Hi InSuk,
I think the general consensus when it comes to building Amber on a Red Hat
system is to install the GCC 4.4 package, since there are reported problems
with the default 4.1.2 compilers.
Good luck!
Jason
On Tue, Dec 21, 2010 at 11:35 AM, InSuk Joung <i.joung.gmail.com> wrote:
> Hi,
> I compiled a recent version of AMBER (as of 12/20/2010) using gnu(4.1.2) +
> mpich2-1.3.1.
> Serial compilation had no problem, but there was a problem with the
> parallel
> version.
>
> Actually, there was no error in the compilation process, but when I tried
> to
> run, I had a problem.
>
> $ gcc -vUsing built-in specs.
> Target: x86_64-redhat-linux
> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
> --infodir=/usr/share/info --enable-shared --enable-threads=posix
> --enable-checking=release --with-system-zlib --enable-__cxa_atexit
> --disable-libunwind-exceptions --enable-libgcj-multifile
> --enable-languages=c,c++,objc,obj-c++,java,fortran,ada
> --enable-java-awt=gtk
> --disable-dssi --enable-plugin
> --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic
> --host=x86_64-redhat-linux
> Thread model: posix
> gcc version 4.1.2 20080704 (Red Hat 4.1.2-48)
>
> $ cd $AMBERHOME/bin
> $ ./mpirun -np 2 ./sander.MPI
> APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
>
> $ ./mpirun -np 2 ./pmemd.MPI
> APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
>
> No mdout file was created.
>
> However, ptraj.MPI worked fine.
> $ ./mpirun -np 2 ./ptraj.MPI
>
> \-/
> -/- PTRAJ: a utility for processing trajectory files
> /-\
> \-/ Version: "AMBER 11.0 integrated" (4/2010)
> -/- Executable is: "./ptraj.MPI"
> /-\ Running on 2 processor(s)
> \-/ MULTIPTRAJ must be run with <TOP> and <INPUT>.
>
> I switched gnu compiler to Intel and then the weird error has gone.
> Everything seems to be ok.
>
> Did anybody have a similar experience and know how to solve the problem?
>
> --
> Best,
> InSuk Joung
> _______________________________________________
> 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. Graduate Student
352-392-4032
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Received on Tue Dec 21 2010 - 11:00:06 PST
