nvcc Compiler error: __shared__ variables cannot have external linkage

	extern __shared__ int col_ssd[1000]; //wrong

Work around

Do not specify __shared__ array sizes in source code. Has to be done at run time, eg via third argument on kernel launch <<<grid, block, bytes of shared memory per block>>>.

Source code 

	extern __shared__ int col_ssd[];
Notice empty [].

Two dimensional array shared memory

extern __shared__ __align__(4) char shared_start[];
For sm_13 etc., use __align__(4) to ensure that later on the nvcc 6.0 compiler knows that shared_start is aligned on a 4 byte boundary. 
typedef unsigned int temptype_u4[4];
typedef char         temptype_char5[5];
temptype_u4*    ks          = (temptype_u4*)    &shared_start[shared_one];
temptype_u4*    ls          = (temptype_u4*)    &ks[MAX_SEQUENCE_LENGTH];
temptype_char5* eligible_cs = (temptype_char5*) &ls[MAX_SEQUENCE_LENGTH];
shared_one is a macro allowing space for other variables in __shared__ memory. In this example, since shared_start elements are a byte wide, shared_one must be a multiple of four. MAX_SEQUENCE_LENGTH is a macro (which need not be a multiple of four).

Example of using two dimensional array in shared memory: 

eligible_cs[current_stage][no_of_eligible_cs++] = 1;

W.B.Langdon Back 12 June 2014 (last update 16 Jun 2014)