Hi Jason,
My replies to your comments are as below. Thank you very much!
On Fri, Oct 14, 2011 at 6:20 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, Oct 13, 2011 at 11:21 PM, Mo Chen <mc842.cornell.edu> wrote:
>
> > Dear Amber users/developers,
> > I have a problem installing parallel version of amber in my machine. I
> was
> > trying to compile amber using intel compiler and mpich2 library. And my
> > procedure was shown as below:
> >
> > chen.sugar9:~$ tar xzvf amber11-06-26-2011.tgz
> >
>
> Does this tarball contain Amber11 + AmberTools 1.5?
>
>
> > chen.sugar9:~$ cd amber11
> > chen.sugar9:~$ echo $SHELL
> > /bin/bash
> > chen.sugar9:~$ echo "export AMBERHOME=$PWD" >> ~/.bashrc
> > chen.sugar9:~$ echo "export PATH=$PATH:$AMBERHOME/bin" >> ~/.bashrc
> > chen.sugar9:~$ source ~/.bashrc
> > chen.sugar9:~$ wget
> http://ambermd.org/bugfixes/AmberTools/1.5/bugfix.all
> > chen.sugar9:~$ patch -p0 -N < bugfix.all
> > chen.sugar9:~$ rm bugfix.all
> > chen.sugar9:~$ cd AmberTools/src/
> > chen.sugar9:~/AmberTools/src$ ./configure intel
> > chen.sugar9:~/amber11/AmberTools/src$ make install
> > chen.sugar9:~/amber11/AmberTools/src$ cd
> > chen.sugar9:~$ cd $AMBERHOME
> > chen.sugar9:~/amber11$ wget
> > http://ambermd.org/bugfixes/11.0/bugfix.1to17.tar.bz2
> > chen.sugar9:~/amber11$ wget
> > http://ambermd.org/bugfixes/11.0/apply_bugfix.x
> > chen.sugar9:~/amber11$ ./apply_bugfix.x bugfix.1to17.tar.bz2 ( this
> does
> > not work)
> >
>
> This is way too vague. What do you mean it didn't work? What errors did
> you get? Until this step works, there's really little point in going
> further with the Amber 11 installation.
>
I will put the path in front of the tar file, as said by Niel. Hopefully it
will work.
>
>
> > chen.sugar9:~/amber11$ cd AmberTools/src/
> > chen.sugar9:~/AmberTools/src$ ./configure intel
> > chen.sugar9:~/amber11/AmberTools/src$ cd $AMBERHOME
> >
>
> After this step you should be running the AT15_Amber11.py script if you are
> building AmberTools 1.5 + Amber11. The instructions are stated at the end
> of the configure script.
>
>
I did not see AT15_Amber11.py in $AMBERHOME directory. I was told that the
amber11-06-26-2011.tgz file contains both amber11 and AmberTools. And after
I did the patch -p0 -N < bugfix.all, there was AT15_amber11.py.orig and
AT15_amber11.py.rej files. So I thought it had been run automatically.
>
> > chen.sugar9:~/amber11$ cd src/
> > chen.sugar9:~/amber11/src$ make serial
> > chen.sugar9:~/amber11/src$ cd $AMBERHOME
> > chen.sugar9:~/amber11$ cd AmberTools/src/
> > chen.sugar9:~/AmberTools/src$ tar xzvf mpich2_1.3.1.orig.tar.gz
> > chen.sugar9:~/AmberTools/src$ ./configure_mpich2 intel
> > chen.sugar9:~/amber11/AmberTools/src$ ./configure -mpi intel
> > chen.sugar9:~/amber11/AmberTools/src$ cd ../../src
> > chen.sugar9:~/amber11/src$ make clean
> > chen.sugar9:~/amber11/src$ make parallel
> >
> > Then, at the end, the error message was as below and there is no pmemd
> > executable in $AMBERHOME/bin. I also tried to follow the README file in
> > pmemd directory to install pmemd, but it did not work either. Could
> anyone
> > help me with this? Many thanks!
> >
> > rism3d_opendx.f:167:0: error: unterminated #if
> >
>
> To me, this is indicative of a badly applied patch. Did you see any errors
> applying patches? Somehow an #endif was dropped from one of the source
> files, preventing the preprocessor from finishing...
>
> My suspicion is that your tarball doesn't contain quite what you think it
> contains, so you should extract a fresh copy of Amber11 and AmberTools 1.5,
> then try your above sequence (but make sure you run the AT15_Amber11.py
> script before trying to build Amber11).
>
> HTH,
> Jason
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 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
Received on Fri Oct 14 2011 - 11:30:04 PDT
