AMBER Archive (2008)

Subject: RE: AMBER: Error while compiling Amber

From: Ross Walker (
Date: Sat Feb 09 2008 - 11:58:59 CST

Hi Lili,
You should check the manual for mpich2 - this version of mpi requires a
demon to be running (in this case called MPD) on all of the nodes on which
you want the code to run. This typically means setting up a machine file or
equivalent that is read by mpd.
If you just want to run this on the local machine to which you are logged in
then you can try.
mpd &
export DO_PARALLEL='mpirun =np 4'
make test.parallel
All the best

|\oss Walker

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| San Diego Supercomputer Center |
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From: [] On Behalf Of
Lili Peng
Sent: Friday, February 08, 2008 17:52
Subject: Re: AMBER: Error while compiling Amber

Hi Dr. Case,
Thank you for your help. I added the parser.c file, and the serial
compilation of AMBER worked.
... Though I have another problem now. It's about compiling Sander in
parallel. Although I've searched the mailing list archives extensively,
none of what's been discussed addresses the issue. It has to do with the
make install function, and I'm trying to do a test run of sander. I have
already compiled my MPI library (the MPICH2 version). Here's my input code
(in bold) and the errors:
$ export AMBERHOME="/nas/lpeng/src/amber9"
$ export MPI_HOME="/nas/lpeng/opt"
$ export CC=icc
$ export FC=ifort
$ ./configure --prefix=/nas/lpeng/opt CC=$CC FC=$FC
$ make
$ make install
$ ./configure -mpich2 -p4 -static ifort_ia32
$ make parallel
... and Amber 9 was compiled successfully. Following the compiling
instructions, I continued on..
$ export DO_PARALLEL="/nas/lpeng/src/mpich2-1.0.6p1/bin/mpirun -np 4"
$ make test.sander
Then I get the error:
make: *** No rule ot make target 'test.sander'. Stop.
I also tried:
$ make test.parallel
..and receive in response:
export TESTsander=/nas/lpeng/src/amber9/exe/sander.MPI/exe/sander.MPI; make
make[1]: Entering directory `/nas/lpeng/src/amber9/test'
cd dmp; ./Run.dmp
This test not set up for parallel
 cannot run in parallel with #residues < #pes
cd adenine; ./Run.adenine
This test not set up for parallel
 cannot run in parallel with #residues < #pes
cd cytosine; ./Run.cytosine cannot connect to local mpd
(/tmp/mpd2.console_lpeng); possible causes:
  1. no mpd is running on this host
  2. an mpd is running but was started without a "console" (-n option)
In case 1, you can start an mpd on this host with:
    mpd &
and you will be able to run jobs just on this host.
For more details on starting mpds on a set of hosts, see
the MPICH2 Installation Guide.
  ./Run.cytosine: Program error
make[1]: *** [test.sander.BASIC] Error 1
make[1]: Leaving directory `/nas/lpeng/src/amber9/test'
make: *** [test.sander.BASIC.MPI] Error 2
Do you have any leads on what is causing this to occur? Any input from your
end would be greatly appreciated.
On 07/02/2008, David A. Case <> wrote:

On Thu, Feb 07, 2008, Lili Peng wrote:
> *$ ./configure -p4 ifort_x86_64*

What kind of machine are you compiling on? On the one hand, you say "-p4"
(which is for Pentium IV), yet you also say x86_64, which is a very
type of architecture.

Typing "uname -m" should give you the information you need. Then choose the
correct options.

> *$ ./configure -p4 ifort_ia32 *
> yacc parser.y
> make[2]: execvp: yacc: Permission denied

It looks like you got a lot further this time, so my guess is that you are
an ia32 (aka i386 aka i686) system. You should see that sander and lots of
other programs have been compiled. For the above problem:

First, try "which yacc" and try to find out if it exists, and if so, why
   you are getting permission denied.

Second, try "which bison": if it looks like you have permissions to run
add the line

YACC = bison -y

to your config.h file (in $AMBERHOME/src).

Or, if neither work, put the attached parser.c file in
$AMBERHOME/src/leap/src/leap, and try again.


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