Re: [AMBER] Amber11 parallel testing error

From: Zhu, James <James.Zhu.ARS.USDA.GOV>
Date: Thu, 3 Feb 2011 13:37:24 -0500

Hi Dan,

The output for mpicc -show is:

[jzhu.jzhu-desktop test]$ mpicc -show
gcc -I/home/jzhu/bin/amber11/AmberTools/include -pthread -L/home/jzhu/bin/amber11/AmberTools/lib -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl

The tail of neb_gb_partial_XX.out files is :

 begin time read from input coords = 0.000 ps

           Begin reading energy term weight changes/NMR restraints
 TEMP0 0 35000 0.000000 300.000000 0 0

                          ** No restraint defined **

                  Done reading weight changes/NMR restraints

 Number of triangulated 3-point waters found: 0
| Atom division among processors:
| 0 22
| Running AMBER/MPI version on 1 nodes

| MULTISANDER: 4 groups. 1 processors out of 4 total.

I ran make test.neb with 8 threads, the outcome was the same as 4 threads.


-----Original Message-----
From: Daniel Roe []
Sent: Wednesday, February 02, 2011 5:02 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Amber11 parallel testing error


On Wed, Feb 2, 2011 at 3:53 PM, Zhu, James <> 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
libXt-devel.x86_64 1.0.7-1.fc13

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.


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Received on Thu Feb 03 2011 - 11:00:04 PST
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