Try CI with current gmsh version

docker/Dockerfile.noble

@@ -20,11 +20,13 @@ RUN apt-get update && \
      echo "Europe/London" > /etc/timezone && \
      apt-get -y install fluidity-dev texlive-pstricks texlive texlive-latex-extra texlive-science python3-pip python3-junit.xml && \
      apt-get -y install sudo flex bison && \
+     apt-get -y install gmsh && \
      apt-get clean
 
 # Use old version of gmsh in CI to avoid mesh-sensitive tests failing
-WORKDIR /usr/local
-RUN curl -fsL https://gmsh.info/bin/Linux/gmsh-2.16.0-Linux64.tgz | tar --strip-components=1 -zxf -
+# WORKDIR /usr/local
+# RUN curl -fsL https://gmsh.info/bin/Linux/gmsh-2.16.0-Linux64.tgz | tar --strip-components=1 -zxf -
+RUN gmsh --version
 
 ENV OMPI_MCA_btl_vader_single_copy_mechanism=none
 ENV OMPI_MCA_rmaps_base_oversubscribe=1

docker/actions/Dockerfile.actions.noble

@@ -1,4 +1,4 @@
-FROM fluidity/baseimages:noble
+FROM fluidity/baseimages:noble-gmsh4
 
 USER root
 

python/fluidity/diagnostics/gmshtools.py

@@ -290,6 +290,9 @@ def ReadBinaryMshV2(fileHandle, dataSize):
 
 
 def ReadBinaryMshV4(fileHandle, dataSize):
+    raise Warning("Fluidity's gmshtools does not correctly read physical surface ids "
+                  "for meshes in .msh format version 4. If these are required save your .msh-file"
+                  "in .msh format version 2 (e.g. using -format msh2 on the command line).")
     if dataSize == 4:
         sizeFormat = "i"
     elif dataSize == 8:
@@ -410,6 +413,10 @@ def ReadBinaryMshV4(fileHandle, dataSize):
             if swap:
                 sArr.byteswap()
 
+            # NOTE: these are not the physical and elementary tags
+            # that are expected in msh2 format. Physical tags
+            # can only be found by also reading in the separate
+            # "Entities" section
             ids = [entityTag, sArr[0]]
             nodes = FromGmshNodeOrder(utils.OffsetList(sArr[1:], -1), type)
             element = elements.Element(nodes, ids)
@@ -519,6 +526,9 @@ def ReadAsciiMshV2(fileHandle):
 
 
 def ReadAsciiMshV4(fileHandle):
+    raise Warning("Fluidity's gmshtools does not correctly read physical surface ids "
+                  "for meshes in .msh format version 4. If these are required save your .msh-file"
+                  "in .msh format version 2 (e.g. using -format msh2 on the command line).")
     line = ReadNonCommentLine(fileHandle)
     assert line == "$EndMeshFormat"
 
@@ -594,6 +604,10 @@ def ReadAsciiMshV4(fileHandle):
             lineSplit = line.split()
             assert len(lineSplit) == 1 + type.GetNodeCount()
 
+            # NOTE: these are not the physical and elementary tags
+            # that are expected in msh2 format. Physical tags
+            # can only be found by also reading in the separate
+            # "Entities" section
             ids = [entityTag, int(lineSplit[0])]
             nodes = FromGmshNodeOrder([int(node) - 1 for node in lineSplit[1:]], type)
             element = elements.Element(nodes, ids)

tests/channel_wind_drag_rotated/Makefile

@@ -1,7 +1,7 @@
 PROJECT = channel
 
 input: clean
-	gmsh -3 -o channel.msh src/channel.geo
+	gmsh -3 -format msh 2 -o channel.msh src/channel.geo
 	../../bin/transform_mesh '(cos(1.)*x-sin(1.0)*y,sin(1.)*x+cos(1.)*y,z)' channel