Re: AMBER: pmemd install error

From: Ji-Lai Li <jlutcc.gmail.com>
Date: Sun, 28 Jan 2007 19:18:05 -0800

Dear Prof. Case,
 I am depressed with pmemd install now. I tried many times and by many
means, but all failed.

The EV was set to: (as Bob Duke suggested at amber web)
setenv PREPROCFLAGS "-DDIRFRC_VECT_OPT"
setenv CPP "/lib/cpp -traditional "
setenv OPT_LO "ifort -c -auto -tpp7 -mp1 -O0"
setenv OPT_MED "ifort -c -auto -tpp7 -mp1 -O2"
setenv OPT_HI "ifort -c -auto -tpp7 -xW -mp1 -ip -O3"
setenv LOAD "ifort"
setenv LOADLIB " -limf -lsvml "
setenv MPI_HOME /home/mds/progpack/openmpi-1.1.3/build/
setenv MPI_INCLUDE $MPI_HOME/include
setenv MPI_LIBDIR $MPI_HOME/lib
setenv MPILIB "-L$MPI_LIBDIR -lmpich"
setenv PREPROCFLAGS "-DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_VECT_OPT"
setenv CPP "/lib/cpp -traditional -I$MPI_INCLUDE"
setenv OPT_LO "ifort -c -auto -tpp7 -mp1 -O0"
setenv OPT_MED "ifort -c -auto -tpp7 -mp1 -O2"
setenv OPT_HI "ifort -c -auto -tpp7 -xW -mp1 -ip -O3"
setenv LOAD "ifort"
setenv LOADLIB " -limf -lsvml $MPILIB"

1. the config.h file was created by "./configure linux_em64t ifort mpich"

MATH_DEFINES =
MATH_LIBS =
IFORT_RPATH = /home/mds/progpack/openmpi-1.1.3
/build/lib:/opt/intel/mkl/9.0/lib:/opt/intel/cce/9.1.044/lib:/opt/intel/cce/9.1.044/lib:/opt/intel/fce/9.0/lib:/opt/intel/fce/9.0/lib:/usr/local/gcc411/lib64:/usr/pgi/linux86-64/6.0/bin:/home/mds/amber9/antechamber-
1.27
/bin:/home/mds/amber9/perl:/home/mds/amber9/exe:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/home/mds/g03C02/g03/bsd:/home/mds/g03C02/g03/local:/home/mds/g03C02/g03/extras:/home/mds/g03C02/g03
MATH_DEFINES = -DMKL
MATH_LIBS = -L/opt/intel/mkl/9.0/lib/em64t -lmkl_em64t -lpthread
FFT_DEFINES = -DPUBFFT
FFT_INCLUDE =
FFT_LIBS =
NETCDF_HOME =
NETCDF_DEFINES =
NETCDF_MOD =
NETCDF_LIBS =
MPI_HOME = /home/mds/progpack/openmpi-1.1.3/build/
MPI_DEFINES = -DMPI -DSLOW_NONBLOCKING_MPI
MPI_INCLUDE = -I$(MPI_HOME)/include
MPI_LIBDIR = $(MPI_HOME)/lib
MPI_LIBS = -L$(MPI_LIBDIR) -lmpich
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 = -tpp7 -O0
F90_OPT_MED = -tpp7 -O2
F90_OPT_HI = -tpp7 -xW -ip -O3
F90_OPT_DFLT = $(F90_OPT_HI)

CC = gcc
CFLAGS =

LOAD = ifort
LOADFLAGS =
LOADLIBS = -limf -lsvml -Wl,-rpath=$(IFORT_RPATH)
and the prompt is (the ifort.txt attachment):
fortcom: Error: parallel_dat.f90, line 96: Cannot open include file '
mpif-common.h'
      include 'mpif-common.h'
--------------^
fortcom: Error: parallel_dat.f90, line 227: This name does not have a type,
and must have an explicit type. [MPI_COMM_WORLD]
    call mpi_abort(mpi_comm_world, i, err_ret_code)
-------------------^
compilation aborted for parallel_dat.f90 (code 1)
make[1]: *** [parallel_dat.o] Error 1
make[1]: Leaving directory `/home/mds/amber9/src/pmemd/src'
make: *** [install] Error 2

2. when the "ifort" was replaced by "mpif90", and the EV were also changed,
 it prompts:
............
gfortran: language W not recognized
...................
 and many unrecongnized languages and I paste the error as an attachment
mpif90.txt.

  Does anybody know how to fix this problem?
  Many thanks!

Ji-Lai Li



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Received on Wed Jan 31 2007 - 06:07:42 PST
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