CHARMM on the Terra
The Terra TR2000 system is available for batch usage only; all CHARMM
work should be submitted to the batchq named t2 since only one
process at a time may use the 16 Alpha chip parallel ring. As on the
HPs, batchq jobs are run from the current working directory, which may
be on any volume accessible via the /v automount service. As always,
input scripts should be thoroughly tested (with fewer steps) on a single
processor host before submitting work to a precious parallel queue. Be
sure to read the restrictions section, and note the distinct
syntax.
The syntax for using the program is:
charmm INP=file.inp OUT=file.out [ [param:value] ...]
The file prefixes INP= and OUT= must be upper case, and no whitespace
(space, tab) is permitted; inp=file.inp will not work, nor will
INP = file.inp
- charmm
- A script in /usr/local/bin on the Terra machine (t2.mgsl.dcrt)
- file.inp
- A text file containing CHARMM input commands, using the command syntax described in usage.doc.
The actual name used for file.inp is up to the user, although it is useful to use short names which hint at the overall purpose, e.g. makpsf.inp
- file.out
- The log file for the CHARMM run, containing echoed commands, and various amounts of command output. The output print level may be increased or decreased in general, and procedures such as minimization and dynamics have printout frequency specifications.
- param:value
- CHARMM script parameters (essentially user defined variables) may optionally be defined on Unix shell command line, using the form param:value; the value is substituted for occurrences of @param in the input script.
- all input files must be in card format (RTF, PARAM, PSF, etc.)
- pathnames using /v do not work for the CHARMM open command; use
relative pathnames, e.g. ../ or subdir, or perhaps a (temporary) link
- many extra features are not included; also NOGRAPHICS, NOVIBRAN, NOMISC
- the HP home directory is used for accounts, but not all HP accounts are
necessarily valid on the Terra
- most /usr/local/bin commands from the HP system are not present; besides
the (modified) charmm command, only number and tcsh are available
Since none of the copies of CHARMM run on the host with OSF1 (DEC Unix),
only the cu_cp process (which handles I/O) is seen with the qb
command. Also, the CHARMM output stream is written in 64K chunks, and the
temporary output log Tfortout.0 is generally incomplete. The best
means of following job progress is to observe the changes in size of the
output trajectory file, e.g. dyn.trj
The Terra can get hung from time to time, and the dq script cannot
be used to kill the active job. To terminate an active job on the Terra, login
to t2.mgsl.dcrt and kill the process named toslgo (Terra Operating
System Load and GO). [This is the process on the OSF1 host which loads the
CHARMM executable image onto each of the processors in the parallel ring, and
the last command executed in the charmm cover script.]
Information and HTML pages provided by:
NIH/NHLBI/LBC Computational Biophysics Section
FDA/CBER/OVRR Biophysics Laboratory
Terra Overview / rvenable@deimos.cber.nih.gov