Re: AMBER: amber9 compile problem

From: Henk Meij <>
Date: Mon, 11 Jun 2007 15:04:05 -0400

Ross, here it is.

 1001 cd /share/apps/amber/
 1002 mkdir 9_ifort
 1003 cd 9_ifort/
 1004 tar zxf /share/apps/src/amber9.tgz
 1005 mv amber9/* .
 1006 rmdir amber9/
 1007 sh < /share/apps/src/amber9_bugfix.cmd
 1008 cd src
 1009 export PATH=/usr/local/topspin/mpi/mpich/bin:$PATH
 1010 export MPI_HOME=/usr/local/topspin/mpi/mpich
 1011 export AMBERHOME=/share/apps/amber/9_ifort
 1012 export MKL_HOME=/share/apps/intel/cmkl/9.1

[root.swallowtail]# which mpif90.i
[root.swallowtail]# which ifort

[root.swallowtail]# ./configure -mpich ifort_x86_64

AMBERHOME is set to /share/apps/amber/9_ifort
Setting up Amber configuration file for architecture: ifort_x86_64
Using parallel communications library: mpich
MPI_HOME is set to /usr/local/topspin/mpi/mpich
./configure: line 300: /usr/local/topspin/mpi/mpich/bin/mpif90: No such file or directory
MKL_HOME is set to /share/apps/intel/cmkl/9.1
Using MKL libraries from /share/apps/intel/cmkl/9.1/lib/em64t

"make parallel" yields an error when compiling
"ifort -FR -o sander.MPI evb_vars.o ..."

evb_init.o(.text+0x69e): In function `evb_init_':
: undefined reference to `mpi_bcast_'
-lots of these-

i've seen dac's fix for this but adding -fsecond-underscore does not fix the problem.
meaning i have to have clean source code for topspin and compile with -fno-secoond-underscore?


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Received on Wed Jun 13 2007 - 06:07:23 PDT
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