Comments for OpenMD

Comment on Installing OpenMD prerequisites by Building and Installing OpenMD 1.0 « OpenMD

Building and Installing OpenMD 1.0 « OpenMD — Thu, 24 Jan 2013 20:31:34 +0000

[...] going to assume here that you have already built and installed all of the prerequisites. If you haven’t done that, go install all of the required stuff and come back. We’ll [...]

Comment on Building and Installing OpenMD 2 by Building and Installing OpenMD 1.0 « OpenMD

Building and Installing OpenMD 1.0 « OpenMD — Thu, 24 Jan 2013 20:29:22 +0000

[...] now quite outdated. As of OpenMD version 2.0, the build system has changed significantly. We have a new set of instructions to build and install OpenMD 2.0. We’re going to assume here that you have already built and installed all of the [...]

Comment on Building and Installing OpenMD 2 by Converting a protein structure for use with OpenMD « OpenMD

Converting a protein structure for use with OpenMD « OpenMD — Thu, 24 Jan 2013 20:27:09 +0000

[...] require some hand adjustment of the input files. Assuming you’ve gotten a version of OpenMD built and installed (along with all of the prerequisite software), we’ll try to walk you through the steps [...]

Comment on Building and Installing OpenMD 2 by Simple liquid simulations using OpenMD « OpenMD

Simple liquid simulations using OpenMD « OpenMD — Thu, 24 Jan 2013 20:25:05 +0000

[...] require some hand adjustment of the input files. Assuming you’ve gotten a version of OpenMD built and installed (along with all of the prerequisite software), we’ll walk you through building the liquid [...]

Comment on Installing OpenMD prerequisites by Building and Installing OpenMD 2 « OpenMD

Building and Installing OpenMD 2 « OpenMD — Thu, 24 Jan 2013 20:18:53 +0000

[...] going to assume here that you have already built and installed all of the prerequisites. If you haven’t done that, go install all of the required stuff and come back. We’ll [...]

Comment on Installing OpenMD prerequisites by Building and Installing OpenMD 2 « OpenMD

Building and Installing OpenMD 2 « OpenMD — Sun, 07 Oct 2012 18:50:40 +0000

[...] [...]

Comment on OpenMD version 1.1.5 by OpenMD version 1.1.5 released

OpenMD version 1.1.5 released — Tue, 24 Jan 2012 19:01:26 +0000

[...] via OpenMD version 1.1.5 « OpenMD. [...]

Comment on Building and Installing OpenMD 1.0 by Lynn Meredith

Lynn Meredith — Thu, 19 Jan 2012 14:49:56 +0000

OK, I got it compiled and installed. However, when I executed opened I get the following error:

openmd(48775) malloc: *** error for object 0x104c4a440: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Abort

It’s probably something simple, but I don’t see it.

Thanks, Lynn

Comment on Building and Installing OpenMD 1.0 by Dan Gezelter

Dan Gezelter — Wed, 18 Jan 2012 19:51:30 +0000

Lynn,

I just uploaded a maintenance release (1.1.5) that should fix this problem. I’m guessing that your version of openmpi was compiled with a relatively new version of gcc / g++, which is more strict about namespaces. We’ve fixed the problem in SquareMatrix, and it should be OK with the newer compilers.

Comment on Building and Installing OpenMD 1.0 by Lynn Meredith

Lynn Meredith — Wed, 18 Jan 2012 18:48:36 +0000

Got an error trying to install …

/opt/local/bin/openmpic++ -DSVN_REV=”" -DFRC_PATH=”/opt/local/openmd/forceFields” -Os -c -I../../src -I/opt/local/include -I/opt/local/include -I/opt/local/include/openbabel-2.0 RigidBody.cpp -o ../../obj/RigidBody.o
In file included from RigidBody.cpp:43:
In file included from ../../src/primitives/RigidBody.hpp:54:
In file included from ../../src/primitives/StuntDouble.hpp:56:
../../src/math/SquareMatrix3.hpp:420:5: error: use of undeclared identifier ‘jacobi’
jacobi(a, w, v);
^
RigidBody.cpp:191:14: note: in instantiation of member function ‘OpenMD::SquareMatrix3::diagonalize’
requested here
Mat3x3d::diagonalize(Itmp, evals, sU_);
^
../../src/math/SquareMatrix.hpp:207:16: note: must qualify identifier to find this declaration in dependent base
class
static int jacobi(SquareMatrix& a, Vector& d,
^
1 error generated.
make[1]: *** [../../obj/RigidBody.o] Error 1
/opt/local/bin/openmpic++ -DSVN_REV=”" -DFRC_PATH=”/opt/local/openmd/forceFields” -DIS_MPI -Os -c -I../../src -I/opt/local/include -I/opt/local/include -I/opt/local/include/openbabel-2.0 RigidBody.cpp -o ../../MPIobj/RigidBody.o
In file included from RigidBody.cpp:43:
In file included from ../../src/primitives/RigidBody.hpp:54:
In file included from ../../src/primitives/StuntDouble.hpp:56:
../../src/math/SquareMatrix3.hpp:420:5: error: use of undeclared identifier ‘jacobi’
jacobi(a, w, v);
^
RigidBody.cpp:191:14: note: in instantiation of member function ‘OpenMD::SquareMatrix3::diagonalize’
requested here
Mat3x3d::diagonalize(Itmp, evals, sU_);
^
../../src/math/SquareMatrix.hpp:207:16: note: must qualify identifier to find this declaration in dependent base
class
static int jacobi(SquareMatrix& a, Vector& d,
^
1 error generated.
make[1]: *** [../../MPIobj/RigidBody.o] Error 1

make[1]: Target `_installall’ not remade because of errors.
make: *** [src/primitives/.install] Error 2