Siesta v4.1.b3 openmpi compilation with slurm example
SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simu...
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2018
El 7 docker upgrade to docker Ce
yum erase *docker* -y yum-config-manager –add-repo “https://download.docker.com/linux/centos/docker-ce.repo” yum install docker-ci -y systemctl stop...
Module usage search in splunk
https://slurp.unl.edu:8000/en-US/account/login?return_to=%2Fen-US%2Fapp%2Flauncher%2Fhome HCC username and password “Launch search app” “Lmod loggin...
Conda build
Tensorflow 1.10.1 https://www.tensorflow.org/install/source#tested_source_configurations https://github.com/tensorflow/tensorflow/blob/v1.10.1/tensorflow/too...
Hcc Puppet
https://hcc-git.unl.edu/red-puppet.git git clone git@hcc-git.unl.edu:red-puppet
Jupyter Notebook Customized Kernels
```bash module load anaconda conda create -n tensorflow-keras tensorflow keras ipykernel python=3.6
Conda project
New Project ```bash mkdir packages/blast cd packages/blast cp ../../anaconda-project.yml.example ./anaconda-project.yml anaconda-project add-env-spec -n blas...
Octopus intel Mkl openmpi
Octopus FFTW3 OpenMPI Intel-MKL GSL
Boost openmpi
Boost $ ./bootstrap.sh --prefix=/home/username/usr $ vim boost_1_55_0/tools/build/v2/user-config.jam using mpi ；#add this to the last line $ ./b2 install --p...
Xdmod boot from snapshot
OpenStack Flavor: general-xlarge Boot from snapshot: “hcc-xdmod prod snap 3/8/18” Security Groups: Port 8080/tcp; default Net...
Slurm cluster usage per group
$ sreport cluster AccountUtilizationByUser accounts=swanson start=1/1/17 end=12/31/17 -t Hour ---------------------------------------------------------------...
Lustre Acl Control
get the ACL’s for /home/usera [usera@login-damiana ~]# lfs lgetfacl /home/usera # file: home/usera # owner: usera # group: users user::rwx group::--- other:...
2017
Slurm Setup
OS is CentOS 7
Comsol v5.3 linux server
Problem: VM run out of entropy cat /proc/sys/kernel/random/entropy_avail 13
R package installations
To see the directories that R searches for libraries, from within R you can do: .libPaths();
Xalt server setup
OpenStack Manage Security Group Rules: XALT
Time sync using chrony
chrony is a versatile implementation of the Network Time Protocol (NTP). It can synchronize the system clock with NTP servers, reference clocks (e.g. GPS rec...
Apache ssl
xdmod.conf ```bash Redirect HTTP to HTTPS <VirtualHost *:80> ServerName hcc-xdmod.unl.edu Redirect / https://hcc-xdmod.unl.edu </VirtualHost&g...
Xdmod fresh install
yum install epel-release -y yum install https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm -y yum groupinstall "Development Tools" -y yum...
Xdmod purge
```bash mysql Welcome to the MariaDB monitor. Commands end with ; or \g. Your MariaDB connection id is 1299 Server version: 5.5.50-MariaDB MariaDB Server
2016
Install Perl Module In User Directory
option 1 echo 'eval $(perl -Mlocal::lib)' >> ~/.bashrc source ~/.bashrc cpan cpan> install Module::Load::Conditional
Globus Connect Cli File Transfer
Add ssh key to your Globus account. instruction ssh jingchao@cli.globusonline.org $ transfer -- hcc#tusker/home/swanson/jingchao/file1 hcc#crane/home/sw...
Rmpi Cluster Installation
module load compiler/gcc openmpi R export R_LIBS=$HOME/R/x86_64-pc-linux-gnu-library/3.3 mkdir -p $HOME/R/x86_64-pc-linux-gnu-library/3.3 wget https://cran.r...
Enable Ldap Centos7 Vm
Only essential commands are listed. Confidential info varies by sites.
Duo Integration With Xdmod Simplesamlphp
To reduce noise, turn off SElinux and firewall. Clone the simplesamlphp-duosecurity repo and put it in /usr/share/xdmod/vendor/simplesamlphp/simplesamlp...
Xdmod Multiple Clusters Ingestor
Setup daily cron job on each cluster running command: