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
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)
chen.sugar9:~/amber11$ cd AmberTools/src/
chen.sugar9:~/AmberTools/src$ ./configure intel
chen.sugar9:~/amber11/AmberTools/src$ cd $AMBERHOME
chen.sugar9:~/amber11$ 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
make[2]: *** [rism3d_opendx.o] Error 1
make[2]: Leaving directory `/home/chen/amber11/AmberTools/src/rism'
make[1]: *** [librism_mpi] Error 2
make[1]: Leaving directory `/home/chen/amber11/src/sander'
make: *** [parallel] Error 2
Best,
Mo
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Received on Thu Oct 13 2011 - 20:30:03 PDT
