Thanks a lot Ross and Jason.
I extracted fresh source code and applied latest bug fixes.
Then compiled the source again with the same old config.h.
Installation completed successfully (with several warnings related to unused variable declaration- I think we can ignore
it safely)
Actually there is some glitch in submitting the job to the cluster (nothing related to Amber), so I could't test it.
Thanks a lot for your valuable suggestions & prompt responses.
Have a great day !!!
Hi Senthil,
Error: Syntax error in data declaration at (1)
In file prmtop_dat.f90:1622
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The bugfix.all file you used to patch your amber10 tree must have been out
of date since this problem (a typo in the bugfix patch file) was fixed about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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Received on Wed May 12 2010 - 08:30:05 PDT
