Posts by Year

2020

Lammps compilation on nersc

NOTE: NERSC provides compiled LAMMPS binaries as modules. This tutorial is for users with modified source code.

Download nimh data with ndatools

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...

Create R environment using conda

```bash #install Miniconda mkdir ~/conda; cd ~/conda wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-...

Rstudio installation with conda

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...

R jupyter notebook kernal

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. `...

Aepera quick setup

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...

2019

Ms word replace line break with return

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...

Matlab parallel server

This document provides the steps to configure MATLAB to submit jobs to a cluster, retrieve results, and debug errors.

Check whether infiniband is being used

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...

Matlab alexnet support package install

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 shared conda environment

create a shared location in $COMMON mkdir /common/GROUP/conda chown :GROUP conda chmod 770 conda create conda env in the shared location ...

Slurm_cgroup_memory_usage

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}

2018

Coldfront deployment

install LDAP dependences yum install python-devel openldap-devel -y pip install django-auth-ldap pip install python-ldap ldap3

Notes on hcc purge

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...

Smileimpi compilation

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 ...

Anvil add new user

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...

Cp2k compilation with plumed

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...

Acs reviewing certificate

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...

My elsevier reviews profile

Peer review is the cornerstone of science, and Elsevier is dedicated to supporting and recognizing our journals’ reviewers. My Elsevier Reviews Profile aims ...

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

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...

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

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

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...