Dear Ross:
Thanks. Static serial compilation of amber9 on linux debian amd64 etch failed
(in my hands).
I first run
./configure -static ifort_x86_64
as user. That set the time corresponding to this command (2007-06-28 09:11) for
the following files: antechamber configure pbsa ptraj sander, while it failed
to create config.h, at least it was not created into /src.
The error was somewhat cryptic:
./configure: line 1264: config.h: Permission denied
The configuration file, config.h was successfully created.
_________
Make serial (or make) issued as user returned that "make" should be run after
./configure.
__________
Then, without modifying anything (configure was "root root", while all other
files were "1006 513") I repeated the ./configure as above, though as superuser
(at 16:07).
The config.h was created in /src (bearing the time of the command 16:07) and no
error was reported. All files previously set at the time of the ./configure
command (antechamber ...sander) were left at that initial time (09:11).
# make serial (as superuser)
resulted in:
cd lib make install
make[1]: Entering directory '/usr/local/amber9/src/lib'
cpp -traditional -P new2oldparm.f > _new2oldparm.f
ifort -c -w95 -mp1 -O0 -o new2oldparm.o _newoldparm.f
make[1]: ifort: Command not found
make[1]: *** [new2oldparm.o] Error127
make[1]: Leaving directory '/use/local/amber9/src/lib'
make: *** [serial] Error 2
_________________
the intel fortran comp is at
/opt/intel/fce/9.1.036/bin which is on my path, and this this contains, inter
alia, "ifort".
If I understand make should be told where to find ifort; as superuser my PATH
is not recognized. On the other hand, I tried first "make clean" as superuser,
than "make serial" as user, getting
cpp -traditional -P new2oldparm.f > _new2oldparm.f
/bin/sh: _new2oldparm.f:Permission denied.
Grateful for help.
francesco pietra
--- Ross Walker <ross.rosswalker.co.uk> wrote:
> Dear Francesco,
>
> I would advise you build the serial version first for two reasons.
>
> 1) Most of the auxiliary tools are not built in the parallel version (i.e.
> leap, ptraj etc...)
>
> 2) Debugging in parallel is really dificult so you should make sure
> everything works in serial before doing this.
>
> If you have a copy of the Intel compilers then don't worry about g95 etc. Do
> the following.
>
> 1) extract the tar file to a dir - e.g. /usr/local/amber9
>
> 2) set AMBERHOME=/usr/local/amber9
>
> 3) obtain the latest bugfix.all from the amber website and apply it to the
> tree.
>
> 4) configure for serial (e.g. ./configure -static ifort_x86_64)
>
> 5) cd $AMBERHOME/src
>
> 6) make
>
> 7) cd ../test
>
> 8) make - check TEST_FAILURES.dat for any failures. If everything is good
> move on to parallel compilation.
>
> 9) verify that MPI_HOME points to the correct place
>
> 10) verify that your MPI was built with the same version of the ifort
> compiler
>
> 11) cd $AMBERHOME/src
>
> 12) ./configure -openmpi ifort_x86_64
>
> 13) make clean; make parallel
>
> 14) set up the mpi environment so you can mpirun...
>
> 15) export DO_PARALLEL='mpirun -np 2' - or whatever your mpi environment
> needs.
>
> 16) cd ../test; make test.parallel (check TEST_FAILURES.dat)
>
> If this all works then you can also build pmemd for parallel - see
> $AMBERHOME/src/pmemd.
>
> All the best
> Ross
>
>
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
> > -----Original Message-----
> > From: owner-amber.scripps.edu
> > [mailto:owner-amber.scripps.edu] On Behalf Of Francesco Pietra
> > Sent: Wednesday, June 27, 2007 07:59
> > To: Amber
> > Subject: Fwd: Re: AMBER: $AMBERHOME on PATH
> >
> > Setting of env variables is obviously correct as indicated
> > below. I am here
> > again to ask if step 2c of readme on amber9 CD should really
> > be carried out as
> > indicated, i.e., compiling serially with g95.
> >
> > That question because I'll move as soon as possible to
> > parallel compilation
> > with intel compilers (having already compiled and installed
> > openmpi with them).
> > In other words, will step 4 (compile with intels) compile
> > everything with
> > intels or some non-parallelized modules will remain compiled with g95?
> >
> > That just to know
> >
> > Thanks
> >
> > francesco pietra
> >
> >
> >
> > --- Francesco Pietra <chiendarret.yahoo.com> wrote:
> >
> > > Date: Wed, 27 Jun 2007 07:30:09 -0700 (PDT)
> > > From: Francesco Pietra <chiendarret.yahoo.com>
> > > Subject: Fwd: Re: AMBER: $AMBERHOME on PATH
> > > To: Amber <amber.scripps.edu>
> > >
> > > Please, see note about "printenv" below
> > >
> > > --- Francesco Pietra <chiendarret.yahoo.com> wrote:
> > >
> > > > Date: Tue, 26 Jun 2007 13:15:11 -0700 (PDT)
> > > > From: Francesco Pietra <chiendarret.yahoo.com>
> > > > Subject: Re: AMBER: $AMBERHOME on PATH
> > > > To: amber.scripps.edu
> > > >
> > > > David:
> > > > Following your warning that setting AMBERHOME must
> > precede that of PATH...,
> > > I
> > > > commented out "PATH .." in my .bashrc. That failed to
> > bring back the env
> > > var
> > > > AMBERHOME, while ":exe" disappered from PATH ... , as
> > obtained from
> > > printenv.
> > > >
> > > > Then I set in my .bashrc the following two lines:
> > > >
> > > > AMBERHOME=/usr/local/amber9
> > > >
> > > > PATH=$PATH:$AMBERHOME/exe; export AMBERHOME PATH
> > > >
> > > > Now
> > > >
> > > >
> > > > $ echo $AMBERHOME
> > > > /usr/local/amber9
> > > >
> > > >
> > > >
> > > > $ echo $AMBERHOME/exe
> > > > /usr/local/amber9/exe
> > > >
> > > >
> > > >
> > > > $ printenv
> > > >
> > > > reports /usr/local/amber9/exe
> > >
> > > NOTE: of course the outcome of "printenv" should be read,
> > inter alia, as
> > > follows:
> > >
> > >
> > > PATH=/home ............:/usr/local/amber9/exe
> > >
> > > and
> > >
> > > AMBERHOME=/usr/local/amber9
> > >
> > > >
> > > >
> > > > Are these settings correct?
> > > >
> > > > Thanks
> > > >
> > > > francesco
> > > >
> > > >
> > > > --- "David A. Case" <case.scripps.edu> wrote:
> > > >
> > > > > On Tue, Jun 26, 2007, Francesco Pietra wrote:
> > > > >
> > > > > > I must have done something very silly while at the
> > first steps of
> > > > > installing
> > > > > > amber9. After untarring as described in the readme on
> > the CD, getting
> > > > > > /usr/local/amber9
> > > > > >
> > > > > > I set (bash shell)
> > > > > >
> > > > > > $ AMBERHOME=/usr/local/amber9; export AMBERHOME
> > > > >
> > > > > Did you also put this in your .bashrc? AMBERHOME needs
> > to be set before
> > > > > you refer to it here:
> > > > >
> > > > > > Then I set in my .bashrc
> > > > > >
> > > > > > PATH=$PATH:$AMBERHOME/exe; export AMBERHOME PATH
> > > > > >
> > > > >
> > > > > I'm just guessing here; maybe someone else will see
> > some other problem.
> > > > >
> > > > > ...dac
> > > > >
> > > > >
> > --------------------------------------------------------------
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> > > >
> > > >
> > > >
> > > >
> > > >
> > >
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Received on Sun Jul 01 2007 - 06:07:21 PDT
