Dear all, I am running a NPT simulation of 33,534 tip4P waters, and I am using domain decomposition as the parallelization scheme. Previously, I had been using Gromacs version 4.5.5 but have recently installed and switched to Gromacs version 4.6.1. Using Gromacs 4.5.5 I can successfully run my water box using domain decomposition over many different processor numbers. However the same simulation returns the following error when I try Gromacs 4.6.1
"The initial number of communication pulses is: X 1 Y 1 Z 1 The initial domain decomposition cell size is: X 2.48 nm Y 2.48 nm Z 1.46 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 1 Y 1 Z 1 The minimum size for domain decomposition cells is 1.000 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.40 Y 0.40 Z 0.68 " The above error occurred running over 16 nodes / 128 processors. The system runs for version 4.6.1 for 1,8, and 16 processors but not for 32,64, or 128 processors. I have tried other systems (including NVT, Berendsen/PR barostats, anisotropic/isotropic ) at the higher number of processors using both version 4.5.5 and 4.6.1 and get the same result - v4.5.5 runs fine while v4.6.1 returns the error type listed above. Is anyone else having a similar issue? Is there something I am not considering? Any help would be greatly appreciated! The details I have used to compile each code are below. My log files indicate that I am indeed calling the correct executable at run time. Thanks in advance! Stephanie ------------------------------------------------------------------------------------------- Computer architecture: SUN X6275 blades CPU: 2.93 GHz dual socket/quad core, Nehalem X5570 processors Version 4.5.5 Compiler: openmpi-1.4.3_oobpr_intel-11.1-f064-c064 / intel-11.1-f064-c064 ./configure COMPILER="intel-11.1-f064-c064" CC="mpicc" CXX="mpicpc" CLINKER="mpicc" FC="mpif90" F77="mpif77" --without-x --disable-threads --enable-mpi --enable-shared --prefix=mypath --oldincludedir=mypath Version 4.6.1 Complier: openmpi-1.4.3_oobpr_intel-12.1-2011.7.256 / intel-12.1-2011.7.256 CC=mpicc CXX=mpicxx FC=mpif90 F77=mpif77 cmake -DGMX_CPU_ACCELERATION=SSE2 -DGMX_PREFER_STATIC_LIBS=ON -DBUILD_SHARED_LIBS=OFF -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=mypath -DGMX_DEFAULT_SUFFIX=ON -DGMX_MPI=ON -- 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
