AMBER Archive (2007)

Subject: Re: AMBER: amber9 compile problem

From: Henk Meij (hmeij_at_wesleyan.edu)
Date: Tue Jun 12 2007 - 09:13:01 CDT

Ross, with link in place
-Henk

[root_at_swallowtail src]# make clean
[root_at_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_at_swallowtail src]# which mpif90
/usr/local/topspin/mpi/mpich/bin/mpif90
[root_at_swallowtail src]# which ifort
/share/apps/intel/fce/9.1.043/bin/ifort

[root_at_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_at_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_at_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_at_scripps.edu [mailto:owner-amber_at_scripps.edu]
> *On Behalf Of *Henk Meij
> *Sent:* Monday, June 11, 2007 12:04
> *To:* amber_at_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_at_swallowtail]# which mpif90.i
> /usr/local/topspin/mpi/mpich/bin/mpif90.i
> [root_at_swallowtail]# which ifort
> /share/apps/intel/fce/9.1.043/bin/ifort
>
> [root_at_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
>
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu