暗能星系

zhanglu

docker volume create mysql
docker run -d --privileged=true
-v mysql:/var/lib/mysql
-p 3306:3306 --name=mysql -e MYSQL_ROOT_PASSWORD=slurm mysql:8.0.33 --lower-case-table-names=1

zhanglu

sleep 30s
docker exec -it mysql mysql -u root -e "CREATE DATABASE slurm" -pslurm
docker exec -it mysql mysql -u root -D slurm6 -e "source /slurm.sql" -pslurm

zhanglu

slurm.sql

zhanglu

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

zhanglu

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

zhanglu

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+).*"
  }
}

}

zhanglu

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"
}
}

zhanglu

hello1.wdl

zhanglu

    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}"
    """

zhanglu

    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}"
    """

zhanglu

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

zhanglu

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

zhanglu

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

zhanglu

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

zhanglu

{
"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": []
}

zhanglu

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

zhanglu

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

zhanglu

B型家族性高胆固醇血症

zhanglu

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

zhanglu

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

tmp