I'm using the intel compiler suite (icc, ifort) on Ubuntu 9.04 with mpich2
using a core 2 quad intel processor. mpicc originally used gcc, but I
recompiled it to use icc. I agree that replacing an executable with a
man-page is not a good idea, and it would probably call failures in the
event I tried to use binary trajectory files. Even after I fixed mpich2, I
got the error one more time, but for some reason I haven't been able to get
it again, so I don't know if it was a real problem or if it was how I fixed
it.
As for the success message, compiling amber/ambertools in serial and amber
in parallel gives a message like:
Installation of Amber11 (serial) is complete at Thu Sep 10 12:15:40 EDT
2009.
but upon completing make -f Makefile_at parallel, the text stream stops at :
/bin/mv ptraj.MPI /scr/arwen_3/swails/newamber/amber11/bin
make[1]: Leaving directory `/scr/arwen_3/swails/newamber/amber11/src/ptraj'
But since there were no errors I'm assuming everything was built properly.
Thanks,
Jason Swails
On Thu, Sep 10, 2009 at 8:28 AM, case <case.biomaps.rutgers.edu> wrote:
> On Wed, Sep 09, 2009, Jason Swails wrote:
> >
> > This is my last email for tonight, I promise (as it's the last issue I
> had
> > during compilation). I finished compiling the whole suite in serial, but
> > ambertools failed when I tried compiling it in parallel (amber itself
> worked
> > in parallel). The error message I got was:
>
> Can you specify your compiler, OS, and mpi version? What does "mpicc
> -show"
> report? And, what flags did you use for the configure script?
> I haven't seen this problem on the systems I have tested.
>
> >
> >
> > /usr/bin/install -c -m 755 ncmpigen
> > /home/swails/newamber/9.09.09/amber11/src/pnetcdf/bin/ncmpigen
> > /usr/bin/install: cannot stat `ncmpigen': No such file or directory
>
> This implies that an earlier error occurred (in the "make" step) where
> ncmpigen should have been created. You will probably need to look at the
> complete log file, and try to figure out what happened at the "cd ncgen &&
> make" step.
>
> >
> > going into the directory AMBERHOME/src/pnetcdf/src/utils/ncgen , I saw
> that
> > ncmpigen was called ncmpigen.1 for some reason, though I don't know if
> that
> > file was created during installation or if it preexisted. cp ncmpigen.1
> > ncmpigen in that directory....
>
> Well, "ncmpigen" is an executable file and "ncpmigen.1" is a man page. So
> that copy operation would seem to be pretty dangerous -- probably ncmpigen
> is
> never used.
>
> > there was no success message afterwards like there is for everything
> else,
> > but there was also no error message).
>
> Can you explain what you mean by "success message"?
>
> ....dac
>
>
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Received on Mon Sep 14 2009 - 13:40:37 PDT
