Dear amber users,
Very thanks for your former suggestion.
Tonight, I tried to install mmpbsa.py based on your suggestions.
1) put the path in the .bashrc
export AMBERHOME=/home/r.yu/amber11
export PATH=$AMBERHOME/bin\:/home/r.yu/amber10/bin\:$PATH
2)
sudo mv /home/r.yu/amber10/bin/nab /home/r.yu/amber10/bin/nab-1.2
sudo ln -s /home/r.yu/amber11/bin/nab /home/r.yu/amber10/bin
3)
cd $AMBERHOME/src/mmpbsa_py
make serial
make parallel
r.yu.euphoria:~/amber11/src/mmpbsa_py$ make serial
/bin/bash setup.sh
Python version 2 detected. No file conversion necessary.
/bin/cp MMPBSA.py *pyc /home/r.yu/amber11/bin
/home/r.yu/amber11/bin/nab -o mmpbsa_py_nabnmode mmpbsa_entropy.nab
/home/r.yu/amber11/lib/libnab.a(sff.o): In function `mme_timer':
sff.c:(.text+0x2b40): undefined reference to `lam_mpi_comm_world'
sff.c:(.text+0x2b4e): undefined reference to `lam_mpi_max'
sff.c:(.text+0x2b53): undefined reference to `lam_mpi_double'
sff.c:(.text+0x2bda): undefined reference to `MPI_Allreduce'
/home/r.yu/amber11/lib/libnab.a(sff.o): In function `mpierror':
sff.c:(.text+0x86c6): undefined reference to `lam_mpi_comm_world'
sff.c:(.text+0x86cc): undefined reference to `lam_mpi_min'
sff.c:(.text+0x86df): undefined reference to `lam_mpi_int'
sff.c:(.text+0x86e9): undefined reference to `MPI_Allreduce'
sff.c:(.text+0x8701): undefined reference to `MPI_Finalize'
/home/r.yu/amber11/lib/libnab.a(sff.o): In function `mpiinit':
sff.c:(.text+0xca2c): undefined reference to `MPI_Init'
sff.c:(.text+0xca4d): undefined reference to `lam_mpi_comm_world'
sff.c:(.text+0xca52): undefined reference to `MPI_Comm_rank'
sff.c:(.text+0xca62): undefined reference to `lam_mpi_comm_world'
sff.c:(.text+0xca67): undefined reference to `MPI_Comm_size'
So I went back to re-install the tool.1.4 again, and found the same problem. Can you give me more suggestions.
I am really appreciated for your suggestions again!
Best wishes,
Rilei Yu
--- 10年5月29日，周六, Jason Swails <jason.swails.gmail.com> 写道：
发件人: Jason Swails <jason.swails.gmail.com>
主题: Re: [AMBER] MMPBSA.py update install problem
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2010年5月29日,周六,上午4:38
On Fri, May 28, 2010 at 1:20 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > When you install AmberTools 1.4 you will not need to uninstall AmberTools
> > 1.2 or Amber 10. Instead, just place the path for Amber 11 (export
> > AMBERHOME=/usr/local/amber11) before defining the path for Amber 10
> > (AMBERHOME=/usr/local/amber10) in your .bashrc file. This will set up
> your
> > environment such that the computer will look for the executable files in
> > Amber 11 *before* the executable files in Amber 10, which is what you
> want.
>
> It doesn't work this way - your environment has only one AMBERHOME
> variable, it is not like a path where directories are indexed
> sequentially.
>
Yes. One at a time. To install amber10, though, AMBERHOME needs to point to
/usr/local/amber10 temporarily (while the install is taking place). Then it
should point to /usr/local/amber11 to install AmberTools 1.4, and it should
remain pointing to /usr/local/amber11 after it's done (since AmberTools
makes the most use of AMBERHOME; indeed probably the only use of it).
However, in order for MMPBSA.py to operate successfully, both
/usr/local/amber10/bin and /usr/local/amber11/bin must be in the PATH, with
/usr/local/amber11 coming first so AmberTools-1.4 binaries are used before
AmberTools-1.2 that reside in /usr/local/amber10. This is what Bill meant,
I believe. (Though defining AMBERHOME a second time in the .bashrc does
overwrite the first definition).
For installing MMPBSA.py, though, you should probably create a symbolic link
from nab in /usr/local/amber11/bin to the directory /usr/local/amber10/bin
in order to build the nmode program with the proper nab compiler. You can
do this as follows:
sudo mv /usr/local/amber10/bin/nab /usr/local/amber10/bin/nab-1.2
sudo ln -s /usr/local/amber11/bin/nab /usr/local/amber10/bin
I used sudo because typically users don't have write permissions in
/usr/local, but if you changed the ownership of /usr/local/amber10 and 11,
then you don't need the sudo (but if you don't need the sudo, you generally
know you don't...)
What this does is to move nab from AT 1.2 "out of the way" so that a soft
link can be put in /usr/local/amber11/bin, so that MMPBSA.py installation
will use that.
Ideally what should be in your .bashrc should look something like this:
export AMBERHOME=/usr/local/amber11
export PATH=$AMBERHOME/bin\:/usr/local/amber10/bin\:$PATH
Hope this helps,
Jason
> Bill
>
> _______________________________________________
> 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 Sat May 29 2010 - 04:30:04 PDT
