genostack部署问题记录

zhanglu

1. 网络

未发现网卡,不能自动连网
执行:
dhclient

2. 跑流程时 Cannot allocate memory错误

编辑/etc/sysctl.conf
vm.overcommit_memory=1
sysctl -p 使配置文件生效

3、硬盘开机直接挂载

编辑/etc/fstab　文件
添加：/dev/sda1 /test ext3 defaults 0 0

注意事项：调研动态自动获取ip ，如何实现ip变动时简化系统配置

anneng

问题现象：
某客户本地电脑无法上网，流程运行过程中提示找不到本地的docker镜像

解决办法：
将cromwell配置为本地方式，只从本地启动docker

修改
/home/anneng/app/genostack_test/genostack_project/config/local.conf
添加内容

docker {
hash-lookup {
# 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 and gcr
method = "local"
}
}

完整 local.conf

database {
profile = "slick.jdbc.PostgresProfile$"
db {
driver = "org.postgresql.Driver"
url = "jdbc:postgresql://{{ip}}:{{db_port}}/cromwell"
user = "{{db_user}}"
password = "{{db_password}}"
port = {{db_port}}
connectionTimeout = 5000
}
}
akka.http.server.request-timeout = 100s

backend {
default = LocalExample

providers {
LocalExample {
actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
config {
run-in-background = true
runtime-attributes = """
String? docker
String? docker_user
"""

    # Submit string when there is a "docker" runtime attribute.
    submit-docker = """
    docker run \
      --rm -i \
      ${"--user " + docker_user} \
      --entrypoint ${job_shell} \
      -v ${cwd}:${docker_cwd} \
      -v {{ project_root }}/genostack_project/cromwell/cromwell-executions:/cromwell-executions \
      -v {{ project_root }}/genostack_project/cromwell/cromwell-executions:{{ project_root }}/genostack_project/cromwell/cromwell-executions \
      ${docker} ${docker_script}
    """
    job-id-regex = "Submitted batch job (\\d+).*"
  }
}

}
}