<?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[cromwell + tesk 重启及gpu支持]]></title><description><![CDATA[<h2>1. cromwell-51代码修改：</h2>
<pre><code>GpuTypeValidation.scala
GpuValidation.scala
TesResponseJsonFormatter.scala
TesRuntimeAttributes.scala
TesTask.scala
</code></pre>
<h2>2. tesk-api修改：</h2>
<pre><code>TesKubernetesConverter.java
TesResources.java
</code></pre>
<h3>2.1 添加gpu支持参数</h3>
<h3>2.2 taskmaster挂在映射</h3>
<h2>3. tesk-core修改:</h2>
<h3>3.1 taskmaster将输入path 和url 做软连接；</h3>
<h3>3.2 修改taskmaster核心逻辑，支持本地路径；</h3>
]]></description><link>http://an.forum.genostack.com/topic/941/cromwell-tesk-重启及gpu支持</link><generator>RSS for Node</generator><lastBuildDate>Sat, 13 Jun 2026 09:37:56 GMT</lastBuildDate><atom:link href="http://an.forum.genostack.com/topic/941.rss" rel="self" type="application/rss+xml"/><pubDate>Tue, 04 Jul 2023 07:05:32 GMT</pubDate><ttl>60</ttl><item><title><![CDATA[Reply to cromwell + tesk 重启及gpu支持 on Fri, 07 Jul 2023 04:10:28 GMT]]></title><description><![CDATA[<h2>cromwell 重启wdl编写和测试规范：</h2>
<h3>1. wdl数据类型：</h3>
<ul>
<li>
<p dir="auto">列表文件类型：<br />
File file = “/tmp/a.txt”</p>
</li>
<li>
<p dir="auto">列表字符串类型：<br />
String str  = “abc”</p>
</li>
</ul>
<p dir="auto">注意点：路径参数：使用String<br />
当task输出是一个路径时：</p>
<pre><code>output {
        File metadata_result = "metadata.tsv"
        File data_dir = "data"
        File fqc_dir = "data1"
        String fqc_dir_str = "${fqc_dir}"
    }
</code></pre>
<p dir="auto">先使用File data_dir = "data",  才能接收到 "data"的完整路径， 但是在后续使用当中需要将File类型的路径转化成 String,   String fqc_dir_str = "${fqc_dir}",</p>
<p dir="auto">因为： 在File类型里，callcaching  hash不支持File类型的path,<br />
如果在输出里用File接收，在输入里用String,使用，则会导致输入的hash值判定为新值，该步骤就无法参与重启</p>
<p dir="auto">后续编写WDL测试规范：</p>
<ol>
<li>功能测试：</li>
<li>重启测试</li>
</ol>
]]></description><link>http://an.forum.genostack.com/post/2274</link><guid isPermaLink="true">http://an.forum.genostack.com/post/2274</guid><dc:creator><![CDATA[zhanglu]]></dc:creator><pubDate>Fri, 07 Jul 2023 04:10:28 GMT</pubDate></item><item><title><![CDATA[Reply to cromwell + tesk 重启及gpu支持 on Tue, 04 Jul 2023 08:13:52 GMT]]></title><description><![CDATA[<p dir="auto">cromwell+tesk支持重启：<br />
cromwell 配置文件</p>
<pre><code>
call-caching {

  enabled = true

}

backend {
  default = TESK

  providers {
    TESK {
      actor-factory = "cromwell.backend.impl.tes.TesBackendLifecycleActorFactory"
      config {
        root = "/cephfs_data/genostack_v3/genostack_cromwell/tmp/cromwell-executions"
#         root = "ftp://192.168.0.135/pub/cromwell-executions"
        dockerRoot = "/cromwell-executions"
        endpoint = "http://192.168.0.135:8080/ga4gh/tes/v1/tasks"
       # endpoint = "http://192.168.0.135:31903/v1/tasks"
        glob-link-command = "ls -L GLOB_PATTERN 2&gt; /dev/null | xargs -I ? ln -s ? GLOB_DIRECTORY"
      }
    }
  }
}



docker {
  hash-lookup {
    # Set this to match your available quota against the Google Container Engine API
    #gcr-api-queries-per-100-seconds = 1000

    # Time in minutes before an entry expires from the docker hashes cache and needs to be fetched again
    #cache-entry-ttl = "20 minutes"

    # Maximum number of elements to be kept in the cache. If the limit is reached, old elements will be removed from the cache
    #cache-size = 200

    # How should docker hashes be looked up. Possible values are "local" and "remote"
    # "local": Lookup hashes on the local docker daemon using the cli
    # "remote": Lookup hashes on docker hub, gcr, gar, quay
    method = "local"
  }
}
</code></pre>
<p dir="auto">注意： docker.hash-lookup.method 要为local，等于remote时，cromwell会从远程仓库去取docker的hash值，一旦获取失败，callcaching就会关闭，导致后续所有的caching 和hash Miss, 无法使用重启</p>
]]></description><link>http://an.forum.genostack.com/post/2252</link><guid isPermaLink="true">http://an.forum.genostack.com/post/2252</guid><dc:creator><![CDATA[zhanglu]]></dc:creator><pubDate>Tue, 04 Jul 2023 08:13:52 GMT</pubDate></item><item><title><![CDATA[Reply to cromwell + tesk 重启及gpu支持 on Tue, 04 Jul 2023 07:10:01 GMT]]></title><description><![CDATA[<p dir="auto">支持gpu参考 <a href="https://www.yii666.com/blog/413659.html?action=onAll" rel="nofollow ugc">https://www.yii666.com/blog/413659.html?action=onAll</a></p>
<ol>
<li>安装支持gpu版本的docker</li>
<li>配置docker和gpu驱动；</li>
<li>创建k8s对gpu支持；</li>
</ol>
]]></description><link>http://an.forum.genostack.com/post/2251</link><guid isPermaLink="true">http://an.forum.genostack.com/post/2251</guid><dc:creator><![CDATA[zhanglu]]></dc:creator><pubDate>Tue, 04 Jul 2023 07:10:01 GMT</pubDate></item></channel></rss>