blast_gpu

zhanglu

依赖软件: cuda7.4 gcc4.8.2 g++4.8.2, make, perl

1. 编译blast

wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+-src.tar.gz
tar -xvzf ncbi-blast-2.2.28+-src.tar.gz
cd ncbi-blast-2.2.28+-src/c++
./configure --without-debug --with-mt --without-boost  --with-optimization
make

注意：--without-debug 非debug模式 --with-mt 多线程

2. 编译gpu_blast

wget http://thales.cheme.cmu.edu/gpublast/gpu-blast-1.1_ncbi-blast-2.2.28.tar.gz
tar -xzf gpu-blast-1.1_ncbi-blast-2.2.28.tar.gz
ls
gpu_blast  install  ncbi-blast-2.2.28+-src  README
sudo sh ./install
Do you want to install GPU-BLAST on an existing installation of "blastp" [yes/no]
yes: you will be asked for the installation directory of the "blastp" executable
no: will download and install "ncbi-blast-2.2.28+-src"
yes
Please input the installation directory of "blastp" of "ncbi-blast-2.2.28+-src"
/home/ploskas/blast/ncbi-blast-2.2.28+-src/c++/GCC482-Debug64/bin/

3. 构建数据库

/cephfs_data/app/blast_gpu/ncbi-blast-2.2.28+-src/c++/GCC480-Debug64/bin/makeblastdb -in mitofish_v3.88.fa -dbtype nucl -out test
/cephfs_data/app/blast_gpu/ncbi-blast-2.2.28+-src/c++/GCC480-Debug64/bin/blastn -query t1.fa -db test -out my_results.out -outfmt 6 -num_threads 4

4. 运行测试

time /cephfs_data/app/blast_gpu/ncbi-blast-2.2.28+-src/c++/GCC480-ReleaseMT64/bin/blastp -query /cephfs_data/app/blast_gpu/database/test.fa -db /cephfs_data/app/blast_gpu/database/nr -gpu t -num_threads 30

zhanglu

测试记录

gpu

time /cephfs_data/app/blast_gpu/ncbi-blast-2.2.28+-src/c++/GCC480-ReleaseMT64/bin/blastp -query /cephfs_data/app/blast_gpu/database/test.fa -db /cephfs_data/app/blast_gpu/database/nr -gpu t -num_threads 30

real	24m43.524s
user	65m41.063s
sys	0m17.254s

cpu

time /cephfs_data/app/blast_gpu/ncbi-blast-2.2.28+-src/c++/GCC480-ReleaseMT64/bin/blastp -query /cephfs_data/app/blast_gpu/database/test.fa -db /cephfs_data/app/blast_gpu/database/nr -gpu f -num_threads 30

real	181m37.406s
user	5399m40.966s
sys	6m51.770s

zhanglu

@zhanglu 编译GPU_BLAST时，

/cephfs_data/app/blast_gpu/ncbi-blast-2.2.28+-src/c++/GCC480-ReleaseMT64/build/Makefile.mk
修改
CONF_LIBS = -lm -lgpublast -lcudart
添加 -pthread
CONF_LIBS = -lm -lgpublast -lcudart -pthread

zhanglu

测试

gpu

time /cephfs_data/app/blast_gpu/ncbi-blast-2.2.28+-src/c++/GCC480-ReleaseMT64/bin/blastp -query /cephfs_data/app/blast_gpu/database/test2.fa -db /cephfs_data/app/blast_gpu/database/nr -gpu t -num_threads 30

real	13m42.160s
user	38m52.082s
sys	0m13.170s

cpu

time /cephfs_data/app/blast_gpu/ncbi-blast-2.2.28+-src/c++/GCC480-ReleaseMT64/bin/blastp -query /cephfs_data/app/blast_gpu/database/test2.fa -db /cephfs_data/app/blast_gpu/database/nr -gpu f -num_threads 30

real 23m23.076s
user 695m50.953s
sys 1m35.377s