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Progress Towards Development of Male Contraceptive Pill

MSI PI and Director of the Institute for Therapeutics Discovery and Development Gunda Georg presented research at this week’s American Chemical Society National Meeting that describes progress towards development of a male contraceptive pill. The research describes adjustments made to various...

Computed Pathways of Biomass Molecules

Abstract: 
<h3 class="red">Computed Pathways of Biomass Molecules</h3><p>These researchers are using Gaussian to perform calculations of energetics of reactants, products, and intermediates of reaction pathways of biomass-derived compounds.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/dcb68bf42025544db3edab668789c84e/10990">main page</a>.</p>
Group name: 
dauenha0

How do I transfer data on Second Tier Storage between users?

An approved self-service workflow has been developed by MSI to detail the process in transferring data from one user to another using Second Tier Storage. A good example of a use case for this scenario is when one member of a group is leaving the University and wants to transfer all data they own...

mpiBLAST

Software Description: 

mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST. mpiBLAST takes advantage of distributed computational resources, i.e., a cluster, through explicit MPI communication and thereby utilizes all available resources unlike standard NCBI BLAST which can only take advantage of shared-memory multi-processor computers. The primary advantage to using mpiBLAST versus traditional NCBI BLAST is performance. mpiBLAST can increase performance by several orders of magnitude while still retaining identical results as output from NCBI BLAST.

 

Additional Information
Software Support Level: 
Primary Support
Software Access Level: 
Open Access
PBS Example: 
An example PBS script for submitting mpiBLAST jobs to the queue is shown below.
#!/bin/bash -l
#PBS -l nodes=30:ppn=8,walltime=24:00:00
#PBS -m abe
#PBS -M USERNAME@umn.edu

module load mpiblast
cd /lustre/USERNAME

mpiexec -np 240 mpiblast -i test.fasta -p blastx -d uniref90.fasta \
        -m 9 -o blastx.out --use-virtual-frags &> blastx.error
The --use-virtual-frags option should provide a small speedup and solves the problem of full local scratch spaces. The -m 9 option generates easily-parsed tab-delimited output.
 
Software Categories: 
Software Interactive/GUI: 
No
General Linux Documentation: 
To initialize this software in a Linux environment run the command:
module load mpiblast
Before running mpiBLAST, a configuration file must be created.  Create the file ~/.ncbirc (in your home directory) with the contents
[mpiBLAST]
Shared=/lustre/USERNAME/blastdb
Local=/scratch

[NCBI]
Data=/soft/mpiblast/VER/ncbi/data

[BLAST]
BLASTDB=/lustre/USERNAME/blastdb
BLASTMAT=/soft/mpiblast/VER/ncbi/data
where VER is the version of mpiBLAST you are using.  Also, create the folder /lustre/USERNAME/blastdb and copy an exisiting mpiBLAST database:
​mkdir -p /lustre/USERNAME/blastdb
cp /project/db/mpiblast/uniref90.fasta.* /lustre/USERNAME/blastdb
mpiBLAST cannot use serial ncbi BLAST databases (such as those in /project/db/blast/current). You must create an mpiBLAST database using mpiformatdb (uniref90.fasta db takes ~10 minutes to build, nr takes ~1hr).  Below is an example of using mpiformatdb:
cd /lustre/USERNAME/blastdb
wget url.to.dataset/dataset.fasta
module load mpiblast
mpiformatdb --nfrags=16 -i uniref90.fasta
It is highly recommended that the number of fragments is the exact same number of cores performing the search, or, when that is not possible, that the number of fragments is an exact multiple of the number of cores, thus avoiding load unbalance, which degrades performance.  On Itasca, 16 is the recommended value for number of fragments.
 

What are the software service levels?

Software is classified according to two service levels: Primary Support Secondary Support Primary Support These are the major software packages supported by the Minnesota Supercomputing Institute. In the case of application software, a Primary Support software is one that is widely utilized by MSI...

Computer & Visualization Labs

Laboratories In addition to providing supercomputing facilities, MSI also has four computational laboratories: All MSI labs have 24 hour continuous access via U Card reader. Lab workstations have access to MSI software and shared global filesystems. Scientific Development and Visualization...

What is the difference between the Shared and Public directories?

The Shared directory (/home/ group /shared) is used to share files among group members. All members of a group have access to their group's Shared directory. Any files that multiple users in the same group need access to should be stored here. Users can read and write to the Shared directory of...

National Cancer Institute work by MSI

MSI has created extensions for the National Cancer Institute's caGrid system. caGrid supports caBIG, the National Cancer Institute's Cancer Biomedical Informatics Grid initiative, which links cancer researchers and their data. caGrid provides researchers at different institutions tools that allow...

Developer to Teach Hands-On PETSc Tutorial on Sep 30

posted on September 4, 2013 Dr. Matthew G. Knepley , University of Chicago , will present a hands-on tutorial for PETSc at MSI on September 30. Dr. Knepley is one of the authors of the widely used PETSc library for scientific computing from Argonne National Laboratory , and is a principal designer...

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