AMBER Archive (2006)

Subject: Re: AMBER: parallel installation of amber8 on HP cluster

From: Michael Crowley (crowley_at_scripps.edu)
Date: Wed Jul 26 2006 - 13:52:09 CDT

Dear Manish,
This appears to be from code that mpif.h included in _egb.f:

      include 'mpiof.h'

since I cannot find it anywhere in the amber8 code for egb.f or any _egb.f
that I produce. So, aside from having the admin folks at your site make
the mpi to behave like a vendor, native mpi by putting the libs and include
files in standard places, you will have to add the following to your
compiler lines inside config,h. on the end of the FFLAGS and FOPTFLAGS,
add

-I/opt/hpmpi//include

and see if that helps ifort find the include file. The trouble is that
amber expects the include files to be handled by the preprocessor, and be all
done by the time the fortran compiler gets the code in the form of the _files
(_egb.f). We do not expect to see any fortran "include" statements there and
so do not provide a path for looking for those include files. Thus, even
though you have MPICH_HOME set, only the preprocessor knows where to look for
the include files, not ifort. I am telling you to add the above information
to the FFLAGS and FOPTFLAGS so ifort will know where to look other than the
current directory.

The other option is to have your admin make the mpi behave like native mpi and
then you will be able to use the config file generated with:
./configure -mpi ifort

Good luck.
Mike

On Wednesday 26 July 2006 10:54, Manish Datt wrote:
> hi
>
> thanks david and mike for your respective responses.
>
> i tried configuring with ./configure -mpich ifort.
> on doing make parallel i am getting following error
>
> ######################################
> [mdatt_at_n288 src]$ make parallel
> Starting installation of Amber8 (parallel) at Wed Jul 26 22:20:23 IST
> 2006.
> mkdir ../exe
> mkdir: cannot create directory `../exe': File exists
> make: [parallel] Error 1 (ignored)
> cd sander; make parallel
> make[1]: Entering directory `/nfsexportn277/mdatt/amber8/src/sander'
> cpp -traditional -I/opt/hpmpi//include -P
> -I/nfsexportn277/mdatt/amber8//src/inc
> lude -DMPI trace.f > _trace.f
> ifort -c -w95 -mp1 -ip -O3 -FR -o trace.o _trace.f
> cpp -traditional -I/opt/hpmpi//include -P
> -I/nfsexportn277/mdatt/amber8//src/inc
> lude -DMPI lmod.f > _lmod.f
> ifort -c -w95 -mp1 -ip -O3 -FR -o lmod.o _lmod.f
> cpp -traditional -I/opt/hpmpi//include -P
> -I/nfsexportn277/mdatt/amber8//src/inc
> lude -DMPI decomp.f > _decomp.f
> ifort -c -w95 -mp1 -O0 -FR -o decomp.o _decomp.f
> cpp -traditional -I/opt/hpmpi//include -P
> -I/nfsexportn277/mdatt/amber8//src/inc
> lude -DMPI icosasurf.f > _icosasurf.f
> ifort -c -w95 -mp1 -ip -O3 -FR -o icosasurf.o _icosasurf.f
> cpp -traditional -I/opt/hpmpi//include -P
> -I/nfsexportn277/mdatt/amber8//src/inc
> lude -DMPI egb.f > _egb.f
> ifort -c -w95 -mp1 -ip -O3 -FR -o egb.o _egb.f
> fortcom: Error: _egb.f, line 645: Cannot open include file 'mpiof.h'
> include 'mpiof.h'
> ---------------^
> compilation aborted for _egb.f (code 1)
> make[1]: *** [egb.o] Error 1
> make[1]: Leaving directory `/nfsexportn277/mdatt/amber8/src/sander'
> make: *** [parallel] Error 2
> ########################################
>
> again the nature of problem has not changed since the file mpiof.h is
> there in the folder /opt/hpmpi/include/ which is there in the path. also
> the variable $MPICH_HOME was set to /opt/hpmpi/ before making
> configuration file.
>
> kindly help me to get out of this.
>
> regards,
>
> Manish Datt
> Research Scholar
> Bioinformatics Centre
> Institute of Microbial Technology
> Sector 39A, Chandigarh-160036
> India.
>
> On Wed, 26 Jul 2006, David A. Case wrote:
> > On Wed, Jul 26, 2006, Manish Datt wrote:
> > > i`m trying to install parallel version of amber8 on HP 288 node XC
> > > cluster. after installing the serial version and doing make clean. the
> > > configuration file was made using ./configure -mpi ifort.
> >
> > The "-mpi" flag is only for "native" mpi, and assumes that all include
> > files are in places like /usr/include where they will automatically be
> > found. Locations under /opt are not automatically searched.
> >
> > > ifort -c -w95 -mp1 -ip -O3 -FR -o icosasurf.o _icosasurf.f
> > > cpp -traditional -P -I/nfsexportn277/mdatt/amber8//src/include -DMPI
> > > egb.f > _egb.f
> > > egb.f:131: mpif.h: No such file or directory
> > >
> > > the file mpif.h is there in the folder /opt/hpmpi/include/ which is
> > > there in the path. also the variable $MPICH_HOME has been defined to
> > > /opt/hpmpi/.
> >
> > It sounds like you are using MPICH (?) since you set $MPICH_HOME. If so,
> > you need to use "-mpich" (not "-mpi") as the flag to configure.
> >
> > ...good luck..dac
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu 

-- 
-----------------------------------------------------------------
Physical mail:   Dr. Michael F. Crowley
                 Department of Molecular Biology, TPC6
                 The Scripps Research Institute
                 10550 North Torrey Pines Road
                 La Jolla, California 92037

Electronic mail: crowley_at_scripps.edu
Telephone:         858/784-9290
Fax:               858/784-8688
-----------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu