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Computer
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Clusters
Our five clusters are Xerxes, Darius2, Darius1, Cyrus1, and Quantum2. See below for additional information. For information about using Gaussian at MIT, see below.
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Darius1
Hostname: darius1.csbi.mit.edu
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Darius1
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is
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a
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35-node
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cluster,
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installed April 2010.
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Information
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about
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Darius
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can
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be
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found
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on
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its
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...
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.
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Cyrus1
Hostname: cyrus1.csbi.mit.edu
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Cyrus1
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is
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a
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24-node
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cluster,
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installed
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December
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2008.
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Please
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note
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that
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the
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CSBi
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network,
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on
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which
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Cyrus1
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is
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hosted,
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does
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not
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allow
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access
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from
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IP
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addresses
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external
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to
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MIT.
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For
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remote
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access
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to
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Cyrus1,
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see
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the
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...
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.
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Status notes
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Node 10 (n010)
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is
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currently
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inaccessible.
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Node
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information
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The
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table
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below
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lists
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the
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memory
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and
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swap
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file
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size
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of
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each
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node
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on
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Cyrus1,
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along
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with
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the
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amount
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of
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space
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used
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and
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free
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in
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each
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node's
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local
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/scratch/
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directory.
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This
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information
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is
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current
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as
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of
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April
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1,
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2010.
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node | memory (MB) |
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swap |
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(MB) |
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scratch |
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used |
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scratch |
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free |
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head | 7982 | 16386 |
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|
n001 | 7982 | 8197 | 147G | 52G |
n002 | 7982 | 8197 | 51G | 148G |
n003 | 7982 | 8197 | 50G | 149G |
n004 | 7982 | 8197 | 102G | 97G |
n005 | 7982 | 8197 | 29G | 170G |
n006 | 7982 | 8197 | 11G | 188G |
n007 | 7982 | 8197 | 47G | 152G |
n008 | 7982 | 8197 | 66G | 133G |
n009 | 7982 | 8197 | 84G | 115G |
n010 |
|
|
|
|
n011 | 7982 | 8197 | 27G | 171G |
n012 | 7982 | 8197 | 126G | 73G |
n013 | 7982 | 8197 | 23G | 176G |
n014 | 7982 | 8197 | 50M | 198G |
n015 | 7982 | 8197 | 22G | 177G |
n016 | 7982 | 8197 | 33M | 198G |
n017 | 7982 | 8197 | 63G | 135G |
n018 | 7982 | 8197 | 60G | 139G |
n019 | 7982 | 8197 | 2.1G | 196G |
n020 | 7982 | 8197 | 61G | 138G |
n021 | 7982 | 8197 | 33M | 198G |
n022 | 7982 | 8197 | 90G | 109G |
n023 | 7982 | 8197 | 33G | 166G |
n024 | 7982 | 8197 | 29G | 170G |
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Quantum2
Hostname: quantum2.mit.edu
Quantum2 is a 20-node cluster installed in October 2007, which features high-memory nodes for quantum-chemical calculations.
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Available Software
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VMD 1.8.7 has been installed, and is working with a user's local Xwindows server. The executable is "/usr/local/vmd-1.8.7"
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(actually
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not
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a
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binary
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executable,
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but
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a
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script),
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and
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can
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be
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invoked
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using
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"vmd-1.8.7."
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A
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number
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of
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software
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packages
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have
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been
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installed
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in
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/home/gpw501/software/
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Please
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contact
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gwood@mit.edu
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for
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any
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questions;
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a
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very
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limited
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usage
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guide
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is
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given
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below.
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GAMESS-US
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quantum
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chemistry
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package.
| Code Block |
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} Usage: /home/gpw501/software/gamess/rungms JOB VERNO NCPUS >& JOB.log & JOB is the name of JOB.inp file to be executed VERNO is the current version of gamess (01 at the time of writing) NCPUS number of cpus you must make a scratch directory that matches your user name on the node you are running from i.e. /scratch/$USER {code} See [GAMESS homepage|http://www.msg.ameslab.gov/GAMESS/] for more details. [CPMD|http://www.cpmd.org/] (QMMM version) |
See GAMESS homepage for more details.
CPMD (QMMM version) plane-wave/PP
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quantum
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CP
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and
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BO
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dynamics.
| Code Block |
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} Usage: mpirun -n NCPUS cpmd.x JOB PATH-TO-PPs >& JOB.out & mpirun should be set to /opt/openmpi/tcp-gnu/bin/mpirun in your .bashrc NCPUS number of cpus JOB name of job file to be executed PATH-TO-PPs the path to a pseudo potential library (see for eg /home/gpw501/software/cpmd/pseudos/ ) JOB.out name of output file {code} [Amber 10|http://ambermd.org/] molecular dynamics program. Executables are located in |
Amber 10 molecular dynamics program. Executables are located in /home/gpw501/software/amber10/exe/
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Gromacs molecular dynamics program. Was installed as root so binaries for MD and the gromacs tools are located in /usr/local/bin/.
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propka
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electrostatic
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and
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pka
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computations
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for
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proteins.
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See
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/home/gpw501/software/propka2.0src/README_PROPKA2.0
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Status notes
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Nodes 4 and 14 (n004 and n014) are currently inaccessible, due to apparent hard disk problems.
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Node information
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The table below lists the memory and swap file size of each node on Quantum2, along with the amount of space used and free in each node's local /scratch/ directory. This information is current as of April 1, 2010.
node | memory (MB) | swap (MB) | scratch used | scratch free |
n001 | 7970 | 16386 | 104G | 90G |
n002 | 7970 | 16386 | 163G | 31G |
n003 | 7970 | 16386 | 13G | 181G |
n004 |
|
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n005 | 7970 | 16386 | 150G | 44G |
n006 | 7970 | 16386 | 138G | 56G |
n007 | 7970 | 16386 | 194G | 0 |
n008 | 7970 | 16386 | 182G | 12G |
n009 | 7970 | 16386 | 155G | 39G |
n010 | 7970 | 16386 | 133G | 61G |
n011 | 7970 | 16386 | 143G | 51G |
n012 | 7970 | 16386 | 122G | 72G |
n013 | 7970 | 16386 | 153G | 41G |
n014 |
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n015 | 7970 | 16386 | 6.8G | 187G |
n016 | 7970 | 16386 | 15G | 180G |
n017 | 3942 | 16386 | 22G | 172G |
n018 | 7970 | 16386 | 16G | 178G |
n019 | 16026 | 16386 | 39G | 155G |
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Gaussian03 at MIT
MIT currently has a site license to run Gaussian03 on IS&T-owned computers, such as those in Athena clusters. For more information, see Gaussian on Athena. For information about creating/submitting Gaussian jobs, see these notes from the 10.675J course taught at MIT: Basics of Running G03.