On Mon, May 10, 2010 at 9:07 AM, jaya c.jose <jayacjose.gmail.com> wrote:
> Dear Prof.Case,
>
> I opened charmm.f90 file and found that all modules have the same name
> "charmm_mod".The second module starting at the line275 with the declaration
> "module charmm_mod" so I think it should be like that itself.
> (First module is from line 52 to line 225 and line 225 is "end module
> charmm_mod" )
>
>
> I have given the following commands to apply bugfix
> patch -p0 -N -r patch-rejects < bugfix.all
> patch -p0 <bugfix.26 > chk
>
> I changed the name of the directory where MKL files are installed as
> "/opt/intel/mkl/10.0.3.020". <http://10.0.3.020/man/man3> But now also it
> showing the same error message
> when giving the command "make install".
>
> Thanking you
> Jaya
>
Did you unpack a clean copy of pmemd before you tried to apply the patches
and reinstall? If not, that is likely your problem (since attempting to
patch an improperly patched source rarely leads to success).
You can do this by the following: (make sure amber10.tar.bz2 is present in
the directory containing $AMBERHOME and that the $AMBERHOME directory has
amber10 at the end of it)
tar jxvf amber10.tar.bz2 amber10/src/pmemd
This should unpack strictly the pmemd source code and nothing else (thereby
overwriting the present, most likely corrupted, files).
Then try to apply the patches, reconfigure, and reinstall (don't forget to
make clean though, since unpacking in this manner will NOT remove old object
files and binaries that may be left over).
Good luck!
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon May 10 2010 - 07:00:03 PDT
