On 25/03/2011 8:36 AM, Adam Herbst wrote:
Thank you all for your help! I ran
make distclean
and re-configured in the GROMACS source folder via
sudo ./configure --prefix=$SOFT --with-gsl --enable-threads
CFLAGS="$CFLAGS -I$SOFT/include" LDFLAGS="$LDFLAGS -L$SOFT/lib"
sudo make -j $NCPU
sudo make install
As a general rule, one should minimize the use of super-user accounts.
You never know when some idiot has messed up the configure script, and
running it as super-user can trash your machine. It is safer to maintain
the source code in a directory writable by whoever will be building it.
Now "configure" and "make" can be run as a normal user. Only the step
that needs write access to system areas needs sudo, i.e. "make install".
Another good idea is to keep separate an unmodified version of GROMACS
and your modified one. Now you you just source the GMXRC from the
version you want to use. Then if you run into some problem, you can
sometimes immediately establish that it wasn't the fault of your changed
code. Alternatively or additionally, using "./configure --suffix=_m" (or
whatever) gives you confirmation of which version you are using every
time you use it.
Mark
where SOFT is the installation directory for FFTW3 and GSL, and NCPU
is the number of processors (24) in my machine. I found if I didn't
specify the CFLAGS and LDFLAGS when running configure (even if they
were already environment variables with the proper paths), I got an
error that the FFTW3 header file or library couldn't be found.
Now when I run mdrun, it automatically uses multiple threads and goes
just as fast as before my changes. Thanks again,
Adam
On Thu, Mar 24, 2011 at 9:00 AM, Mark Abraham <[email protected]
<mailto:[email protected]>> wrote:
On 24/03/2011 11 <tel:24%2F03%2F2011%2011>:51 PM, Adam Herbst wrote:
Dear GROMACS users,
I successfully installed GROMACS 4.5.1 several months ago on a
Mac Pro with 12 CPUs, and the "mdrun" command (not "mpirun
mdrun_mpi") allows parallel simulations--it automatically uses
multiple processors, while the number of processors can be
manually specified as N with the flag "mdrun -nt N". I
understand that this is a feature of GROMACS 4 and later.
Yes, threading, enabled by default, and mutually incompatible with
MPI.
Now I am making minor changes to the mdrun source code, and I
want to recompile such that the parallel version of mdrun is
updated with my changes. But when I run:
make mdrun (or just make)
make install-mdrun (or just make install)
from the top-level source directory, the only executables that
are updated are the ones with the _mpi suffix, such as
mdrun_mpi. The version of mdrun in src/kernel/ is updated,
but this one has no -nt flag and cannot seem to run on
multiple processors. And when I run
Subsequently you have configured with --enable-mpi, so threading
is disabled. Now everything is probably a mess.
mpirun -np N mdrun_mpi [options],
the same simulation is started separately on each processor,
leading to a crash. If I use
mpirun -np 1 -cpus-per-proc N mdrun_mpi [options],
I get an error message that this is not supported on my
computer ("An attempt to set processor affinity has failed").
I can't configure the input .tpr file for parallel because
grompp doesn't have the -np flag in GROMACS 4.
How can I update the parallel-capable "mdrun" executable with
my changes?
Run "make distclean" and then re-configure.
Mark
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