#################

ERIXdxl setup

################# ssh ma695@erisxdl.partners.org

cd xdl

Conda

module load Anaconda3 conda create -n cas-designer python=3.8 conda activate cas-designer conda install cuda

Podman

podman pull nvidia/cuda:11.0-base podman pull nvcr.io/nvidia/opencl:runtime-ubuntu18.04 podman pull gcr.io/aryeelab/cas-designer podman images

podman run --rm -it gcr.io/aryeelab/cas-designer /bin/bash

podman run --rm -it nvcr.io/nvidia/cuda:11.0-base nvidia-smi

podman run --rm -it nvidia/opencl:runtime-ubuntu18.04 /bin/bash

###################

Set up GCP host

################### gcloud beta compute --project=aryeelab instances create cas-designer --zone=us-central1-a --machine-type=n1-standard-8 --subnet=default --network-tier=PREMIUM --metadata=google-logging-enabled=true --maintenance-policy=TERMINATE --service-account=303574531351-compute@developer.gserviceaccount.com --scopes=https://www.googleapis.com/auth/devstorage.read_only,https://www.googleapis.com/auth/logging.write,https://www.googleapis.com/auth/monitoring.write,https://www.googleapis.com/auth/servicecontrol,https://www.googleapis.com/auth/service.management.readonly,https://www.googleapis.com/auth/trace.append --accelerator=type=nvidia-tesla-k80,count=1 --image=ubuntu-2004-focal-v20210623 --image-project=ubuntu-os-cloud --boot-disk-size=20GB --boot-disk-type=pd-balanced --boot-disk-device-name=cas-designer --no-shielded-secure-boot --shielded-vtpm --shielded-integrity-monitoring --metadata-from-file=startup-script=/Users/maryee/Documents/cas-designer/gcp_host_setup.sh

See gcp_host_setup.sh for startup script

gcloud beta compute ssh --zone "us-central1-a" "cas-designer" --project "aryeelab"

Test docker GPU

sudo docker run --rm --gpus all nvidia/cuda:11.3.1-base nvidia-smi

##########################

Docker Container setup

##########################

sudo docker run --gpus all --rm -it gcr.io/aryeelab/cas-designer /bin/bash

Genome FASTA

mkdir GRCh38 cd GRCh38 gsutil -m cp gs://genomics-public-data/references/GRCh38/* . gunzip *

docker build -t gcr.io/aryeelab/cas-designer .

WDL

With options (for monitoring)

java -Dconfig.file=cromwell-gcp.conf -jar /usr/local/Cellar/cromwell/65/libexec/cromwell.jar run -o cromwell-gcp-options.conf -i CD_EMX1_2_1_1.json cas-designer.wdl

Assuming the monitoring option is in the main conf file. (Does not work?)

java -Dconfig.file=cromwell-gcp.conf -jar /usr/local/Cellar/cromwell/65/libexec/cromwell.jar run -i CD_EMX1_2_1_1.json cas-designer.wdl

################################################

Highest GCP NVIDIA for WDL? 460.73.01

Cos

cos-extensions install gpu sudo mkdir /mnt/disks/scratch sudo mount -t tmpfs tmpfs /mnt/disks/scratch/

docker run --rm -it nvidia/cuda:11.3.1-base-ubuntu20.04 /bin/bash

docker run --rm -it
--volume /var/lib/nvidia/lib64:/usr/local/nvidia/lib64
--volume /var/lib/nvidia/bin:/usr/local/nvidia/bin
--device /dev/nvidia0:/dev/nvidia0
--device /dev/nvidia-uvm:/dev/nvidia-uvm
--device /dev/nvidiactl:/dev/nvidiactl
nvidia/cuda:11.3.1-base-ubuntu20.04 /bin/bash

docker run --rm -it
--volume /var/lib/nvidia/lib64:/usr/local/nvidia/lib64
--volume /var/lib/nvidia/bin:/usr/local/nvidia/bin
--device /dev/nvidia0:/dev/nvidia0
--device /dev/nvidia-uvm:/dev/nvidia-uvm
--device /dev/nvidiactl:/dev/nvidiactl
nvidia/opencl:runtime-ubuntu18.04 /bin/bash

gcloud compute scp --zone "us-central1-a" --project "aryeelab" EMX1_fasta.fa a100:/home/maryee/ gcloud compute scp --zone "us-central1-a" --project "aryeelab" CD_EMX1_4_2_2.txt a100:/home/maryee/

gcloud beta compute ssh --zone "us-central1-a" "instance-1" --project "aryeelab"

time cas-designer CD_EMX1_4_2_2.txt

/data/molpath/genomes/GRCh38/Homo_sapiens/NCBI/GRCh38/Sequence/

cd bin &&
wget https://versaweb.dl.sourceforge.net/project/cas-offinder/Binaries/2.4/Linux64/cas-offinder &&
chmod +x cas-offinder