I am trying to render plants with transparent textures. I use discard in the shader that creates the shadow map, but I get blocky holes in the shadow:

This is the shader that I'm using:

		uniform mediump vec2 uvOffset;
		uniform highp mat4 matrixPVM;
		attribute highp vec3 inVertex;
		attribute mediump vec2 texCoordAttr;
		varying mediump vec2 texCoordVar;
		void main(void)
		{
			gl_Position = matrixPVM * vec4(inVertex, 1.0);
			texCoordVar = texCoordAttr.st + uvOffset.st;
		}

		uniform sampler2D sampler2d;
		varying mediump vec2 texCoordVar;
		void main(void)
		{
			lowp vec4 texColor = texture2D(sampler2d, texCoordVar);
			if (texColor.a < 0.001) discard;
		}

As you can see the opaque objects have the shadow rendered correctly. I tried doubling the resolution of the map and changing the alpha compare number, but makes no difference.

Anyone know a solution to this problem?

Does it help if you set gl_FragColor to something (e.g. vec4(1.0, 1.0, 1.0, 1.0)) ?

No. Makes no difference

If it is only happening on transparent objects, then I would check the alpha values of your textures. But then I see that floating leather (?) patch that clearly isn't transparent and it too has holes in the shadow. :/

Maybe a precision issue? Have you tried removing the "lowp" qualifier?

Finally, I figured it out.

When creating the shadow I called glActiveTexture(GL_TEXTURE1) to deactivate the shadow map texture, but I forgot to call glActiveTexture(GL_TEXTURE0) again when creating the shadow, so the texture being read was just random jibberish.

Thanks for the help anyways ;)