Compiling NAMD_2.9b2_Source with GCC 4.7.0

From: Fabien Archambault (
Date: Fri Mar 30 2012 - 08:25:18 CDT

Dear list,

I tried to compile NAMD using GCC 4.7.0 and the OpenMPI 1.4.5 on CentOS 6.2
but it fails at some point. When I try using Intel Compiler 12.1 and the
OpenMPI compiled with it all works.

All steps for charm-6.4.0 work. The error occurs when doing make in
g++ -m64 -O3 -I.rootdir/charm-6.4.0/mpi-linux-x86_64/include
-DCMK_OPTIMIZE=1 -Isrc -Iinc -Iplugins/include -DSTATIC_PLUGIN
-I.rootdir/tcl/include -DNAMD_TCL -I.rootdir/fftw/include -DNAMD_FFTW
-DNAMD_VERSION=\"2.9b2\" -DNAMD_PLATFORM=\"Linux-x86_64-MPI\"
-DUSE_NODEPATCHMGR -fexpensive-optimizations -ffast-math -o
obj/ComputeAngles.o -c src/ComputeAngles.C
In file included from inc/NamdHybridLB.decl.h:10:0,
                 from inc/LdbCoordinator.decl.h:8,
                 from src/LdbCoordinator.h:24,
                 from src/ComputeSelfTuples.h:11,
                 from src/ComputeAngles.h:11,
                 from src/ComputeAngles.C:15:
.rootdir/charm-6.4.0/mpi-linux-x86_64/include/CentralLB.h: In member
function 'void
.rootdir/charm-6.4.0/mpi-linux-x86_64/include/CentralLB.h:166:16: warning:
converting 'false' to pointer type 'bool*' [-Wconversion-null]
In file included from src/ComputeAngles.h:11:0,
                 from src/ComputeAngles.C:15:
src/ComputeSelfTuples.h: In instantiation of 'void ComputeSelfTuples<T, S,
P>::initialize() [with T = AngleElem; S = angle; P = AngleValue]':
src/ComputeAngles.C:193:1: required from here
src/ComputeSelfTuples.h:147:7: error: 'setNumPatches' was not declared in
this scope, and no declarations were found by argument-dependent lookup at
the point of instantiation [-fpermissive]
src/ComputeSelfTuples.h:147:7: note: declarations in dependent base
'Compute' are not found by unqualified lookup
src/ComputeSelfTuples.h:147:7: note: use 'this->setNumPatches' instead
make: *** [obj/ComputeAngles.o] Error 1

I tried patching the file src/ComputeSelfTuples.h as suggested by the GCC

Then everything compiles but when running the apoa1 simulation I get:
Charm++> Running on MPI version: 2.1
Charm++> level of thread support used: MPI_THREAD_SINGLE (desired:
Charm++> Running on non-SMP mode
Converse/Charm++ Commit ID: v6.4.0-beta1-0-g5776d21

namd2:26972 terminated with signal 11 at PC=3fe5e0947f SP=7fff890eb9e0.
CharmLB> Load balancer assumes all CPUs are same.
mpirun noticed that process rank 9 with PID 26972 on node node036 exited on
signal 11 (Segmentation fault).

I hope this can be fixed easily. I am no expert of C++ so I cannot
expertise more the problem.

Fabien Archambault

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