[MUMmerGPU-devel] Problems compiling mummergpu 2.0

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Hi everyone,

I'm trying to compile mummergpu2 but i'm having problems with it. My system:

Fedora 10 x86_64
GeForce 8800 GTS
gcc version 4.3.2
Cuda compilation tools, release 2.3, V0.2.1221


This is what I'm obtaining:

rm -f ../obj/release/mummergpu_gold.cpp_o ../obj/release/suffix-tree.cpp_o
../obj/release/PoolMalloc.cpp_o ../obj/release/mummergpu.cu_o
rm -f ../lib/libmummergpu.a
rm -f ../obj/release/mummergpu_main.cpp_o
rm -f ../bin/release/mummergpu
g++  -W -Wall -Wimplicit -Wswitch -Wformat -Wchar-subscripts -Wparentheses
-Wmultichar -Wtrigraphs -Wpointer-arith -Wcast-align -Wreturn-type
-Wno-unused-function   -I. -I/usr/local/cuda/include  -DUNIX -O3 -o
../obj/release/mummergpu_gold.cpp_o -c mummergpu_gold.cpp
g++  -W -Wall -Wimplicit -Wswitch -Wformat -Wchar-subscripts -Wparentheses
-Wmultichar -Wtrigraphs -Wpointer-arith -Wcast-align -Wreturn-type
-Wno-unused-function   -I. -I/usr/local/cuda/include  -DUNIX -O3 -o
../obj/release/suffix-tree.cpp_o -c suffix-tree.cpp
suffix-tree.cpp: In function ‘const char* substr(const char*, int, int)’:
suffix-tree.cpp:50: error: ‘strncpy’ was not declared in this scope
suffix-tree.cpp: In constructor ‘EventTime_t::EventTime_t()’:
suffix-tree.cpp:84: error: ‘memset’ was not declared in this scope
suffix-tree.cpp: In constructor ‘SuffixTree::SuffixTree(const char*)’:
suffix-tree.cpp:333: error: ‘strlen’ was not declared in this scope
suffix-tree.cpp: In function ‘void getReferenceString(const char*, char**,
size_t*)’:
suffix-tree.cpp:1670: error: ‘strdup’ was not declared in this scope
suffix-tree.cpp:1671: error: ‘strlen’ was not declared in this scope
suffix-tree.cpp: In function ‘void getQueriesTexture(int, char**, size_t*,
int**, char***, int**, unsigned int*, unsigned int*, unsigned int, int,
bool)’:
suffix-tree.cpp:1787: error: ‘strdup’ was not declared in this scope
suffix-tree.cpp:1890: error: ‘strdup’ was not declared in this scope
suffix-tree.cpp: In function ‘int addToBuffer(char*)’:
suffix-tree.cpp:2108: error: ‘strlen’ was not declared in this scope
suffix-tree.cpp:2113: error: ‘strncpy’ was not declared in this scope
suffix-tree.cpp:2122: error: ‘strncpy’ was not declared in this scope
suffix-tree.cpp: In function ‘void printAlignmentsOld(ReferencePage*,
char*, int, int, int, int, int, bool, bool)’:
suffix-tree.cpp:2398: error: ‘strlen’ was not declared in this scope
suffix-tree.cpp: In function ‘void printAlignments(ReferencePage*,
Alignment*, char*, int, TextureAddress, int, int, int, bool, bool)’:
suffix-tree.cpp:2435: error: ‘strlen’ was not declared in this scope
make: *** [../obj/release/suffix-tree.cpp_o] Error 1

So, I don't program in c++ but I checked the code and according to the
error the problem begins here:

char substrbuffer[1024];
const char * substr(const char * str, int start, int len)

str, start and len are not getting values for some reason. Hence, the
other variables that take their values using the previous ones, are also
empy.

Other things is that there's a new CUDA 3.0 which I also tried and give me
the same problem.

Any ideas?



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