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 - 07:00:02 PDT
