Thanks for the responses!
noemil lets it get past the configure step! It then crashes quickly in the
"make install" with:
...[lots of lines]....
mpicc -fPIC -O0 -h gnu -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-DBINTRAJ -DHASGZ -D__PLUMED_HAS_DLOPEN -DMPI -c -o symtab.o symtab.c
mpicc -fPIC -O0 -h gnu -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-DBINTRAJ -DHASGZ -D__PLUMED_HAS_DLOPEN -DMPI -c -o verbose.o
verbose.c
mpicc -fPIC -O0 -h gnu -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-DBINTRAJ -DHASGZ -D__PLUMED_HAS_DLOPEN -DMPI -c -o warshall.o
warshall.c
/opt/cray/pe/cce/8.5.7/cray-binutils/x86_64-pc-linux-gnu/bin/ld: cannot
find -lmpi
main.o: In function `create_file_names':
/p/home/tschutt7/Software/amber16/AmberTools/src/byacc/main.c:268: warning:
the use of `mktemp' is dangerous, better use `mkstemp'
Makefile:34: recipe for target '/p/home/tschutt7/Software/amber16/bin/yacc'
failed
make[2]: *** [/p/home/tschutt7/Software/amber16/bin/yacc] Error 1
make[2]: Leaving directory '/p/home/tschutt7/Software/
amber16/AmberTools/src/byacc'
Makefile:145: recipe for target 'cray_parallel' failed
make[1]: *** [cray_parallel] Error 2
make[1]: Leaving directory '/p/home/tschutt7/Software/
amber16/AmberTools/src'
Makefile:7: recipe for target 'install' failed
make: *** [install] Error 2
going to the sander directory - "make install" returns:
make: *** No rule to make target 'cray_parallel', needed by 'install'. Stop.
and attempting "make parallel" returns:
....[lots of lines]...
ftn -DBINTRAJ -DMPI -DSANDER -c -O0 -fPIC -O0 -emf -f free
-I/p/home/tschutt7/Software/amber16/include -I/opt/cray/pe/netcdf-
hdf5parallel/4.4.1.1/CRAY/8.3/include -o np_force.SANDER.o np_force.F90
ftn -DBINTRAJ -DMPI -DSANDER -c -fPIC -O0 -emf -f free
-I/p/home/tschutt7/Software/amber16/include -I/opt/cray/pe/netcdf-
hdf5parallel/4.4.1.1/CRAY/8.3/include -I../sander \
-o density.SANDER.o density.F90
_REAL_ function density_atom(dist)
^
ftn-828 crayftn: ERROR DENSITY_ATOM, File = density.F90, Line = 763, Column
= 30
Procedure "DENSITY_ATOM" is defined in multiple places. Argument 1 has
INTENT(IN) in one definition but not the other.
Makefile:254: recipe for target 'density.SANDER.o' failed
make[1]: *** [density.SANDER.o] Error 1
make[1]: Leaving directory '/p/home/tschutt7/Software/
amber16/AmberTools/src/pbsa'
Makefile:492: recipe for target 'libpbsa' failed
make: *** [libpbsa] Error 2
I don't know if this is cray support issues in general or if our new
machine is just That awkward or... Regardless, Thanks for helping! Let me
know your thoughts on the most promising of the above three approach(es)?
On Thu, Sep 21, 2017 at 3:46 PM, David A Case <david.case.rutgers.edu>
wrote:
> Sending this again, because my laptop crashed just as I was mailing this,
> and I'm not sure if it was really mailed or not.....dac
>
>
> ----- Forwarded message from David A Case <david.case.rutgers.edu> -----
>
> Date: Thu, 21 Sep 2017 22:43:37 +0200
> From: David A Case <david.case.rutgers.edu>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Is it possible to compile without linking C++ and
> fortran?
>
> On Thu, Sep 21, 2017, Timothy Schutt wrote:
> >
> > Sorry to be a hassle again. Still trying to get Amber to work on this
> Cray
> > XC40/50 system. Is it possible to compile amber without C++ linking to
> > fortran, perhaps without cuda or EMIL features?
>
> Sorry crays are giving you so much trouble! You can use the "-noemil"
> flag to configure to turn off emil compiling. Then, after configure try
> going directly to AmberTools/src/sander and typing "make install" (or
> perhaps "make parallel" -- I'm travelling right now. That should(!?!) get
> you sander.MPI. Please don't be shy about letting us know whether this
> does
> or does not work....
>
> I'm not sure what to do about the cpptraj.MPI problem: maybe Dan will have
> a good suggestion.
>
> >
> > Error! Could not link C++ mpi code using mpi fortran linker:
> > "ftn "
> > [C++ / fortran / MPI] cross-linking is needed for cuda_parallel and EMIL
> > builds.
> > Try: "mpif90 -show"
> > Configure failed due to the errors above!
>
> If you are lucky, adding the -noemil flag will eliminate this error.
> If not, you might try going
> to AMBERHOME/AmberTools/src, edit the configure2 script so that it doesn't
> exit after the above message.
>
> > Is there a way to turn off cuda_parallel and EMIL builds? (I'm not asking
> > for cuda in the configure flags but it's still partly trying apparently?)
> > At the moment mostly I just need sander.mpi and cpptraj?
>
> As an aside: thanks for sending the information you have so far: it's
> pretty
> clear that we have let Cray support wither (wasn't that long ago that
> things
> worked there....)
>
> ....dac
>
>
> ----- End forwarded message -----
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Sep 21 2017 - 14:30:03 PDT
