Hi,
Thanks for the input. Amber Tools installation completed successfully.
However, the test suite gave the following result.
Finished test suite for AmberTools at Wed Jun 1 09:35:49 MDT 2011.
make[1]: Target `test.serial' not remade because of errors.
make[1]: Leaving directory `/home/common/packages/amber11/AmberTools/test'
281 file comparisons passed
4 file comparisons failed
64 tests experienced errors
Test log file saved as logs/test_at_serial/2011-06-01_09-26-02.log
Test diffs file saved as logs/test_at_serial/2011-06-01_09-26-02.diff
1. It says test.serial was not remade.
Should I be worried about this?
2. The 4 tests that failed were to do with NAB
Please advise.
Vivek
On Tue, May 31, 2011 at 10:14 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> This is due to io.c being patched twice. Replace
> $AMBERHOME/AmberTools/src/ptraj/io.c with the attached io.c, that
> should fix it.
>
> -Dan
>
> On Tue, May 31, 2011 at 10:35 PM, Vivek Shankar Bharadwaj
> <vbharadw.mymail.mines.edu> wrote:
> > Hi dac,
> >
> > Thanks for the patch. I used the patch on the unpatched version of files.
> >
> > I get a new error now,
> >
> > a - wallclock.o
> > ranlib arpack.a
> > mv arpack.a /home/common/packages/amber11/lib
> > make[2]: Leaving directory
> > `/home/common/packages/amber11/AmberTools/src/arpack'
> > gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o main.o
> > main.c
> > gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o
> rdparm.o
> > rdparm.c
> > gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o
> dispatch.o
> > dispatch.c
> > gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o help.o
> > help.c
> > gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o
> utility.o
> > utility.c
> > gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o
> second.o
> > second.c
> > gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o io.o
> io.c
> > io.c:782:5: error: conflicting types for ‘gzipFileSize’
> > io.c:681:15: note: previous definition of ‘gzipFileSize’ was here
> > io.c:814:5: error: conflicting types for ‘bzip2FileSize’
> > io.c:728:15: note: previous definition of ‘bzip2FileSize’ was here
> > io.c:840:5: error: conflicting types for ‘zipFileSize’
> > io.c:755:15: note: previous definition of ‘zipFileSize’ was here
> > make[1]: *** [io.o] Error 1
> > make[1]: Leaving directory
> > `/home/common/packages/amber11/AmberTools/src/ptraj'
> > make: *** [serial] Error 2
> >
> > What could this be due to?
> >
> > Please Advice.
> >
> > Vivek
> >
> > On Mon, May 30, 2011 at 7:43 PM, case <case.biomaps.rutgers.edu> wrote:
> >
> >> On Mon, May 30, 2011, Vivek Shankar Bharadwaj wrote:
> >> >
> >> > escf = escf + pm6_correction()
> >> > 1
> >> > Error: Function 'pm6_correction' at (1) has no IMPLICIT type
> >>
> >> OK: my bad. The sqm routines that ship with AmberTools1.5 are actually
> >> those
> >> that were present in Amber11, not our most recent ones.
> >>
> >> You can try the attached patch (fingers crossed; use the files before
> you
> >> applied the previous patch I posted). But I'm hoping Andy or someone
> >> familier
> >> with sqm will vet this to see if it both makes sense, and is consistent
> >> with
> >> current code.
> >>
> >> Thanks for the report....dac
> >>
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Wed Jun 01 2011 - 18:30:03 PDT
