AMBER: Compiling parallel Amber9 on Linux cluster

From: Jesus Angulo <>
Date: Wed, 9 May 2007 12:27:23 +0200

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 - 06:07:05 PDT
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