Job Scheduling The acm headnode serves a great many purposes including being the file server, subnet manager, gateway and license manager. This means its important ...

ACM The ACM cluster (Applied and Computational Mathematics) is purchased by several members in the Math department at FSU Currently the cluster consists of two distinctly ...

FAQ How do I get an account on acm? If you already have an SCS account access can be requested by going to https://tsg.scs.fsu.edu/scsum, logging in, selecting request ...

File Systems Local Storage The file system is currently configured as a raid 10 device on the head node formatted with ext3 providing 1.4TB of usable shared storage ...

N/A JazcekBraden 02 Apr 2008

N/A JazcekBraden 02 Apr 2008

There is plenty of software installed but of note to document gcc 4.1.2 gfortran 4.1.2 PGI compilers (inlcuding high performance fortran, f90, f77 ...

Everything is in Flux As the applications of the acm cluster have not been completely defined, the systems usage policy and configuration will change in order to ...

Running Jobs on Anfinsen The Anfinsen cluster is an owner based access SCS resource. The Anfinsen cluster is configured to serve long running batch style jobs, by ...

Anfinsen The Anfinsen cluster was funded by the School of Computational Science (SCS) and has been a major resource for computational biophysics research in SCS. ...

Anfinsen FAQ General frequently asked questions about the Anfinsen cluster. Table of Contents How do I get an account on anfinsen? Anfinsen is an owner based ...

File System setup on anfinsen Every user's home directory is auto generated when the users logs into anfinsen and this directory is mounted across all anfinsen ...

Open Issues on the Anfinsen Cluster Table of Contents No known issues at this time We are not aware of any issues with Anfinsen cluster. AnfinsenLog JeffMcDonald ...

Anfinsen User Knowledge Base This page exists to facilitate the transfer of knowledge among users of the AnfinsenCluster, such as more detailed description of ...

Anfinsen System Status Ganglia A system called Ganglia can be used to view the status of the anfinsen compute nodes. Ganglia has a graphical and a command line interface ...

Running Jobs on Aster The Aster cluster is an owner based access SCS resource. The Aster cluster is configured to serve long running batch style jobs, by using either ...

Aster The Aster cluster was purchased by Dr. Christopher Tam (Math Department) and the Boing Company for a joint research project, entitled "Modeling of Large Scale ...

Aster FAQ General frequently asked questions about the Aster cluster. Table of Contents How do I get an account on aster? Aster is an owner based resource. Accounts ...

File System setup on Aster Every user's home directory is auto mounted on Aster and this directory is mounted across all Aster compute nodes. The shared ...

Open Issues on the Aster Cluster Table of Contents No known issues at this time We are not aware of any issues with Aster cluster. AsterLog Permissions ...

Aster User Knowledge Base This page exists to facilitate the transfer of knowledge among users of the AsterCluster, such as more detailed description of installed ...

Aster System Status Ganglia A system called Ganglia can be used to view the status of the Aster compute nodes. Ganglia has a graphical and a command line interface ...

Available Software General Access Resources Job Submission Tools Version Classroom Hallway Desktops GP VisLab Condor 7.0.1 ...

Running Jobs on Bruce The Bruce cluster is an owner based access SCS resource. The Bruce cluster is configured to serve long running batch style jobs, by using either ...

Bruce Bruce was purchased with money from the startup fund from FSU research foundation, which was provided for Dr. Wei Yang. The projects being carried on Bruce ...

Bruce FAQ General frequently asked questions about the Bruce cluster. Table of Contents How do I get an account on bruce? Bruce is an owner based resource. Accounts ...

File System setup on Bruce Every user's home directory is auto generated when the users logs into bruce and this directory is mounted across all bruce compute ...

Open Issues on the Bruce Cluster Table of Contents No known issues at this time We are not aware of any issues with Bruce cluster. JeffMcDonald 06 Nov 2006 ...

Bruce User Knowledge Base This page exists to facilitate the transfer of knowledge among users of the BruceCluster, such as more detailed description of installed ...

Bruce System Status Ganglia A system called Ganglia can be used to view the status of the bruce compute nodes. Ganglia has a graphical and a command line interface ...

YusongLiu 11 Jan 2007

YusongLiu 11 Jan 2007

Connection to SCS Computing Resources An SCS account is required to connect to most of the computing resources available at SCS (see RequestAccount for more information ...

Computing at SCS FAQ General frequently asked questions about using SCS's computing resources. Table of Contents Why doesn't my VPN connection to SCS allow connections ...

Reading/writing a List of Ascii Numbers: C Consider a file with the following structure 10 // number of points 4 // number of columns 34 64 23 10 ...

Running Jobs No limitations are placed on user desktops for running jobs. Desktops machines provisioned with desks support condor job submission and sge ...

Desktop FAQ Frequently asked questions about using the DESKTOP computing resources. See also the General FAQ. Table of Contents Why isn't software X available ...

File System setup on desktops Each user's home directory is auto mounted from fs. Individual disks sizes vary. For desks systems, users are generally ...

Desktop Open Issues JeffMcDonald 25 Oct 2006

Collected user wisdom JeffMcDonald 25 Oct 2006

Desktop System Status Ganglia A system called Ganglia can be used to view the status of the desks nodes. Systems outside of the desks provisioning are not monitored ...

Desktops The desktop systems at SCS generally defines all of the computational systems which people as their SCS/internet access point. The desktops generally are ...

Reading/writing a Fortran List of Ascii Numbers: Fortran 77 Consider a file with the following structure 10 // number of points 4 // number of columns 34 64 ...

Reading/Writing a Fortran List of Ascii Numbers using Fortran 90 Consider a file with the following structure 10 // number of points 4 // number of columns 34 ...

GP GP is the General Purpose Cluster. The current hardware configuration consists of the following: Lots of computers configured with: Lots of different ...

SCS Graduate Student Office Hours Evan Bollig (Vislab Room 428) Tuesday 14:00 17:00 Wednesday 12:00 17:00 Thursday 14:00 17:00 ...

Grove Grove was purchased with money from an Information Technology Research (ITR) grant from the Natioinal Science Foundation entitled Building the Tree of Life ...

Hydra Hydra was purchased using startup funds provided to Dr. Shanbhag and is used to execute mesoscopic simulations of polymer solutions and melts. It is well known ...

Reading/writing a Fortran List of Ascii Numbers: Java Consider an input file with the following asci structure 10 // number of points 4 // number of columns ...

VolkanSevim 15 Oct 2007 Using !LaTeX !LaTeX is a document preparation system developed by Leslie Lamport in 1985. It is based on a typesetting language called Tex ...

The matsim cluster is an owner based cluster which is not available for in general SCS use. The matsim cluster is configured to serve long running batch style jobs ...

Matsim The Matsim cluster is owned by Dr. Anter El Azab and is intended to support his research requirements and those associated with the recently approved Center ...

Matsim FAQ General frequently asked questions about the Matsim cluster, this includes matsim and matsim ib: Table of Contents How do I get an account on matsim ...

The matsim and matsim ib segments of the cluster have been configured to run independently of each other and as such as seperate filesystems and home directories. ...

As the matsim nodes and matsim ib nodes have slightly different hardware confiugrations, it difficult to provide a common environment across them. Currently the only ...

Information will be posted here are issues arise and are solved by users of the cluster JazcekBraden 30 Jan 2008

The system is current up and running to specifications. Using HPL test compiled against openmpi benchmarks of 720 GFLOPS have been achieved. JazcekBraden 30 Jan ...

Running Jobs on Mendel Mendel accepts valid ssh logons from all domains and does not require any specialized batch submission mechanism, though it does support Condor ...

Mendel Mendel is now retired! Its functions have been ported to the new FSU HPC. Mendel was a dedicated bioinformatics server managed by SCS for the FSU biosciences ...

Mendel FAQ General Frequently Asked Questions about the Mendel server. Table of Contents Why don't I have a Mendel account, when I have other SCS accounts? Mendel ...

File System setup on Mendel Mendel does NOT share its file system with any other SCS systems at this time. Every user has a dedicated home directory in ...

Open Issues on the Mendel Server Table of Contents Mendel does not update its finger data. Mendel reports all users have "Never logged in" in spite of users' ...

Mendel User Knowledge Base This page exists to facilitate the transfer of knowledge among users of the Mendel bioinformatics server, such as more detailed description ...

Mendel System Status Mendel will only respond to 'ping' from within the SCS domain. While logged onto Mendel 'top' prvides a dynamic usage summary. Ganglia ...

Migrate on the SCS Condor cluster (Standard universe) 1) log in one of the SCS master nodes SCS has several master nodes in the the Condor Pool. You may ...

Migrate on the SCS Condor cluster (Vanilla universe) 1) log in one of the SCS master nodes SCS has several master nodes in the the Condor Pool. You may or ...

MrBayes on the SCS Condor cluster (Standard universe) Prepare a !MrBayes batch file Before we start pratice !MrBayes on condor, it is usful to set up a directory ...

MrBayes on the SCS Condor cluster (Vanilla universe) 1) log in one of the SCS master nodes SCS has several master nodes in the the Condor Pool. You may or ...

Running Jobs on Olga The Olga cluster is an owner based access SCS resource. The Olga cluster is configured to serve long running batch style jobs, by using either ...

Olga The Olga cluster is a small cluster being used primarily as an application server for the research group of Max Gunzburger. You can find information about Max ...

Olga FAQ General frequently asked questions about the Olga cluster. Table of Contents How do I get an account on Olga? Olga is an owner based resource. Accounts ...

File System setup on Olga Every user's home directory is auto generated when the users logs into Olga and this directory is mounted across all Olga compute nodes ...

Open Issues on the Olga Cluster Table of Contents No known issues at this time We are not aware of any issues with Olga cluster. SivaSakti 11 Jul 2007

Olga User Knowledge Base This page exists to facilitate the transfer of knowledge among users of the OlgaCluster, such as more detailed description of installed ...

Olga System Status Ganglia A system called Ganglia can be used to view the status of the Olga compute nodes. Ganglia has a graphical and a command line interface ...

How to Submit PAUP Jobs in the Standard Universe (Checkpointing) Prepare a PAUP batch file For this example you'll need two files one containing a NEXUS ...

Running PAUP Jobs in the Vanilla Universe (no checkpointing) Prepare a PAUP batch file For this example you'll need two file one containing a NEXUS dataset ...

VolkanSevim 6 Nov 2007 Advanced Scripting: Perl and Gnuplot For a brief introduction to Perl and Gnuplot see perl.odp. A Simple Project: Text Extraction and Plotting ...

Petal The Petal cluster was funded by the School of Computational Science (SCS) and has been a major resource for Computational Evolutionary Biology (CEB) research ...

Portland Group Compilers at SCS Description PGI provides High performance Compilers optimizing parallel Fortran, C and C compilers for 32 bit x86 and 64 bit x64 ...

Running Jobs on Phoenix The Phoenix cluster is a general access SCS resource. The Phoenix cluster is configured to serve long running batch style jobs, by using ...

Compiling on Phoenix Condor compile Intel C/C 9 Intel Fortran 9 gcc 3.2.2 pgi compilers Supported Applications on Pheonix Gromacs 3.3.1 ...

Phoenix FAQ General frequently asked questions about the Phoenix cluster. Table of Contents Why do my jobs terminate after running about 30 minutes on phoenix ...

File System setup on phoenix Every user's home directory is auto generated when the users logs into phoenix and this directory is mounted across all phoenix compute ...

Open Issues on the Phoenix Cluster Table of Contents No known issues at this time We are not aware of any issues with Phoenix cluster.

Phoenix User Knowledge Base This page exists to facilitate the transfer of knowledge among users of the PhoenixCluster, such as more detailed description of ...

Phoenix System Status Ganglia A system called Ganglia can be used to view the status of the phoenix compute nodes. Ganglia has a graphical and a command line interface ...

Running Jobs on Prism The Prism cluster is a general access SCS resource providing applications. The Prism cluster is configured to serve short, interactive jobs ...

Prism FAQ Frequently asked questions about using the PRISM computing resources. See also the General FAQ. Table of Contents How can I get an account on the prism ...

File System setup on prism Each user's home directory is auto mounted from fs when the users does a qlogin or qsh to prism. Each disk has approximately ...

Open Issues on the prism cluster JeffMcDonald 25 Oct 2006

Collected Wisdom of users. JeffMcDonald 25 Oct 2006

Prism System Status Ganglia A system called Ganglia can be used to view the status of the prism000 nodes. Ganglia has a graphical and a command line interface. To ...

Reading/writing a List of Ascii Numbers: ruby Ruby is probably the most elegant (and the slowest) scripting language (choices are perl, python, ruby). Consider a ...

General Overview of SGE and Condor These resources can be used with general purpose clusters like prism, tempest, and phoenix. You can look at the job restrictions ...

Sax The Sax cluster was purchased through a DURIP grant from Army, entitled "A Laboratory for Distributed and Grid Computing" and awarded to Michael Mascagni and ...

ARPACK Library at SCS Description ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. The package is designed to compute ...

Amira General Description Amira is an advanced 3D visualization toolkit designed to handle large datasets, volume renderings and a multitude of other visualization ...

The Blas Library Description The (Basic Linear Algebra Subprograms) are routines that provide standard building blocks for performing basic vector and matrix operations ...

!CHARMM at SCS Description CHARMM(Chemistry at HARvard Macromolecular Mechanics) is a program for macromolecular simulations, including energy minimization, molecular ...

Condor

Desktop Cluster JeffMcDonald 19 Oct 2006

FFTW Library at SCS Description FFTW ( The Fastest Fourier Transform in the West ) is a C subroutine library for computing the discrete Fourier transform (DFT) in ...

GCC at SCS Description “GCC” is a common shorthand term for the GNU Compiler Collection. This is both the most general name for the compiler, and the name used when ...

Gromacs Libraries at SCS Description GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with ...

Hallway Machines JeffMcDonald 19 Oct 2006

Intel Compilers at SCS Description The intel compilers provide improved performance over the GNU C/C compilers. This compiler product automatically optimizes and ...

LAM MPI at SCS Description LAM (Local Area Multicomputer) is an open source implementation of the Message Passing Interface (MPI) standard. The MPI standard is the ...

Lapack Libraries at SCS Description LAPACK, a Linear Algebra Package library, is written in Fortran77 and provides routines for solving systems of simultaneous ...

!MPE at SCS Description MPE is a software package for MPI ( Message Passing Interface ) programmers. The package provides users with a number of useful tools for ...

Maple General Description Maple is a general purpose computer algebra system, that can be used to solve mathematical problems and produce high quality technical graphics ...

Mathematica General Description Mathematica is a computer algebra system originally conceived by Stephen Wolfram, developed by a team of mathematicians and programmers ...

!MathWorks MATLAB General Description MATLAB is a high level technical computing language and interactive environment for algorithm development, data visualization ...

MATLAB Graphics Learning of MATLAB Graphics Graphics Manual Central User contributions with source code especially note the "Gallery" category. Examples ...

Mpich2 at SCS Description MPICH2 is a freely available, portable implementation of MPI, the Standard for message passing libraries. It implements both MPI 1 and MPI ...

Netbeans General Description Netbeans is an ide for developing Java Home Page: http://www.netbeans.org/ General Tutorials http://www.netbeans.org/kb/index.html ...

!OpenMPI at SCS Description Open MPI is a project combining technologies and resources from several other projects (FT MPI, LA MPI, LAM/MPI, and PACX MPI) in order ...

PETSC at SCS Description PETSc, pronounced PET see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific ...

FACILITIES, COMPUTATIONAL INFRASTRUCTURE download text version: Facilities2008.txt The SCS plays a major role in the support of FSU's cyber infrastructure ...

SGE at SCS Description The primary job submission queue is managed by the Sun Grid Engine (SGE). It allows you to request the necessary resources and it will find ...

Super LU Super LU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. The ...

Tecplot General Description Tecplot is a data visualization package developed explicitly for engineers and scientists. Home Page: http://www.tecplot.com/products ...

Totalview General Description !TotalView is a source and machine level debugger with support for Fortran, C, C , !OpenMP, MPI, and threads. Home Page: http://www ...

VMD General Description VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3 D graphics and built ...

Introduction to Shell Scripting Before starting this Seminar Slides Introduction to Shell Scripting Command Notes This will help you to remember ...

Material Related to the Seminar: "Beginners Shell Scripting for Batch Jobs" Slides Seminar Slides: Beginners Shell Scripting for Batch Jobs NOTE: These ...

Notes on Installing Software in the !VisLab This document provides notes for installing software on the machines in the SCS !VisLab. General Procedure for Software ...

SpitFireCluster The SpitFireCluster cluster is owned by Prof. Robert van Engelen's group. We recently acquired 8 PS3 machines for research in the ACIS (advanced ...

SpitFire frequently asked questions. JeffMcDonald 11 Mar 2008

Information about the !SpitFire File System JeffMcDonald 11 Mar 2008

Open Issues for the !SpitFire Cluster JeffMcDonald 11 Mar 2008

User knowledgebase for !SpitFire JeffMcDonald 11 Mar 2008

The status of !SpitFire JeffMcDonald 11 Mar 2008

Stella Stella was purchased from startup funds for Dr. Nymeyer provided by the FSU research foundation. Stella is dedicated to the development of newer, faster methods ...

System Status JimWilgenbusch 31 Aug 2006

SCS Technical Topics Series Wednesdays, 1:30 to 2:30 Dirac Science Library, 1st Floor Room 152. Feb. 14 Introduction to SCS !VisLab resources and a quick ...

SCS Technical Workshop Series Wednesdays, 10:00 to 11:00 Dirac Science Library, 1st Floor Room 152 The SCS Technical Workshop Series consists of 12 one hour labs ...

SCS Technical Workshop Series The SCS Technical Workshop Series consists of one hour labs designed to give students and faculty hands on experience with a variety ...

Running Jobs on Tempest The Tempest cluster is a general access SCS resource. The Tempest cluster is configured to serve long running batch style jobs, by using ...

Tempest The Tempest cluster was funded by Sun Microsystems through an Academic Excellence Grant obtained by members of the Technical Support Group and has been a ...

Tempest FAQ General frequently asked questions about the Tempest cluster. Table of Contents Why do my jobs terminate after running about 30 minutes on tempest ...

File System setup on tempest Each user's home directory is auto mounted from the SCS shared file server when the users log in.

Open Issues on the Tempest Cluster Table of Contents No known issues at this time We are not aware of any issues with Tempest cluster.

Tempest User Knowledge Base This page exists to facilitate the transfer of knowledge among users of the TempestCluster, such as more detailed description of ...

Tempest System Status Ganglia A system called Ganglia can be used to view the status of the tempest compute nodes. Ganglia has a graphical and a command line interface ...

Introduction to Unix Basic Unix Commands Directory Navigation pwd (present working directory) type pwd to list the present working directory ls ...

Condor at SCS About Condor Condor is a batch system for queuing, scheduling, and prioritizing compute intensive jobs. It is developed by the team at the University ...

Visualization Laboratory The Visualization Laboratory has one 9.2 Tbyte file system attached to four graphic workstations. Their characteristics are listed below ...

Images Produced in the !VisLab Screenshots from the !VisLab Nothing of interest at this point Other Screenshots Produced at SCS Image Caption ...

SCS !VisLab: Hardware Mission File System PowerWall FAQ NEW CUDA FAQ NEW Available Software Images Videos Tutorials ...

Videos Produced by the !VisLab Videos Produced in the Vislab Nothing of interest available at this time. Videos from SCS (non VisLab) Nothing at this time ...

Amira Tutorial for Creating Stereo (3D) Movies This material is based upon work supported by the National Science Foundation under No. 0722782. Creating the Movie ...

CUDA FAQ Setting up CUDA CUDA in your home directory Problem CUDA may not be installed in a global location on all systems that have CUDA GPUs Applies ...

Compilation

Frequently Asked Questions Are there backups? There are no backups. Users have access to scratch1/ and scratch2/ partitions in their home directory for the ...

User Feedback Make a Comment We encourage feedback on our tutorial notes, or any questions/comments users may have regarding the !VisLab. NOTE: you must have ...

File Structure and Backups File System The Visualization Lab supports Fedora Core 5 on all its systems, with the exception of a single iMac with OS X. The four ...

Material Related to the !VisLab and Amira Introductory Seminar Slides Seminar Slides: Introduction to the SCS VisLab plus A Layman's Guide to Amira NOTE ...