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-- Jason Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 On May 29, 2010, at 7:21 AM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote: > 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 > _______________________________________________ > 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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sat May 29 2010 - 07:00:03 PDT