Center for Computational Molecular Science and Technology Georgia Institute of Technology Center for Computational Molecular Science and Technology School of Chemistry and Biochemistry

CCMST Weekly News, April 29 2011

April 29, 2011 3:24 pm EDT

1. Announcements
2. Statistics
3. Tip of the Week

ANNOUNCEMENTS

Upcoming Seminars

May 2, 2011 7:30 PM – 9:00 PM
Emory University, 316 Atwood Hall
AACP Seminar Series
Prof. John Yates, University of Virginia
Photochemical Behavior of TiO2- Following Electron and Hole Behavior

May 5, 2011 11:00 AM - 12 AM
IBB, Suddath Seminar Room 1128
COPE Seminar
Professor Paul Burn, School of Chemistry and Molecular Biosciences, The University of Queensland, Australia
Probing Organic Optoelectronic Film Morphology with Neutrons

May 5, 2011 4:00 PM – 5:00 PM MoSE 3201A
Physical Chemistry Seminar Series
Prof. Lillian Chong, University of Pittsburgh
Molecular simulations of protein binding and switching

May 6, 2011 3:00 PM – 5:00 PM MoSE 4202-A
Thesis Defense - Ms. Ashley Tucker
Complex dynamics and phase behavior in non-equilibrium models: From Lorentz models to liquid crystals

Ggate Online after Upgrade

Ggate has now resumed production after the upgrade. Please note the following:

  1. There are now 30 nodes actives, for a total of 640 processors. One node (n2) developed an hardware problem, and we are waiting for a replacement part. Two of the GPU nodes (n29 and n30) are excluded from the queue for the moment for testing.
  2. The Icebreaker is not yet available. The configuration should be finalized in the following days.
  3. All submission scripts should work as before. If you plan on running a GPU enabled code through the queue please contact Massimo, as the submission process of GPU jobs has not been finalized yet.

Please contact Massimo (massimo.malagoli@chemistry.gatech.edu) if you have any question.

STATISTICS

GGATE

Uptime: 1 day
/home directory usage: 14% (9.5 TB available)
/backups directory usage: 53%

Utilization for period from: 03/29/2011 to: 04/28/2011

Note: Full statistics for ggate are available online at: http://ggate.chemistry.gatech.edu:8080 (the link works only for the Gatech Chemistry network)

FGATE

Uptime: 105 days
/home directory usage: 80% (1.2 TB available)
/backups directory usage: 98%

LSF usage for Week 16 (4/18-4/24) (times are in minutes)
GroupJobsTotal CPUAvg CPUAvg WaitAvg Trnr.
Bredas 38 148105 8% 3897 5852 8118
Hernandez 117 61041 3% 522 1438 2110
Sherrill 578 224812 12% 389 833 1273
Other 5 26650 1% 5330 0 2776
Total 738 460608 24% 624 1182 1769

Note: percentages refer to the total CPU time available for the period.

Most productive user of the Week: loriab 224678.

EGATE

Uptime: 53 days
/theoryfs/common directory usage: 82% (124 GB available)
/theoryfs/ccmst directory usage: 93% (64 GB available)

LSF usage for Week 16 (4/18-4/24) (times are in minutes)
GroupJobsTotal CPUAvg CPUAvg WaitAvg Trnr.
Hernandez 1364 283087 19% 208 83 434
Other 423 117608 8% 278 0 281
Total 1787 400696 27% 224 64 398

Note: percentages refer to the total CPU time available for the period.

Most productive user of the Week: galen 249239.

TIP OF THE WEEK

By Massimo

Working on Ggate: Hardware Configuration

Now that ggate has reached its full configuration, let's take some time to review the hardware configuration of the cluster:

Node Name Functionality Processor Memory Disk Interconnection
Infiniband Gigabit Ethernet
Greengate Login 2.0 GHz, 16 cores AMD Opteron 6128 64 GB 11TB /home + 11 TB /backup x x
n0-n1 Fat nodes (MEMP_8, RAM_256GB) 2.0 GHz, 32 cores AMD Opteron 6128 256 GB 2.5 TB local scratch (/scratch) x x
n2-n11 Thin nodes (MEMP_2, RAM_64GB) 2.0 GHz, 32 cores AMD Opteron 6128 64 GB 2.5 TB local scratch (/scratch) x x
n12-n15 Fat nodes (MEMP_8, RAM_128GB) 2.0 GHz, 16 cores AMD Opteron 6128 128 GB 2.5 TB local scratch (/scratch) x x
Icebreaker Fast scratch storage 2.27 GHz, 8 cores Intel E5520 24 GB 24 TB x x
n13-n29 GPU nodes (Tesla) 2.0 GHz, 16 cores AMD Opteron 6128, 2 NVIDIA C1060 64 GB (CPU) + 8 GB (GPU) 2.5 TB local scratch (/scratch) x x
n30-n31 GPU nodes (Fermi) 2.0 GHz, 16 cores AMD Opteron 6128, NVIDIA C2070 64 GB (CPU) + 6 GB (GPU) 2.5 TB local scratch (/scratch) x x
Total   720 2.0 GHz AMD Opteron cores, 30 C1060 + 2 C2070 GPU (Total 8096 thread processors) 2240 GB DDR3 Memory + 132 GB GPU memory (DDR3 + DDR5) 134 TB x x

Do you have usage tips that you want to share with the other CCMST users? Please send them to Massimo (massimo.malagoli@chemistry.gatech.edu) for inclusion in the Tip of the Week section.