NAMD compile error

From: itvasile_at_nipne.ro
Date: Tue Dec 16 2008 - 10:43:20 CST

Hello,

I'm trying to compile NAMD 2.6 from source on a Linux CentOS 5.2 64bit
cluster. I have Myrinet 2000 interconnection with MX 1.2.7 driver and
mpich-mx 1.2.7..7.

First of all I've downloaded the latest charm++ from the site and build it
with: ./build charm++ mpi-linux-x86_64 mpicxx --no-shared -O2
-DCMK_OPTIMIZE
It said "Build successful", I made some tests (megatest) and it run
without any errors.

I've written my own .arch, .tcl and .fftw files adapted from
"Linux-amd64". I've downloaded fftw and tcl version amd64, make the
adjustments then:
./config tcl fftw Linux-x86_64
cd Linux-x86_64
make

After a lot of "good" messages it ends with:
~~~~~~~~~~~~
mpicc -Isrc -I/opt/NAMD_2.6_Source/tcl/linux-amd64/include -DNAMD_TCL -O3
-m64 -march=nocona -fexpensive-optimizations -ffast-math
-DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-x86_64\" -o flipdcd
src/flipdcd.c || \
        echo "#!/bin/sh\necho unavailable on this platform" > flipdcd; \
        chmod +x flipdcd
src/flipdcd.c: In function 'main':
src/flipdcd.c:39: warning: incompatible implicit declaration of built-in
function 'exit'
mpicc -Isrc -I/opt/NAMD_2.6_Source/tcl/linux-amd64/include -DNAMD_TCL -O3
-m64 -march=nocona -fexpensive-optimizations -ffast-math
-DNAMD_VERSION=\"2.6\" -DNAMD_PLATFORM=\"Linux-x86_64\" -o flipbinpdb
src/flipbinpdb.c || \
        echo "#!/bin/sh\necho unavailable on this platform" > flipbinpdb; \
        chmod +x flipbinpdb
src/flipbinpdb.c: In function 'main':
src/flipbinpdb.c:28: warning: incompatible implicit declaration of
built-in function 'exit'
src/flipbinpdb.c:33: warning: incompatible implicit declaration of
built-in function 'exit'
src/flipbinpdb.c:38: warning: incompatible implicit declaration of
built-in function 'exit'
src/flipbinpdb.c:45: warning: incompatible implicit declaration of
built-in function 'exit'
src/flipbinpdb.c:51: warning: incompatible implicit declaration of
built-in function 'exit'
src/flipbinpdb.c:62: warning: incompatible implicit declaration of
built-in function 'exit'
~~~~~~~~~~~~~~~

I must mention that I tried compiling with the compilers from mpich-mx
1.2.7..7, based on GNU gcc 4.1.2.
Any help is highly appreciated.
Thank you

_____________________________________________________________________
   Dipl. Eng. Drd. Ionut VASILE
   Junior Researcher
   Horia Hulubei National Institute of Physics and Nuclear Engineering
   ROMANIA
   http://www.nipne.ro

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