暗能星系
    • 登录
    • 搜索

    tmp

    张渌
    2
    262
    1755
    正在加载更多帖子
    • 从旧到新
    • 从新到旧
    • 最多赞同
    回复
    • 在新帖中回复
    登录后回复
    此主题已被删除。只有拥有主题管理权限的用户可以查看。
    • Z
      zhanglu 最后由 编辑

      #!/bin/bash
      #SBATCH -J test
      #SBATCH -N 1
      #SBATCH -n 1
      #SBATCH --comment=test
      date
      hostname
      touch /cephfs_data/aaaaaaaaaaaa.txt
      sleep 10s
      date

      1 条回复 最后回复 回复 引用 0
      • Z
        zhanglu 最后由 编辑

        在node03上执行
        1.lammps

        cd /home/user/Desktop/rigid
        source /opt/intel/oneapi/setvars.sh
        gpu
        mpirun -np 20 /opt/software/lammps-7Feb2024/src/lmp_oneapi -sf gpu -pk gpu 1 neigh no -in in.rigid
        cpu
        mpirun -np 20 /opt/software/lammps-7Feb2024/src/lmp_oneapi < in.rigid

        1 条回复 最后回复 回复 引用 0
        • Z
          zhanglu 最后由 编辑

          database {
          profile = "slick.jdbc.PostgresProfile$"
          db {
          driver = "org.postgresql.Driver"
          url = "jdbc:postgresql://172.17.0.1:5437/cromwell"
          user = "postgres"
          password = "genostack123456"
          port = 5437
          connectionTimeout = 5000
          }
          }
          akka.http.server.request-timeout = 100s
          docker {
          hash-lookup {
          method = "local"
          }
          }

          backend {
          default = slurm

          providers {
          slurm {
          actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
          config {
          runtime-attributes = """
          Int cpu = 2
          String? docker
          """
          root = "/cephfs_data/slurm_hpc2/genostack_v3/genostack_cromwell/cromwell-executions"
          dockerRoot = "/cephfs_data/slurm_hpc2/genostack_v3/genostack_cromwell/cromwell-executions"
          submit-docker = """
          # Pull the image using the head node, in case our workers don't have network access
          docker pull ${docker}

                sbatch \
        -J ${job_name} \
        -D ${cwd} \
        ${"-c " + cpu} \
       --wrap "docker run -v /cephfs_data/slurm_hpc2:/cephfs_data/slurm_hpc2 ${docker} ${job_shell} ${docker_script}"
    """
    kill = "scancel ${job_id}"
    check-alive = "squeue -j ${job_id}"
    job-id-regex = "Submitted batch job (\\d+).*"
  }
}

          }

          1 条回复 最后回复 回复 引用 0
          • Z
            zhanglu 最后由 编辑

            workflow hello {
            String aaa = "aaaaaaaaaaaaaa"
            call path_to_pair {
            input:
            aaa = aaa
            }
            }
            task path_to_pair {
            String aaa
            command {
            sleep 20s
            echo '${aaa}' > out.txt
            }
            runtime {
            cpu: 1
            docker: "dockerhub.genostack.com:8090/library/fileparse:v1"
            }
            output {
            File out = "out.txt"
            }
            }

            1 条回复 最后回复 回复 引用 0
            • Z
              zhanglu 最后由 编辑

              hello1.wdl

              1 条回复 最后回复 回复 引用 0
              • Z
                zhanglu 最后由 编辑 

                    submit = """
        sbatch \
          --wait \
          -J ${job_name} \
          -D ${cwd} \
          -t ${runtime_minutes} \
          ${"-c " + cpus} \
          --mem-per-cpu=${requested_memory_mb_per_core} \
          --wrap "/bin/bash ${docker_script}"
    """
                1 条回复 最后回复 回复 引用 0
                • Z
                  zhanglu 最后由 编辑 

                      submit = """
        sbatch -J ${job_name} -D ${cwd} -o ${out} -e ${err} -t ${runtime_minutes} -p ${queue} \
        ${"-n " + cpus} \
        --mem-per-cpu=${requested_memory_mb_per_core} \
        --wrap "/usr/bin/env bash ${script}"
    """
                  1 条回复 最后回复 回复 引用 0
                  • Z
                    zhanglu 最后由 编辑

                    mpirun -np 20 /opt/software/lammps-7Feb2024/src/lmp_oneapi -sf gpu -pk gpu 1 neigh no -in in.rigid

                    1 条回复 最后回复 回复 引用 0
                    • Z
                      zhanglu 最后由 编辑

                      nerdctl pull dyrnq/pause:3.9
                      nerdctl pull dyrnq/coredns:v1.10.1
                      nerdctl pull dyrnq/k8s-dns-node-cache:1.22.20
                      nerdctl pull dyrnq/metrics-server:v0.6.4
                      nerdctl pull dyrnq/local-volume-provisioner:v2.5.0
                      nerdctl pull dyrnq/controller:v1.8.1
                      nerdctl pull dyrnq/csi-attacher:v3.3.0
                      nerdctl pull dyrnq/csi-provisioner:v3.0.0
                      nerdctl pull dyrnq/csi-snapshotter:v5.0.0
                      nerdctl pull dyrnq/csi-resizer:v1.3.0
                      nerdctl pull dyrnq/csi-node-driver-registrar:v2.4.0
                      nerdctl pull dyrnq/livenessprobe:v2.5.0
                      nerdctl pull dockergroo/cluster-proportional-autoscaler:v1.8.8

                      nerdctl tag dyrnq/pause:3.9 registry.k8s.io/pause:3.9
                      nerdctl tag dyrnq/pause:3.9 registry.k8s.io/kube-proxy/pause:3.9
                      nerdctl tag dyrnq/coredns:v1.10.1 registry.k8s.io/coredns/coredns:v1.10.1
                      nerdctl tag dyrnq/k8s-dns-node-cache:1.22.20 registry.k8s.io/dns/k8s-dns-node-cache:1.22.20
                      nerdctl tag dyrnq/metrics-server:v0.6.4 registry.k8s.io/metrics-server/metrics-server:v0.6.4
                      nerdctl tag dyrnq/local-volume-provisioner:v2.5.0 registry.k8s.io/sig-storage/local-volume-provisioner:v2.5.0
                      nerdctl tag dyrnq/controller:v1.8.1 registry.k8s.io/ingress-nginx/controller:v1.8.1
                      nerdctl tag dyrnq/csi-attacher:v3.3.0 registry.k8s.io/sig-storage/csi-attacher:v3.3.0
                      nerdctl tag dyrnq/csi-provisioner:v3.0.0 registry.k8s.io/sig-storage/csi-provisioner:v3.0.0
                      nerdctl tag dyrnq/csi-snapshotter:v5.0.0 registry.k8s.io/sig-storage/csi-snapshotter:v5.0.0
                      nerdctl tag dyrnq/csi-resizer:v1.3.0 registry.k8s.io/sig-storage/csi-resizer:v1.3.0
                      nerdctl tag dyrnq/csi-node-driver-registrar:v2.4.0 registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.4.0
                      nerdctl tag dyrnq/livenessprobe:v2.5.0 registry.k8s.io/sig-storage/livenessprobe:v2.5.0
                      nerdctl tag dockergroo/cluster-proportional-autoscaler:v1.8.8 registry.k8s.io/cpa/cluster-proportional-autoscaler:v1.8.8
                      nerdctl pull dyrnq/kube-apiserver:v1.27.7
                      nerdctl tag dyrnq/kube-apiserver:v1.27.7 registry.k8s.io/kube-apiserver:v1.27.7
                      nerdctl pull dyrnq/kube-controller-manager:v1.27.7
                      nerdctl tag dyrnq/kube-controller-manager:v1.27.7 registry.k8s.io/kube-controller-manager:v1.27.7
                      nerdctl pull dyrnq/kube-scheduler:v1.27.7
                      nerdctl tag dyrnq/kube-scheduler:v1.27.7 registry.k8s.io/kube-scheduler:v1.27.7
                      nerdctl pull dyrnq/kube-proxy:v1.27.7
                      nerdctl tag dyrnq/kube-proxy:v1.27.7 registry.k8s.io/kube-proxy:v1.27.7

                      初于钟情:
                      qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads bold_derep1_seqs.qza --i-reference-taxonomy bold_derep1_taxa.qza --o-classifier bold_derep1_classifier.qza

                      初于钟情:
                      qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads bold_anml_seqs.qza --i-reference-taxonomy bold_anml_taxa.qza --o-classifier bold_anml_classifer_anneng.qza &

                      nerdctl pull docker/desktop-kubernetes-pause:3.5
                      nerdctl tag docker/desktop-kubernetes-pause:3.5 k8s.gcr.io/pause:3.5

                      nerdctl pull cnplat/kube-scheduler:v1.19.13
                      nerdctl tag cnplat/kube-scheduler:v1.19.13 k8s.gcr.io/kube-scheduler:v1.19.13

                      nerdctl pull kubeon/pause:3.5
                      nerdctl tag kubeon/pause:3.5 k8s.gcr.io/pause:3.5

                      nerdctl pull dockerhub.genostack.com:8090/library/k8s.gcr.io/kube-scheduler:v1.19.13
                      nerdctl tag dockerhub.genostack.com:8090/library/k8s.gcr.io/kube-scheduler:v1.19.13 k8s.gcr.io/kube-scheduler:v1.19.13

                      nerdctl pull jupyterhub/configurable-http-proxy:4.5.0
                      nerdctl tag jupyterhub/configurable-http-proxy:4.5.0 jupyterhub/configurable-http-proxy:4.5.0

                      nerdctl rmi k8s.gcr.io/kube-scheduler:v1.19.13 --force
                      nerdctl rmi k8s.gcr.io/pause:3.5 --force

                      1 条回复 最后回复 回复 引用 0
                      • Z
                        zhanglu 最后由 编辑

                        nerdctl pull docker/desktop-kubernetes-pause:3.5
                        nerdctl tag docker/desktop-kubernetes-pause:3.5 k8s.gcr.io/pause:3.5

                        nerdctl pull cnplat/kube-scheduler:v1.19.13
                        nerdctl tag cnplat/kube-scheduler:v1.19.13 k8s.gcr.io/kube-scheduler:v1.19.13

                        nerdctl pull kubeon/pause:3.5
                        nerdctl tag kubeon/pause:3.5 k8s.gcr.io/pause:3.5

                        nerdctl pull dockerhub.genostack.com:8090/library/k8s.gcr.io/kube-scheduler:v1.19.13
                        nerdctl tag dockerhub.genostack.com:8090/library/k8s.gcr.io/kube-scheduler:v1.19.13 k8s.gcr.io/kube-scheduler:v1.19.13

                        nerdctl pull jupyterhub/configurable-http-proxy:4.5.0
                        nerdctl tag jupyterhub/configurable-http-proxy:4.5.0 jupyterhub/configurable-http-proxy:4.5.0

                        nerdctl rmi k8s.gcr.io/kube-scheduler:v1.19.13 --force
                        nerdctl rmi k8s.gcr.io/pause:3.5 --force

                        1 条回复 最后回复 回复 引用 0
                        • Z
                          zhanglu 最后由 编辑

                          nerdctl pull dyrnq/csi-node-driver-registrar:v2.9.1
                          nerdctl pull dyrnq/csi-resizer:v1.9.2
                          nerdctl pull dyrnq/csi-provisioner:v3.6.2
                          nerdctl pull dyrnq/csi-snapshotter:v6.3.2
                          nerdctl pull dyrnq/csi-attacher:v4.4.2
                          nerdctl tag dyrnq/csi-node-driver-registrar:v2.9.1 registry.k8s.io/sig-storage/csi-node-driver-registrar:v2.9.1
                          nerdctl tag dyrnq/csi-resizer:v1.9.2 registry.k8s.io/sig-storage/csi-resizer:v1.9.2
                          nerdctl tag dyrnq/csi-provisioner:v3.6.2 registry.k8s.io/sig-storage/csi-provisioner:v3.6.2
                          nerdctl tag dyrnq/csi-snapshotter:v6.3.2 registry.k8s.io/sig-storage/csi-snapshotter:v6.3.2
                          nerdctl tag dyrnq/csi-attacher:v4.4.2 registry.k8s.io/sig-storage/csi-attacher:v4.4.2

                          1 条回复 最后回复 回复 引用 0
                          • Z
                            zhanglu 最后由 编辑

                            {
                            "url":"/home/genostack/workspace/test/sample.vcf",
                            "data_detection": ["561","297","363","556","446","417","382","338","431","18","286","295","356","375","406","326","562","35","61","359","26","163","69","336","45","370","91","63","426","94","103","50","70","20","174","30","251","47","109","148","23","74","555","557","12","418","87","310","355","19","17","83","281","283","419","304","395","404","369","8","298","54","374","300","483","518","464","474","333","187","496","66","68","67","560","11","416","16","420","503","78","143","402","272","81","421","40","422","226","65","55","9","77","153","202","60","339","444","53","386","379","277","414","85","367","387","371","312","64","408","390","334","276","179","33","354","472","274","228","351","384","152","486","505","199","481","240","182","450","337","280","327","289","209","176","263","291","380","377","500","275","75","432","399","378","436","443","456","278","314","335","292","190","391","341","460","449","452","302","321","485","198","440","476","495","383","330","361","407","150","466","126","13","101","211","185","477","479","497","396","388","307","348","389","293","32","400","37","360","403","34","296","364","427","368","411","318","340","349","430","362","309","475","439","373","457","366","96","365","458","465","106","80","57","93","320","517","52","41","124","86","31","73","316","39","98","471","22","322","342","270","453","398","352","350","357","433","405","4","42","62","305","376","249","104","242","10","223","217","268","559","7","97","2","285","325","558","287","313","288","3","331","345","5","27","438","282","353","441","343","372","308","205","139","506","191","225","315","284","442","501","435","434","306","164","259","100","347","188","468","467","328","158","180","173","424","303","447","410","344","448","413","401","512","319","423","513","428","459","445","461","279","301","72","224","429","454","262","317","392","412","290","294","409","511","397","323","425","140","385","437","451","273","487","469","136","488","499","137","346","490","254"],
                            "data_module": []
                            }

                            1 条回复 最后回复 回复 引用 0
                            • Z
                              zhanglu 最后由 编辑

                              http://192.168.0.143:8086/gene/file/read

                              1 条回复 最后回复 回复 引用 0
                              • Z
                                zhanglu 最后由 编辑

                                id 272
                                name 3-羟-3-甲基戊二酰辅酶A裂解酶缺乏症
                                rsid rs763494292
                                geneType AC
                                spare A
                                genetypes AC,CC,AA
                                Gene HMGCL
                                result 携带

                                1 条回复 最后回复 回复 引用 0
                                • Z
                                  zhanglu 最后由 编辑

                                  B型家族性高胆固醇血症

                                  1 条回复 最后回复 回复 引用 0
                                  • Z
                                    zhanglu 最后由 编辑

                                    马德隆畸形
                                    geneType CG
                                    spare G,T
                                    gene SHOX
                                    genetypes CG,CT,CC,GG,TT
                                    result 携带

                                    1 条回复 最后回复 回复 引用 0
                                    • Z
                                      zhanglu 最后由 编辑

                                      酪氨酸血症II型
                                      geneType AG
                                      spare A
                                      gene TAT
                                      genetypes AG,GG,AA
                                      result 携带

                                      1 条回复 最后回复 回复 引用 0
                                      • Z
                                        zhanglu 最后由 编辑

                                        SELECT
                                        rs.rsid AS rsId,
                                        rg.pair AS genotype,
                                        rd.spare AS spare,
                                        rd.score AS genotypeScore,
                                        rd.pk AS pk,
                                        rd.efficacy AS efficacy,
                                        rd.toxicity AS toxicity,
                                        rd.dosage AS dosage,
                                        rd.freq AS freq,
                                        rd.detection_id AS detectionId,
                                        rd.description,
                                        report_genes.name as gene
                                        FROM
                                        report_detection_genotype as rd
                                        LEFT JOIN report_genotypes as rg ON rg.ID = rd.genotype_id
                                        LEFT JOIN report_snp as rs ON rs.ID = rg.snp_id
                                        LEFT JOIN report_genes on report_genes.id = rs.genes_id
                                        WHERE
                                        rd.detection_id IN

                                        1 条回复 最后回复 回复 引用 0
                                        • Z
                                          zhanglu 最后由 编辑

                                          a.txt

                                          1 条回复 最后回复 回复 引用 0
                                          • Z
                                            zhanglu 最后由 编辑

                                            kubectl get jobs -o json | jq -r '.items[] | select((.status.succeeded//0) > 0) | .metadata.name' | xargs kubectl delete job

                                            1 条回复 最后回复 回复 引用 0
                                            • First post
                                              Last post
                                            Powered by 暗能星系