Thank you all for your help! I ran<div><br></div><div> make distclean</div><div><br></div><div>and re-configured in the GROMACS source folder via</div><div><br></div><div> sudo ./configure --prefix=$SOFT --with-gsl --enable-threads CFLAGS="$CFLAGS -I$SOFT/include" LDFLAGS="$LDFLAGS -L$SOFT/lib"</div>
<div> sudo make -j $NCPU</div><div> sudo make install</div><div><br></div><div>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.</div>
<div><br></div><div>Now when I run mdrun, it automatically uses multiple threads and goes just as fast as before my changes. Thanks again,</div><div><br></div><div>Adam</div><div><br><br><div class="gmail_quote">On Thu, Mar 24, 2011 at 9:00 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im">On <a href="tel:24%2F03%2F2011%2011" target="_blank">24/03/2011 11</a>:51 PM, Adam Herbst wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear GROMACS users,<br>
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.<br>
</blockquote>
<br></div>
Yes, threading, enabled by default, and mutually incompatible with MPI.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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:<br>
<br>
make mdrun (or just make)<br>
make install-mdrun (or just make install)<br>
<br>
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<br>
</blockquote>
<br></div>
Subsequently you have configured with --enable-mpi, so threading is disabled. Now everything is probably a mess.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
mpirun -np N mdrun_mpi [options],<br>
<br>
the same simulation is started separately on each processor, leading to a crash. If I use<br>
<br>
mpirun -np 1 -cpus-per-proc N mdrun_mpi [options],<br>
<br>
I get an error message that this is not supported on my computer ("An attempt to set processor affinity has failed").<br>
<br>
I can't configure the input .tpr file for parallel because grompp doesn't have the -np flag in GROMACS 4.<br>
<br>
How can I update the parallel-capable "mdrun" executable with my changes?<br>
</blockquote>
<br></div>
Run "make distclean" and then re-configure.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
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