Haystack (Oct 2009 – June 2013)
MERCURY SGI Altix 3700 Bx2
Summary
- SGI Altix 3700 Bx2 has
- 128 1.6GHz Intel Itanium2 processors with 6MB last level cache each
- 640GB of globally shared memory
- 7.2TB RAID5 SGI InfiniteStorage 220
- NUMAlink interconnect
- a single image of Novell SUSE Linux Enterprise Server 10.0 SP2 + SGI ProPack 6
Hardware Configuration
- It physically appears as
- Two 40U SGI racks
- 8 compute (CR) bricks and 2 router(R) brick per rack
- First rack has an I/O (IX) brick and the second rack has an IS220 storage unit
- Three power bays per rack Each one of the 16 CR-bricks have 8 single core Intel Itanium2 processors
- CR-bricks interconnected to R-bricks and IX-bricks via 80 NUMAlink cables
- IX-brick has 10/100/1000 ethernet, CDROM, 11 PCIX slots, 2 146GB System Disks
- The storage unit is an SGI InfiniteStorage220; 2 Trays – 7.2TB RAID5, 4 – 4+1, 1 Hot Spare 21 – 450GB 15K RPM SAS Drives
Software
- The machine the following software and more will be added as necessary.
- Chemistry
- Gaussian09 C.03; Gaussian03 Rev. D.03, E.03
ii.NWchem 5.1.1
iii. PSI 3.4
- AMBER 9.1
- MPQC 2.4
- ORCA 2.8
- General tools aside from what is available in stock SLES 10.2
- Intel Compilers (11.0+)
- Intel MKL libraries (10.2+)
iii. OpenMPI 1.4.2+
- SGI MPT 1.23
- SGI Propack 6
Access
- The machine is accessible to MERCURY members.
- MERCURY members
i.You can access the machine (haystack) through MERCURY resources at Hamilton College
ssh username@jake.hpc.hamilton.edu. From jake, ssh haystack
(Email Steve Young at Hamilton or Berhane Temelso at Bucknell if you have any questions.)
ii.Here are a few details on using haystack. – Home directories are NFS mounted from Hamilton servers,. so expect some latency when you first log in
– Binaries are also NFS mounted from Hamilton. All the applications you ran on Hamilton’s SGI Altix machines will run on haystack.
– Since there is no queue manager (PBS, SGE, LSF … etc) running on haystack, you have to run everything interactively and take precautions to ensure the machine is not overloaded.
– 64 of the 128 CPUs are always available, but the other 64 are powered on or off depending on the machine’s use. In the summer when there is a lot of need for computer time, the machine operates at full capacity. During the academic year, half the machine’s capacity is sufficient to meet computational needs.
- Bucknell community
i.You can request for accounts
(Email: Berhane Temelso)
- You can access the machine from campus using ssh (ssh username@haystack.bucknell.edu)
iii. For security reasons, the machine is not accessible directly from outside of campus. You would need to
- Either need to use a Bucknell VPN tunnel to access the machine using ssh OR
- You can log into a Bucknell server (say linuxremote.eg.bucknell.edu) and ssh to haystack from there. The second method is typically faster