[gmx-users] MPICH, SMP,--disable-nice

Erik Lindahl erik at theophys.kth.se
Sat Jan 5 13:42:52 CET 2002

Mehmet Suezen wrote:

> Dear Eric,
> Many thanks for your kind help.
> Actually I mistimed it. What does --disable-nice means? where I couldn't
> find its description in the help.
> After all I tried with and without --disable-nice (cos it advised in
> INSTALL file of the distribution.)
> No affect on result. Executable with MPICH just appeared very short time
> drop then. It is really a
> strange behavior.

By default, the cpu-intensive programs like mdrun are run at nice 19 so
you can have them in the background on your workstation. The nicelevel can
be set with the -nice option, though.

This will only have effect on the runtime if you have more than one
job on the machine.

Since some systems (like Cygwin) don't have process priorities it can be
turned off,
but keep it on a unix system.

> Let me ask some question on this problem:
> (i.)  How could I ensure that mdrun uses MPICH libraries? Except than
> giving as an  environment variable before
>       compilation or as LD_LIBRARY_PATH?

 Not sure - there is some information in our faq on how to link with
MPI libraries
without using a command like "mpicc", but this is probably better answered by
the MPICH documentation!

> (ii.) Does SMP machines makes difference on compilation procedure? Where
> I don't think.

Nope, although you can get a faster compile by using both processors:

make MAKE="make -j2 "



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