AMBER Archive (2008)

Subject: RE: AMBER: amber 9 compilation error with mvapich and intel compilers

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Dec 22 2008 - 11:46:58 CST

Hi Amit,

 

I would recommend doing the following. Firstly make sure that the version of
mvapich you are linking to was built with the same compiler as you are using
to build AMBER. For example the following comes from Ranger
(http://www.tacc.utexas.edu/resources/hpcsystems/) and highlights how I
compiled amber9 with mvapich on it:

 

login3% which mpif90

/opt/apps/pgi7_2/mvapich/1.0.1/bin/mpif90

 

The path here implies that PGI v7.2 was used to build this version of
MVAPICH. If your system admin is any good they should have built several
versions of mvapich for each different compiler option on your machine. We
can further check what compiler is being used by asking the mpif90 script
what it is actually doing:

 

login3% mpif90 -show

ln -s /opt/apps/pgi7_2/mvapich/1.0.1/include/mpif.h mpif.h

pgf90 -Wl,-rpath,/opt/apps/pgi7_2/mvapich/1.0.1/lib/shared -Wl,-rpath-link
-Wl,/opt/apps/pgi7_2/mvapich/1.0.1/lib/shared
-L/opt/apps/pgi7_2/mvapich/1.0.1/lib/shared
-L/opt/apps/pgi7_2/mvapich/1.0.1/lib -lmpichf90nc -lmpichfarg -lmpich
-L/opt/ofed//lib64/ -libverbs -libumad -lpthread -lpthread -lrt

 

Here we see if runs pgf90. We can then check that the pgf90 in our path is
the same version as was used for mvapich:

 

login3% which pgf90

/opt/apps/pgi/7.2-5/linux86-64/7.2-5/bin/pgf90

 

All looks good. Next we can configure amber9:

 

setenv AMBERHOME ~/amber9

tar xvzf amber9.tgz

cd amber9

wget http://ambermd.org/bugfixes/9.0/bugfix.all

patch -p0 -N -r patch_rejects < bugfix.all

cd src

./configure -mpi pgf90

 

Edit config.h and change all occurrences of pgf90 to mpif90. Also remove all
occurrences of -lmpi.

 

On the end of the FPPFLAGS line add:
-I/opt/apps/pgi7_2/mvapich/1.0.1/include/

 

Since 64 bit pgi compilations used to fail with the version of PGI available
at AMBER 9 release it also forced 32 bit compilation which with v7.2 we can
now allow - so also remove -tp p7 and -m32. (Just be sure to run all the
test cases and make sure they work.) - other compilers such as ifort do not
have this issue.

 

make parallel

 

This should compile properly - then you can go on and run the parallel tests
as normal.

 

All the best

Ross

 

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Amit Bajaj
Sent: Sunday, December 21, 2008 9:42 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: amber 9 compilation error with mvapich and intel
compilers

 

dear david

we used mvapich 1.x so we provided option "mpich" while generating config.h

Thanks

 

Best rgds

Amit

D M Systems Pvt. Ltd.

B-127, Shivalik, ND – 17

Ph – 26691429/2344

98112-07764

 

“One never reaches anywhere sitting on the shore”

David A. Case wrote:

On Sat, Dec 20, 2008, Amit Bajaj wrote:
  

We are trying to compile Amber 9 (sander) with mvapich(we got it as part of
mellanox OpenFabrics Enterprise Distribution for Linux on RHEL 4(64 bit) on
Intel 5400 series processor
    

 
How did you configure the system? Amber 9's configure script does not
offer any option for mvapich, so I'm assuming you must have done some
editing of config.h (or something) on your own.
 
  

/usr/mpi/intel/mvapich-1.0.1/lib/libmpich.a(viapriv.o)(.text+0x155): In
function `viadev_ext_sendq_send':
: undefined reference to `prepare_coalesced_pkt'
    

 
Note that these are undefined references coming from the mpi library,
which suggests that you are not linking in the correct libraries. Be
sure you can compile and run the test cases (or other simple MPI
programs) that come with you mpi installation.
 
...dac
 
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