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-   -   Issue with CUDA-BlastP (http://www.molecularstation.com/forum/bioinformatics/74709-issue-cuda-blastp.html)

abhicdac 12-21-2010 07:07 AM

Issue with CUDA-BlastP
 
I found the error while i am running the command in installation of CUDABLASTP
:

make all 2>&1 | tee LOG-MAKEALL-CUDABLASTP
Makefile:101: warning: overriding commands for target `clean'
../../common/common.mk:469: warning: ignoring old commands for target `clean'
gcc -I include -O3 -c -o obj/CUDA-BLASTP.o src/CUDA-BLASTP.c
src/CUDA-BLASTP.c:155: warning: conflicting types for ‚blastp‚
src/CUDA-BLASTP.c:127: warning: previous implicit declaration of ‚blastp‚ was here
gcc -I include -O3 -c -o obj/sequential_alignments.o src/sequential_alignments.c
gcc -I include -O3 -c -o obj/descriptions.o src/descriptions.c
gcc -I include -O3 -c -o obj/encoding.o src/encoding.c
gcc -I include -O3 -c -o obj/fasterGappedExtension.o src/fasterGappedExtension.c
gcc -I include -O3 -c -o obj/gappedExtension.o src/gappedExtension.c
gcc -I include -O3 -c -o obj/gappedScoring.o src/gappedScoring.c
gcc -I include -O3 -c -o obj/global.o src/global.c
gcc -I include -O3 -c -o obj/CUDA-hitMatrix.o src/CUDA-hitMatrix.c
gcc -I include -O3 -c -o obj/karlin.o src/karlin.c
gcc -I include -O3 -c -o obj/memBlocks.o src/memBlocks.c
gcc -I include -O3 -c -o obj/memSingleBlock.o src/memSingleBlock.c
gcc -I include -O3 -c -o obj/oldGappedScoring.o src/oldGappedScoring.c
gcc -I include -O3 -c -o obj/oldSemiGappedScoring.o src/oldSemiGappedScoring.c
gcc -I include -O3 -c -o obj/parameters.o src/parameters.c
src/parameters.c: In function ‚parameters_processArguments‚:
src/parameters.c:180: warning: excess elements in array initializer
src/parameters.c:180: warning: (near initialization for ‚parameters_arguments‚)
gcc -I include -O3 -c -o obj/print.o src/print.c
gcc -I include -O3 -c -o obj/PSSMatrix.o src/PSSMatrix.c
gcc -I include -O3 -c -o obj/qPosList.o src/qPosList.c
gcc -I include -O3 -c -o obj/readFasta.o src/readFasta.c
gcc -I include -O3 -c -o obj/readFile.o src/readFile.c
gcc -I include -O3 -c -o obj/scoreMatrix.o src/scoreMatrix.c
gcc -I include -O3 -c -o obj/semiGappedScoring.o src/semiGappedScoring.c
gcc -I include -O3 -c -o obj/statistics.o src/statistics.c
gcc -I include -O3 -c -o obj/CUDA-ungappedExtension.o src/CUDA-ungappedExtension.c
gcc -I include -O3 -c -o obj/CUDA-DFA.o src/CUDA-DFA.c
gcc -I include -O3 -c -o obj/smithWatermanTraceback.o src/smithWatermanTraceback.c
gcc -I include -O3 -c -o obj/smithWatermanScoring.o src/smithWatermanScoring.c
gcc -I include -O3 -c -o obj/unpack.o src/unpack.c
gcc -I include -O3 -c -o obj/index.o src/index.c
gcc -I include -O3 -c -o obj/postings.o src/postings.c
gcc -I include -O3 -c -o obj/writedb.o src/writedb.c
gcc -I include -O3 -c -o obj/readdb.o src/readdb.c
gcc -I include -O3 -c -o obj/CUDA-search.o src/CUDA-search.c
src/CUDA-search.c:685:2: warning: no newline at end of file
gcc -I include -O3 -c -o obj/wildcards.o src/wildcards.c
gcc -I include -O3 -c -o obj/seg.o src/seg.c
In file included from src/seg.c:10:
src/genwin.c: In function ‚opendbase‚:
src/genwin.c:90: warning: incompatible implicit declaration of built-in function ‚malloc‚
src/genwin.c:94: warning: incompatible implicit declaration of built-in function ‚strlen‚
src/genwin.c:96: warning: incompatible implicit declaration of built-in function ‚strcpy‚
src/genwin.c:97: warning: incompatible implicit declaration of built-in function ‚strcat‚
src/genwin.c:103: warning: incompatible implicit declaration of built-in function ‚strlen‚
src/genwin.c:105: warning: incompatible implicit declaration of built-in function ‚strcpy‚
src/genwin.c: In function ‚firstseq‚:
src/genwin.c:167: warning: incompatible implicit declaration of built-in function ‚exit‚
src/genwin.c: In function ‚openwin‚:
src/genwin.c:215: warning: incompatible implicit declaration of built-in function ‚malloc‚
src/genwin.c: In function ‚compon‚:
src/genwin.c:342: warning: incompatible implicit declaration of built-in function ‚calloc‚
src/genwin.c: In function ‚stateon‚:
src/genwin.c:372: warning: incompatible implicit declaration of built-in function ‚malloc‚
src/genwin.c: In function ‚entropy_init‚:
src/genwin.c:413: warning: incompatible implicit declaration of built-in function ‚malloc‚
src/genwin.c: In function ‚readentry‚:
src/genwin.c:493: warning: incompatible implicit declaration of built-in function ‚malloc‚
src/genwin.c: In function ‚readhdr‚:
src/genwin.c:568: warning: incompatible implicit declaration of built-in function ‚exit‚
src/genwin.c:571: warning: incompatible implicit declaration of built-in function ‚malloc‚
src/genwin.c:619: warning: incompatible implicit declaration of built-in function ‚exit‚
src/genwin.c:622: warning: incompatible implicit declaration of built-in function ‚memcpy‚
src/genwin.c: In function ‚readseq‚:
src/genwin.c:730: warning: incompatible implicit declaration of built-in function ‚malloc‚
src/genwin.c:788: warning: incompatible implicit declaration of built-in function ‚strlen‚
src/genwin.c: In function ‚tmalloc‚:
src/genwin.c:847: warning: incompatible implicit declaration of built-in function ‚malloc‚
src/genwin.c:851: warning: incompatible implicit declaration of built-in function ‚exit‚
src/genwin.c:854: warning: cast from pointer to integer of different size
src/genwin.c: In function ‚tfree‚:
src/genwin.c:869: warning: cast from pointer to integer of different size
src/seg.c: In function ‚seg_segSequence‚:
src/seg.c:52: warning: incompatible implicit declaration of built-in function ‚malloc‚
src/seg.c:54: warning: incompatible implicit declaration of built-in function ‚strlen‚
src/seg.c: In function ‚getparams‚:
src/seg.c:105: warning: incompatible implicit declaration of built-in function ‚exit‚
src/seg.c: In function ‚segseq‚:
src/seg.c:196: warning: incompatible implicit declaration of built-in function ‚malloc‚
src/seg.c: In function ‚seqent‚:
src/seg.c:228: warning: incompatible implicit declaration of built-in function ‚malloc‚
src/seg.c: In function ‚singreport‚:
src/seg.c:573: warning: incompatible implicit declaration of built-in function ‚memset‚
src/seg.c: In function ‚prettyreport‚:
src/seg.c:642: warning: incompatible implicit declaration of built-in function ‚exit‚
src/seg.c: In function ‚seqout‚:
src/seg.c:802: warning: incompatible implicit declaration of built-in function ‚strlen‚
src/seg.c:830: warning: incompatible implicit declaration of built-in function ‚exit‚
src/seg.c: In function ‚usage‚:
src/seg.c:900: warning: incompatible implicit declaration of built-in function ‚exit‚
In file included from CUDA_Blast.cu:13:
./CUDA_Blast_kernel.cu:559:40: warning: no newline at end of file
CUDA_Blast.cu:606:2: warning: no newline at end of file
In file included from CUDA_Blast.cu:13:
./CUDA_Blast_kernel.cu:559:40: warning: no newline at end of file
CUDA_Blast.cu:606:2: warning: no newline at end of file
In file included from CUDA_Blast.cu:13:
./CUDA_Blast_kernel.cu:559:40: warning: no newline at end of file
CUDA_Blast.cu:606:2: warning: no newline at end of file
In file included from CUDA_Blast.cu:13:
./CUDA_Blast_kernel.cu:559:40: warning: no newline at end of file
CUDA_Blast.cu:606:2: warning: no newline at end of file
CUDA_Blast.cu: In function ‚void CUDA_blast(TGPUplan*)‚:
CUDA_Blast.cu:97: warning: passing ‚double‚ for argument 4 to ‚cudaError_t cudaMallocArray(cudaArray**, const cudaChannelFormatDesc*, size_t, size_t, unsigned int)‚
CUDA_Blast.cu:98: warning: converting to ‚unsigned int‚ from ‚double‚
CUDA_Blast.cu:109: warning: passing ‚double‚ for argument 4 to ‚cudaError_t cudaMallocArray(cudaArray**, const cudaChannelFormatDesc*, size_t, size_t, unsigned int)‚
CUDA_Blast.cu:110: warning: converting to ‚unsigned int‚ from ‚double‚
CUDA_Blast.cu:120: warning: passing ‚double‚ for argument 3 to ‚cudaError_t cudaMemcpyToSymbol(const T&, const void*, size_t, size_t, cudaMemcpyKind) [with T = int [400]]‚
gcc -I include -O3 -lm -o CUDA-BLASTP obj/CUDA-BLASTP.o obj/sequential_alignments.o obj/descriptions.o obj/encoding.o obj/fasterGappedExtension.o obj/gappedExtension.o obj/gappedScoring.o obj/global.o obj/CUDA-hitMatrix.o obj/karlin.o obj/memBlocks.o obj/memSingleBlock.o obj/oldGappedScoring.o obj/oldSemiGappedScoring.o obj/parameters.o obj/print.o obj/PSSMatrix.o obj/qPosList.o obj/readFasta.o obj/readFile.o obj/scoreMatrix.o obj/semiGappedScoring.o obj/statistics.o obj/CUDA-ungappedExtension.o obj/CUDA-DFA.o obj/smithWatermanTraceback.o obj/smithWatermanScoring.o obj/unpack.o obj/index.o obj/postings.o obj/writedb.o obj/readdb.o obj/CUDA-search.o obj/wildcards.o obj/seg.o obj/x86_64/release/CUDA_Blast.cu.o -L/usr/local/cuda/lib64 -L../../lib -L../../common/lib/linux -L../../../shared//lib -lcudart -L/usr/local/cuda/lib64 -L../../lib -L../../common/lib/linux -L../../../shared//lib -lcudart -lcutil_x86_64 -lshrutil_x86_64
/usr/bin/ld: cannot find -lcutil_x86_64
collect2: ld returned 1 exit status
make: *** [CUDA-BLASTP] Error 1

mfursov 12-22-2010 08:58 AM

Re: Issue with CUDA-BlastP
 
GCC linker is failed to find cutil_x86_64 library. This library must be provided by NVidia SDK.
Check if this library exists on your PC and add the folder with the library to the linker path using -L option:
-L <path_to_the_folder_with_library>

If you have no NVidia SDK installed, install it first.


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