Lammps compilation on nersc
NOTE: NERSC provides compiled LAMMPS binaries as modules. This tutorial is for users with modified source code.
NOTE: NERSC provides compiled LAMMPS binaries as modules. This tutorial is for users with modified source code.
In order to access NIMH Data Archive, users need to apply for an account using this link. Project PI needs to add the new user to their project for data acce...
```bash #install Miniconda mkdir ~/conda; cd ~/conda wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-...
In Anaconda Prompt conda create -n newEnv conda activate newEnv - y conda install spyder-kernels -y conda install ... where python Copy the Python environme...
Install Miniconda if you haven’t done so. mkdir ~/conda; cd ~/conda wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh bash Mi...
Install Miniconda and configure Jupyter notebook to run R kernals. First make sure X11 forwarding works on your local machine. Then follow the steps below. `...
Use the GNU du command [jingchao@login.crane hao]$ du --apparent-size -sh 11T . [jingchao@login.crane hao]$ du -sh 3.2T .
Aspera is IBM’s high-performance file transfer software which allows for the transfer large files and data sets with predictable, reliable and secure deliver...
This is mostly used for preparing a reponse letter for journal reviews. Copying/pasting reviewers’ comments to a MS Word file ends up with lots of line break...
```bash #!/bin/sh Change the job name, if you want to #SBATCH –job-name=pendulum
This document provides the steps to configure MATLAB to submit jobs to a cluster, retrieve results, and debug errors.
Check for number incrementals in files at /sys/class/infiniband/mlx4_0/ports/1/counters/ watch -n .5 -diff=cumm 'grep -H . /sys/class/infiniband/mlx4_0/ports...
If Deep Learning Toolbox Model for AlexNet Network support package is not installed, then the function provides a link to the required support package in the...
create a shared location in $COMMON mkdir /common/GROUP/conda chown :GROUP conda chmod 770 conda create conda env in the shared location ...
Put the line below at the end of a slurm submit script to find out the memory usage. cgget -g memory /slurm/uid_${UID}/job_${SLURM_JOB_ID}
Global lock. usermod.py --lock user
install LDAP dependences yum install python-devel openldap-devel -y pip install django-auth-ldap pip install python-ldap ldap3
```console [root@beta ~]# source keystonerc_admin
Crane/Tusker purged files are temporarily stored at /lustre/backup/robinhood/YYYY-WXX (YYYY=year and XX=week number) for 2 weeks. Files beyond 2 weeks are...
wget https://github.com/lammps/lammps/archive/stable_22Aug2018.tar.gz tar zxvf stable_22Aug2018.tar.gz cd lammps-stable_22Aug2018/src for i in BODY ...
Compile OpenMPI with MPI_THREAD_MULTIPLE support. ./configure --enable-mpi-thread-multiple ml load compiler/gcc/4.9 openmpi/1.10 phdf5/1.8 python/3.6 ...
From Tusker/Crane, ssh beta.anvil.hcc.unl.edu sudo su - source /root/keystonerc_admin /util/accounts-mgmt-cli/anvilman.py -v -g GROUPNAME -u USERNAM...
Building Your Own FFTW3 Interface Wrapper Library source /util/opt/lmod/lmod/init/profile ml load compiler/intel/16 cd /util/comp/intel/2016.3/mkl/interfaces...
Click the button to see and download your peer review activity certificate. We hope you will display it with the same pride we take in working with such an a...
Peer review is the cornerstone of science, and Elsevier is dedicated to supporting and recognizing our journals’ reviewers. My Elsevier Reviews Profile aims ...
SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simu...
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...
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...
Tensorflow 1.10.1 https://www.tensorflow.org/install/source#tested_source_configurations https://github.com/tensorflow/tensorflow/blob/v1.10.1/tensorflow/too...
https://hcc-git.unl.edu/red-puppet.git git clone git@hcc-git.unl.edu:red-puppet
```bash module load anaconda conda create -n tensorflow-keras tensorflow keras ipykernel python=3.6
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 FFTW3 OpenMPI Intel-MKL GSL
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...
OpenStack Flavor: general-xlarge Boot from snapshot: “hcc-xdmod prod snap 3/8/18” Security Groups: Port 8080/tcp; default Net...
$ sreport cluster AccountUtilizationByUser accounts=swanson start=1/1/17 end=12/31/17 -t Hour ---------------------------------------------------------------...
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:...
OS is CentOS 7
Problem: VM run out of entropy cat /proc/sys/kernel/random/entropy_avail 13
To see the directories that R searches for libraries, from within R you can do: .libPaths();
OpenStack Manage Security Group Rules: XALT
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...
xdmod.conf ```bash Redirect HTTP to HTTPS <VirtualHost *:80> ServerName hcc-xdmod.unl.edu Redirect / https://hcc-xdmod.unl.edu </VirtualHost&g...
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...
```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
option 1 echo 'eval $(perl -Mlocal::lib)' >> ~/.bashrc source ~/.bashrc cpan cpan> install Module::Load::Conditional
Add ssh key to your Globus account. instruction ssh jingchao@cli.globusonline.org $ transfer -- hcc#tusker/home/swanson/jingchao/file1 hcc#crane/home/sw...
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...
Only essential commands are listed. Confidential info varies by sites.
To reduce noise, turn off SElinux and firewall. Clone the simplesamlphp-duosecurity repo and put it in /usr/share/xdmod/vendor/simplesamlphp/simplesamlp...
Setup daily cron job on each cluster running command: