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Seventh Graders Introduced to Supercomputing

On July 1, Brian Ropers-Huilman, MSI Director of Systems Administration and Technical Operations, spoke to a group of seventh-grade students about MSI, high-performance computing, and programming for computers. The students are taking a class in Math and Programming as part of the Minnesota...

IBM Town Hall Meeting, September 20

posted on September 12, 2013 As part of the ongoing selection process for the next HPC system at MSI, MSI has invited top high performance computing vendors to present their high performance computing portfolios and roadmaps to users in a Town Hall setting. IBM will be on-site Friday, September 20...

Computational Studies in Cell Motility

Abstract: 

Computational Studies in Cell Motility

Cell locomotion plays an essential role during embryonic development, angiogenesis, tissue regeneration, the immune response, and wound healing in multicellular organisms. Movement is a very complex process that involves the spatial and temporal control and integration of a number of sub-processes, including the transduction of chemical or mechanical signals from the environment, intracellular biochemical responses, and translation of the intra- and extracellular signals into a mechanical response. While many single-celled organisms use flagella or cilia to swim, there are two basic modes of movement used by eukaryotic cells that lack such structures - mesenchymal and amoeboid. The former, which can be characterized as "crawling" in fibroblasts or "gliding" in keratocytes, involves the extension of finger-like pseudopodia and/or broad flat lamellipodia, whose protrusion is driven by actin polymerization at the leading edge. In the amoeboid mode, which does not rely on strong adhesion, cells are more rounded and employ shape changes to move - in effect "jostling through the crowd" or "swimming." Here force generation relies more heavily on actin bundles and on the control of myosin contractility. Leukocytes use this mode for movement through the extracellular matrix when adhesion molecules have been knocked out. However, recent experiments have shown that numerous cell types display enormous plasticity in locomotion, in that they sense the mechanical properties of their environment and adjust the balance between the modes. Thus pure crawling and pure swimming are the extremes on a continuum of locomotion strategies, but many cells can sense their environment and use the most efficient strategy in a given context.

One objective of this research is to understand how shape changes can propel cells, the forces that drive the shape changes, and what determines the efficiency of a stroke. Another objective is to understand the cytoskeletal changes needed to produce the shape changes, beginning with blebbing. Blebs result from actomyosin contractions of the cortex, which cause either transient detachments or local rupturing of the cortex. While much less studied than actin-driven extensions, blebs are used as an alternate mechanism for movement by many cell types, and also play a role during cytokinesis and apoptosis.

Another major aspect of this research concerns the signaling networks that control the dynamic rearrangements of the actin cytoskeleton. The pathways involve Rho GTPases that act as molecular switches that relay extracellular signals, both receptor-mediated signals and mechanical signals transduced via integrin-mediated adhesion to the extracellular matrix. Recent experimental work has shed light on the networks involved, but a synthesis of these results into an integrated model that can predict how the balances between the pathways determine whether the amoeboid or mesenchymal mode prevails is needed.

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Group name: 
othmerhg

Checkpointing

Abstract

Checkpointing HPC applications has been a challenging, but highly desired functionality for saving the state of long-running applications. This functionality hedges against failure modes from unexpected events that can cause premature failure of an application.
 

Itasca - where one can do the checkpointing right now.

        login to itasca

              ssh username@itasca.msi.umn.edu

Checkpoint serial jobs

Compile your job

       module load intel

       icc  -o my_test my_app.c  -lcr

or

       ifort -o my_test  my_app.f -lcr  
 

Run your job

      qsub -I -l node=1:ppn=8,mem=10gb,walltime=2:00:00

      cd $wrk # where your job

      cr_run ./my_test &

Find the job PID

   PS=`ps -u szhang | grep my_test`

   PID=${PS:0:6}
 

  PID=`echo "${PID:0:6}" | sed 's/ //g' `
  cr_checkpoint --signal=2 --term $PID

To verify   checkpointing  success

    tail  context.$PID

To checkpoint again and terminate the job 

   cr_checkpoint  --term $PID

To restart the job from the status of last chechpointing

  cr_restart context.$PID

 

Checkpoint OpenMP  jobs

Compile your job

       module load intel

       icc  -o my_test -openmp  my_app.c  -lcr

or

       ifort -o my_test   -openmp my_app.f -lcr  
 

Run your job

      qsub -I -l node=1:ppn=8,mem=10gb,walltime=2:00:00

      cd $wrk # where your job

      export OMP_NUM_THREADS=4

      cr_run ./my_test &

Find the job PID and checkpoint the job

   PS=`ps -u szhang | grep my_test`

   PID=`echo "${PID:0:6}" | sed 's/ //g' `

   cr_checkpoint --signal=2 --term $PID

To verify   checkpointing  success

    tail  context.$PID

To checkpoint again and terminate the job 

   cr_checkpoint  --term $PID

To restart the job from the status of last chechpointing

  export OMP_NUM_THREADS=4

 cr_restart context.$PID

 

Checkpoint MPI  jobs

Compile your job

       module load intel ompi/1.6.3-blcr/intel

       mpicc  -o my_test   my_app.c 

or

       mpif77 -o my_test    my_app.f
 

Where to store the checkpointing file

Please create a  .openmpi in your home directory, generate a file named as mca-params.conf under    .openmpi. the mca-params.conf file should contain the path to the directory where you want to store the checkpointing files. Here is an example:

     cat /home/support/szhang/.openmpi/mca-params.conf
     snapc_base_global_snapshot_dir=/lustre/cr_files
     crs_base_snapshot_dir=/lustre/cr_files/local

Run your job

      qsub -I -l node=4:ppn=8,mem=10gb,walltime=2:00:00

      cd $wrk # where your job

      mpirun  -am ft-enable-cr -np 32 ./my_test &

Find the job PID and checkpoint it:

      pid=`ps -u szhang | grep mpirun`

      jid=`echo "${pid:0:6}" | sed 's/ //g' `

     export jid
     ompi-checkpoint $jid

To verify  checkpointing  success

    ls -al /lustre/cr_files | grep $jid

To checkpoint again and terminate the job 

   ompi-checkpoint --term $jid

To restart the job from the status of last chechpointing

cd  /lustre/cr_files/

 ompi-restart  /lustre/cr_files/ompi_global_snapshot_$jid.ckpt/

 

 

  I/O Performance

 

MSI Purchases New Storage System

UPDATE: The new storage system will be activated on January 9, 2013. All data should be migrated to the new system during January - July 2013. Complete information can be found on the Panasas Migration Guide webpage. The Minnesota Supercomputing Institute (MSI) is putting into a production a new...

Discovery of Compounds That Inhibit Select RNA Viruses

Abstract: 

Discovery of Compounds That Inhibit Select RNA Viruses

These researchers' main interests are identifying anti-viral drug targets for major human pathogens and evaluating small molecules for their ability to inhibit those targets and virus replication. They employ four main approaches to uncover small molecules that inhibit the replication and pathogenesis of viruses:

  • Conduct phenotypic screens to evaluate anti-viral activity of small molecules.
  • Collaborate with medicinal chemists, computational chemists, and structural biologists to rationally design small molecule inhibitors of established and novel viral drug targets.
  • Design and implement high throughput screening to identify small molecules that inhibit known and novel viral drug targets.
  • Understand mechanism of effect of small molecule inhibitors.

Passage of virus in the presence of inhibitors will generate resistant virus and the researchers can sequence viral genomes to understand which viral gene products are important for inhibition and aspects of those proteins that interact with inibitors. They use MSI resources to help analyze large amounts of nucleic acid sequence data to understand how inhibitors function. In addition, the researchers are developing reagents to understand replication of RNA viruses such as coronaviruses and to screen for coronavirus inhibitors. They have used MSI resources previously to analyze the nucleic acid sequence data from a candidate viral repicon and are continuing that analysis.

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Group name: 
geraghty

12/3/12: MSI at CSE Family Fun Fair

MSI participated in the College of Science and Engineering’s Family Fun Fair on November 17, 2012. This annual event, which is designed to introduce children to science and math in fun and interactive ways, had nearly 2,500 participants this year. At the MSI booth, hundreds of kids created models...

The Impact of Emerging Technologies on the Design of Computer Systems

Abstract: 

The Impact of Emerging Technologies on the Design of Computer Systems

The overall goal of this group’s work is to develop computer systems that satisfy a desired set of constraints. These constraints typically require non-obvious trade-offs in performance, power consumption, cost, and reliability. The researchers are particularly interested in how changes in the underlying technology, such as the trend towards smaller feature sizes in VLSI circuits and new types of technologies, affect how computer systems will be designed in the future. They are working on several interrelated projects in this broad area, including the development of techniques to automatically classify the benchmark programs used to evaluate the performance of computer systems, techniques to statistically evaluate large design spaces, and studying how spintronics components might be used to design computer systems.   

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Group name: 
liljadj

HP Town Hall Meeting, September 17

posted on September 12, 2013 As part of the ongoing selection process for the next HPC system at MSI, MSI has invited top high performance computing vendors to present their high performance computing portfolios and roadmaps to users in a Town Hall setting. HP will be on-site Tuesday, September 17...

Impact of Alcohol and Drug Use on the Development of Neural Connections During Adolescence and Young Adulthood

Abstract: 

Impact of Alcohol and Drug Use on the Development of Neural Connections During Adolescence and Young Adulthood           

The primary aims of this ongoing longitudinal study are to conduct a comprehensive investigation of brain development during adolescence and early adulthood and to determine how brain development is altered when individuals begin to use alcohol (as well as other drugs, such as marijuana) during this period. The researchers employ an extensive two-day data collection protocol at each study time point, consisting of behavioral assessments (interviews, questionnaires, computerized testing), brain magnetic resonance imaging (MRI; high resolution anatomical scans, several types of diffusion scans, spectroscopy, resting functional scans), and electroencephalography (EEG). They also have a one-time collection of genetic data (single-nucleotide polymorphisms). Data collection waves occur at two-year intervals and currently the researchers are completing their fifth assessment. In their analyses within and across these types of data, the researchers investigate the refinement of brain network connectivity during normal adolescent development and identify alterations due to alcohol and drug use. MSI resources are heavily used to achieve this “connectivity” aspect of this brain-behavior research, which relates directly to the goals of the Human Connectome Project. For example, using high-resolution anatomical MRI scans, the researchers extract complete representations of the cortical surface in both brain hemispheres; using diffusion MRI scans they compute measures of the microstructural organization of neural fibers that connect brain regions, and then conduct a “virtual dissection” of these fibers using probabilistic tractography; using resting functional MRI scans they measure neurophysiological activity across multiple overlapping brain networks; using EEG recordings they identify the coordinated synchronization of electrophysiological activity within brain networks in response to external stimuli; and so on. MSI resources are used in all of these analyses, for both data preprocessing and permutation-based statistics. 

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Group name: 
lucianam

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