AMBER Archive (2008)

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

From: amit (amit_at_dmsystems.in)
Date: Mon Dec 22 2008 - 12:15:34 CST

dear all

thanks a ton ross, we got it compiled

  

-- 

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”

-----Original Message-----
From: "Ross Walker" <ross_at_rosswalker.co.uk>
To: <amber_at_scripps.edu>
Date: Mon, 22 Dec 2008 09:46:58 -0800
Subject: RE: AMBER: amber 9 compilation error with mvapich and intel   
compilers

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
 
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu
  
----------------------------------------------------------------------- The 
AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, 
send "unsubscribe amber" (in the *body* of the email) to 
majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu