Having successfully navigated serial and parallel Amber10 installs under Ubuntu 8.10, I am pleased to report that the process for Amber11 with OpenMPI (from apt-get, one doesn't have to build from scratch) under Ubuntu 10.10 is seemingly much easier (and have it here so I don't forget). There is a bit of persnicketiness to the order of the serial and parallel installs that must be kept track of (and I'm building in serial-to-parallel order), but the process is otherwise straightforward.
For organizational purposes, I'm building amber11 in my $HOME directory. This removes some of the PATH issues with sudo-ing aspects of the install (and can be moved into another directory after the build is complete).
1. apt-get Installs
The search for dependent programs and libraries is a long and involved one given how many programs I have installed. Therefore, instead of trying to find all of the amber-dependent installs for successful building, I'm simply providing the list of everything I have on the test machine. As hard drives are cheap and Ubuntu will warn of conflicts, I recommend simply installing the below and accepting the 100 Mb hit to NOT have to find the smallest apt-get set (yes, some of these are obviously not needed).
sudo apt-get install build-essential cmake doxygen freeglut3-dev g++-multilib gcc-multilib gettext gnuplot ia32-libs lib32asound2 lib32gcc1 lib32gcc1-dbg lib32gfortran3 lib32gomp1 lib32mudflap0 lib32ncurses5 lib32nss-mdns lib32z1 libavdevice52 libc6-dev-i386 libc6-i386 libfreeimage-dev libglew1.5-dev libopenal1 libopenexr-dev libpng12-dev libqt4-dev libssl-dev libstdc++6-4.3-dbg libstdc++6-4.3-dev libstdc++6-4.3-doc libxi-dev libxml-simple-perl libxmu-dev mercurial nfs-common nfs-kernel-server portmap python2.6-dev rpm ssh
The above said, there are some obvious most-important installs that have to be there (according to the "official" Ubuntu amber11 install summary at ambermd.org/ubuntu.html). You could try to work with only these first if you were in a diagnostic mood today:
sudo apt-get install bison csh flex fort77 g++ gcc gfortran libbz2-dev libnetcdf-dev libopenmpi-dev libxext-dev libxt-dev openmpi-bin patch tcsh xorg-dev zlib1g-dev
With that, we move onto the AmberTools 1.5 install.
2. AmberTools 1.5 (Serial)
The AmberTools build process deals with PATH specifications for both it and Amber, then walks you through patching and a successful build.
user@machine:~$ tar xjf AmberTools-1.5.tar.bz2 user@machine:~$ cd amber11/ user@machine:~/amber11$ echo "export AMBERHOME=$PWD" >> ~/.bashrc user@machine:~/amber11$ echo "export PATH=$PATH:$AMBERHOME/bin" >> ~/.bashrc user@machine:~/amber11$ source ~/.bashrc user@machine:~/amber11$ wget http://ambermd.org/bugfixes/AmberTools/1.5/bugfix.all user@machine:~/amber11$ patch -p0 < bugfix.all user@machine:~/amber11$ rm bugfix.all user@machine:~/amber11$ cd AmberTools/src/ user@machine:~/amber11/AmberTools/src$ ./configure gnu user@machine:~/amber11/AmberTools/src$ make install user@machine:~/amber11/AmberTools/src$ cd
3. Amber 11 (Serial Install)
For the Amber build, not building the serial version first will produce the following error (which you may or may not be searching against in google presently):
Warning: Deleted feature: PAUSE statement at (1) cpp -traditional -P -DBINTRAJ -DMPI svbksb.f > _svbksb.f mpif90 -c -O3 -mtune=generic -ffree-form -o svbksb.o _svbksb.f cpp -traditional -P -DBINTRAJ -DMPI pythag.f > _pythag.f mpif90 -c -O3 -mtune=generic -ffree-form -o pythag.o _pythag.f Error: a serial version of libFpbsa.a must be built before parallel build. make[2]: *** [libFpbsa.parallel] Error 2 make[2]: Leaving directory `/home/genomebio/amber11/AmberTools/src/pbsa' make[1]: *** [libpbsa] Error 2 make[1]: Leaving directory `/home/genomebio/amber11/src/sander' make: *** [parallel] Error 2
The "gnu" is also important, as there appears to be some kind of formatting (fortran-specific) issue with some files in the non-gnu build attempt that produces the following error if you just blindly run a ./configure:
Error: Unclassifiable statement at (1) constants.f:39.1: double precision, parameter :: two = 2.0d0 1 Error: Non-numeric character in statement label at (1) constants.f:39.1: double precision, parameter :: two = 2.0d0 1 Error: Unclassifiable statement at (1) constants.f:40.1: double precision, parameter :: three = 3.0d0 1 Error: Non-numeric character in statement label at (1) Fatal Error: Error count reached limit of 25. make[1]: *** [constants.o] Error 1 make[1]: Leaving directory `/home/user/amber11/src/sander' make: *** [parallel] Error 2
With that, the serial build is below, including bug fixes.
user@machine:~$ tar xfj Amber11.tar.bz2 user@machine:~$ cd $AMBERHOME user@machine:~/amber11$ wget http://ambermd.org/bugfixes/11.0/bugfix.all user@machine:~/amber11$ wget http://ambermd.org/bugfixes/11.0/apply_bugfix.x user@machine:~/amber11$ chmod +x ./apply_bugfix.x user@machine:~/amber11$ ./apply_bugfix.x bugfix.all user@machine:~/amber11$ cd AmberTools/src/ user@machine:~/amber11/AmberTools/src$ ./configure gnu user@machine:~/amber11/AmberTools/src$ cd $AMBERHOME user@machine:~/amber11$ ./AT15_Amber11.py user@machine:~/amber11$ cd src/ user@machine:~/amber11/src$ make serial
4. Amber 11 (Parallel)
Hopefully the serial build ran non-problematically. The parallel install works just as simply provided you run the process in the order below. The key steps are the "make clean," new ./configure, re-run of ./AT_Amber11.py, and the other "make clean."
user@machine:~/amber11/src$ cd $AMBERHOME user@machine:~/amber11$ cd AmberTools/src/ user@machine:~/amber11/AmberTools/src$ make clean user@machine:~/amber11/AmberTools/src$ ./configure -mpi gnu user@machine:~/amber11/AmberTools/src$ cd $AMBERHOME user@machine:~/amber11$ ./AT15_Amber11.py user@machine:~/amber11$ cd src/ user@machine:~/amber11/src$ make clean user@machine:~/amber11/src$ make parallel
5. Amber 11 (Tests)
Finally, testing the install. Nothing specific to be done as far as the code is concerned, simply running the tests.
user@machine:~/amber11/src$ cd .. user@machine:~/amber11$ cd test/ user@machine:~/amber11/test$ make -f Makefile user@machine:~/amber11/test$
From the out-of-the-box installation above, my test results complete as follows:
365 file comparisons passed 15 file comparisons failed 0 tests experienced errors Test log file saved as logs/test_amber_serial/2011-07-14_11-19-47.log Test diffs file saved as logs/test_amber_serial/2011-07-14_11-19-47.diff
The failed tests include those already mentioned by the Amber developers to fail. This list is provided at the end of the AT15_Amber11.py results:
NOTE: Because PBSA has changed since Amber 11 was released, some tests are known to fail and others are known to quit in error. These can be safely ignored. Tests that error: Tests in $AMBERHOME/test/sander_pbsa_frc Run.argasp.min Run.dadt.min Run.dgdc.min Run.lysasp.min Run.polyALA.min Run.polyAT.min Run.argasp.min Run.dadt.min Run.dgdc.min Run.lysasp.min Run.polyALA.min Run.polyAT.min Run.argasp.min Run.dadt.min Run.dgdc.min Run.lysasp.min Run.polyALA.min Run.polyAT.min Tests that produce possible FAILUREs: cd sander_pbsa_ipb2 && ./Run.110D.min cd sander_pbsa_lpb && ./Run.lsolver.min (only some of them fail here) cd sander_pbsa_tsr && ./Run.tsrb.min cd sander_pbsa_decres && ./Run.pbsa_decres mm_pbsa.pl tests 02, 03, and 05
6. Quick Summary
For ease of copy-and-paste-ing, the command list is below:
apt-get
sudo apt-get install build-essential cmake doxygen freeglut3-dev g++-multilib gcc-multilib gettext gnuplot ia32-libs lib32asound2 lib32gcc1 lib32gcc1-dbg lib32gfortran3 lib32gomp1 lib32mudflap0 lib32ncurses5 lib32nss-mdns lib32z1 libavdevice52 libc6-dev-i386 libc6-i386 libfreeimage-dev libglew1.5-dev libopenal1 libopenexr-dev libpng12-dev libqt4-dev libssl-dev libstdc++6-4.3-dbg libstdc++6-4.3-dev libstdc++6-4.3-doc libxi-dev libxml-simple-perl libxmu-dev mercurial nfs-common nfs-kernel-server portmap python2.6-dev rpm ssh sudo apt-get install bison csh flex fort77 g++ gcc gfortran libbz2-dev libnetcdf-dev libopenmpi-dev libxext-dev libxt-dev openmpi-bin patch tcsh xorg-dev zlib1g-dev
AmberTools
tar xjf AmberTools-1.5.tar.bz2 cd amber11/ echo "export AMBERHOME=$PWD" >> ~/.bashrc echo "export PATH=$PATH:$AMBERHOME/bin" >> ~/.bashrc source ~/.bashrc wget http://ambermd.org/bugfixes/AmberTools/1.5/bugfix.all patch -p0 < bugfix.all rm bugfix.all cd AmberTools/src/ ./configure gnu make install cd
Amber 11 (Serial)
tar xfj Amber11.tar.bz2 cd $AMBERHOME wget http://ambermd.org/bugfixes/11.0/bugfix.all wget http://ambermd.org/bugfixes/11.0/apply_bugfix.x chmod +x ./apply_bugfix.x ./apply_bugfix.x bugfix.all cd AmberTools/src/ ./configure gnu cd $AMBERHOME ./AT15_Amber11.py cd src/ make serial
Amber 11 (Parallel)
cd $AMBERHOME cd AmberTools/src/ make clean ./configure -mpi gnu cd $AMBERHOME ./AT15_Amber11.py cd src/ make clean make parallel
Amber Tests
cd .. cd test/ make -f Makefile
7. And Furthermore…
I tried the above on an old linux box running Intrepid Ibex (8.10), which counts as an End-Of-Life (Obsolete) version. Running all of the apt-get installs will work despite 8.10 not existing in the standard package locations, but you have to make the following addition to /etc/apt/sources.list.
sudo pico /etc/apt/sources.list
And copy-and-paste the following (this all taken from help.ubuntu.com/community/EOLUpgrades/Intrepid):
## EOL upgrade sources.list # Required deb http://old-releases.ubuntu.com/ubuntu/ intrepid main restricted universe multiverse deb http://old-releases.ubuntu.com/ubuntu/ intrepid-updates main restricted universe multiverse deb http://old-releases.ubuntu.com/ubuntu/ intrepid-security main restricted universe multiverse