nvbio::host_atomic_sub(nvbio::uint32*, nvbio::uint32)’:
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:133: error: ‘__ATOMIC_RELAXED’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:133: error: ‘__atomic_fetch_sub’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp: In function ‘nvbio::int64 nvbio::host_atomic_sub(nvbio::int64*, nvbio::int64)’:
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:147: error: ‘__ATOMIC_RELAXED’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:147: error: ‘__atomic_fetch_sub’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp: In function ‘nvbio::uint64 nvbio::host_atomic_sub(nvbio::uint64*, nvbio::uint64)’:
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:160: error: ‘__ATOMIC_RELAXED’ was not declared in this scope
/home/masaki/nvidia/nvbio/nvbio/basic/atomics.cpp:160: error: ‘__atomic_fetch_sub’ was not declared in this scope
make[2]: *** [nvbio/CMakeFiles/nvbio.dir/basic/atomics.cpp.o] Error 1
make[1]: *** [nvbio/CMakeFiles/nvbio.dir/all] Error 2
make: *** [all] Error 2

My suspicion is that it is because I'm using an older version of gcc. I am, however, running this on a machine that I do not have root permissions. Can anyone confirm my suspicions or provide me with some insight into what I might do?

Thanks! 

[Nuno Subtil]

We’ve seen similar errors before, they are indeed caused by using a version of gcc that is too old.

You’ll need a newer version of gcc to compile nvbio — we’ve been using 4.9 internally, although I believe 4.6 and above should work.

Nuno

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[Stanley Fujimoto]

Thanks so much for the quick response! I really appreciate it.

[Richard Casey]

We're using gcc v.4.9.2 but get exactly the same error messages in the same file.  Not sure what to do next.

[M. Stanley Fujimoto]

I found success using gcc 4.7.2 with cuda 6.5.14.

--

Stanley Fujimoto

Computational Science Laboratory

Brigham Young University

sfuj...@gmail.com

208.391.3208

[W Langdon]

May be check paths etc.
Errors relate to feature added to gcc in (about) gcc 4.7, which suggests you
are picking up include files from an older version of gcc. As already posted,
we also (eventually) got nvBIO to compile with gcc 4.7.2
Bill

[Stanley Fujimoto]

you might also make sure that you're environment variables are correct. i needed to have CC and CXX set. i have the following lines in my .bashrc:

export CC=/apps/gcc/4.7.2/bin/gcc

export CXX=/apps/gcc/4.7.2/bin/g++

[Richard Casey]

We had luck compiling on Ubuntu v.14.04 with gcc v.4.8 and cuda v.6.5 and set CC/CXX env vars.  Running well now.