Tabitha,
> /usr/include/bits/mathcalls.h:350: error: inline function âint
> __signbitl(long double)â cannot be declared weak
>
> cuda/3.0
> mpich2/1.2.1-ch3nemesis-gcc44
> openmpi/1.4.1-gcc44-rhel5
>
> gcc/4.4.2-rhel5
This is not an AMBER problem per se. Did you try compiling the CUDA_SDK?
Gcc4.4 is NOT currently supported by the nvcc compilers.. I believe the
current solution is to compile yourself up a copy of gcc 4.3 and use that.
If I recall correctly RedHat 5 is NOT gcc4.4 based so you must have somehow
upgraded things to 4.4 from 4.1 anyway.
Here are some instructions from OpenSuse that you should be able to adapt to
get gcc 4.3 installed. Alternatively just modify all your paths so you are
using the stock gcc 4.1 that comes with Redhat 5.
1) install gcc 4.3
$> sudo zypper install gcc43 gcc43-c++ gcc43-fortran
2) Make new links for gcc version 4.3
$> mkdir /opt/gcc-43
$> ln -s /usr/bin/gcc-4.3 /opt/gcc-43/gcc
$> ln -s /usr/bin/g++-4.3 /opt/gcc-43/g++
$> ln -s /usr/bin/gfortran-4.3 /opt/gcc-43/gfortran
3) Use gcc 4.3 with nvcc
Invoke nvcc with "--compiler-bindir /opt/gcc-4.3"
For PMEMD:
$> cd $AMBERHOME/AmberTools/src
$> ./configure -cuda gnu
Edit config.h: append "--compiler-bindir /opt/gcc-4.3" to the NVCC build
flags
$> cp config.h $AMBERHOME/src/
$> cd $AMBERHOME/src
$> make cuda
All the best
Ross
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Received on Wed May 12 2010 - 12:30:09 PDT
