Dear Dan,
Thanks for your guidance.
My problem was resolved.
Best,
Shahab
On Wed, Oct 12, 2016 at 5:02 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> If all you need is 'rdparm' don't try to build the parallel version of
> ptraj; just re-run AmberTools configure for serial, then try to make
> ptraj/rdparm, e.g.
>
> cd $AMBERHOME
> ./configure gnu
> cd $AMBERHOME/AmberTools/src/ptraj
> make install
>
> -Dan
>
> On Wed, Oct 12, 2016 at 8:18 AM, shahab shariati
> <shahab.shariati.gmail.com> wrote:
> > Dear David,
> >
> > Now, the AMBERHOME variable setting is ok.
> >
> > After using make install,
> >
> > ------------------------------------------------------------
> --------------------
> > [root.ibbs ptraj]# make install
> > cd pdb && make
> > make[1]: Entering directory
> > `/export/apps/amber/amber14/AmberTools/src/ptraj/pdb'
> > 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 /export/apps/amber/amber14/lib
> > make[1]: Leaving directory
> > `/export/apps/amber/amber14/AmberTools/src/ptraj/pdb'
> > cd ../arpack && make
> > make[1]: Entering directory
> > `/export/apps/amber/amber14/AmberTools/src/arpack'
> > make[1]: Nothing to be done for `install'.
> > make[1]: Leaving directory
> > `/export/apps/amber/amber14/AmberTools/src/arpack'
> > mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
> > -DHASBZ2 -DMPI -I/export/apps/amber/amber14/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
> >
> > ------------------------------------------------------------
> --------------------
> >
> > This time, I encountered with only one error (Error 1).
> >
> > On Wed, Oct 12, 2016 at 4:29 AM, David A Case <david.case.rutgers.edu>
> > wrote:
> >
> >> On Tue, Oct 11, 2016, shahab shariati wrote:
> >>
> >> > [root.ibbs ptraj]# make install
> >> > cd pdb && make
> >> > make[1]: Entering directory `/share/apps/2_amber/amber14/
> >> AmberTools/src/ptraj/pdb'
> >>
> >> Here you are in the tree /share/apps/2_amer/amber14....
> >>
> >> > mv: cannot move `libpdb.a' to `/export/apps/amber/amber14/lib': No
> such
> >> > file or directory
> >>
> >> Here, it looks like your AMBERHOME variable is set to
> >> /export/apps/amber/amber14.
> >>
> >> I suspect that, as the message says, you don't have an
> >> /export/apps/amber/amber14/lib directory, and that you AMBERHOME
> variable
> >> is
> >> probably set incorrectly.
> >>
> >> Having said that, the advice to move to acpype sounds like a much better
> >> solution.
> >>
> >> ....dac
> >>
> >> [Aside: don't install Amber as root! Take the time to learn how to
> avoid
> >> doing this.]
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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Received on Wed Oct 12 2016 - 12:30:02 PDT
