Hi Senthil,
Did you "make clean" before compiling parallel version? I compiled a new
version of Amber today and forgot to "make clean" after the serial version
and got weird results. Your problems look similar. Good luck.
Sid
> glb_natex(:) = 0
> 1
>
> The bugfix.all file you used to patch your amber10 tree must have been out
> of date since this problem (a typo in the bugfix patch file) was fixed
> about
> a month ago.
>
> I suggest untarring the original Amber10.tar.bz2 and AmberTools1.2.tar.bz2
> files to give yourself a completely clean tree. Then re-download and apply
> the bugfixes and try again.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> > Behalf Of Senthil Natesan
> > Sent: Wednesday, May 12, 2010 6:58 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] PMEMD installation with gfortran
> >
> >
> >
> > Thanks Prof. Case and Jason. I sincerely appreciate your time and help.
> >
> > I explicitly added MPI_INCLUDE path and it seems that it found mpif.h.
> > Now there is a long list of errors mainly related to prmtop_dat.f90.
> > please see the
> > attached text file. I am copying my latest config.h here
> >
> > MATH_DEFINES =
> > MATH_LIBS =
> > FFT_DEFINES = -DPUBFFT
> > FFT_INCLUDE =
> > FFT_LIBS =
> > NETCDF_HOME =
> > NETCDF_DEFINES =
> > NETCDF_MOD =
> > NETCDF_LIBS =
> > MPI_HOME = /usr/mpi/gcc/mvapich-1.1.0
> > MPI_LIBDIR2 = /usr/mpi/gcc/mvapich-1.1.0/lib/shared
> > MPI_DEFINES = -DMPI
> > MPI_INCLUDE =-I$(MPI_HOME)/include
> > MPI_LIBDIR = $(MPI_HOME)/lib
> > MPI_LIBS =
> > DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> > CPP = /usr/bin/cpp
> > CPPFLAGS = -traditional -P
> > F90_DEFINES = -DFFTLOADBAL_2PROC
> >
> > F90 = mpif90
> > MODULE_SUFFIX = mod
> > F90FLAGS = -c
> > F90_OPT_DBG = -g -ftrace=full
> > F90_OPT_LO = -O0
> > F90_OPT_MED = -O2
> > F90_OPT_HI = -O3
> > F90_OPT_DFLT = $(F90_OPT_HI)
> > CC = gcc
> > CFLAGS =
> >
> > LOAD = mpif90
> > LOADFLAGS =
> > LOADLIBS =
> >
> > thanks a lot.
> >
> > Senthil Natesan
> >
> >
> > ________________________________
> > From: Jason Swails <jason.swails.gmail.com>
> > To: AMBER Mailing List <amber.ambermd.org>
> > Sent: Wed, May 12, 2010 8:41:17 AM
> > Subject: Re: [AMBER] PMEMD installation with gfortran
> >
> > On Wed, May 12, 2010 at 8:19 AM, case <case.biomaps.rutgers.edu> wrote:
> >
> > > On Tue, May 11, 2010, Senthil Natesan wrote:
> > >
> > > > /lib/cpp -traditional -P -DPUBFFT -DMPI -DDIRFRC_EFS -
> > DDIRFRC_COMTRANS
> > > -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC pmemd_lib.fpp pmemd_lib.f90
> > > > pmemd_lib.fpp:40: error: mpif.h: No such file or directory
> > >
> > > Note that in your earlier post, you had lines like this:
> > >
> > > /lib/cpp -traditional -P -I/usr/mpi/gcc/mvapich-1.1.0/include -
> > DPUBFFT
> > > -DMPI
> > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> > >
> > > The underlined part above is now missing; it is set up when the
> > configure
> > > script asks where your MPI is located. You need to get the "-I" flag
> > back
> > > in there.
> > >
> >
> > Sorry. I told him to take that out expecting mpif90 to take care of
> > it. Of
> > course, the compiler wrappers have no bearing on the preprocessor, so
> > that
> > won't do much good for this line. This is the first time I noticed it
> > was a
> > cpp call that was messing up, so of course mpif90 won't help here.
> >
> > (I did suggest he put it back in MPI_INCLUDE in my previous email, if
> > that
> > makes up for things).
> >
> > All the best,
> > Jason
> >
> >
> > > ...good luck...dac
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> >
>
>
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>
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Received on Fri May 14 2010 - 23:00:05 PDT
