ptraj.MPI is not built anymore (I don't think we build or release pnetcdf
anymore, either). There's a note
http://ambermd.org/doc12/ <-- at the
bottom of that page about that.
All the best,
Jason
On Wed, May 2, 2012 at 3:15 PM, Jodi Ann Hadden <jodih.uga.edu> wrote:
> I am noticing that ptraj.MPI is not being generated by the default build
> protocol for AMBER12 on any of the machines I've compiled it on. These are
> either fully patched versions of AMBER12 or recent git pulls. Any
> suggestions?
>
> Two examples machine configurations are:
>
> RHEL6 server, gnu 4.4.6, mvapich2 1.4.1p1
> RHEL5, gnu 4.4.6, openMPI 1.4.2
>
> I'm just doing what I though was the standard procedure now:
>
> ./configure gnu
> make -j4 install
> make test
> ./configure -mpi gnu
> make -j4 install
> make test
>
> Everything appears to compile fine, all the tests pass, everything seems
> normal and in working order, but ptraj.MPI is missing. Is there a command I
> can use to try to build it individually? I tried going down into
> $AMBERHOME/AmberTools/src/ptraj and doing a make clean/make, but got an
> error about a missing file:
>
> [installer.tolkien ptraj]$ make
> cd pdb && make
> make[1]: Entering directory
> `/programs/gpu/mmpbsa_test/amber12/AmberTools/src/ptraj/pdb'
> mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -c
> -o pdbrun.o pdbrun.c
> mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -c
> -o pdb_read.o pdb_read.c
> mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -c
> -o pdb_sprntf.o pdb_sprntf.c
> mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -c
> -o pdb_sscanf.o pdb_sscanf.c
> mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -c
> -o pdb_write.o pdb_write.c
> mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -c
> -o ms.o ms.c
> ar rv libpdb.a pdbrun.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o
> ms.o
> ar: creating libpdb.a
> a - pdbrun.o
> a - pdb_read.o
> a - pdb_sprntf.o
> a - pdb_sscanf.o
> a - pdb_write.o
> a - ms.o
> ranlib libpdb.a
> mv libpdb.a /programs/gpu/mmpbsa_test/amber12/lib
> make[1]: Leaving directory
> `/programs/gpu/mmpbsa_test/amber12/AmberTools/src/ptraj/pdb'
> cd ../arpack && make
> make[1]: Entering directory
> `/programs/gpu/mmpbsa_test/amber12/AmberTools/src/arpack'
> make[1]: Nothing to be done for `install'.
> make[1]: Leaving directory
> `/programs/gpu/mmpbsa_test/amber12/AmberTools/src/arpack'
> mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI
> -I/programs/gpu/mmpbsa_test/amber12/include -o main.o main.c
> In file included from ptraj.h:80,
> from main.c:114:
> netcdf_ptraj.h:4:39: error: ../../include/pnetcdf.h: No such file or
> directory
> In file included from ptraj.h:80,
> from main.c:114:
> netcdf_ptraj.h:18: error: expected declaration specifiers or ‘...’ before
> ‘nc_type’
> make: *** [main.o] Error 1
> [installer.tolkien ptraj]$
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed May 02 2012 - 13:00:02 PDT
