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Tree [r62] / History
| File | Date | Author | Commit |
|---|---|---|---|
| cluster-configs | 2021-04-22 | yassinesouilmi | [r40] adding README file and support for S3 upload |
| dev | 2021-12-09 | fschwarz | [r61] adjusted path to humante-mapstat-weight.py in s... |
| profiles | 2021-04-22 | yassinesouilmi | [r40] adding README file and support for S3 upload |
| refg | 2021-05-17 | rokofler | [r49] HGDP929.tsv |
| scripts | 2022-12-29 | rokofler | [r62] added matrix conversion script |
| test | 2021-03-13 | yassinesouilmi | [r34] adding cpu, mem, disk resources to Snakefile; A... |
| README.md | 2021-04-22 | yassinesouilmi | [r40] adding README file and support for S3 upload |
| Snakefile | 2021-04-22 | yassinesouilmi | [r40] adding README file and support for S3 upload |
| config.yaml | 2021-03-13 | yassinesouilmi | [r33] moving input specs to config file |
| environment.yaml | 2021-03-18 | yassinesouilmi | [r36] Adding drmaa library to the environment setup |
Read Me
1. Configure cluster
1.1. Get required software
sudo apt update -y
sudo apt install -y openjdk-8-jre-headless subversion
cd /shared/ ; \
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh ; \
bash Miniconda3-latest-Linux-x86_64.sh ; \
source ~/.bashrc ;\
rm Miniconda3-latest-Linux-x86_64.sh ; \
conda install -c conda-forge mamba
svn checkout --username=yassinesouilmi svn+ssh://yassinesouilmi@svn.code.sf.net/p/human-te-dynamics/svn/ human-te-dynamics-svn ; \
cd /shared/human-te-dynamics-svn/ ; \
mamba env update -n base --file environment.yaml
1.2. Fix slurm
1) First log in to the compute node from the head node and grab the "RealMemory" config in the node by running /opt/slurm/sbin/slurmd -C (as you did already)
2) Log out of the compute node back to the head node
3) Edit /opt/slurm/etc/slurm.conf and add NodeName=DEFAULT RealMemory=[RealMemory number] BEFORE include slurm_parallelcluster_nodes.conf
4) Log back into the compute node
5) Run sudo service slurmd restart
5) Log back out of the compute node
7) Run sudo service slurmctl restart
8)Check your work with scontrol show nodes
NodeName=ip-10-255-1-17 CPUs=32 Boards=1 SocketsPerBoard=1 CoresPerSocket=16 ThreadsPerCore=2 RealMemory=127459
UpTime=0-00:16:01
