RE: AMBER: amber9 compile problem

From: Ross Walker <>
Date: Mon, 11 Jun 2007 15:06:30 -0700

Hi Henk,
Can you create a symbolic link that points /usr/local/topspin/mpi/mpich/bin/mpif90 to /usr/local/topspin/mpi/mpich/bin/mpif90.i
And then try running configure again and then make clean / make parallel.
Configure calls mpif90 as part of the configuration to find out where all the libraries are and below it didn't manage to run it because your mpif90 is actually called mpif90.i
Then get back to me with the next problem and we can work from there.
All the best

|\oss Walker

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From: [] On Behalf Of Henk Meij
Sent: Monday, June 11, 2007 12:04
Subject: Re: AMBER: amber9 compile problem

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 - 06:07:25 PDT
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