Hi all, Thanks for your observations and suggestions. I had neglected to install mpi4py, which was the original problem. I installed that and I can run parallel yt scripts, however, I'm still having trouble with using inline yt. I've pasted the error I now get below. It is not very informative (to me at least); the keyboard interrupt is the symptom, not the cause of the problem, I think. I'm doing this on trestles and I tried to use their parallel debugger ddt to get some more information. ddt seems to indicate that one of the processes is looking for a file called mpi4py.MPI.c in the /tmp directory, which I don't really understand, and maybe is a red herring. I don't have any problems with single processor jobs. I installed yt using shared libraries by adding the --enable-shared flag to the configure statement for python in the install script. I've also pasted the enzo make file that I'm using below. I'm thinking that I somehow have messed up the libraries or include files. If anyone has successfully used inline yt on trestles and has any advice, I'd love to hear it. Thanks for all your help Christine Error: MPI_Init: NumberOfProcessors = 3 warning: the following parameter line was not interpreted: TestStarParticleEnergy = 0.00104392468495 warning: the following parameter line was not interpreted: TestStarParticleDensity = 1.0 warning: the following parameter line was not interpreted: TestStarParticleStarMass = 100.0 ****** ReadUnits: 2.748961e+37 1.000000e-24 3.018025e+20 3.150000e+13 ******* Global Dir set to . Initialdt in ReadParameterFile = 4.815337e-05 InitializeNew: Starting problem initialization. Central Mass: 6813.382812 Allocated 1 particles Initialize Exterior ExtBndry: BoundaryRank = 3 ExtBndry: GridDimension = 104 104 104 ExtBndry: NumberOfBaryonFields = 6 InitializeExternalBoundaryFace SimpleConstantBoundary FALSE End of set exterior InitializeNew: Initial grid hierarchy set InitializeNew: Partition Initial Grid 0 Enter CommunicationPartitionGrid. PartitionGrid (on all processors): Layout = 1 1 3 NumberOfNewGrids = 3 GridDims[0]: 98 GridDims[1]: 98 GridDims[2]: 33 32 33 StartIndex[0]: 0 StartIndex[1]: 0 StartIndex[2]: 0 33 65 Call ZeroSUS on TopGrid ENZO_layout 1 x 1 x 3 Grid structure: 1576 SubGrids structure: 4728 Re-set Unigrid = 0 Grid distribution Delete OldGrid OldGrid deleted Exit CommunicationPartitionGrid. InitializeNew: Finished problem initialization. Initializing Python interface Successfully read in parameter file StarParticleTest.enzo. INITIALIZATION TIME = 9.38615084e-01 Beginning parallel import block. MPI process (rank: 1) terminated unexpectedly on trestles-12-20.local Exit code -5 signaled from trestles-12-20 Traceback (most recent call last): File "<string>", line 1, in <module> File "./user_script.py", line 1, in <module> from yt.pmods import * File "/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/pmods.py", line 364, in <module> from yt.mods import * File "/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/pmods.py", line 234, in __import_hook__ q, tail = __find_head_package__(parent, name) File "/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/pmods.py", line 323, in __find_head_package__ q = __import_module__(head, qname, parent) File "/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/pmods.py", line 268, in __import_module__ pathname,stuff,ierror = mpi.bcast((pathname,stuff,ierror)) File "/home/csimpson/yt-x86_64-shared/src/yt-hg/yt/pmods.py", line 201, in bcast return MPI.COMM_WORLD.bcast(obj,root) KeyboardInterrupt Caught fatal exception: 'Importing user_script failed!' at InitializePythonInterface.C:108 Backtrace: BT symbol: ./enzo.exe [0x41ff8a] BT symbol: ./enzo.exe [0x727e14] BT symbol: ./enzo.exe [0x421147] BT symbol: /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c0121d994] BT symbol: ./enzo.exe(__gxx_personality_v0+0x3d9) [0x41fea9] terminate called after throwing an instance of 'EnzoFatalException' Make file: #======================================================================= # # FILE: Make.mach.trestles # # DESCRIPTION: Makefile settings for the Trestles Resource at SDSC/UCSD # # AUTHOR: John Wise (jwise@astro.princeton.edu) # # DATE: 07 Dec 2010 # # #======================================================================= MACH_TEXT = Trestles MACH_VALID = 1 MACH_FILE = Make.mach.trestles MACHINE_NOTES = "MACHINE_NOTES for Trestles at SDSC/UCSD: \ Load these modules, \ 'module add intel/11.1 mvapich2/1.5.1p1'" #----------------------------------------------------------------------- # Compiler settings #----------------------------------------------------------------------- LOCAL_MPI_INSTALL = /home/diag/opt/mvapich2/1.5.1p1/intel/ LOCAL_PYTHON_INSTALL = /home/csimpson/yt-x86_64-shared/ #LOCAL_COMPILER_DIR = /opt/pgi/linux86-64/10.5 LOCAL_COMPILER_DIR = /opt/intel/Compiler/11.1/072 LOCAL_HYPRE_INSTALL = # With MPI MACH_CPP = cpp MACH_CC_MPI = $(LOCAL_MPI_INSTALL)/bin/mpicc # C compiler when using MPI MACH_CXX_MPI = $(LOCAL_MPI_INSTALL)/bin/mpicxx # C++ compiler when using MPI MACH_FC_MPI = $(LOCAL_MPI_INSTALL)/bin/mpif90 # Fortran 77 compiler when using MPI MACH_F90_MPI = $(LOCAL_MPI_INSTALL)/bin/mpif90 # Fortran 90 compiler when using MPI MACH_LD_MPI = $(LOCAL_MPI_INSTALL)/bin/mpicxx # Linker when using MPI # Without MPI MACH_CC_NOMPI = $(LOCAL_COMPILER_DIR)/bin/intel64/icc # C compiler when not using MPI MACH_CXX_NOMPI = $(LOCAL_COMPILER_DIR)/bin/intel64/icpc # C++ compiler when not using MPI MACH_FC_NOMPI = $(LOCAL_COMPILER_DIR)/bin/intel64/ifort # Fortran 77 compiler when not using MPI MACH_F90_NOMPI = $(LOCAL_COMPILER_DIR)/bin/intel64/ifort # Fortran 90 compiler when not using MPI MACH_LD_NOMPI = $(LOCAL_COMPILER_DIR)/bin/intel64/icpc # Linker when not using MPI #----------------------------------------------------------------------- # Machine-dependent defines #----------------------------------------------------------------------- # Defines for the architecture; e.g. -DSUN, -DLINUX, etc. MACH_DEFINES = -DLINUX -DH5_USE_16_API #----------------------------------------------------------------------- # Compiler flag settings #----------------------------------------------------------------------- MACH_CPPFLAGS = -P -traditional MACH_CFLAGS = MACH_CXXFLAGS = MACH_FFLAGS = MACH_F90FLAGS = MACH_LDFLAGS = #----------------------------------------------------------------------- # Precision-related flags #----------------------------------------------------------------------- MACH_FFLAGS_INTEGER_32 = -i4 MACH_FFLAGS_INTEGER_64 = -i8 MACH_FFLAGS_REAL_32 = -r4 MACH_FFLAGS_REAL_64 = -r8 #----------------------------------------------------------------------- # Optimization flags #----------------------------------------------------------------------- MACH_OPT_WARN = -Wall # Flags for verbose compiler warnings MACH_OPT_DEBUG = -O0 -g # Flags for debugging # Flags for high conservative optimization #MACH_OPT_HIGH = -O1 -ftz -mieee-fp -fp-speculation=off -prec-sqrt -prec-div MACH_OPT_HIGH = -O2 # Note that this breaks determinism, which is why it's commented out! # MACH_OPT_AGGRESSIVE = -O3 # Flags for aggressive optimization # This is the best we can do, from what I can tell. #MACH_OPT_AGGRESSIVE = -O1 -ftz -mieee-fp -fp-speculation=off -prec-sqrt -prec-div #----------------------------------------------------------------------- # Includes #----------------------------------------------------------------------- LOCAL_INCLUDES_MPI = LOCAL_INCLUDES_HDF5 = -I/home/csimpson/yt-x86_64-shared/include # HDF5 includes LOCAL_INCLUDES_HYPRE = LOCAL_INCLUDES_PAPI = # PAPI includes LOCAL_INCLUDES_PYTHON = -I$(LOCAL_PYTHON_INSTALL)/include/python2.7 \ -I$(LOCAL_PYTHON_INSTALL)/lib/python2.7/site-packages/numpy/core/include MACH_INCLUDES = $(LOCAL_INCLUDES_HDF5) MACH_INCLUDES_PYTHON = $(LOCAL_INCLUDES_PYTHON) MACH_INCLUDES_MPI = $(LOCAL_INCLUDES_MPI) MACH_INCLUDES_HYPRE = $(LOCAL_INCLUDES_HYPRE) MACH_INCLUDES_PAPI = $(LOCAL_INCLUDES_PAPI) #----------------------------------------------------------------------- # Libraries #----------------------------------------------------------------------- LOCAL_LIBS_MPI = LOCAL_LIBS_HDF5 = -L/home/csimpson/yt-x86_64-shared/lib -lhdf5 # HDF5 libraries LOCAL_LIBS_HYPRE = LOCAL_LIBS_PAPI = # PAPI libraries LOCAL_LIBS_PYTHON = -L$(LOCAL_PYTHON_INSTALL)/lib -lpython2.7 \ -lreadline -ltermcap -lutil #LOCAL_LIBS_MACH = -L$(LOCAL_COMPILER_DIR)/lib \ # -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lrt LOCAL_LIBS_MACH = -L$(LOCAL_COMPILER_DIR)/lib/intel64 -lifcore -lifport MACH_LIBS = $(LOCAL_LIBS_HDF5) $(LOCAL_LIBS_MACH) MACH_LIBS_MPI = $(LOCAL_LIBS_MPI) MACH_LIBS_HYPRE = $(LOCAL_LIBS_HYPRE) MACH_LIBS_PAPI = $(LOCAL_LIBS_PAPI) MACH_LIBS_PYTHON = $(LOCAL_LIBS_PYTHON)