http://archive.ambermd.org/201011/0185.html
On Thu, Feb 3, 2011 at 2:19 PM, Zhu, James <James.Zhu.ars.usda.gov> wrote:
> Hi Dan,
>
> I expect to see a sander.RISM.MPI in amber11/bin folder, but the file does
> not exist after compiling.
>
> James
>
> -----Original Message-----
> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> Sent: Wednesday, February 02, 2011 5:02 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Amber11 parallel testing error
>
> Hi,
>
> On Wed, Feb 2, 2011 at 3:53 PM, Zhu, James <James.Zhu.ars.usda.gov> wrote:
> > 3) What parallel library was used (e.g. mpich1, mpich2, openmpi etc)
> >
> > Openmpi-1.4.1/lib (? I do not know where to look for)
>
> What is the output of 'mpicc -show' (where mpicc is the mpi command
> used to compile your parallel version of amber)? Did you use the
> ./configure_openmpi script or is this a version of openmpi that came
> with your system?
>
> >
> > 4) Are there any error messages in the output files produced by the
> > test (neb_gb_partial_XX.out files)?
> >
> > It is a long file and I do not know where to check.
>
> Typically the error will be printed at the end of the file. Try 'tail
> neb_gb_partial_*.out' and see what prints.
>
> >
> > Also, can you repeat just the NEB tests with 8 threads (type 'make
> > test.neb') and see if the error still occurs?
> >
> > I ran it but it is still running after 15 min. How long does this take?
>
> 15 minutes is probably too long. I will run some tests with openmpi
> and see if I can recreate your problem.
>
> >
> > I also got this warning when I ran ./configure -mpi gnu and I checked
> that the files as shown in the following.
> >
> > [jzhu.jzhu-desktop src]$ ./configure -mpi gnu
> > Your AMBERHOME environment variable should be set to
> /home/jzhu/bin/amber11
> >
> > Warning: the X11 libraries are not in the usual location !
>
> Not too worrisome; this means you don't have the development version
> of the X libraries (including header files) which are necessary for
> compiling e.g. Xleap. If you don't use xleap you can specify the
> '-noX11' option to configure. Otherwise you need to install the
> necessary package, and possibly set the XHOME and/or XLIBS variables
> in config.h. So for example on my fedora14 machine if I type:
>
> $ yum list libXt-devel*
> Loaded plugins: langpacks, presto, refresh-packagekit
> Adding en_US to language list
> Available Packages
> libXt-devel.i686 1.0.7-1.fc13
> fedora
> libXt-devel.x86_64 1.0.7-1.fc13
> fedora
>
> I can see I dont have the libraries installed, so I can do something
> like 'yum install libXt-devel.x86_64' and everything should be OK.
>
> I'll get back to you and let you know if I can reproduce the error.
>
> -Dan
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Feb 03 2011 - 12:00:03 PST
