RE: AMBER: Compiling parallel Amber9 on Linux cluster

From: Ross Walker <>
Date: Wed, 9 May 2007 08:27:36 -0700

Dear Jesus,
Your config.h file looks very non-standard to me. Did you modify it beyond
what configure created for you?
For example how did the following end up in the AMBERBUILDFLAGS?
Then further down you have what I suspect is causing your problem:


I take it you added the "-nus" to get it to link against openmpi. And this
is likely the problem since I suspect the external flush routine should
actually be flush_ and the compiler is stripping this because of "-nus" and
therefore you get an undefined reference.

My advice is to do the following. Download a fresh copy of either openmpi or
mpich2 (I recommend mpich2 since I find the performance is typically
slightly better). Then build this copy of mpi using the intel compiler. Then
make sure MPI_HOME is set to where you installed the copy of mpi and that
your path etc points to the correct copy of mpi.

Then from a freshly cleaned copy of amber 9 do:

cd $AMBERHOME/src/

./configure -openmpi -p4 ifort_ia32

Note replace -openmpi with -mpich2 if you plan to use mpich2

Do not modify the config.h file in anyway, it should not be necessary and
just makes debugging harder.


make parallel

Hopefully this time it will work.

Good luck,


|\oss Walker

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From: [] On Behalf Of
Jesus Angulo
Sent: Wednesday, May 09, 2007 03:27
Subject: AMBER: Compiling parallel Amber9 on Linux cluster

Dear Amber users,
I have been looking for an answer to my question at the reflector but I
couldn't find any, so first I would like to apologize in case the fix to
this problem has previously been posted and I didn't get it. I'm using
Amber9 serial version on a Beowulf cluster of 12 nodes with 2 Intel-Xeon
(2.8 GHz) per node running Linux version 2.4.22 with Red-Hat release 9, and
till now is working fine. Then, I wanted to install the parallel version,
using openmpi1.2, and basically following the instructions on the Amber9
manual. As with the serial version, I'd like to compile the programme with
Intel compilers (version 8.0). Unfortunately after doing "make clean" at the
"src" directory and doing "make parallel" using the attached config.h file,
I've got messages indicating that seemingly the process is running OK until
a final message breaks the compilation process:
        ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
        ../lib/nxtsec.o ../lib/sys.a -L/usr/local/lib -lmpi_f90 -lmpi_f77
-lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -ldl
../lib/sys.a(sys.o)(.text+0xb): In function `amflsh':
 : undefined reference to `flush'
make[1]: *** [sander.MPI] Error 1
make[1]: Leaving directory `/usr/local/amber9/src/sander'
make: *** [parallel] Error 2

I have been trying to modify different things on the config file, but I
didn't succeed. Could any of you please give me a hint about how to proceed
to fix this problem?.
Thank you very much in advance!
Jesús Angulo


Dr. Jesús Angulo

Carbohydrate Group. Bio-Organic Department

Instituto de Investigaciones Químicas (C.S.I.C.)

Américo Vespucio, 49

41092 – Sevilla, Spain

Phone. +34 954489500 (Ext. 9609)

Fax +34 954460565



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Received on Sun May 13 2007 - 06:07:11 PDT
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