<?xml version="1.0" encoding="UTF-8"?><rss xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:content="http://purl.org/rss/1.0/modules/content/" xmlns:atom="http://www.w3.org/2005/Atom" version="2.0"><channel><title><![CDATA[SegAlign  使用GPU来加速比对]]></title><description><![CDATA[<p dir="auto"><a href="https://github.com/gsneha26/SegAlign" rel="nofollow ugc">https://github.com/gsneha26/SegAlign</a><br />
SegAlign:A Scalable GPU-Based Whole Genome Aligner<br />
1.编译<br />
git clone <a href="https://github.com/gsneha26/SegAlign.git" rel="nofollow ugc">https://github.com/gsneha26/SegAlign.git</a><br />
export PROJECT_DIR=$PWD/SegAlign<br />
cd $PROJECT_DIR<br />
//由于大服务器已经安装了cuda 可以使用-c 来避免再次安装cuda<br />
./scripts/installUbuntu.sh -c</p>
<p dir="auto">一个错误：<br />
CMake Error at CMakeLists.txt:3 (project):<br />
No CMAKE_CUDA_COMPILER could be found.<br />
Tell CMake where to find the compiler by setting either the environment<br />
variable "CUDACXX" or the CMake cache entry CMAKE_CUDA_COMPILER to the full<br />
path to the compiler, or to the compiler name if it is in the PATH.<br />
添加 cuda的相关变量：<br />
export CUDA_HOME=/usr/local/cuda<br />
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib64:/usr/local/cuda/extras/CUPTI/lib64<br />
export PATH=$PATH:$CUDA_HOME/bin</p>
<p dir="auto">//系统在安装软件的时候老是报munge错误 是etc权限导致的<br />
sudo chmod -R u=rwx,g=rx,o=rx /etc<br />
● munge.service - MUNGE authentication service<br />
Loaded: loaded (/lib/systemd/system/munge.service; enabled; vendor preset: enabled)<br />
Active: failed (Result: exit-code) since Sun 2021-07-25 17:23:17 CST; 15ms ago<br />
Docs: man:munged(8)<br />
Process: 36517 ExecStart=/usr/sbin/munged (code=exited, status=1/FAILURE)</p>
<p dir="auto">Jul 25 17:23:17 anneng01 systemd[1]: Starting MUNGE authentication service...<br />
Jul 25 17:23:17 anneng01 munged[36517]: munged: Error: Keyfile is insecure: group-writable permissions without sticky bit set on "/etc"<br />
Jul 25 17:23:17 anneng01 systemd[1]: munge.service: Control process exited, code=exited status=1<br />
Jul 25 17:23:17 anneng01 systemd[1]: munge.service: Failed with result 'exit-code'.<br />
Jul 25 17:23:17 anneng01 systemd[1]: Failed to start MUNGE authentication service.</p>
<p dir="auto">//执行faToTwoBit时老是报段错误<br />
gdb /usr/local/bin/faToTwoBit 后发现文件可能有问题<br />
"/usr/local/bin/faToTwoBit": not in executable format: File truncated<br />
(gdb) q<br />
重新安装后正常</p>
]]></description><link>http://an.forum.genostack.com/topic/360/segalign-使用gpu来加速比对</link><generator>RSS for Node</generator><lastBuildDate>Sat, 13 Jun 2026 09:36:51 GMT</lastBuildDate><atom:link href="http://an.forum.genostack.com/topic/360.rss" rel="self" type="application/rss+xml"/><pubDate>Sat, 24 Jul 2021 09:40:17 GMT</pubDate><ttl>60</ttl><item><title><![CDATA[Reply to SegAlign  使用GPU来加速比对 on Thu, 29 Jul 2021 05:47:35 GMT]]></title><description><![CDATA[<p dir="auto">实现机制：<br />
1.算法<br />
Smith-Waterman (SW) algorithm 算法是经典的局部比对算法，复杂度O(L r *L q )和序列的长度相关， Lr、Lq是要比对的两条序列。对于全基因组比对就无法满足性能要求，whole genome alignment algorithm (LASTZ)　基于BLAST的启发式seed-filter-extend算法，专门针对全基因组的比对进行的改进。<br />
LASTZ的算法分为下面三个阶段：<br />
<img src="/assets/uploads/files/1627452165854-88112bce-b3b2-4d3c-8188-e5299aa41f1d-image.png" alt="88112bce-b3b2-4d3c-8188-e5299aa41f1d-image.png" class=" img-responsive img-markdown" /><br />
(1)Seeding<br />
使用尽可能完全匹配的片段(K-Mer)作为种子,　并把所有的种子保存为一张查询表。这些种子通常也就10几个碱基，因此假阳性很高，需要在下一步进行过滤。<br />
(2)Filter<br />
过滤步骤性能消耗占整个过程的98%以上。该算法对种子在两个方向进行延长，并计算比对的评分，评分低于某个阈值H x时终止延长。通过这些阈值的就是高分序列对high-scoring segment pair (HSP)，传递到下一步继续进行分析。HSP 大约100个碱基左右。<br />
(3)采用动态规划(Dynamic programming)算法将HSP延长到1000个碱基左右。<br />
2.GPU　单节点加速<br />
Streaming Multiproces-sors (SMs)</p>
<p dir="auto">3.Spark　多节点加速</p>
]]></description><link>http://an.forum.genostack.com/post/710</link><guid isPermaLink="true">http://an.forum.genostack.com/post/710</guid><dc:creator><![CDATA[anneng]]></dc:creator><pubDate>Thu, 29 Jul 2021 05:47:35 GMT</pubDate></item><item><title><![CDATA[Reply to SegAlign  使用GPU来加速比对 on Sun, 25 Jul 2021 11:14:18 GMT]]></title><description><![CDATA[<p dir="auto">用自带的文件做了一个对比:<br />
//GPU的时间是 6min多<br />
run_segalign ce11.fa cb4.fa --output=ce11.cb4.maf<br />
//CPU的时间是 超过1个小时<br />
time lastz ce11.fa[multiple]  cb4.fa[multiple] --format=maf &gt; cell.cb4.lastz.maf</p>
]]></description><link>http://an.forum.genostack.com/post/696</link><guid isPermaLink="true">http://an.forum.genostack.com/post/696</guid><dc:creator><![CDATA[anneng]]></dc:creator><pubDate>Sun, 25 Jul 2021 11:14:18 GMT</pubDate></item></channel></rss>