Thank you very much for your answer, After setting up some qm/mm runs, I clearly understand what you mean. Wow, the qm calculations are some cpu eating monsters... M.
On Fri, Jun 8, 2012 at 3:46 PM, Gerrit Groenhof <[email protected]> wrote: > YOucan only use one thread in mdrun, but more than one in ORCA. Try to > estimate the ratio of computation time spent between the QM and MM > calculation to get an idea of why we never bothered to parallellize the MM > part. > > Hope this helps, > > Gerrit > > >> >> 4. QM/MM Calculation with Orca (Minos Matsoukas) >> >> >> Dear GROMACS Users, >> >> I am using Gromacs with ORCA for a qm calculation, but I can only use >> 1 processor for mdrun. >> >> If I place the line !PAL4 in the topol.ORCAINFO and run mdrun -nt 1, >> it works, and ORCA parallelizes correctly for 4 processors, although >> mdrun only runs one thread. >> >> If I place the line !PAL4 in the topol.ORCAINFO and run mdrun -nt 4, >> it doesn‚t work. mdrun crashes with a segmentation fault error : >> >> Back Off! I just backed up md.log to ./#md.log.35# >> Reading file topol.tpr, VERSION 4.5.5 (single precision) >> Starting 4 threads >> QM/MM calculation requested. >> QM/MM calculation requested. >> QM/MM calculation requested. >> QM/MM calculation requested. >> there we go! >> there we go! >> there we go! >> there we go! >> Layer 0 >> nr of QM atoms 73 >> QMlevel: B3LYP/STO-3G >> >> /opt/soft/orca_2_9_1_linux_x86-64/opt/soft/orca_2_9_1_linux_x86-64... >> orca initialised... >> Segmentation fault (core dumped) >> >> >> Is this because mdrun can only run with 1 thread when used with ORCA ? >> >> Here‚s some information : >> OS: CentOS 6.2 x86_64 kernel 2.6.32-220 >> GROMACS: 4.5.5 compiled with options : --with-qmmm-orca >> --without-qmmm-gaussian >> ORCA: 2.9.1 for x86_64 >> OPENMPI: 1.4.3 >> >> My minimization mdp file is: >> ------------ >> ; >> ; Input file >> ; >> title = Yo ; a string >> cpp = /lib/cpp ; c-preprocessor >> integrator = cg ; >> ;integrator = l-bfgs >> >> rlist = 1.0 ; cut-off for ns >> rvdw = 1.0 ; cut-off for vdw >> rcoulomb = 1.5 ; cut-off for coulomb >> ; Energy minimizing stuff >> ; >> nsteps = 200 >> emtol = 10 >> emstep = 0.1 >> ;define = -DPOSRES >> constraints = none >> QMMM = yes >> QMMM-grps = MOL >> QMMMscheme = normal >> QMbasis = STO-3g >> QMmethod = b3lyp >> QMcharge = 1 >> QMmult = 1 >> ------------- >> >> Thanks in advance > > -- > 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 -- 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
