AMBER Archive (2009)

Subject: [AMBER] amber10 pmemd fail

From: Aragorn Steiger (aragorn_at_wayne.edu)
Date: Fri Dec 11 2009 - 14:35:49 CST

Hello everyone,

I would like a bit of advice. I have compiled pmemd for a researcher here at Wayne State. When we run it it dies at varying points. We get various errors from mpirun such as:

p8_15722: (1054.988281) net_recv failed for fd = 9
p8_15722: p4_error: net_recv read, errno = : 110
p14_21538: p4_error: Found a dead connection while looking for messages: 9

I am using various libraries from MKL, ifort, and mvapich. The config file that I am using is below:

IFORT_RPATH = /wsu/arch/amd64/compilers/intel/ifort-11.1.056/lib/intel64:/wsu/arch/amd64/lib/l_mkl_p_10.2.2.025/lib/em64t:/wsu/arch/amd64/mvapich-1.1/lib:/wsu/arch/amd64/lib/l_mkl_p_10.2.2.025:/usr/local/lib:/u
sr/local/lib:/wsu/usr/local/lib:/usr/local/pgsql/lib
MATH_DEFINES = -DMKL
MATH_LIBS = /wsu/arch/amd64/intel/mkl/10.0.1.014/lib/em64t/libmkl_em64t.a -L/wsu/arch/amd64/lib/l_mkl_p_10.2.2.025/lib/em64t -lguide -lpthread
FFT_DEFINES = -DPUBFFT
FFT_INCLUDE =
FFT_LIBS =
NETCDF_HOME =
NETCDF_DEFINES =
NETCDF_MOD =
NETCDF_LIBS =
MPI_HOME = /wsu/arch/amd64/mvapich-1.1
MPI_LIBDIR2 = /wsu/lib64
MPI_DEFINES = -DMPI
MPI_INCLUDE = -I$(MPI_HOME)/include
MPI_LIBDIR = $(MPI_HOME)/lib
MPI_LIBS = -L$(MPI_LIBDIR) -lmpich /usr/lib64/libibverbs.so.1 -lpthread
DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
CPP = /lib/cpp
CPPFLAGS = -traditional -P
F90_DEFINES = -DFFTLOADBAL_2PROC

F90 = ifort
MODULE_SUFFIX = mod
F90FLAGS = -c -auto
F90_OPT_DBG = -g -traceback
F90_OPT_LO = -O0
F90_OPT_MED = -O2
F90_OPT_HI = -xP -ip -O3
F90_OPT_DFLT = $(F90_OPT_HI)

CC = gcc
CFLAGS =

LOAD = ifort
LOADFLAGS =
LOADLIBS = -limf -lsvml -Wl,-rpath=$(IFORT_RPATH)

I am wondering if someone could suggest a course of action?

Thank You,

Aragorn Steiger
Senior Systems Software Engineer
Wayne State University
Computing & Information Technology
Scientific Computing
(313) 577-9601

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