RE: AMBER: amber9 compile problem

From: Ross Walker <ross.rosswalker.co.uk>
Date: Mon, 11 Jun 2007 09:16:58 -0700

Dear Henk,
 
The problems are likely occuring because you are using the wrong Intel compiler. You are using the 32 bit version of the compiler on a x86_64 machine - hence why you keep seeing problems relating to incompatible libraries. Uninstall the 32 bit version of the compiler and go get the x86_64 version. This will get installed in /opt/intel/fce/9.1.xxx
 
Note the "e" on the end of "fce". You may already have this version installed in which case you need to source the vars scripts in this directory in place of the ones you are currently sourcing. Also, don't mess with LD_LIBRARY_PATH, the ifortvars script should do this for you.
 
I suggest trying the folloing.
 
1) Obtain the fce and cce versions of the compilers and check that these are being referenced by ifort and icc:
 
   which ifort
 
2) Delete your amber9 directory and create a brand new one from the amber9.tgz file on the cd.
 
3) Apply bugfix.all from the amber website.
 
4) Make sure you have the default roll up of the mpich installed and working. Check that /usr/local/topspin/mpi/mpich/bin in your path
 
5) export AMBERHOME=/directory/where/you/uncompressed/sander
    export MPI_HOME=/usr/local/topspin/mpi/mpich/
 
6) cd $AMBERHOME/src/
    ./configure -mpich ifort_x86_64
    Check for any error messages from configure here.
 
7) make parallel
 
Then from this please report any and all error messages. In this way we will be able to determine exactly what you did and address the problems step by step rather than chasing errors that may have come from modifying the config.h file in some unknown way etc etc.
 
Good luck...
 
Ross
 
 
 

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|\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 |

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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of Henk Meij
Sent: Monday, June 11, 2007 06:51
To: amber.scripps.edu
Subject: Re: AMBER: amber9 compile problem


ross, i plead ignorance to the question "does mpif90.i actually call the intel compiler?", i was hoping ;0 ...

i tried in vain compiling the source code that comes with the "roll" in /usr/local/topspin/mpi/mpich/src after reading all the messages about mpi, ib libs and amber all need to be compiled with same compiler. and i can't find a topspin src tarball although i have not gone to cisco yet.

here is the info on compiling with ifort ... first i hit an error during the configure stage dealing with line 300 of the configure program

./configure: line 300: /usr/local/topspin/mpi/mpich/bin/mpif90: No such file or directory

line 300 loadlib=`$MPI_HOME/bin/mpif90 -show | perl -p -e 's/(-[lL]\S+\s)|\S+\s/$1/g'`
line 301 # old: loadlib="-L$MPI_HOME/lib -lfmpich -lmpich -lpmpich"

then on first massive compilation, a slightly different error

ld: skipping incompatible /share/apps/intel/cmkl/9.1/lib/em64t/libvml.so when searching for -lvml
ld: cannot find -lvml
make[1]: *** [sander.MPI] Error 1
make[1]: Leaving directory `/share/apps/amber/9_ifort/src/sander'
make: *** [parallel] Error 2
[root.swallowtail src]# file /share/apps/intel/cmkl/9.1/lib/em64t/libvml.*
/share/apps/intel/cmkl/9.1/lib/em64t/libvml.so: ELF 64-bit LSB shared object, AMD x86-64, version 1 (SYSV), not stripped

i do see libvml.so in lib/64 and lib/32 inside $MKL_HOME and when i add those paths to config.h i get past that error (it skips over lib/64 and thus picks up the one in lib./32) and then i run into

/share/apps/intel/cmkl/9.1lib/64/libmkl_lapack.a: could not read symbols: bad value

ofcourse thoroughly confusing the compiler. so why ifort not compile amber cleanly, iow back tot he libvml error?

-Henk


Hi Henk,



  

-> i then edit config.h and change all ifort occurences to mpif90.i

    



I suspect this is part of the problem. Did you try it without changing the compiler command? With ifort it should be linking the correct libraries. Note does mpif90.i actually call the intel compiler?

 

  

ld: skipping incompatible

/usr/local/topspin/mpi//mpich/lib64/libmpichf90_i.so when

searching for

-lmpichf90_i

ld: skipping incompatible

/usr/local/topspin/mpi//mpich/lib64/libmpichf90_i.a when searching for

-lmpichf90_i

    



You see this message because the compiler is trying to link a 64 bit library with a 32 bit object file. So what is happening here is that you are on an x86_64 machine with the correct 64 bit mpi libraries but mpif90.i is setup incorrectly so it is acting as a wrapper for the 32 bit version of the compiler.



Note you appear to be using the 32 bit version of the intel compilers:



  

. /share/apps/intel/cc/9.1.047/bin/iccvars.sh

. /share/apps/intel/fc/9.1.043/bin/ifortvars.sh

    



note the fc and cc. I would go and download and install the 64 bit versions (x86_64, NOT the IA64 version) which will be in fce and cce directories and then make sure you source these config files. If mpif90.i just calls ifort then you will be fine since "which ifort" should return the fce version. However, if it uses the full path then you will have modify things so it calls the correct version.



Make sure you do a make clean before recompiling.



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 | 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.





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Received on Wed Jun 13 2007 - 06:07:21 PDT
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