RE: AMBER: Fwd: Amber9 parallel compilation openmpi issues

From: Francesco Pietra <>
Date: Wed, 25 Jul 2007 10:07:15 -0700 (PDT)

Dear Ross:
Sorry. I understand your irritation. People are in vacation and I managed

Seemingly, everything reduces to having taken /usr/local/openmpi-1.2.3 as the
installation dir, while it is for the openmpi source. Not a minor
misunderstanding. I have no excuse.

~$ which mpif90



~$ mpif90 --showme

/opt/intel/fce/9.1.036/bin/ifort -I/usr/local/include -pthread -I/usr/local/lib
-L/usr/local/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl
-Wl,--export-dynamic -lnsl -lutil

report correctly (as far as I can understand) and I'll refrain from posting
hurriedly at next attempts to compile Amber. A positive note from my side: my
very large non-polymeric natural products behave perfectly at steps 1-5 of your
tutorial B1, and I have not yet investigated the arrangement of water beyond
what you indicated. Not tried step 6 yet. Wait for parallelization.

francesco pietra

--- Ross Walker <> wrote:

> Dear Francesco,
> > Analysis of config.h and errors.log by comepetents in
> > openmpi, who do not know
> > Amber, may help. It is clear at this point that the issue can
> > only be solved
> > with help from Amber compilation experts. Notice please that
> The issue here is that you are greatly over complicating things by trying to
> resolve things in ten different directions at once, giving different error
> messages to different people and generally just confusing everybody.
> The key problem I believe is that you are receiving error messages early on
> in the process that you are ignoring and proceeding to the next step
> blindly. Then things are failing further down the line and it is at this
> point that you post all the errors and people are left trying to work how on
> earth this happened when all the previous steps (as you state) worked
> without error. This results in people wasting a lot of time trying to work
> out what is the bug in the Amber configure script that would cause this,
> given that it works on a such large number of other machines. This just
> results in everybody wasting time and the problem not getting solved.
> The analogous experimental scenario would be designing a 10 stage synthesis
> and not bother to to use NMR etc on each step to make sure it made what you
> wanted. So step 2 fails and gives you a completely different product that
> you expected but you carry on blindly. Then when you get to say stage 8 it
> makes a ton of decomposed brown goo and this point you go and ask someone
> why step 8 of your proposed synthesis doesn't work and this person then
> spends ages trying to work such a simple step as step 8 doesn't work when
> they have used it all the time in their work...
> So lets take this in small steps one at a time and hopefully we can work out
> where the problem occurs and fix it so that you can run Amber in parallel.
> Firstly lets start with the mpi installation. I suspect that this has not
> been correctly installed or has been installed to a directory other than you
> think it has. Do you specifically know where you installed openMPI? From
> what I can gather you are pointing MPI_HOME to the directory of the original
> source code and not where you actually installed it. So I suspect the chain
> of events is something like this:
> 1) Assume that openMPI installed correctly but with no idea what directory
> it installed to.
> 2) Do not bother to check that openMPI test cases work.
> 3) Point MPI_HOME to the source directory for openMPI assuming that this is
> where it installed.
> 4) execute amber's configure script - configure most likely gives a warning
> about missing mpif.h etc etc - you ignore this warning and do not feel it
> necessary to report it in your list of things that went wrong.
> 5) having ignored the warning you then attempt to build amber anyway and get
> a whole load of unresolved dependencies and then post to the amber list
> claiming that nothing works. \
> The key point here is that the error could have been picked up at a number
> of steps. At the openMPI build step by not running the tests there and or
> not making sure you actually knew where things were installed.
> At the configure stage when you would have received a warning.
> Start by building openMPI giving it a prefix for the directory you want it
> installed in. Also make sure that you will use the same compiler as you will
> for Amber 9. I guess ifort. You can leave the c compiler as gcc it makes no
> difference. Be sure to check that the openMPI configure script does indeed
> use the compiler you chose.
> Then once this is done and you have done make install go take a look in the
> directory you gave with the prefix and make sure things like mpif90 are
> present. See if you can build some simple example mpi programs - I assume
> openMPI comes with a tests suite. Add the bin directory of this install
> directory to your path and then logout and log back in and make sure that
> >which mpirun / >which mpf90 etc are returning the path you expect.
> You most likely have multiple MPI installations on your system and you need
> to make sure you are actually using the one you want to use - don't just
> assume it.
> There will probably be a ton of MPI stuff from LAM MPI installed in /usr/bin
> etc all built against g77 - Wow you just have to love the ANARCHY that is
> Linux :-(... You need to make sure the path to your custom installed MPI is
> before /usr/bin /bin /usr/lib etc etc so put it at the front of your path
> variable and make sure when you execute mpif90 etc it does indeed use the
> correct one.
> If the above does not return the path where you installed openMPI (or says
> command not found) then you need to fix this BEFORE attempting to build
> amber.
> Alternatively if you have admins for this machine who complain that openMPI
> is in use by other applications etc and you cannot change it then get them
> to install you a copy of openMPI on the machine that is built against ifort
> and have them provide you with the necessary modifications to your
> .bashrc/.cshrc etc in order to use this openMPI instead of the default one.
> If they complain then just tell them "tough it is your job so get on with
> it" - If they don't know how to do it then they are pretty useless admins
> for a cluster so have them fired and find someone else who knows what they
> are doing.
> Once you have sorted this and have a working MPI installation with a mpif90
> --showme that reports the correct fortran compiler and you know what to set
> MPI_HOME to then proceed to building Amber. First run configure and check
> for any and all warnings / errors and act on them. If you don't understand
> them then STOP at this point and ask the mailing list.
> Then go ahead and build AMBER and hopefully this time it will work. If not
> then before you modify anything / tweak paths etc then post to the AMBER
> list with the errors and details about what you did - what configure
> reported, what arguments you gave configure etc. Running "env" to show all
> your environment variables can also help.
> All the best
> Ross
> /\
> \/
> |\oss Walker
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- |
> | | PGP Key available on request |
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Received on Sun Jul 29 2007 - 06:07:12 PDT
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