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 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]>wrote: > On 24/03/2011 11:51 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 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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