RE: AMBER: amber9 compile problem

From: Ross Walker <ross.rosswalker.co.uk>
Date: Tue, 12 Jun 2007 10:04:54 -0700

Hi Henk,
 
For some reason it looks like your mpi libraries are distributed in two directories, /usr/local/topspin/mpi/mpich/lib64 and
/usr/local/topspin/lib64/. The mpif90_i script should have taken care of this though. For some reason here though it isn't picking up the second search path. In your config.h file can you try specifying -L/usr/local/topspin/lib64/ before the -lvapi or alternatively try creating a link to libvapi.a and libvapi.so in /usr/local/topspin/mpi/mpich/lib64. Same for any other libraries in /usr/local/topspin/lib64/ that it can't find. I know this is a bit of a hack but hopefully it will work and get you a compiled executable.
 
All the best
Ross

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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of Henk Meij
Sent: Tuesday, June 12, 2007 07:13
To: amber.scripps.edu
Subject: Re: AMBER: amber9 compile problem


Ross, with link in place

-Henk



[root.swallowtail src]# make clean

[root.swallowtail src]# ./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

MKL_HOME is set to /share/apps/intel/cmkl/9.1

Using MKL libraries from /share/apps/intel/cmkl/9.1/lib/em64t



The configuration file, config.h, was successfully created.



[root.swallowtail src]# which mpif90

/usr/local/topspin/mpi/mpich/bin/mpif90

[root.swallowtail src]# which ifort

/share/apps/intel/fce/9.1.043/bin/ifort



[root.swallowtail src]# make parallel



first error when compiling sander.MPI

IPO link: can not find -lmpif90_i

ifort: error: problem during multi-file optimization compilation (code 1)



so i changed config.h

#LOADLIB= -L/usr/local/topspin/mpi/mpich/lib -lmpichf90_i ...

LOADLIB= -L/usr/local/topspin/mpi/mpich/lib64 -lmpichf90_i ...



reran, and now have error

IPO link: can not find -lvapi

ifort: error: problem during multi-file optimization compilation (code 1)



[root.swallowtail src]# file /usr/local/topspin/lib64/libvapi.*

/usr/local/topspin/lib64/libvapi.a: current ar archive

/usr/local/topspin/lib64/libvapi.so: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped







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
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk <http://www.rosswalker.co.uk/> | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.

 


  _____

From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of Henk Meij
Sent: Monday, June 11, 2007 12:04
To: amber.scripps.edu
Subject: Re: AMBER: amber9 compile problem


Ross, here it is.
-Henk



 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

/usr/local/topspin/mpi/mpich/bin/mpif90.i

[root.swallowtail]# which ifort

/share/apps/intel/fce/9.1.043/bin/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?



-Henk

    






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Received on Wed Jun 13 2007 - 06:07:33 PDT
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