[gmx-users] mdrun failed
Hi dear gmx-usersI want to simulate gold surface - proteininteraction by GOLP-CHARMM forcefield. In md step, after 7 ps , without anyreason mdrun failed. md.mdp contains: title = gold cpp = cpp include = ; RUN CONTROL PARAMETERS integrator = md ;comm_mode = Linear ;nstcomm = 1 ;comm_grps = Protein non-Protein ;nstcalcenergy = 1 ; ENERGY MINIMIZATIONOPTIONS ; Force tolerance andinitial step-size emtol = 500.0 emstep = 0.001 tinit = 0.000 dt = 0.001 nsteps = 10 ; OUTPUT CONTROL OPTIONS nstxout = 3000 nstvout = 3000 nstfout = 0 nstlog = 1 nstenergy = 3000 ;nsttcouple = 5 ; Output frequency andprecision for xtc file nstxtcout = 3000 xtc-precision = 3000 ; NEIGHBORSEARCHINGPARAMETERS ; Periodic boundaryconditions: xyz (default), no (vacuum) pbc = xyz periodic_molecules = yes ; nblistcut-off rlist = 1.10 ; OPTIONS FORELECTROSTATICS AND VDW ; Method for doingelectrostatics coulombtype = PME r_coulomb= 1.1 ;pme_order = 6 ;fourierspacing = 0.10 ewald_rtol = 1e-06 ewald_geometry = 3d ; Method for doing Vander Waals vdw-type= switch ; cut-offlengths rvdw-switch = 0.90 rvdw= 1.10 ; OPTIONS FORBONDS constraints = all-bonds constraint-algorithm= Lincs lincs-order = 8 lincs-iter = 12 ; Lincs will write awarning to the stderr if in one step a bond ; rotates over moredegrees than lincs-warnangle = 90 ; OPTIONS FOR WEAKCOUPLING ALGORITHMS ; Temperature coupling Tcoupl = Nose-Hoover nhchainlength = 1 ; Groups to coupleseparately tc-grps =ProteinNon-Protein ; Time constant (ps) andreference temperature (K) tau-t = 0.2 0.2 ref-t = 310 310 ; Non-equilibrium MDstuff freezegrps = slab freezedim = Y Y Y Fatemeh Ramezani mdrun command is: nohup mdrun -s md.tpr-o md.trr -c md.pdb -g md.log -e md.edr -nt 3 -dd 1 -pin on -pinoffset 1 & the last line of md.log is: Step Time Lambda 7460 7.46000 0.0 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 5.39081e+04 1.47221e+04 3.15826e+03 -1.85050e+03 1.80904e+04 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential 2.97824e+05 2.17254e+12 -6.91585e+06 3.01612e+04 2.17254e+12 Kinetic En. Total Energy Conserved En. TemperaturePressure (bar) 7.71065e+14 7.73237e+14 9.41950e+16 2.61554e+11 2.41578e+12 Constr. rmsd 1.15453e-01 The last line of nohup.out is: Changing nstlist from10 to 40, rlist from 1.1 to 1.1 Using 1 MPI thread Using 3 OpenMP threads Applying core pinning offset 1 Setting the maximum number of constraint warnings to -1 Back Off! I just backed up fws_md3.trr to ./#fws_md3.trr.20# Back Off! I justbacked up traj_comp.xtc to ./#traj_comp.xtc.22# Back Off! I justbacked up md3.edr to ./#md3.edr.20# starting mdrun 'Protein in water' 10 steps, 100.0ps. Can you help me to prevent from mdrun failing? Thank you very much Fatemeh Ramezani -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] mdrun failed
Hello: I try to submit Gromacs job with command: mpirun -np 2 mdrun_mpi -s md.tpr -g -v but it failed with messages: -- It looks like opal_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during opal_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): opal_shmem_base_select failed -- Returned value -1 instead of OPAL_SUCCESS -- *** An error occurred in MPI_Init *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, ***and potentially your MPI job) [cudaA:5978] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed! -- I first compiled openmpi with command: ./configure --prefix=/soft/openmpi-1.7.5_intel CC=icc F77=ifort FC=ifort CXX=icpc then gromacs-4.6.5 was compiled with command: env CC=icc F77=ifort CXX=icpc CMAKE_PREFIX_PATH=/soft/intel/mkl/include/fftw:/soft/openmpi-1.7.5 cmake .. -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF -DCMAKE_INSTALL_PREFIX=/soft/gromacs-4.6.5 -DGMX_FFT_LIBRARY=mkl -DGMX_MPI=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda thank you very much. ALbert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun failed
First, check your install of MPI works on a simple test program. Then, check that GROMACS cmake picked up the MPI you expected, and that that's really the one you're using at run time. Mark On Thu, May 15, 2014 at 3:28 PM, Albert mailmd2...@gmail.com wrote: Hello: I try to submit Gromacs job with command: mpirun -np 2 mdrun_mpi -s md.tpr -g -v but it failed with messages: -- It looks like opal_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during opal_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): opal_shmem_base_select failed -- Returned value -1 instead of OPAL_SUCCESS -- *** An error occurred in MPI_Init *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, ***and potentially your MPI job) [cudaA:5978] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed! -- I first compiled openmpi with command: ./configure --prefix=/soft/openmpi-1.7.5_intel CC=icc F77=ifort FC=ifort CXX=icpc then gromacs-4.6.5 was compiled with command: env CC=icc F77=ifort CXX=icpc CMAKE_PREFIX_PATH=/soft/intel/mkl/include/fftw:/soft/openmpi-1.7.5 cmake .. -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF -DCMAKE_INSTALL_PREFIX=/soft/gromacs-4.6.5 -DGMX_FFT_LIBRARY=mkl -DGMX_MPI=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda thank you very much. ALbert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun failed
Hello Mark: thanks a lot for reply. The MPI works fine in my machine when I run another problem. How can I check whether gromacs cmake picked up the MPI that I expected? I've already specified with options: CMAKE_PREFIX_PATH=/soft/intel/mkl/include/fftw:/soft/openmpi-1.7.5 thx a lot Albert On 05/15/2014 05:35 PM, Mark Abraham wrote: First, check your install of MPI works on a simple test program. Then, check that GROMACS cmake picked up the MPI you expected, and that that's really the one you're using at run time. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun failed
Try mdrun -version and have a look at the flags and stuff. Do a make VERBOSE=1 and check the compile line doesn't refer to some other MPI. Inspect the CMakeCache.txt in the cmake build directory. Mark On Thu, May 15, 2014 at 5:39 PM, Albert mailmd2...@gmail.com wrote: Hello Mark: thanks a lot for reply. The MPI works fine in my machine when I run another problem. How can I check whether gromacs cmake picked up the MPI that I expected? I've already specified with options: CMAKE_PREFIX_PATH=/soft/intel/mkl/include/fftw:/soft/openmpi-1.7.5 thx a lot Albert On 05/15/2014 05:35 PM, Mark Abraham wrote: First, check your install of MPI works on a simple test program. Then, check that GROMACS cmake picked up the MPI you expected, and that that's really the one you're using at run time. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
