Hello,
The errors you have now appear to be related to a corrupted version of
pmemd. I would suggest removing the pmemd source code and extracting a
fresh copy from the tarball. You can do this via the following, assuming
the amber11.tar.bz2 file is in the parent directory of $AMBERHOME:
cd $AMBERHOME/src/
rm -fr pmemd
cd ../../
tar jxvf amber11.tar.bz2 amber10/src/pmemd
This will selectively extract the pmemd source code into that directory.
After that, apply the latest bug fixes (there have been new ones posted --
see the amber website for them). Then recompile. Note that your current
config.h file looks good, so you may want to save that before you delete the
pmemd directory.
Good luck!
Jason
On Wed, May 12, 2010 at 9:58 AM, Senthil Natesan <sen.natesan.yahoo.com>wrote:
>
>
> Thanks Prof. Case and Jason. I sincerely appreciate your time and help.
>
> I explicitly added MPI_INCLUDE path and it seems that it found mpif.h.
> Now there is a long list of errors mainly related to prmtop_dat.f90.
> please see the
> attached text file. I am copying my latest config.h here
>
> MATH_DEFINES =
> MATH_LIBS =
> FFT_DEFINES = -DPUBFFT
> FFT_INCLUDE =
> FFT_LIBS =
> NETCDF_HOME =
> NETCDF_DEFINES =
> NETCDF_MOD =
> NETCDF_LIBS =
> MPI_HOME = /usr/mpi/gcc/mvapich-1.1.0
> MPI_LIBDIR2 = /usr/mpi/gcc/mvapich-1.1.0/lib/shared
> MPI_DEFINES = -DMPI
> MPI_INCLUDE =-I$(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
>
>
>
>
> _______________________________________________
> 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
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Received on Wed May 12 2010 - 07:30:03 PDT
