Dear all, In an attempt to speed up things, I tried to calculate an hessian matrix in parallel, using two processors and it finished in about half the time when compared to a single-node run. However, the parallel run produces an .mtx file that has about half the size of the one obtained in the single-node run. Running g_nmeig_d on the .mtx from the parallel run generates negative eigenvalues, while eigenvalues from the single-node run are OK.
Is this a known issue? I could not found anything in the archives. mdrun_d_mpi runs just fine in parallel with integrator=steep or md, and produces the expected error with l-bfgs. This is with gromacs 4.0.5 and 4.0.7, compiled in 64 bit, double precision, with or without mpi, in a Mac (OSX 10.5.8). Commands used: grompp_d -f nm.mdp -c lbfgs.gro -t lbfgs.trr -p protMg.top -o nm.tpr mpirun -np $NSLOTS /usr/local/gromacs/bin/mdrun_d_mpi -s nm.tpr -v -deffnm nm -mtx hessian.mtx g_nmeig_d -f hessian.mtx -s nm.tpr Thanks for your time, Rui Rodrigues -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
