AMBER Archive (2004)

Subject: AMBER: Building the parallel version in AMBER 8 and GIBBS

From: Ilyas Yildirim (
Date: Tue Nov 09 2004 - 21:03:54 CST

Dear all,

I have a dual processor PC (two P3-600Mhz CPU), linux installed on it.
(RedHat WS Enterprise) I have installed AMBER 8 and when I tried to follow
the parallel version installation, it failed. I used the following

# make clean
# ./configure -mpi ifort
# make parallel

And the error I got is as following:
new_time.o(.text+0x7d5): In function `profile_time_':
: undefined reference to `mpi_send_'
new_time.o(.text+0xc43): In function `profile_time_':
: undefined reference to `mpi_recv_'
make[1]: *** [sander] Error 1
make[1]: Leaving directory `/rna2/programs/amber8/src/sander'
make: *** [parallel] Error 2

Can you tell me what my mistake is? Or is not it possible to build the
parallel version into a dual processor machine?

Another question I have is about GIBBS. I am going to do some free
energy perturbations and am planning to use GIBBS for that. Can I do the
free energy perturbation in sander too? If not, is it possible to
explicitely install just GIBBS into AMBER 8? I have the previous ver of
AMBER, too. (AMBER 7)

Thanks in advance.

  Ilyas Yildirim
  - Department of Chemisty       -                              -
  - University of Rochester      -                              -
  - Hutchison Hall, Office B10   - Ph.:(585) 503 44 00 (Cell)   -
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) -
  -                     -

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