...
Darius
...
is
...
a
...
32-node
...
cluster
...
with
...
InfiniBand
...
QDR
...
interconnections.
...
It
...
runs
...
...
...
(Linux
...
kernel
...
version
...
2.6),
...
which
...
is
...
closely
...
related
...
to
...
Red
...
Hat
...
Enterprise
...
Linux.
...
Its
...
hostname
...
is
...
darius1.csbi.mit.edu.
...
The
...
CSBi
...
firewall
...
is
...
configured
...
to
...
accept
...
connections
...
only
...
from
...
MIT
...
IP
...
addresses,
...
so
...
users
...
should
...
connect
...
to
...
MITNet
...
through
...
...
...
for
...
off-campus
...
use.
...
Installed software
software | location of source code or executable |
|---|---|
NAMD 2.7b2 | /share/apps/NAMD_2.7b2_Source/Linux-x86_64-OpenMPI |
...
Charm++ |
...
6.2 |
...
/share/apps/charm-6.2.0/mpi-linux-x86_64-mpicxx |
...
VMD |
...
1.8.7 |
...
/share/apps/vmd-1.8.7/LINUXAMD64 |
...
AmberTools |
...
1.4 |
...
/share/apps/amber11 |
...
CHARMM |
...
c35b2 |
...
not |
...
yet |
...
installed, |
...
source |
...
in |
...
/share/apps/c35b2 |
...
GNUPLOT |
...
4.0 |
...
/usr/bin/gnuplot |
...
Grace |
...
5.1 |
...
/usr/bin/xmgrace |
...
Octave |
...
3.0.5 |
...
/usr/bin/octave |
...
GROMACS-MPI |
...
4.0.7 |
...
/usr/bin/g_mdrun_mpi |
...
The
...
OpenMPI,
...
Mvapich,
...
and
...
Mvapich2
...
libraries
...
all
...
use
...
the
...
Infiniband
...
interface.
...
libraries | location |
|---|---|
OpenMPI | /usr/mpi/gcc/openmpi-1.4.1 |
...
Mvapich | /usr/mpi/gcc/mvapich-1.2.0 |
...
Mvapich2 | /usr/mpi/gcc/mvapic2-1.4.1 |
...
Platform |
...
MPI, |
...
aka |
...
HP-MPI |
...
/opt/hpmpi |
...
Note
...
that
...
the
...
mpicc,
...
mpicxx,
...
mpif77,
...
mpif90,
...
etc.,
...
all
...
refer
...
to
...
the
...
OpenMPI
...
versions,
...
when
...
using
...
the
...
default
...
path.
...
Performance
Using the 92 katom ApoA1 benchmark with NAMD 2.7,
...
performance
...
appears
...
to
...
compare
...
very
...
favorably
...
with
...
previously
...
benchmarked
...
clusters:
...
its
...
[processor
...
cores
...
X
...
time
...
per
...
step
...
]
...
values
...
(corresponding
...
to
...
the
...
ordinate
...
on
...
the
...
...
on
...
the
...
linked
...
page)
...
vary
...
from
...
1.8
...
sec
...
(8
...
CPUs)
...
to
...
2.1
...
sec
...
(128
...
CPUs).
Using the queue system
All programs run on Darius must use the queue system. Users can check what jobs are running using qstat; XWindows users can try xpbs, although load times are long. Users can submit their jobs using the qsub command:
| Code Block |
|---|
!apoa_bench_scan.png|thumbnail! h4. Using the queue system All programs run on Darius must use the queue system. Users can check what jobs are running using {{qstat}}; XWindows users can try {{xpbs}}, although load times are long. Users can submit their jobs using the {{qsub}} command: {code} qsub jobscript.sh {code} |
Here
...
is
...
an
...
example
...
of
...
a
...
simple
...
PBS
...
script,
...
which
...
is
...
like
...
an
...
ordinary
...
BASH
...
script,
...
but
...
with
...
the
...
addition
...
of
...
special
...
#PBS
...
directives:
| Code Block |
|---|
} #!/bin/bash #PBS -k o #PBS -N apoa #PBS -l nodes=1:ppn=4,walltime=12:00:00 #PBS -j oe cd /home/musolino/namd/apoa1 /usr/mpi/gcc/openmpi-1.4.1/bin/mpirun /share/apps/NAMD_2.7b2_Source/Linux-x86_64-OpenMPI/namd2 apoa1.namd {code} h4. Notes on compiling NAMD |
Notes on compiling NAMD 2.6
...
- Run
./config
...
Linux-amd64-MPI.<postfix>
...
- to
...
- create
...
- an
...
- installation.
...
- <Postfix>
...
- is
...
- any
...
- label
...
- you
...
- wish
...
- to
...
- append
...
- to
...
- the
...
- NAMD
...
- directory.
...
- The
...
- new
...
- Charm++
...
- and
...
- NAMD
...
- 2.7
...
- use
...
- different
...
- platform
...
- names
...
- than
...
- they
...
- did
...
- in
...
- the
...
- past(e.g.
...
Linux-x86_64-OpenMPI
...
- for
...
- NAMD
...
- 2.7
...
- and
...
- Charm++
...
- 6.2,
...
- but
...
Linux-amd64-MPI
...
- for
...
- NAMD
...
- 2.6.
...
- This
...
- causes
...
- problems
...
- when
...
- looking
...
- for
...
- the
...
- Charm++
...
- installation,
...
- so
...
- edit
...
Make.charm
...
- in
...
- NAMD
...
- directory:
...
Code Block
...
CHARMBASE = /share/apps/charm-6.2.0/mpi-linux-x86_64-mpicxx
...
- Then edit
Makearchin theLinux-amd64-MPI.postfix
...
- directory
...
- as
...
- follows,
...
- by
...
- changing
...
- the
...
CHARM=...
...
- line:
...
Code Block
...
include .rootdir/Make.charm include .rootdir/arch/Linux-amd64-MPI.arch CHARM = $(CHARMBASE) NAMD_PLATFORM = $(NAMD_ARCH)-MPI include .rootdir/arch/$(NAMD_ARCH)$(NAMD_SUBARCH).base
...
- Try
makein the installation directory.
Other notes
Using the Mac OS 10.6 X11 client, XWindows is working, with small utilities like xcalc and xpbs, and with VMD 1.8.7.
...
VMD
...
performance
...
seems
...
sluggish,
...
however.
...
Note:
...
when
...
connecting
...
with
...
"ssh
...
-X",
...
starting
...
VMD
...
consistently
...
leads
...
to
...
a
...
crash
...
of
...
the
...
X11
...
client.
...
Connecting
...
with
...
"ssh
...
-Y"
...
(which
...
disables
...
X11
...
security
...
protocols,
...
for
...
trusted
...
connections)
...
works
...
instead.
...
This
...
problem
...
has
...
occurred
...
with
...
other
...
computers
...
in
...
the
...
past,
...
and
...
it's
...
not
...
clear
...
whether
...
this
...
is
...
a
...
bug
...
in
...
VMD,
...
the
...
X11
...
installation
...
on
...
the
...
cluster,
...
or
...
the
...
Mac
...
OS
...
10.6
...
X11
...
client.