Well if you want spheres you could use instancing and draw those sphere in big chunks(or in one chunk depends on your case).
Otherwise if it is suitable for you you could draw them as points. Both OpenGL and D3D support drawing directly points on the screen with customizable size.
@work we've simulate particles and in order to draw a preview of those particle we just draw them as points(GL_POINTS or D3D11_PRIMITIVE_TOPOLOGY_POINTLIST) and give the user an integer that specifies the size of those points. It works like a charm.