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

[Erik Lindahl]

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
cpu-intensive
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 "

Cheers,

Erik