Charm++ parallel programming system

[Hideaki Kikuchi <hideaki.kikuchi AT ndsu.edu>]

Hi,

 

I downloaded NAMD 2.10b1 and was trying build the binary with Intel cluster studio 2013 sp1 on the cluster with Intel Xeon IvyBridge and Mellanox FDR IB connection.

When I tried to build charm++ I got following error:

../bin/charmc  -optimize -production  -DCMK_OPTIMIZE=1  -I.   -c -o controlPoints.o controlPoints.C

../bin/charmc  -optimize -production  -DCMK_OPTIMIZE=1  -I.   -c -o arrayRedistributor.o arrayRedistributor.C

../bin/charmc  -optimize -production  -DCMK_OPTIMIZE=1  -I.   -c -o cp_effects.o cp_effects.C

../bin/charmc  -optimize -production  -DCMK_OPTIMIZE=1  -I.   -c -o trace-controlPoints.o trace-controlPoints.C

../bin/charmc  -optimize -production  -DCMK_OPTIMIZE=1  -I.   -c -o mpi-interoperate.o mpi-interoperate.C

In file included from /global/opt/intel/impi/4.1.3.049/intel64/include/mpi.h(1279),

                 from mpi-interoperate.h(9),

                 from mpi-interoperate.C(3):

/global/opt/intel/impi/4.1.3.049/intel64/include/mpicxx.h(95): catastrophic error: #error directive: "SEEK_SET is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h"

  #error "SEEK_SET is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h"

   ^

 

compilation aborted for mpi-interoperate.C (code 4)

Fatal Error by charmc in directory /home/xxxx/NAMD_2.10b1_Source/charm-6.6.0-rc4/mpi-linux-x86_64-ifort-mpicxx/tmp

   Command mpiicpc -O3 -axAVX -mavx -ip -I../bin/../include -D__CHARMC__=1 -DCMK_OPTIMIZE=1 -I. -O2 -U_FORTIFY_SOURCE -fno-stack-protector -c mpi-interoperate.C -o mpi-interoperate.o returned error code 4

charmc exiting...

gmake: *** [mpi-interoperate.o] Error 1

-------------------------------------------------

Charm++ NOT BUILT. Either cd into mpi-linux-x86_64-ifort-mpicxx/tmp and try

to resolve the problems yourself, visit

http://charm.cs.illinois.edu/

for more information. Otherwise, email the developers at charm AT cs.illinois.edu

 

According to Intel website, I should add “-DMPICH_IGNORE_CXX_SEEK” to avoid the issue. But I am not sure where to define the macro. Can you help me solve the issue?

 

Thanks.

 

Hideaki Kikuchi, Ph.D.

HPC Manager / Center for Computationally Assisted Science and Technology
NORTH DAKOTA STATE UNIVERSITY
 
236A Research 2
Dept. 4100, PO Box 6050
Fargo, ND  58108-6050

 

Street / Delivery Address
1735 NDSU Research Park Dr.
Fargo, ND 58102

phone: 701.231.8303

fax: 701.231.5873

email: hideaki.kikuchi AT ndsu.edu